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McClellan JM, Zoghbi AW, Buxbaum JD, Cappi C, Crowley JJ, Flint J, Grice DE, Gulsuner S, Iyegbe C, Jain S, Kuo PH, Lattig MC, Passos-Bueno MR, Purushottam M, Stein DJ, Sunshine AB, Susser ES, Walsh CA, Wootton O, King MC. An evolutionary perspective on complex neuropsychiatric disease. Neuron 2024; 112:7-24. [PMID: 38016473 PMCID: PMC10842497 DOI: 10.1016/j.neuron.2023.10.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/09/2023] [Accepted: 10/26/2023] [Indexed: 11/30/2023]
Abstract
The forces of evolution-mutation, selection, migration, and genetic drift-shape the genetic architecture of human traits, including the genetic architecture of complex neuropsychiatric illnesses. Studying these illnesses in populations that are diverse in genetic ancestry, historical demography, and cultural history can reveal how evolutionary forces have guided adaptation over time and place. A fundamental truth of shared human biology is that an allele responsible for a disease in anyone, anywhere, reveals a gene critical to the normal biology underlying that condition in everyone, everywhere. Understanding the genetic causes of neuropsychiatric disease in the widest possible range of human populations thus yields the greatest possible range of insight into genes critical to human brain development. In this perspective, we explore some of the relationships between genes, adaptation, and history that can be illuminated by an evolutionary perspective on studies of complex neuropsychiatric disease in diverse populations.
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Affiliation(s)
- Jon M McClellan
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Anthony W Zoghbi
- Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joseph D Buxbaum
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carolina Cappi
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - James J Crowley
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jonathan Flint
- Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Dorothy E Grice
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Suleyman Gulsuner
- Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Conrad Iyegbe
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sanjeev Jain
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bengaluru 560029, India
| | - Po-Hsiu Kuo
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei 100, Taiwan
| | | | | | - Meera Purushottam
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bengaluru 560029, India
| | - Dan J Stein
- SAMRC Unit on Risk and Resilience in Mental Disorders, Department of Psychiatry, University of Cape Town, Cape Town, South Africa
| | - Anna B Sunshine
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA; Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Ezra S Susser
- Department of Epidemiology, Mailman School of Public Health, and New York State Psychiatric Institute, Columbia University, New York, NY 10032, USA
| | - Christopher A Walsh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Olivia Wootton
- SAMRC Unit on Risk and Resilience in Mental Disorders, Department of Psychiatry, University of Cape Town, Cape Town, South Africa
| | - Mary-Claire King
- Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
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Benoit C, Carlson RJ, King MC, Horn DL, Rubinstein JT. Behavioral characterization of the cochlear amplifier lesion due to loss of function of stereocilin (STRC) in human subjects. Hear Res 2023; 439:108898. [PMID: 37890241 PMCID: PMC10756798 DOI: 10.1016/j.heares.2023.108898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/12/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023]
Abstract
Loss of function of stereocilin (STRC) is the second most common cause of inherited hearing loss. The loss of the stereocilin protein, encoded by the STRC gene, induces the loss of connection between outer hair cells and tectorial membrane. This only affects the outer hair cells (OHCs) function, involving deficits of active cochlear frequency selectivity and amplifier functions despite preservation of normal inner hair cells. Better understanding of cochlear features associated with mutation of STRC will improve our knowledge of normal cochlear function, the pathophysiology of hearing impairment, and potentially enhance hearing aid and cochlear implant signal processing. Nine subjects with homozygous or compound heterozygous loss of function mutations in STRC were included, age 7-24 years. Temporal and spectral modulation perception were measured, characterized by spectral and temporal modulation transfer functions. Speech-in-noise perception was studied with spondee identification in adaptive steady-state noise and AzBio sentences with 0 and -5 dB SNR multitalker babble. Results were compared with normal hearing (NH) and cochlear implant (CI) listeners to place STRC-/- listeners' hearing capacity in context. Spectral ripple discrimination thresholds in the STRC-/- subjects were poorer than in NH listeners (p < 0.0001) but remained better than for CI listeners (p < 0.0001). Frequency resolution appeared impaired in the STRC-/- group compared to NH listeners but did not reach statistical significance (p = 0.06). Compared to NH listeners, amplitude modulation detection thresholds in the STRC-/- group did not reach significance (p= 0.06) but were better than in CI subjects (p < 0.0001). Temporal resolution in STRC-/- subjects was similar to NH (p = 0.98) but better than in CI listeners (p = 0.04). The spondee reception threshold in the STRC-/- group was worse than NH listeners (p = 0.0008) but better than CI listeners (p = 0.0001). For AzBio sentences, performance at 0 dB SNR was similar between the STRC-/- group and the NH group, 88 % and 97 % respectively. For -5 dB SNR, the STRC-/- performance was significantly poorer than NH, 40 % and 85 % respectively, yet much better than with CI who performed at 54 % at +5 dB SNR in children and 53 % at + 10 dB SNR in adults. To our knowledge, this is the first study of the psychoacoustic performance of human subjects lacking cochlear amplification but with normal inner hair cell function. Our data demonstrate preservation of temporal resolution and a trend to impaired frequency resolution in this group without reaching statistical significance. Speech-in-noise perception compared to NH listeners was impaired as well. All measures were better than those in CI listeners. It remains to be seen if hearing aid modifications, customized for the spectral deficits in STRC-/- listeners can improve speech understanding in noise. Since cochlear implants are also limited by deficient spectral selectivity, STRC-/- hearing may provide an upper bound on what could be obtained with better temporal coding in electrical stimulation.
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Affiliation(s)
- Charlotte Benoit
- Virginia Merrill Bloedel Hearing Research Center, Department of Otolaryngology-Head and Neck Surgery, University of Washington, Seattle, WA, USA.
| | - Ryan J Carlson
- Departments of Genome Sciences and Medicine, University of Washington, Seattle, WA, USA
| | - Mary-Claire King
- Departments of Genome Sciences and Medicine, University of Washington, Seattle, WA, USA
| | - David L Horn
- Virginia Merrill Bloedel Hearing Research Center, Department of Otolaryngology-Head and Neck Surgery, University of Washington, Seattle, WA, USA; Department of Speech and Hearing Sciences, University of Washington, Seattle, WA, USA; Division of Pediatric Otolaryngology, Department of Surgery, Seattle Children's Hospital, Seattle, WA, USA
| | - Jay T Rubinstein
- Virginia Merrill Bloedel Hearing Research Center, Department of Otolaryngology-Head and Neck Surgery, University of Washington, Seattle, WA, USA; Department of Bioengineering, University of Washington, Seattle, WA, USA
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Aburayyan A, Carlson RJ, Rabie GN, Lee MK, Gulsuner S, Walsh T, Avraham KB, Kanaan MN, King MC. A paradoxical genotype-phenotype relationship: Low level of GOSR2 translation from a non-AUG start codon in a family with profound hearing loss. Hum Mol Genet 2023; 32:2265-2268. [PMID: 37074134 PMCID: PMC10321379 DOI: 10.1093/hmg/ddad066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 03/25/2023] [Accepted: 04/10/2023] [Indexed: 04/20/2023] Open
Affiliation(s)
- Amal Aburayyan
- Department of Genome Sciences and Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Hereditary Research Laboratory, Department of Biology, Bethlehem University, Bethlehem, Palestine
| | - Ryan J Carlson
- Department of Genome Sciences and Department of Medicine, University of Washington, Seattle, WA, USA
| | - Grace N Rabie
- Hereditary Research Laboratory, Department of Biology, Bethlehem University, Bethlehem, Palestine
| | - Ming K Lee
- Department of Genome Sciences and Department of Medicine, University of Washington, Seattle, WA, USA
| | - Suleyman Gulsuner
- Department of Genome Sciences and Department of Medicine, University of Washington, Seattle, WA, USA
| | - Tom Walsh
- Department of Genome Sciences and Department of Medicine, University of Washington, Seattle, WA, USA
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Moien N Kanaan
- Hereditary Research Laboratory, Department of Biology, Bethlehem University, Bethlehem, Palestine
| | - Mary-Claire King
- Department of Genome Sciences and Department of Medicine, University of Washington, Seattle, WA, USA
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Carlson RJ, Walsh T, Mandell JB, Aburayyan A, Lee MK, Gulsuner S, Horn DL, Ou HC, Sie KCY, Mancl L, Rubinstein J, King MC. Association of Genetic Diagnoses for Childhood-Onset Hearing Loss With Cochlear Implant Outcomes. JAMA Otolaryngol Head Neck Surg 2023; 149:212-222. [PMID: 36633841 PMCID: PMC9857764 DOI: 10.1001/jamaoto.2022.4463] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/10/2022] [Indexed: 01/13/2023]
Abstract
Importance In the US, most childhood-onset bilateral sensorineural hearing loss is genetic, with more than 120 genes and thousands of different alleles known. Primary treatments are hearing aids and cochlear implants. Genetic diagnosis can inform progression of hearing loss, indicate potential syndromic features, and suggest best timing for individualized treatment. Objective To identify the genetic causes of childhood-onset hearing loss and characterize severity, progression, and cochlear implant success associated with genotype in a single large clinical cohort. Design, Setting, and Participants This cross-sectional analysis (genomics) and retrospective cohort analysis (audiological measures) were conducted from 2019 to 2022 at the otolaryngology and audiology clinics of Seattle Children's Hospital and the University of Washington and included 449 children from 406 families with bilateral sensorineural hearing loss with an onset younger than 18 years. Data were analyzed between January and June 2022. Main Outcomes and Measures Genetic diagnoses based on genomic sequencing and structural variant analysis of the DNA of participants; severity and progression of hearing loss as measured by audiologic testing; and cochlear implant success as measured by pediatric and adult speech perception tests. Hearing thresholds and speech perception scores were evaluated with respect to age at implant, months since implant, and genotype using a multivariate analysis of variance and covariance. Results Of 406 participants, 208 (51%) were female, 17 (4%) were African/African American, 32 (8%) were East Asian, 219 (54%) were European, 53 (13%) were Latino/Admixed American, and 16 (4%) were South Asian. Genomic analysis yielded genetic diagnoses for 210 of 406 families (52%), including 55 of 82 multiplex families (67%) and 155 of 324 singleton families (48%). Rates of genetic diagnosis were similar for children of all ancestries. Causal variants occurred in 43 different genes, with each child (with 1 exception) having causative variant(s) in only 1 gene. Hearing loss severity, affected frequencies, and progression varied by gene and, for some genes, by genotype within gene. For children with causative mutations in MYO6, OTOA, SLC26A4, TMPRSS3, or severe loss-of-function variants in GJB2, hearing loss was progressive, with losses of more than 10 dB per decade. For all children with cochlear implants, outcomes of adult speech perception tests were greater than preimplanted levels. Yet the degree of success varied substantially by genotype. Adjusting for age at implant and interval since implant, speech perception was highest for children with hearing loss due to MITF or TMPRSS3. Conclusions and Relevance The results of this cross-sectional study suggest that genetic diagnosis is now sufficiently advanced to enable its integration into precision medical care for childhood-onset hearing loss.
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Affiliation(s)
- Ryan J. Carlson
- Department of Genome Sciences, University of Washington, Seattle
- Department of Medicine, University of Washington, Seattle
| | - Tom Walsh
- Department of Genome Sciences, University of Washington, Seattle
- Department of Medicine, University of Washington, Seattle
| | - Jessica B. Mandell
- Department of Genome Sciences, University of Washington, Seattle
- Department of Medicine, University of Washington, Seattle
| | - Amal Aburayyan
- Department of Genome Sciences, University of Washington, Seattle
- Department of Medicine, University of Washington, Seattle
| | - Ming K. Lee
- Department of Genome Sciences, University of Washington, Seattle
- Department of Medicine, University of Washington, Seattle
| | - Suleyman Gulsuner
- Department of Genome Sciences, University of Washington, Seattle
- Department of Medicine, University of Washington, Seattle
| | - David L. Horn
- Department of Otolaryngology–Head & Neck Surgery, University of Washington School of Medicine, Seattle
- Division of Pediatric Otolaryngology–Head and Neck Surgery, Seattle Children’s Hospital, Seattle, Washington
| | - Henry C. Ou
- Department of Otolaryngology–Head & Neck Surgery, University of Washington School of Medicine, Seattle
- Division of Pediatric Otolaryngology–Head and Neck Surgery, Seattle Children’s Hospital, Seattle, Washington
| | - Kathleen C. Y. Sie
- Department of Otolaryngology–Head & Neck Surgery, University of Washington School of Medicine, Seattle
- Division of Pediatric Otolaryngology–Head and Neck Surgery, Seattle Children’s Hospital, Seattle, Washington
| | - Lisa Mancl
- Center on Human Development and Disability, University of Washington Medical Center, Seattle
| | - Jay Rubinstein
- Department of Otolaryngology–Head & Neck Surgery, University of Washington School of Medicine, Seattle
- Division of Pediatric Otolaryngology–Head and Neck Surgery, Seattle Children’s Hospital, Seattle, Washington
| | - Mary-Claire King
- Department of Genome Sciences, University of Washington, Seattle
- Department of Medicine, University of Washington, Seattle
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Freund T, Baxter SK, Walsh T, Golan H, Kapelushnik J, Abramsohn-Goldenberg M, Benor S, Sarid N, Ram R, Alcalay Y, Segel R, Renbaum P, Stepensky P, King MC, Torgerson TR, Hagin D. Clinically Complex LRBA Deficiency Due to a Founder Allele in the Georgian Jewish Population. J Clin Immunol 2023; 43:151-164. [PMID: 36063261 DOI: 10.1007/s10875-022-01358-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/15/2022] [Indexed: 01/18/2023]
Abstract
Pathogenic variants in LRBA, encoding the LPS Responsive Beige-Like Anchor (LRBA) protein, are responsible for recessive, early-onset hypogammaglobulinemia, severe multi-organ autoimmunity, and lymphoproliferation, with increased risk for malignancy. LRBA deficiency has a wide clinical spectrum with variable age of onset and disease severity. Three apparently unrelated patients with LRBA deficiency, of Georgian Jewish descent, were homozygous for LRBA c.6640C > T, p.R2214*, leading to a stop upstream of the LRBA BEACH domain. Despite carrying the same LRBA genotype, the three patients differed in clinical course: the first patient was asymptomatic until age 25 years; the second presented with failure to thrive at age 3 months; and the third presented at age 7 years with immune cytopenias and severe infections. Two of the patients developed malignancies: the first patient was diagnosed with recurrent Hodgkin's disease at age 36 years, and the second patient developed aggressive gastric cancer at age 15 years. Among Georgian Jews, the carrier frequency of the LRBA p.R2214* allele was 1.6% (4 of 236 Georgian Jewish controls). The allele was absent from other populations. Haplotype analysis showed a shared origin of the mutation. These three patients revealed a pathogenic LRBA founder allele in the Georgian Jewish population, support the diverse and complex clinical spectrum of LRBA deficiency, and support the possibility that LRBA deficiency predisposes to malignancy.
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Affiliation(s)
- Tal Freund
- Allergy and Clinical Immunology Unit, Department of Medicine, Tel Aviv Sourasky Medical Center and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sarah K Baxter
- Department of Pediatrics, University of Washington and Seattle Children's Research Institute, Seattle, WA, USA.,Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Tom Walsh
- Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Hana Golan
- Pediatric Hematology Oncology Department, Safra Children's Hospital, Sheba Medical Center, Ramat-Gan, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Joseph Kapelushnik
- Department of Pediatric Oncology and Department of Hematology, Faculty of Health Sciences, Soroka Medical Center and The Center of Advanced Research and Education in Reproduction (CARER), Ben-Gurion University of the Negev, Beer Sheva, Israel
| | | | - Shira Benor
- Allergy and Clinical Immunology Unit, Department of Medicine, Tel Aviv Sourasky Medical Center and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nadav Sarid
- Department of Hematology and Stem Cell Transplantation Service, Tel Aviv Sourasky Medical Center and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ron Ram
- Department of Hematology and Stem Cell Transplantation Service, Tel Aviv Sourasky Medical Center and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yifat Alcalay
- Allergy and Clinical Immunology Unit, Department of Medicine, Tel Aviv Sourasky Medical Center and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Reeval Segel
- Shaare Zedek Medical Center and Faculty of Medicine, Medical Genetics Institute, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Paul Renbaum
- Shaare Zedek Medical Center and Faculty of Medicine, Medical Genetics Institute, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Polina Stepensky
- Department of Bone Marrow Transplantation and Cancer Immunotherapy, Faculty of Medicine, Hadassah Medical Center, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mary-Claire King
- Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Troy R Torgerson
- Department of Pediatrics, University of Washington and Seattle Children's Research Institute, Seattle, WA, USA.,Allen Institute for Immunology, Seattle, WA, USA
| | - David Hagin
- Allergy and Clinical Immunology Unit, Department of Medicine, Tel Aviv Sourasky Medical Center and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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Baxter SK, Gulsuner S, Eckert MM, Lee MK, Walsh T, Stevens A, King MC. 906 De novomutations in childhood-onset systemic lupus erythematosus. Genetics 2022. [DOI: 10.1136/lupus-2022-lupus21century.57] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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Felix GES, Guindalini RSC, Zheng Y, Walsh T, Sveen E, Lopes TMM, Côrtes J, Zhang J, Carôzo P, Santos I, Bonfim TF, Garicochea B, Toralles MBP, Meyer R, Netto EM, Abe-Sandes K, King MC, de Oliveira Nascimento IL, Olopade OI. Mutational spectrum of breast cancer susceptibility genes among women ascertained in a cancer risk clinic in Northeast Brazil. Breast Cancer Res Treat 2022; 193:485-494. [PMID: 35353237 PMCID: PMC9090684 DOI: 10.1007/s10549-022-06560-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 02/27/2022] [Indexed: 12/24/2022]
Abstract
PURPOSE There is a paucity of data on the spectrum and prevalence of pathogenic variants among women of African ancestry in the Northeast region of Brazil. METHODS We performed BROCA panel sequencing to identify inherited loss-of-function variants in breast cancer susceptibility genes among 292 Brazilian women referred to a single institution cancer risk assessment program. RESULTS The study included a convenient cohort of 173 women with invasive breast cancer (cases) and 119 women who were cancer-free at the time of ascertainment. The majority of the women self-reported as African-descended (67% for cases and 90.8% for unaffected volunteers). Thirty-seven pathogenic variants were found in 36 (20.8%) patients. While the spectrum of pathogenic variants was heterogeneous, the majority (70.3%) of the pathogenic variants were detected in high-risk genes BRCA1, BRCA2, PALB2, and TP53. Pathogenic variants were also found in the ATM, BARD1, BRIP1, FAM175A, FANCM, NBN, and SLX4 genes in 6.4% of the affected women. Four recurrent pathogenic variants were detected in 11 patients of African ancestry. Only one unaffected woman had a pathogenic variant in the RAD51C gene. Different risk assessment models examined performed well in predicting risk of carrying germline loss-of-function variants in BRCA1 and/or BRCA2 in breast cancer cases. CONCLUSION The high prevalence and heterogenous spectrum of pathogenic variants identified among self-reported African descendants in Northeast Brazil is consistent with studies in other African ancestry populations with a high burden of aggressive young onset breast cancer. It underscores the need to integrate comprehensive cancer risk assessment and genomic testing in the management of newly diagnosed Black women with breast cancer across the African Diaspora, enabling improved cancer control in admixed underserved and understudied populations.
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Affiliation(s)
- Gabriela E S Felix
- Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Bahia, Brazil
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz Bahia, Salvador, Bahia, Brazil
| | - Rodrigo Santa Cruz Guindalini
- Centro de Investigação Translacional em Oncologia (CTO), Instituto do Cancer do Estado de São Paulo (ICESP), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, São Paulo, Brazil
- Instituto D'or de Pesquisa e Ensino, Salvador, Bahia, Brazil
| | - Yonglan Zheng
- Department of Medicine, Center for Clinical Cancer Genetics and Global Health, University of Chicago, Chicago, Illinois, USA
| | - Tom Walsh
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Elisabeth Sveen
- Department of Medicine, Center for Clinical Cancer Genetics and Global Health, University of Chicago, Chicago, Illinois, USA
| | | | - Juliana Côrtes
- Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Bahia, Brazil
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz Bahia, Salvador, Bahia, Brazil
- Universidade do Estado da Bahia, Salvador, Bahia, Brazil
| | - Jing Zhang
- Department of Medicine, Center for Clinical Cancer Genetics and Global Health, University of Chicago, Chicago, Illinois, USA
| | - Polyanna Carôzo
- Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Bahia, Brazil
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz Bahia, Salvador, Bahia, Brazil
- Universidade do Estado da Bahia, Salvador, Bahia, Brazil
| | - Irlânia Santos
- Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | - Thaís Ferreira Bonfim
- Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | | | | | - Roberto Meyer
- Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | - Eduardo Martins Netto
- Laboratório de Pesquisa em Infectologia, Hospital Universitário Prof. Edgard Santos, Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | - Kiyoko Abe-Sandes
- Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | - Mary-Claire King
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Ivana Lucia de Oliveira Nascimento
- Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Bahia, Brazil
- Núcleo de Oncologia da Bahia, Salvador, Bahia, Brazil
| | - Olufunmilayo I Olopade
- Department of Medicine, Center for Clinical Cancer Genetics and Global Health, University of Chicago, 5841 S. Maryland Avenue, MC 2115, Chicago, Illinois, 60637-1470, USA.
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Carlson RJ, Quesnel A, Wells D, Brownstein Z, Gilony D, Gulsuner S, Leppig KA, Avraham KB, King MC, Walsh T, Rubinstein J. Genetic Heterogeneity and Core Clinical Features of NOG-Related-Symphalangism Spectrum Disorder. Otol Neurotol 2021; 42:e1143-e1151. [PMID: 34049328 PMCID: PMC8486042 DOI: 10.1097/mao.0000000000003176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES To better distinguish NOG-related-symphalangism spectrum disorder (NOG-SSD) from chromosomal 17q22 microdeletion syndromes and to inform surgical considerations in stapes surgery for patients with NOG-SSD. BACKGROUND Mutations in NOG cause a variety of skeletal syndromes that often include conductive hearing loss. Several microdeletions of chromosome 17q22 lead to severe syndromes with clinical characteristics that overlap NOG-SSD. Isolated deletion of NOG has not been described, and therefore the contribution of NOG deletion in these syndromes is unknown. METHODS Two families with autosomal dominant NOG-SSD exhibited stapes ankylosis, facial dysmorphisms, and skeletal and joint anomalies. In each family, NOG was evaluated by genomic sequencing and candidate mutations confirmed as damaging by in vitro assays. Temporal bone histology of a patient with NOG-SSD was compared with temporal bones of 40 patients diagnosed with otosclerosis. RESULTS Family 1 harbors a 555 kb chromosomal deletion encompassing only NOG and ANKFN1. Family 2 harbors a missense mutation in NOG leading to absence of noggin protein. The incus-footplate distance of the temporal bone was significantly longer in a patient with NOG-SSD than in patients with otosclerosis. CONCLUSION The chromosomal microdeletion of family 1 led to a phenotype comparable to that due to a NOG point mutation and much milder than the phenotypes due to other chromosome 17q22 microdeletions. Severe clinical findings in other microdeletion cases are likely due to deletion of genes other than NOG. Based on temporal bone findings, we recommend that surgeons obtain longer stapes prostheses before stapes surgery in individuals with NOG-SSD stapes ankylosis.
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Affiliation(s)
- Ryan J Carlson
- Departments of Genome Sciences and Medicine, University of Washington, Seattle, Washington
| | - Alicia Quesnel
- Department of Otolaryngology, Harvard Medical School, Boston, Massachusetts
- Otopathology Laboratory, Massachusetts Eye and Ear, Boston, Massachusetts
| | - Dawson Wells
- Department of Otolaryngology, Harvard Medical School, Boston, Massachusetts
- Otopathology Laboratory, Massachusetts Eye and Ear, Boston, Massachusetts
| | - Zippora Brownstein
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Dror Gilony
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Pediatric Otolaryngology Unit, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Suleyman Gulsuner
- Departments of Genome Sciences and Medicine, University of Washington, Seattle, Washington
| | - Kathleen A Leppig
- Genetic Services, Kaiser Permanente of Washington, Seattle, Washington
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Mary-Claire King
- Departments of Genome Sciences and Medicine, University of Washington, Seattle, Washington
| | - Tom Walsh
- Departments of Genome Sciences and Medicine, University of Washington, Seattle, Washington
| | - Jay Rubinstein
- Virginia Merrill Bloedel Hearing Research Center, Department of Otolaryngology-Head and Neck Surgery, University of Washington, Seattle, Washington
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9
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Miller DE, Sulovari A, Wang T, Loucks H, Hoekzema K, Munson KM, Lewis AP, Fuerte EPA, Paschal CR, Walsh T, Thies J, Bennett JT, Glass I, Dipple KM, Patterson K, Bonkowski ES, Nelson Z, Squire A, Sikes M, Beckman E, Bennett RL, Earl D, Lee W, Allikmets R, Perlman SJ, Chow P, Hing AV, Wenger TL, Adam MP, Sun A, Lam C, Chang I, Zou X, Austin SL, Huggins E, Safi A, Iyengar AK, Reddy TE, Majoros WH, Allen AS, Crawford GE, Kishnani PS, King MC, Cherry T, Chong JX, Bamshad MJ, Nickerson DA, Mefford HC, Doherty D, Eichler EE. Targeted long-read sequencing identifies missing disease-causing variation. Am J Hum Genet 2021; 108:1436-1449. [PMID: 34216551 PMCID: PMC8387463 DOI: 10.1016/j.ajhg.2021.06.006] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/07/2021] [Indexed: 12/28/2022] Open
Abstract
Despite widespread clinical genetic testing, many individuals with suspected genetic conditions lack a precise diagnosis, limiting their opportunity to take advantage of state-of-the-art treatments. In some cases, testing reveals difficult-to-evaluate structural differences, candidate variants that do not fully explain the phenotype, single pathogenic variants in recessive disorders, or no variants in genes of interest. Thus, there is a need for better tools to identify a precise genetic diagnosis in individuals when conventional testing approaches have been exhausted. We performed targeted long-read sequencing (T-LRS) using adaptive sampling on the Oxford Nanopore platform on 40 individuals, 10 of whom lacked a complete molecular diagnosis. We computationally targeted up to 151 Mbp of sequence per individual and searched for pathogenic substitutions, structural variants, and methylation differences using a single data source. We detected all genomic aberrations-including single-nucleotide variants, copy number changes, repeat expansions, and methylation differences-identified by prior clinical testing. In 8/8 individuals with complex structural rearrangements, T-LRS enabled more precise resolution of the mutation, leading to changes in clinical management in one case. In ten individuals with suspected Mendelian conditions lacking a precise genetic diagnosis, T-LRS identified pathogenic or likely pathogenic variants in six and variants of uncertain significance in two others. T-LRS accurately identifies pathogenic structural variants, resolves complex rearrangements, and identifies Mendelian variants not detected by other technologies. T-LRS represents an efficient and cost-effective strategy to evaluate high-priority genes and regions or complex clinical testing results.
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Affiliation(s)
- Danny E Miller
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA.
| | - Arvis Sulovari
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Tianyun Wang
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Hailey Loucks
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Edith P Almanza Fuerte
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Catherine R Paschal
- Department of Laboratories, Seattle Children's Hospital, Seattle, WA 98105, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Tom Walsh
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jenny Thies
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - James T Bennett
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Department of Laboratories, Seattle Children's Hospital, Seattle, WA 98105, USA; Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Ian Glass
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Katrina M Dipple
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Center for Clinical and Translational Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Karynne Patterson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Emily S Bonkowski
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Zoe Nelson
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Audrey Squire
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Megan Sikes
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Erika Beckman
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Robin L Bennett
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Dawn Earl
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Winston Lee
- Department of Genetics and Development, Columbia University, New York, NY 10032, USA; Department of Ophthalmology, Columbia University, New York, NY 10032, USA
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Seth J Perlman
- Department of Neurology, Seattle Children's Hospital, University of Washington, Seattle, WA 98105, USA
| | - Penny Chow
- Department of Pediatrics, Division of Craniofacial Medicine, University of Washington, Seattle, WA 98195, USA
| | - Anne V Hing
- Department of Pediatrics, Division of Craniofacial Medicine, University of Washington, Seattle, WA 98195, USA
| | - Tara L Wenger
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Margaret P Adam
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Angela Sun
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Center for Clinical and Translational Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Christina Lam
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Irene Chang
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Xue Zou
- Program in Computational Biology & Bioinformatics, Duke University, Durham, NC 27710, USA
| | - Stephanie L Austin
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Erin Huggins
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Alexias Safi
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Apoorva K Iyengar
- Department of Biostatistics and Bioinformatics, Duke University; Durham, NC 27708, USA; University Program in Genetics and Genomics, Duke University; Durham, NC 27708, USA
| | - Timothy E Reddy
- Department of Biostatistics and Bioinformatics, Duke University; Durham, NC 27708, USA
| | - William H Majoros
- Department of Biostatistics and Bioinformatics, Duke University; Durham, NC 27708, USA
| | - Andrew S Allen
- Department of Biostatistics and Bioinformatics, Duke University; Durham, NC 27708, USA
| | - Gregory E Crawford
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Priya S Kishnani
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Mary-Claire King
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Tim Cherry
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Jessica X Chong
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Michael J Bamshad
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Heather C Mefford
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Dan Doherty
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Department of Pediatrics, Division of Developmental Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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10
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Feurstein S, Churpek JE, Walsh T, Keel S, Hakkarainen M, Schroeder T, Germing U, Geyh S, Heuser M, Thol F, Pohlkamp C, Haferlach T, Gao J, Owen C, Goehring G, Schlegelberger B, Verma D, Krause DS, Gao G, Cronin T, Gulsuner S, Lee M, Pritchard CC, Subramanian HP, Del Gaudio D, Li Z, Das S, Kilpivaara O, Wartiovaara-Kautto U, Wang ES, Griffiths EA, Döhner K, Döhner H, King MC, Godley LA. Germline variants drive myelodysplastic syndrome in young adults. Leukemia 2021; 35:2439-2444. [PMID: 33510405 PMCID: PMC8725861 DOI: 10.1038/s41375-021-01137-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 12/17/2020] [Accepted: 01/11/2021] [Indexed: 01/29/2023]
Affiliation(s)
- Simone Feurstein
- Department of Medicine, Section of Hematology/Oncology, The University of Chicago Comprehensive Cancer Center, The University of Chicago, Chicago, IL, USA
| | - Jane E Churpek
- Division of Hematology, Medical Oncology, and Palliative Care, Department of Medicine, The University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Tom Walsh
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | - Sioban Keel
- Department of Medicine, Division of Hematology, University of Washington, Seattle, WA, USA
| | - Marja Hakkarainen
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, University of Helsinki, Helsinki, Finland
| | - Thomas Schroeder
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty, University of Duesseldorf, Duesseldorf, Germany
| | - Ulrich Germing
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty, University of Duesseldorf, Duesseldorf, Germany
| | - Stefanie Geyh
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty, University of Duesseldorf, Duesseldorf, Germany
| | - Michael Heuser
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Felicitas Thol
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | | | | | - Juehua Gao
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Carolyn Owen
- Division of Hematology and Hematological Malignancies, University of Calgary, Calgary, AB, Canada
| | - Gudrun Goehring
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | | | - Divij Verma
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Medicine, Frankfurt, Germany
- Department of Medicine, Albert Einstein College of Medicine, New York, NY, USA
| | - Daniela S Krause
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Medicine, Frankfurt, Germany
| | - Guimin Gao
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
| | - Tara Cronin
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Suleyman Gulsuner
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Ming Lee
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Colin C Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | | | - Daniela Del Gaudio
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Zejuan Li
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, TX, USA
| | - Soma Das
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Outi Kilpivaara
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Medical and Clinical Genetics/Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ulla Wartiovaara-Kautto
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, University of Helsinki, Helsinki, Finland
| | - Eunice S Wang
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | | | - Konstanze Döhner
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Hartmut Döhner
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Mary-Claire King
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Lucy A Godley
- Department of Medicine, Section of Hematology/Oncology, The University of Chicago Comprehensive Cancer Center, The University of Chicago, Chicago, IL, USA.
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11
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Yechieli M, Gulsuner S, Ben-Pazi H, Fattal A, Aran A, Kuzminsky A, Sagi L, Guttman D, Schneebaum Sender N, Gross-Tsur V, Klopstock T, Walsh T, Renbaum P, Zeligson S, Shemer Meiri L, Lev D, Shmueli D, Blumkin L, Lahad A, King MC, Levy EL, Segel R. Diagnostic yield of chromosomal microarray and trio whole exome sequencing in cryptogenic cerebral palsy. J Med Genet 2021; 59:759-767. [PMID: 34321325 DOI: 10.1136/jmedgenet-2021-107884] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 07/14/2021] [Indexed: 11/03/2022]
Abstract
OBJECTIVE To determine the yield of genetic diagnoses using chromosomal microarray (CMA) and trio whole exome sequencing (WES), separately and combined, among patients with cryptogenic cerebral palsy (CP). METHODS Trio WES of patients with prior CMA analysis for cryptogenic CP, defined as disabling, non-progressive motor symptoms beginning before the age of 3 years without known cause. RESULTS Given both CMA analysis and trio WES, clinically significant genetic findings were identified for 58% of patients (26 of 45). Diagnoses were eight large CNVs detected by CMA and 18 point mutations detected by trio WES. None had more than one severe mutation. Approximately half of events (14 of 26) were de novo. Yield was significantly higher in patients with CP with comorbidities (69%, 22 of 32) than in those with pure motor CP (31%, 4 of 13; p=0.02). Among patients with genetic diagnoses, CNVs were more frequent than point mutations among patients with congenital anomalies (OR 7.8, 95% CI 1.2 to 52.4) or major dysmorphic features (OR 10.5, 95% CI 1.4 to 73.7). Clinically significant mutations were identified in 18 different genes: 14 with known involvement in CP-related disorders and 4 responsible for other neurodevelopmental conditions. Three possible new candidate genes for CP were ARGEF10, RTF1 and TAOK3. CONCLUSIONS Cryptogenic CP is genetically highly heterogeneous. Genomic analysis has a high yield and is warranted in all these patients. Trio WES has higher yield than CMA, except in patients with congenital anomalies or major dysmorphic features, but these methods are complementary. Patients with negative results with one approach should also be tested by the other.
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Affiliation(s)
- Michal Yechieli
- Obstetrics and Gynecology, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Suleyman Gulsuner
- Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Hilla Ben-Pazi
- Pediatric Neurology, Shaare Zedek Medical Center, Jerusalem, Israel.,Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Aviva Fattal
- Pediatric Neurology Unit, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Adi Aran
- Pediatric Neurology, Shaare Zedek Medical Center, Jerusalem, Israel.,Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Alla Kuzminsky
- Pediatric Neurology Institute, Schneider Children's Medical Center of Israel, Petah Tikva, Israel
| | - Liora Sagi
- Pediatric Neurology Unit, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Dafna Guttman
- Pediatric Rehabilitation Department, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Nira Schneebaum Sender
- Pediatric Neurology Unit, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Varda Gross-Tsur
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.,Pediatric Neurology Unit, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Tehila Klopstock
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.,Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Tom Walsh
- Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Paul Renbaum
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Sharon Zeligson
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | | | - Dorit Lev
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Institute of Medical Genetics, Edith Wolfson Medical Center, Holon, Israel
| | - Dorit Shmueli
- Child Development Services, Clalit Health Services, Tel Aviv, Israel
| | - Luba Blumkin
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Neurology, Edith Wolfson Hospital, Holon, Israel
| | - Amnon Lahad
- Braun School of Public Health, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.,Department of Family Medicine, Clalit Health Services, Jerusalem, Israel
| | - Mary-Claire King
- Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Ephrat Lahad Levy
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.,Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Reeval Segel
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel .,Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
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12
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Abstract
Severe neuropsychiatric disorders are so genetically heterogeneous that virtually every unrelated patient harbors different clinically significant alleles. By studying schizophrenia in the Ashkenazi Jewish founder population, Lencz and co-authors identified rare severe alleles each shared by a few patients. Experimental evaluation of an implicated protocadherin allele revealed failure to form homophilic cellular aggregates as a possible mechanism for defective development of neural circuits.
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Affiliation(s)
- Jon M McClellan
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Mary-Claire King
- Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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13
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Kedar I, Walsh L, Levi GR, Lieberman S, Shtaya AA, Nathan SN, Lagovsky I, Tomashov-Matar R, Goldenberg M, Basel-Salmon L, Katz L, Aleme O, Peretz TY, Hubert A, Rothstein D, Castellvi-Bel S, Walsh T, King MC, Pritchard CC, Levi Z, Half E, Laish I, Goldberg Y. A novel founder MSH2 deletion in Ethiopian Jews is mainly associated with early-onset colorectal cancer. Fam Cancer 2021; 21:181-188. [PMID: 33837488 DOI: 10.1007/s10689-021-00249-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/29/2021] [Indexed: 11/27/2022]
Abstract
Lynch syndrome is an inherited cancer predisposition syndrome caused by germline defects in any of the mismatch repair (MMR) genes. Diagnosis of carriers makes precision prevention, early detection, and tailored treatment possible. Herein we report a novel founder deletion of 18,758 bp, mediated by Alu repeats on both sides, detected in Ethiopian Jews. The deletion, which encompasses exon 9-10 of the MSH2 coding sequence, is associated mainly with early-onset MSH2/MSH6-deficient colorectal cancer (CRC) and liposarcoma. Testing of 35 members of 5 seemingly unrelated families of Ethiopian origin yielded 10/21 (48%) carriers, of whom 9 had CRC. Age at first tumor diagnosis ranged from 16 to 89 years. Carriers from the oldest generations were diagnosed after age 45 years (mean 57), and carriers from the younger generation were diagnosed before age 45 years (mean 30). Awareness of this founder deletion is important to improve patient diagnosis, institute surveillance from an early age, and refer patients for genetic counseling addressing the risk of bi-allelic constitutional MMR deficiency syndrome.
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Affiliation(s)
- I Kedar
- The Raphael Recanati Genetics Institute, Rabin Medical Center - Beilinson Hospital, 39 Jabotinsky St., 4941492, Petach Tikva, Israel
| | - L Walsh
- Departments of Medicine and Genome Sciences, University of Washington, Seattle, WA, USA
| | - G Reznick Levi
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel
| | - S Lieberman
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - A Abu Shtaya
- Department of Internal Medicine, Carmel Medical Center, Haifa, Israel
| | - S Naftaly Nathan
- The Raphael Recanati Genetics Institute, Rabin Medical Center - Beilinson Hospital, 39 Jabotinsky St., 4941492, Petach Tikva, Israel
| | - I Lagovsky
- The Raphael Recanati Genetics Institute, Rabin Medical Center - Beilinson Hospital, 39 Jabotinsky St., 4941492, Petach Tikva, Israel
| | - R Tomashov-Matar
- The Raphael Recanati Genetics Institute, Rabin Medical Center - Beilinson Hospital, 39 Jabotinsky St., 4941492, Petach Tikva, Israel
| | - M Goldenberg
- The Raphael Recanati Genetics Institute, Rabin Medical Center - Beilinson Hospital, 39 Jabotinsky St., 4941492, Petach Tikva, Israel
| | - L Basel-Salmon
- The Raphael Recanati Genetics Institute, Rabin Medical Center - Beilinson Hospital, 39 Jabotinsky St., 4941492, Petach Tikva, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - L Katz
- Department of Gastroenterology and Hepatology, Hadassah Medical Center, Jerusalem, Israel
| | - O Aleme
- Genetics Institute, Emek Medical Center, Afula, Israel
| | - T Yablonski Peretz
- Sharett Institute of Oncology, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - A Hubert
- Gastrointestinal Cancer Center, Sharett Institute of Oncology, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | | | - S Castellvi-Bel
- Gastroenterology Department, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - T Walsh
- Departments of Medicine and Genome Sciences, University of Washington, Seattle, WA, USA
| | - M C King
- Departments of Medicine and Genome Sciences, University of Washington, Seattle, WA, USA
| | - C C Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Z Levi
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Division of Gastroenterology, Rabin Medical Center - Beilinson Hospital, Petach Tikva, Israel
| | - E Half
- Department of Gastroenterology, Rambam Health Care Campus, Haifa, Israel
| | - I Laish
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Gastroenterology Institute, Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Y Goldberg
- The Raphael Recanati Genetics Institute, Rabin Medical Center - Beilinson Hospital, 39 Jabotinsky St., 4941492, Petach Tikva, Israel.
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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14
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Kalra M, Tong Y, Jones DR, Walsh T, Danso MA, Ma CX, Silverman P, King MC, Badve SS, Perkins SM, Miller KD. Cisplatin +/- rucaparib after preoperative chemotherapy in patients with triple-negative or BRCA mutated breast cancer. NPJ Breast Cancer 2021; 7:29. [PMID: 33753748 PMCID: PMC7985189 DOI: 10.1038/s41523-021-00240-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 02/26/2021] [Indexed: 12/18/2022] Open
Abstract
Patients with triple-negative breast cancer (TNBC) who have residual disease after neoadjuvant therapy have a high risk of recurrence. We tested the impact of DNA-damaging chemotherapy alone or with PARP inhibition in this high-risk population. Patients with TNBC or deleterious BRCA mutation (TNBC/BRCAmut) who had >2 cm of invasive disease in the breast or persistent lymph node (LN) involvement after neoadjuvant therapy were assigned 1:1 to cisplatin alone or with rucaparib. Germline mutations were identified with BROCA analysis. The primary endpoint was 2-year disease-free survival (DFS) with 80% power to detect an HR 0.5. From Feb 2010 to May 2013, 128 patients were enrolled. Median tumor size at surgery was 1.9 cm (0-11.5 cm) with 1 (0-38) involved LN; median Residual Cancer Burden (RCB) score was 2.6. Six patients had known deleterious BRCA1 or BRCA2 mutations at study entry, but BROCA identified deleterious mutations in 22% of patients with available samples. Toxicity was similar in both arms. Despite frequent dose reductions (21% of patients) and delays (43.8% of patients), 73% of patients completed planned cisplatin. Rucaparib exposure was limited with median concentration 275 (82-4694) ng/mL post-infusion on day 3. The addition of rucaparib to cisplatin did not increase 2-year DFS (54.2% cisplatin vs. 64.1% cisplatin + rucaparib; P = 0.29). In the high-risk post preoperative TNBC/BRCAmut setting, the addition of low-dose rucaparib did not improve 2-year DFS or increase the toxicity of cisplatin. Genetic testing was underutilized in this high-risk population.
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Affiliation(s)
- Maitri Kalra
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN, USA
| | - Yan Tong
- Department of Biostatistics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - David R Jones
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN, USA
| | - Tom Walsh
- University of Washington, Seattle, WA, USA
| | | | - Cynthia X Ma
- Siteman Cancer Center, Washington University, St. Louis, MO, USA
| | - Paula Silverman
- University Hospitals Ireland Cancer Center, Case Comprehensive Cancer Center, Cleveland, OH, USA
| | | | - Sunil S Badve
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN, USA
| | - Susan M Perkins
- Department of Biostatistics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kathy D Miller
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN, USA.
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15
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King MC. 2020 William Allan Award address: genetics as a way of thinking-cultural inheritance from our teachers. Am J Hum Genet 2021; 108:386-391. [PMID: 33667391 DOI: 10.1016/j.ajhg.2021.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This article is based on the address given by the author at the 2020 virtual meeting of The American Society of Human Genetics (ASHG) on October 26, 2020. The video of the original address can be found at the ASHG website.
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Affiliation(s)
- Mary-Claire King
- Department of Medicine (Medical Genetics) and Department of Genome Sciences, University of Washington, Seattle, WA 98195-7720, USA.
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16
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Walsh T, Gulsuner S, Lee MK, Troester MA, Olshan AF, Earp HS, Perou CM, King MC. Inherited predisposition to breast cancer in the Carolina Breast Cancer Study. NPJ Breast Cancer 2021; 7:6. [PMID: 33479248 PMCID: PMC7820260 DOI: 10.1038/s41523-020-00214-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/17/2020] [Indexed: 11/09/2022] Open
Abstract
The Carolina Breast Cancer Study (CBCS) phases I-II was a case-control study of biological and social risk factors for invasive breast cancer that enrolled cases and controls between 1993 and 1999. Case selection was population-based and stratified by ancestry and age at diagnosis. Controls were matched to cases by age, self-identified race, and neighborhood of residence. Sequencing genomic DNA from 1370 cases and 1635 controls yielded odds ratios (with 95% confidence limits) for breast cancer of all subtypes of 26.7 (3.59, 189.1) for BRCA1, 8.8 (3.44, 22.48) for BRCA2, and 9.0 (2.06, 39.60) for PALB2; and for triple-negative breast cancer (TNBC) of 55.0 (7.01, 431.4) for BRCA1, 12.1 (4.18, 35.12) for BRCA2, and 10.8 (1.97, 59.11) for PALB2. Overall, 5.6% of patients carried a pathogenic variant in BRCA1, BRCA2, PALB2, or TP53, the four most highly penetrant breast cancer genes. Analysis of cases by tumor subtype revealed the expected association of TNBC versus other tumor subtypes with BRCA1, and suggested a significant association between TNBC versus other tumor subtypes with BRCA2 or PALB2 among African-American (AA) patients [2.95 (1.18, 7.37)], but not among European-American (EA) patients [0.62 (0.18, 2.09)]. AA patients with pathogenic variants in BRCA2 or PALB2 were 11 times more likely to be diagnosed with TNBC versus another tumor subtype than were EA patients with pathogenic variants in either of these genes (P = 0.001). If this pattern is confirmed in other comparisons of similarly ascertained AA and EA breast cancer patients, it could in part explain the higher prevalence of TNBC among AA breast cancer patients.
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Affiliation(s)
- Tom Walsh
- Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Suleyman Gulsuner
- Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Ming K Lee
- Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Melissa A Troester
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Andrew F Olshan
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - H Shelton Earp
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Charles M Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Mary-Claire King
- Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA.
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17
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Affiliation(s)
- Ephrat Levy-Lahad
- From the Shaare Zedek Medical Center and the Hebrew University of Jerusalem, Jerusalem (E.L.-L.); and the University of Washington, Seattle (M.-C.K.)
| | - Mary-Claire King
- From the Shaare Zedek Medical Center and the Hebrew University of Jerusalem, Jerusalem (E.L.-L.); and the University of Washington, Seattle (M.-C.K.)
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18
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Auerbach A, Cohen A, Ofek Shlomai N, Weinberg-Shukron A, Gulsuner S, King MC, Hemi R, Levy-Lahad E, Abulibdeh A, Zangen D. NKX2-2 Mutation Causes Congenital Diabetes and Infantile Obesity With Paradoxical Glucose-Induced Ghrelin Secretion. J Clin Endocrinol Metab 2020; 105:5895035. [PMID: 32818257 DOI: 10.1210/clinem/dgaa563] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/14/2020] [Indexed: 12/12/2022]
Abstract
CONTEXT NKX2-2 is a crucial transcription factor that enables specific β-cell gene expression. Nkx2-2(-/-) mice manifest with severe neonatal diabetes and changes in β-cell progenitor fate into ghrelin-producing cells. In humans, recessive NKX2-2 gene mutations have been recently reported as a novel etiology for neonatal diabetes, with only 3 cases known worldwide. This study describes the genetic analysis, distinctive clinical features, the therapeutic challenges, and the unique pathophysiology causing neonatal diabetes in human NKX2-2 dysfunction. CASE DESCRIPTION An infant with very low birth weight (VLBW) and severe neonatal diabetes (NDM) presented with severe obesity and developmental delay already at age 1 year. The challenge of achieving glycemic control in a VLBW infant was unexpectedly met by a regimen of 3 daily doses of long-acting insulin analogues. Sanger sequencing of known NDM genes (such as ABCC8 and EIF2AK3) was followed by whole-exome sequencing that revealed homozygosity of a pathogenic frameshift variant, c.356delG, p.P119fs64*, in the islet cells transcription factor, NKX2-2. To elucidate the cause for the severe obesity, an oral glucose tolerance test was conducted at age 3.5 years and revealed undetectable C-peptide levels with a paradoxically unexpected 30% increase in ghrelin levels. CONCLUSION Recessive NKX2-2 loss of function causes severe NDM associated with VLBW, childhood obesity, and developmental delay. The severe obesity phenotype is associated with postprandial paradoxical ghrelin secretion, which may be related to human β-cell fate change to ghrelin-secreting cells, recapitulating the finding in Nkx2-2(-/-) mice islet cells.
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Affiliation(s)
- Adi Auerbach
- Division of Pediatric Endocrinology, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Amitay Cohen
- Hadassah Mt. Scopus, Department of Pediatrics, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Noa Ofek Shlomai
- Department of Neonatology, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Ariella Weinberg-Shukron
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
- Hadassah Medical School, Hebrew University, Jerusalem 9112102, Israel
| | - Suleyman Gulsuner
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, DC
| | - Mary-Claire King
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, DC
| | - Rina Hemi
- Institute of Endocrinology, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Ephrat Levy-Lahad
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
- Hadassah Medical School, Hebrew University, Jerusalem 9112102, Israel
| | - Abdulsalam Abulibdeh
- Division of Pediatric Endocrinology, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - David Zangen
- Division of Pediatric Endocrinology, Hadassah Hebrew University Medical Center, Jerusalem, Israel
- Hadassah Medical School, Hebrew University, Jerusalem 9112102, Israel
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19
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Walsh T, Casadei S, Munson KM, Eng M, Mandell JB, Gulsuner S, King MC. CRISPR-Cas9/long-read sequencing approach to identify cryptic mutations in BRCA1 and other tumour suppressor genes. J Med Genet 2020; 58:850-852. [PMID: 33060287 PMCID: PMC8046837 DOI: 10.1136/jmedgenet-2020-107320] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/24/2020] [Accepted: 08/27/2020] [Indexed: 01/07/2023]
Abstract
Current clinical approaches for mutation discovery are based on short sequence reads (100-300 bp) of exons and flanking splice sites targeted by multigene panels or whole exomes. Short-read sequencing is highly accurate for detection of single nucleotide variants, small indels and simple copy number differences but is of limited use for identifying complex insertions and deletions and other structural rearrangements. We used CRISPR-Cas9 to excise complete BRCA1 and BRCA2 genomic regions from lymphoblast cells of patients with breast cancer, then sequenced these regions with long reads (>10 000 bp) to fully characterise all non-coding regions for structural variation. In a family severely affected with early-onset bilateral breast cancer and with negative (normal) results by gene panel and exome sequencing, we identified an intronic SINE-VNTR-Alu retrotransposon insertion that led to the creation of a pseudoexon in the BRCA1 message and introduced a premature truncation. This combination of CRISPR-Cas9 excision and long-read sequencing reveals a class of complex, damaging and otherwise cryptic mutations that may be particularly frequent in tumour suppressor genes replete with intronic repeats.
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Affiliation(s)
- Tom Walsh
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Silvia Casadei
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Katherine M Munson
- Department of Genome Sciences, Unversity of Washington, Seattle, Washington, USA
| | - Mary Eng
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Jessica B Mandell
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Suleyman Gulsuner
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Mary-Claire King
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle, Washington, USA
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20
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Kamal L, Pierce SB, Canavati C, Rayyan AA, Jaraysa T, Lobel O, Lolas S, Norquist BM, Rabie G, Zahdeh F, Levy-Lahad E, King MC, Kanaan MN. Helicase-inactivating BRIP1 mutation yields Fanconi anemia with microcephaly and other congenital abnormalities. Cold Spring Harb Mol Case Stud 2020; 6:a005652. [PMID: 33028645 PMCID: PMC7552932 DOI: 10.1101/mcs.a005652] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/11/2020] [Indexed: 02/07/2023] Open
Abstract
Fanconi anemia is a genetically and phenotypically heterogeneous disorder characterized by congenital anomalies, bone marrow failure, cancer, and sensitivity of chromosomes to DNA cross-linking agents. One of the 22 genes responsible for Fanconi anemia is BRIP1, in which biallelic truncating mutations lead to Fanconi anemia group J and monoallelic truncating mutations predispose to certain cancers. However, of the more than 1000 reported missense mutations in BRIP1, very few have been functionally characterized. We evaluated the functional consequence of BRIP1 p.R848H (c.2543G > A), which was homozygous in two cousins with low birth weight, microcephaly, upper limb abnormalities, and imperforate anus and for whom chromosome breakage analysis of patient cells revealed increased mitomycin C sensitivity. BRIP1 p.R848H alters a highly conserved residue in the catalytic DNA helicase domain. We show that BRIP1 p.R848H leads to a defect in helicase activity. Heterozygosity at this missense has been reported in multiple cancer patients but, in the absence of functional studies, classified as of unknown significance. Our results support that this mutation is pathogenic for Fanconi anemia in homozygotes and for increased cancer susceptibility in heterozygous carriers.
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Affiliation(s)
- Lara Kamal
- Molecular Genetics Laboratory, Istishari Arab Hospital, Ramallah, Palestine
- Hereditary Research Laboratory and Department of Biology, Bethlehem University, Bethlehem, Palestine
| | - Sarah B Pierce
- Departments of Medicine and Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Christina Canavati
- Hereditary Research Laboratory and Department of Biology, Bethlehem University, Bethlehem, Palestine
| | - Amal Abu Rayyan
- Hereditary Research Laboratory and Department of Biology, Bethlehem University, Bethlehem, Palestine
| | - Tamara Jaraysa
- Hereditary Research Laboratory and Department of Biology, Bethlehem University, Bethlehem, Palestine
| | - Orit Lobel
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem 9103102, Israel
| | - Suhair Lolas
- Hereditary Research Laboratory and Department of Biology, Bethlehem University, Bethlehem, Palestine
| | - Barbara M Norquist
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington 98195, USA
| | - Grace Rabie
- Hereditary Research Laboratory and Department of Biology, Bethlehem University, Bethlehem, Palestine
| | - Fouad Zahdeh
- Hereditary Research Laboratory and Department of Biology, Bethlehem University, Bethlehem, Palestine
| | - Ephrat Levy-Lahad
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem 9103102, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Mary-Claire King
- Departments of Medicine and Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Moien N Kanaan
- Molecular Genetics Laboratory, Istishari Arab Hospital, Ramallah, Palestine
- Hereditary Research Laboratory and Department of Biology, Bethlehem University, Bethlehem, Palestine
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21
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Bodily WR, Shirts BH, Walsh T, Gulsuner S, King MC, Parker A, Roosan M, Piccolo SR. Effects of germline and somatic events in candidate BRCA-like genes on breast-tumor signatures. PLoS One 2020; 15:e0239197. [PMID: 32997669 PMCID: PMC7526916 DOI: 10.1371/journal.pone.0239197] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/02/2020] [Indexed: 11/19/2022] Open
Abstract
Mutations in BRCA1 and BRCA2 cause deficiencies in homologous recombination repair (HR), resulting in repair of DNA double-strand breaks by the alternative non-homologous end-joining pathway, which is more error prone. HR deficiency of breast tumors is important because it is associated with better responses to platinum salt therapies and PARP inhibitors. Among other consequences of HR deficiency are characteristic somatic-mutation signatures and gene-expression patterns. The term "BRCA-like" (or "BRCAness") describes tumors that harbor an HR defect but have no detectable germline mutation in BRCA1 or BRCA2. A better understanding of the genes and molecular events associated with tumors being BRCA-like could provide mechanistic insights and guide development of targeted treatments. Using data from The Cancer Genome Atlas (TCGA) for 1101 breast-cancer patients, we identified individuals with a germline mutation, somatic mutation, homozygous deletion, and/or hypermethylation event in BRCA1, BRCA2, and 59 other cancer-predisposition genes. Based on the assumption that BRCA-like events would have similar downstream effects on tumor biology as BRCA1/BRCA2 germline mutations, we quantified these effects based on somatic-mutation signatures and gene-expression profiles. We reduced the dimensionality of the somatic-mutation signatures and expression data and used a statistical resampling approach to quantify similarities among patients who had a BRCA1/BRCA2 germline mutation, another type of aberration in BRCA1 or BRCA2, or any type of aberration in one of the other genes. Somatic-mutation signatures of tumors having a non-germline aberration in BRCA1/BRCA2 (n = 80) were generally similar to each other and to tumors from BRCA1/BRCA2 germline carriers (n = 44). Additionally, somatic-mutation signatures of tumors with germline or somatic events in ATR (n = 16) and BARD1 (n = 8) showed high similarity to tumors from BRCA1/BRCA2 carriers. Other genes (CDKN2A, CTNNA1, PALB2, PALLD, PRSS1, SDHC) also showed high similarity but only for a small number of events or for a single event type. Tumors with germline mutations or hypermethylation of BRCA1 had relatively similar gene-expression profiles and overlapped considerably with the Basal-like subtype; but the transcriptional effects of the other events lacked consistency. Our findings confirm previously known relationships between molecular signatures and germline or somatic events in BRCA1/BRCA2. Our methodology represents an objective way to identify genes that have similar downstream effects on molecular signatures when mutated, deleted, or hypermethylated.
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Affiliation(s)
- Weston R. Bodily
- Department of Biology, Brigham Young University, Provo, UT, United States of America
| | - Brian H. Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Tom Walsh
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Suleyman Gulsuner
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Mary-Claire King
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Alyssa Parker
- Department of Biology, Brigham Young University, Provo, UT, United States of America
| | - Moom Roosan
- Pharmacy Practice Department, Chapman University School of Pharmacy, Irvine, CA, United States of America
| | - Stephen R. Piccolo
- Department of Biology, Brigham Young University, Provo, UT, United States of America
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22
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Brownstein Z, Gulsuner S, Walsh T, Martins FTA, Taiber S, Isakov O, Lee MK, Bordeynik-Cohen M, Birkan M, Chang W, Casadei S, Danial-Farran N, Abu-Rayyan A, Carlson R, Kamal L, Arnthórsson AÖ, Sokolov M, Gilony D, Lipschitz N, Frydman M, Davidov B, Macarov M, Sagi M, Vinkler C, Poran H, Sharony R, Samra N, Zvi N, Baris-Feldman H, Singer A, Handzel O, Hertzano R, Ali-Naffaa D, Ruhrman-Shahar N, Madgar O, Sofrin-Drucker E, Peleg A, Khayat M, Shohat M, Basel-Salmon L, Pras E, Lev D, Wolf M, Steingrimsson E, Shomron N, Kelley MW, Kanaan MN, Allon-Shalev S, King MC, Avraham KB. Spectrum of genes for inherited hearing loss in the Israeli Jewish population, including the novel human deafness gene ATOH1. Clin Genet 2020; 98:353-364. [PMID: 33111345 DOI: 10.1111/cge.13817] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 12/26/2022]
Abstract
Mutations in more than 150 genes are responsible for inherited hearing loss, with thousands of different, severe causal alleles that vary among populations. The Israeli Jewish population includes communities of diverse geographic origins, revealing a wide range of deafness-associated variants and enabling clinical characterization of the associated phenotypes. Our goal was to identify the genetic causes of inherited hearing loss in this population, and to determine relationships among genotype, phenotype, and ethnicity. Genomic DNA samples from informative relatives of 88 multiplex families, all of self-identified Jewish ancestry, with either non-syndromic or syndromic hearing loss, were sequenced for known and candidate deafness genes using the HEar-Seq gene panel. The genetic causes of hearing loss were identified for 60% of the families. One gene was encountered for the first time in human hearing loss: ATOH1 (Atonal), a basic helix-loop-helix transcription factor responsible for autosomal dominant progressive hearing loss in a five-generation family. Our results show that genomic sequencing with a gene panel dedicated to hearing loss is effective for genetic diagnoses in a diverse population. Comprehensive sequencing enables well-informed genetic counseling and clinical management by medical geneticists, otolaryngologists, audiologists, and speech therapists and can be integrated into newborn screening for deafness.
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Affiliation(s)
- Zippora Brownstein
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Suleyman Gulsuner
- Departments of Genome Sciences and Medicine, University of Washington, Seattle, Washington, USA
| | - Tom Walsh
- Departments of Genome Sciences and Medicine, University of Washington, Seattle, Washington, USA
| | - Fábio T A Martins
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Shahar Taiber
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Ofer Isakov
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ming K Lee
- Departments of Genome Sciences and Medicine, University of Washington, Seattle, Washington, USA
| | - Mor Bordeynik-Cohen
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Maria Birkan
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.,Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Tel Aviv University Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Weise Chang
- Laboratory of Cochlear Development, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA
| | - Silvia Casadei
- Departments of Genome Sciences and Medicine, University of Washington, Seattle, Washington, USA
| | - Nada Danial-Farran
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.,Genetics Institute, Ha'Emek Medical Center, Afula, Israel.,Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Amal Abu-Rayyan
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.,Department of Biological Sciences, Bethlehem University, Bethlehem, Palestine
| | - Ryan Carlson
- Departments of Genome Sciences and Medicine, University of Washington, Seattle, Washington, USA
| | - Lara Kamal
- Department of Biological Sciences, Bethlehem University, Bethlehem, Palestine
| | - Asgeir Ö Arnthórsson
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Meirav Sokolov
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.,Department of Otolaryngology-Head and Neck Surgery, Schneider Children's Medical Center, Petach Tikva, Israel
| | - Dror Gilony
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.,Department of Otolaryngology-Head and Neck Surgery, Schneider Children's Medical Center, Petach Tikva, Israel
| | - Noga Lipschitz
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.,Department of Otolaryngology-Head and Neck Surgery, Sheba Medical Center, Tel Hashomer, Israel
| | - Moshe Frydman
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.,Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
| | - Bella Davidov
- Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Tel Aviv University Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Michal Macarov
- Department of Human Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Michal Sagi
- Department of Human Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Chana Vinkler
- Institute of Medical Genetics, Wolfson Medical Center, Holon, Israel
| | - Hana Poran
- Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
| | - Reuven Sharony
- Genetics Institute, Meir Medical Center, Kfar Saba and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Na'ama Zvi
- Department of Human Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Hagit Baris-Feldman
- Genetics Institute, Tel-Aviv Sourasky Medical Center and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Amihood Singer
- Community Genetics Department, Public Health Services, Ministry of Health, Ramat Gan, Israel
| | - Ophir Handzel
- Department of Otolaryngology Head and Neck Surgery and Maxillofacial Surgery, Tel-Aviv Sourasky Medical Center and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ronna Hertzano
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Doaa Ali-Naffaa
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.,Human Genetics Institute, Lady Davis Carmel Medical Center, Haifa, Israel
| | - Noa Ruhrman-Shahar
- Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Tel Aviv University Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Ory Madgar
- Department of Otolaryngology-Head and Neck Surgery, Sheba Medical Center, Tel Hashomer, Israel
| | - Efrat Sofrin-Drucker
- Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Tel Aviv University Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Amir Peleg
- Human Genetics Institute, Lady Davis Carmel Medical Center, Haifa, Israel
| | - Morad Khayat
- Genetics Institute, Ha'Emek Medical Center, Afula, Israel
| | - Mordechai Shohat
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.,Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Israel.,Institute of Medical Genetics, Maccabi HMO, Rehovot, Israel
| | - Lina Basel-Salmon
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.,Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Tel Aviv University Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Elon Pras
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.,Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
| | - Dorit Lev
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.,Institute of Medical Genetics, Wolfson Medical Center, Holon, Israel
| | - Michael Wolf
- Department of Otolaryngology-Head and Neck Surgery, Sheba Medical Center, Tel Hashomer, Israel
| | - Eirikur Steingrimsson
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Noam Shomron
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Matthew W Kelley
- Laboratory of Cochlear Development, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA
| | - Moien N Kanaan
- Department of Biological Sciences, Bethlehem University, Bethlehem, Palestine
| | - Stavit Allon-Shalev
- Genetics Institute, Ha'Emek Medical Center, Afula, Israel.,Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Mary-Claire King
- Departments of Genome Sciences and Medicine, University of Washington, Seattle, Washington, USA
| | - Karen B Avraham
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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23
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Abdel-Rahman MH, Sample KM, Pilarski R, Walsh T, Grosel T, Kinnamon D, Boru G, Massengill JB, Schoenfield L, Kelly B, Gordon D, Johansson P, DeBenedictis MJ, Singh A, Casadei S, Davidorf FH, White P, Stacey AW, Scarth J, Fewings E, Tischkowitz M, King MC, Hayward NK, Cebulla CM. Whole Exome Sequencing Identifies Candidate Genes Associated with Hereditary Predisposition to Uveal Melanoma. Ophthalmology 2019; 127:668-678. [PMID: 32081490 DOI: 10.1016/j.ophtha.2019.11.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/13/2019] [Accepted: 11/11/2019] [Indexed: 01/08/2023] Open
Abstract
PURPOSE To identify susceptibility genes associated with hereditary predisposition to uveal melanoma (UM) in patients with no detectable germline BAP1 alterations. DESIGN Retrospective case series from academic referral centers. PARTICIPANTS Cohort of 154 UM patients with high risk of hereditary cancer defined as patients with 1 or more of the following: (1) familial UM, (2) young age (<35 years) at diagnosis, (3) personal history of other primary cancers, and (4) family history of 2 or more primary cancers with no detectable mutation or deletion in BAP1 gene. METHODS Whole exome sequencing, a cancer gene panel, or both were carried out. Probands included 27 patients with familial UM, 1 patient with bilateral UM, 1 patient with congenital UM, and 125 UM patients with strong personal or family histories, or both, of cancer. Functional validation of variants was carried out by immunohistochemistry, reverse-transcriptase polymerase chain reaction, and genotyping. MAIN OUTCOME MEASURES Clinical characterization of UM patients with germline alterations in known cancer genes. RESULTS We identified actionable pathogenic variants in 8 known hereditary cancer predisposition genes (PALB2, MLH1, MSH6, CHEK2, SMARCE1, ATM, BRCA1, and CTNNA1) in 9 patients, including 3 of 27 patients (11%) with familial UM and 6 of 127 patients (4.7%) with a high risk for cancer. Two patients showed pathogenic variants in CHEK2 and PALB2, whereas variants in the other genes each occurred in 1 patient. Biallelic inactivation of PALB2 and MLH1 was observed in tumors from the respective patients. The frequencies of pathogenic variants in PALB2, MLH1, and SMARCE1 in UM patients were significantly higher than the observed frequencies in noncancer controls (PALB2: P = 0.02; odds ratio, 8.9; 95% confidence interval, 1.5-30.6; MLH1: P = 0.04; odds ratio, 25.4; 95% confidence interval, 1.2-143; SMARCE1: P = 0.001; odds ratio, 2047; 95% confidence interval, 52-4.5e15, respectively). CONCLUSIONS The study provided moderate evidence of gene and disease association of germline mutations in PALB2 and MLH1 with hereditary predisposition to UM. It also identified several other candidate susceptibility genes. The results suggest locus heterogeneity in predisposition to UM. Genetic testing for hereditary predisposition to cancer is warranted in UM patients with strong personal or family history of cancers, or both.
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Affiliation(s)
- Mohamed H Abdel-Rahman
- Department of Ophthalmology and Visual Science, Havener Eye Institute, The Ohio State University, Columbus, Ohio; Division of Human Genetics, Department of Internal Medicine, The Ohio State University, Columbus, Ohio.
| | - Klarke M Sample
- Department of Ophthalmology and Visual Science, Havener Eye Institute, The Ohio State University, Columbus, Ohio
| | - Robert Pilarski
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
| | - Tomas Walsh
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Timothy Grosel
- Department of Ophthalmology and Visual Science, Havener Eye Institute, The Ohio State University, Columbus, Ohio
| | - Daniel Kinnamon
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
| | - Getachew Boru
- Department of Ophthalmology and Visual Science, Havener Eye Institute, The Ohio State University, Columbus, Ohio
| | - James B Massengill
- Department of Ophthalmology and Visual Science, Havener Eye Institute, The Ohio State University, Columbus, Ohio
| | - Lynn Schoenfield
- Department of Pathology, The Ohio State University, Columbus, Ohio
| | - Ben Kelly
- The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio
| | - David Gordon
- The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio
| | - Peter Johansson
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Meghan J DeBenedictis
- Department of Ophthalmic Oncology, Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio
| | - Arun Singh
- Department of Ophthalmic Oncology, Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio
| | - Silvia Casadei
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Frederick H Davidorf
- Department of Ophthalmology and Visual Science, Havener Eye Institute, The Ohio State University, Columbus, Ohio
| | - Peter White
- The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio
| | - Andrew W Stacey
- Department of Ophthalmology, University of Washington, Seattle, Washington
| | - James Scarth
- Academic Laboratory of Medical Genetics and National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Ellie Fewings
- Academic Laboratory of Medical Genetics and National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Marc Tischkowitz
- Academic Laboratory of Medical Genetics and National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom; East Anglian Medical Genetics Service, Cambridge University Hospitals, Cambridge, United Kingdom
| | - Mary-Claire King
- Department of Genome Sciences, University of Washington, Seattle, Washington; Department of Medicine, University of Washington, Seattle, Washington
| | | | - Colleen M Cebulla
- Department of Ophthalmology and Visual Science, Havener Eye Institute, The Ohio State University, Columbus, Ohio
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24
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Seo A, Gulsuner S, Pierce S, Ben-Harosh M, Shalev H, Walsh T, Krasnov T, Dgany O, Doulatov S, Tamary H, Shimamura A, King MC. Inherited thrombocytopenia associated with mutation of UDP-galactose-4-epimerase (GALE). Hum Mol Genet 2019; 28:133-142. [PMID: 30247636 DOI: 10.1093/hmg/ddy334] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 09/07/2018] [Indexed: 12/11/2022] Open
Abstract
Severe thrombocytopenia, characterized by dysplastic megakaryocytes and intracranial bleeding, was diagnosed in six individuals from a consanguineous kindred. Three of the individuals were successfully treated by bone marrow transplant. Whole-exome sequencing and homozygosity mapping of multiple family members, coupled with whole-genome sequencing to reveal shared non-coding variants, revealed one potentially functional variant segregating with thrombocytopenia under a recessive model: GALE p.R51W (c.C151T, NM_001127621). The mutation is extremely rare (allele frequency = 2.5 × 10-05), and the likelihood of the observed co-segregation occurring by chance is 1.2 × 10-06. GALE encodes UDP-galactose-4-epimerase, an enzyme of galactose metabolism and glycosylation responsible for two reversible reactions: interconversion of UDP-galactose with UDP-glucose and interconversion of UDP-N-acetylgalactosamine with UDP-N-acetylglucosamine. The mutation alters an amino acid residue that is conserved from yeast to humans. The variant protein has both significantly lower enzymatic activity for both interconversion reactions and highly significant thermal instability. Proper glycosylation is critical to normal hematopoiesis, in particular to megakaryocyte and platelet development, as reflected in the presence of thrombocytopenia in the context of congenital disorders of glycosylation. Mutations in GALE have not previously been associated with thrombocytopenia. Our results suggest that GALE p.R51W is inadequate for normal glycosylation and thereby may impair megakaryocyte and platelet development. If other mutations in GALE are shown to have similar consequences, this gene may be proven to play a critical role in hematopoiesis.
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Affiliation(s)
- Aaron Seo
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | - Suleyman Gulsuner
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | - Sarah Pierce
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | - Miri Ben-Harosh
- Department of Pediatric Hematology/Oncology, Soroka Medical Center, Faculty of Medicine, Ben-Gurion University, Beer Sheva, Israel
| | - Hanna Shalev
- Department of Pediatric Hematology/Oncology, Soroka Medical Center, Faculty of Medicine, Ben-Gurion University, Beer Sheva, Israel
| | - Tom Walsh
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | - Tanya Krasnov
- Pediatric Hematology Laboratory, Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Orly Dgany
- Pediatric Hematology Laboratory, Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Sergei Doulatov
- Department of Medicine, Division of Hematology, University of Washington, Seattle, WA, USA
| | - Hannah Tamary
- Pediatric Hematology Laboratory, Felsenstein Medical Research Center, Petach Tikva, Israel.,Hematology Unit, Schneider Children's Medical Center, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Akiko Shimamura
- Department of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Mary-Claire King
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
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25
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Walsh T, Mandell JB, Norquist BM, Casadei S, Gulsuner S, Lee MK, King MC. Genetic Predisposition to Breast Cancer Due to Mutations Other Than BRCA1 and BRCA2 Founder Alleles Among Ashkenazi Jewish Women. JAMA Oncol 2019; 3:1647-1653. [PMID: 28727877 DOI: 10.1001/jamaoncol.2017.1996] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Importance Among Ashkenazi Jewish women, 3 mutations in BRCA1 and BRCA2 severely increase the risk of breast and ovarian cancer. However, among Ashkenazi Jewish patients with breast cancer who do not carry one of these founder mutations, the likelihood of carrying another pathogenic mutation in BRCA1 or BRCA2 or another breast cancer gene is not known. This information would be valuable to the patient and family for cancer prevention and treatment. Objective To determine the frequency of cancer-predisposing mutations other than the BRCA1 and BRCA2 founder alleles among patients of Ashkenazi Jewish ancestry with breast cancer. Design, Setting, and Participants In this cohort study, genomic DNA of women from 12 major cancer centers with a first diagnosis of invasive breast cancer who identified themselves and all 4 grandparents as Ashkenazi Jewish and participated in the New York Breast Cancer Study (NYBCS) from 1996 to 2000 was sequenced for known and candidate breast cancer genes. Data analysis was performed from July 10, 2014, to March 10, 2017. Main Outcomes and Measures Genomic DNA from all 1007 NYBCS probands was sequenced for 23 known and candidate breast cancer genes using BROCA, a targeted multiplexed gene panel. Results Of the 1007 probands in the study, 903 probands had no founder mutations in BRCA1 or BRCA2; of these probands, 7 (0.8%) carried another pathogenic mutation in BRCA1 or BRCA2, and 31 (3.4%) carried a pathogenic mutation in another breast cancer gene (29 in CHEK2, and 1 each in BRIP1 and NBN). Of all inherited predispositions to breast cancer in the NYBCS, 73.8% (104 of 142) were due to a BRCA1 or BRCA2 founder allele, 4.9% (7 of 142) to another BRCA1 or BRCA2 mutation, and 21.8% (31 of 142) to a mutation in another gene. Overall, 14.1% (142 of 1007) of Ashkenazi Jewish patients with breast cancer in the NYBCS carried a germline mutation responsible for their disease: 11.0% (111 of 1007) in BRCA1 or BRCA2, and 3.1% (31 of 1007) in CHEK2 or another breast cancer gene. Of the 111 patients with BRCA1 or BRCA2 mutations, 57 (51.4%) had a mother or sister with breast or ovarian cancer and 54 patients (48.6%) did not. Conclusions and Relevance Comprehensive sequencing would provide complete relevant genetic information for Ashkenazi Jewish patients with breast cancer.
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Affiliation(s)
- Tom Walsh
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle,Department of Genome Sciences, University of Washington, Seattle
| | - Jessica B Mandell
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle,Department of Genome Sciences, University of Washington, Seattle
| | - Barbara M Norquist
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Washington, Seattle
| | - Silvia Casadei
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle,Department of Genome Sciences, University of Washington, Seattle
| | - Suleyman Gulsuner
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle,Department of Genome Sciences, University of Washington, Seattle
| | - Ming K Lee
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle,Department of Genome Sciences, University of Washington, Seattle
| | - Mary-Claire King
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle,Department of Genome Sciences, University of Washington, Seattle
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26
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Guindalini RSC, Zheng Y, Abe H, Whitaker K, Yoshimatsu TF, Walsh T, Schacht D, Kulkarni K, Sheth D, Verp MS, Bradbury AR, Churpek J, Obeid E, Mueller J, Khramtsova G, Liu F, Raoul A, Cao H, Romero IL, Hong S, Livingston R, Jaskowiak N, Wang X, Debiasi M, Pritchard CC, King MC, Karczmar G, Newstead GM, Huo D, Olopade OI. Intensive Surveillance with Biannual Dynamic Contrast-Enhanced Magnetic Resonance Imaging Downstages Breast Cancer in BRCA1 Mutation Carriers. Clin Cancer Res 2019; 25:1786-1794. [PMID: 30154229 PMCID: PMC6395536 DOI: 10.1158/1078-0432.ccr-18-0200] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 05/23/2018] [Accepted: 08/22/2018] [Indexed: 12/17/2022]
Abstract
PURPOSE To establish a cohort of high-risk women undergoing intensive surveillance for breast cancer.Experimental Design: We performed dynamic contrast-enhanced MRI every 6 months in conjunction with annual mammography (MG). Eligible participants had a cumulative lifetime breast cancer risk ≥20% and/or tested positive for a pathogenic mutation in a known breast cancer susceptibility gene. RESULTS Between 2004 and 2016, we prospectively enrolled 295 women, including 157 mutation carriers (75 BRCA1, 61 BRCA2); participants' mean age at entry was 43.3 years. Seventeen cancers were later diagnosed: 4 ductal carcinoma in situ (DCIS) and 13 early-stage invasive breast cancers. Fifteen cancers occurred in mutation carriers (11 BRCA1, 3 BRCA2, 1 CDH1). Median size of the invasive cancers was 0.61 cm. No patients had lymph node metastasis at time of diagnosis, and no interval invasive cancers occurred. The sensitivity of biannual MRI alone was 88.2% and annual MG plus biannual MRI was 94.1%. The cancer detection rate of biannual MRI alone was 0.7% per 100 screening episodes, which is similar to the cancer detection rate of 0.7% per 100 screening episodes for annual MG plus biannual MRI. The number of recalls and biopsies needed to detect one cancer by biannual MRI were 2.8 and 1.7 in BRCA1 carriers, 12.0 and 8.0 in BRCA2 carriers, and 11.7 and 5.0 in non-BRCA1/2 carriers, respectively. CONCLUSIONS Biannual MRI performed well for early detection of invasive breast cancer in genomically stratified high-risk women. No benefit was associated with annual MG screening plus biannual MRI screening.See related commentary by Kuhl and Schrading, p. 1693.
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Affiliation(s)
- Rodrigo Santa Cruz Guindalini
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, The University of Chicago, Chicago, Illinois
- CLION, CAM Group, Salvador, Bahia, Brazil
- Department of Radiology and Oncology, The State of Sao Paulo Cancer Institute, University of Sao Paulo Medical School, Sao Paulo, São Paulo, Brazil
| | - Yonglan Zheng
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Hiroyuki Abe
- Department of Radiology, The University of Chicago, Chicago, Illinois
| | - Kristen Whitaker
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Toshio F Yoshimatsu
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Tom Walsh
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington
| | - David Schacht
- Department of Radiology, The University of Chicago, Chicago, Illinois
| | - Kirti Kulkarni
- Department of Radiology, The University of Chicago, Chicago, Illinois
| | - Deepa Sheth
- Department of Radiology, The University of Chicago, Chicago, Illinois
| | - Marion S Verp
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Angela R Bradbury
- Department of Medicine, Division of Hematology-Oncology, and Department of Medical Ethics and Health Policy, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jane Churpek
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Elias Obeid
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Jeffrey Mueller
- Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Galina Khramtsova
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Fang Liu
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Akila Raoul
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Hongyuan Cao
- Department of Public Health Sciences, The University of Chicago, Chicago, Illinois
| | - Iris L Romero
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, The University of Chicago, Chicago, Illinois
- Department of Obstetrics and Gynecology, The University of Chicago, Chicago, Illinois
| | - Susan Hong
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, The University of Chicago, Chicago, Illinois
- University of Illinois Cancer Center, University of Illinois - Chicago, Chicago, Illinois
| | - Robert Livingston
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Nora Jaskowiak
- Department of Surgery, The University of Chicago, Chicago, Illinois
| | - Xiaoming Wang
- Computation Institute, The University of Chicago, Chicago, Illinois
| | - Marcio Debiasi
- PUCRS School of Medicine, Porto Alegre, Rio Grande do Sul, Brazil
- Latin American Cooperative Oncology Group (LACOG), Porto Alegre, Rio Grande do Sul, Brazil
| | - Colin C Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Mary-Claire King
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington
| | - Gregory Karczmar
- Department of Radiology, The University of Chicago, Chicago, Illinois.
| | | | - Dezheng Huo
- Department of Public Health Sciences, The University of Chicago, Chicago, Illinois.
| | - Olufunmilayo I Olopade
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, The University of Chicago, Chicago, Illinois.
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27
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Zheng Y, Walsh T, Gulsuner S, Casadei S, Lee MK, Ogundiran TO, Ademola A, Falusi AG, Adebamowo CA, Oluwasola AO, Adeoye A, Odetunde A, Babalola CP, Ojengbede OA, Odedina S, Anetor I, Wang S, Huo D, Yoshimatsu TF, Zhang J, Felix GE, King MC, Olopade OI. Inherited Breast Cancer in Nigerian Women. J Clin Oncol 2018; 36:2820-2825. [PMID: 30130155 PMCID: PMC6161833 DOI: 10.1200/jco.2018.78.3977] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
PURPOSE Among Nigerian women, breast cancer is diagnosed at later stages, is more frequently triple-negative disease, and is far more frequently fatal than in Europe or the United States. We evaluated the contribution of an inherited predisposition to breast cancer in this population. PATIENTS AND METHODS Cases were 1,136 women with invasive breast cancer (mean age at diagnosis, 47.5 ± 11.5 years) ascertained in Ibadan, Nigeria. Patients were selected regardless of age at diagnosis, family history, or prior genetic testing. Controls were 997 women without cancer (mean age at interview, 47.0 ± 12.4 years) from the same communities. BROCA panel sequencing was used to identify loss-of-function mutations in known and candidate breast cancer genes. RESULTS Of 577 patients with information on tumor stage, 86.1% (497) were diagnosed at stage III (241) or IV (256). Of 290 patients with information on tumor hormone receptor status and human epidermal growth factor receptor 2, 45.9% (133) had triple-negative breast cancer. Among all cases, 14.7% (167 of 1,136) carried a loss-of-function mutation in a breast cancer gene: 7.0% in BRCA1, 4.1% in BRCA2, 1.0% in PALB2, 0.4% in TP53, and 2.1% in any of 10 other genes. Odds ratios were 23.4 (95% CI, 7.4 to 73.9) for BRCA1 and 10.3 (95% CI, 3.7 to 28.5) for BRCA2. Risks were also significantly associated with PALB2 (11 cases, zero controls; P = .002) and TP53 (five cases, zero controls; P = .036). Compared with other patients, BRCA1 mutation carriers were younger ( P < .001) and more likely to have triple-negative breast cancer ( P = .028). CONCLUSION Among Nigerian women, one in eight cases of invasive breast cancer is a result of inherited mutations in BRCA1, BRCA2, PALB2, or TP53, and breast cancer risks associated with these genes are extremely high. Given limited resources, prevention and early detection services should be especially focused on these highest-risk women.
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Affiliation(s)
- Yonglan Zheng
- Yonglan Zheng, Shengfeng Wang, Dezheng Huo, Toshio F. Yoshimatsu, Jing Zhang, Gabriela E.S. Felix, and Olufunmilayo I. Olopade, The University of Chicago, Chicago, IL; Tom Walsh, Suleyman Gulsuner, Silvia Casadei, Ming K. Lee, and Mary-Claire King, University of Washington, Seattle, WA; Temidayo O. Ogundiran, Adeyinka Ademola, Adeyinka G. Falusi, Abideen O. Oluwasola, Adewumi Adeoye, Abayomi Odetunde, Chinedum P. Babalola, Oladosu A. Ojengbede, Stella Odedina, Imaria Anetor, University of Ibadan; Clement A. Adebamowo, Centre for Bioethics and Research, Ibadan, Oyo, Nigeria, and University of Maryland School of Medicine, Baltimore, MD; and Gabriela E.S. Felix, Fundação Oswaldo Cruz and Universidade Federal da Bahia, Bahia, Brazil
| | - Tom Walsh
- Yonglan Zheng, Shengfeng Wang, Dezheng Huo, Toshio F. Yoshimatsu, Jing Zhang, Gabriela E.S. Felix, and Olufunmilayo I. Olopade, The University of Chicago, Chicago, IL; Tom Walsh, Suleyman Gulsuner, Silvia Casadei, Ming K. Lee, and Mary-Claire King, University of Washington, Seattle, WA; Temidayo O. Ogundiran, Adeyinka Ademola, Adeyinka G. Falusi, Abideen O. Oluwasola, Adewumi Adeoye, Abayomi Odetunde, Chinedum P. Babalola, Oladosu A. Ojengbede, Stella Odedina, Imaria Anetor, University of Ibadan; Clement A. Adebamowo, Centre for Bioethics and Research, Ibadan, Oyo, Nigeria, and University of Maryland School of Medicine, Baltimore, MD; and Gabriela E.S. Felix, Fundação Oswaldo Cruz and Universidade Federal da Bahia, Bahia, Brazil
| | - Suleyman Gulsuner
- Yonglan Zheng, Shengfeng Wang, Dezheng Huo, Toshio F. Yoshimatsu, Jing Zhang, Gabriela E.S. Felix, and Olufunmilayo I. Olopade, The University of Chicago, Chicago, IL; Tom Walsh, Suleyman Gulsuner, Silvia Casadei, Ming K. Lee, and Mary-Claire King, University of Washington, Seattle, WA; Temidayo O. Ogundiran, Adeyinka Ademola, Adeyinka G. Falusi, Abideen O. Oluwasola, Adewumi Adeoye, Abayomi Odetunde, Chinedum P. Babalola, Oladosu A. Ojengbede, Stella Odedina, Imaria Anetor, University of Ibadan; Clement A. Adebamowo, Centre for Bioethics and Research, Ibadan, Oyo, Nigeria, and University of Maryland School of Medicine, Baltimore, MD; and Gabriela E.S. Felix, Fundação Oswaldo Cruz and Universidade Federal da Bahia, Bahia, Brazil
| | - Silvia Casadei
- Yonglan Zheng, Shengfeng Wang, Dezheng Huo, Toshio F. Yoshimatsu, Jing Zhang, Gabriela E.S. Felix, and Olufunmilayo I. Olopade, The University of Chicago, Chicago, IL; Tom Walsh, Suleyman Gulsuner, Silvia Casadei, Ming K. Lee, and Mary-Claire King, University of Washington, Seattle, WA; Temidayo O. Ogundiran, Adeyinka Ademola, Adeyinka G. Falusi, Abideen O. Oluwasola, Adewumi Adeoye, Abayomi Odetunde, Chinedum P. Babalola, Oladosu A. Ojengbede, Stella Odedina, Imaria Anetor, University of Ibadan; Clement A. Adebamowo, Centre for Bioethics and Research, Ibadan, Oyo, Nigeria, and University of Maryland School of Medicine, Baltimore, MD; and Gabriela E.S. Felix, Fundação Oswaldo Cruz and Universidade Federal da Bahia, Bahia, Brazil
| | - Ming K. Lee
- Yonglan Zheng, Shengfeng Wang, Dezheng Huo, Toshio F. Yoshimatsu, Jing Zhang, Gabriela E.S. Felix, and Olufunmilayo I. Olopade, The University of Chicago, Chicago, IL; Tom Walsh, Suleyman Gulsuner, Silvia Casadei, Ming K. Lee, and Mary-Claire King, University of Washington, Seattle, WA; Temidayo O. Ogundiran, Adeyinka Ademola, Adeyinka G. Falusi, Abideen O. Oluwasola, Adewumi Adeoye, Abayomi Odetunde, Chinedum P. Babalola, Oladosu A. Ojengbede, Stella Odedina, Imaria Anetor, University of Ibadan; Clement A. Adebamowo, Centre for Bioethics and Research, Ibadan, Oyo, Nigeria, and University of Maryland School of Medicine, Baltimore, MD; and Gabriela E.S. Felix, Fundação Oswaldo Cruz and Universidade Federal da Bahia, Bahia, Brazil
| | - Temidayo O. Ogundiran
- Yonglan Zheng, Shengfeng Wang, Dezheng Huo, Toshio F. Yoshimatsu, Jing Zhang, Gabriela E.S. Felix, and Olufunmilayo I. Olopade, The University of Chicago, Chicago, IL; Tom Walsh, Suleyman Gulsuner, Silvia Casadei, Ming K. Lee, and Mary-Claire King, University of Washington, Seattle, WA; Temidayo O. Ogundiran, Adeyinka Ademola, Adeyinka G. Falusi, Abideen O. Oluwasola, Adewumi Adeoye, Abayomi Odetunde, Chinedum P. Babalola, Oladosu A. Ojengbede, Stella Odedina, Imaria Anetor, University of Ibadan; Clement A. Adebamowo, Centre for Bioethics and Research, Ibadan, Oyo, Nigeria, and University of Maryland School of Medicine, Baltimore, MD; and Gabriela E.S. Felix, Fundação Oswaldo Cruz and Universidade Federal da Bahia, Bahia, Brazil
| | - Adeyinka Ademola
- Yonglan Zheng, Shengfeng Wang, Dezheng Huo, Toshio F. Yoshimatsu, Jing Zhang, Gabriela E.S. Felix, and Olufunmilayo I. Olopade, The University of Chicago, Chicago, IL; Tom Walsh, Suleyman Gulsuner, Silvia Casadei, Ming K. Lee, and Mary-Claire King, University of Washington, Seattle, WA; Temidayo O. Ogundiran, Adeyinka Ademola, Adeyinka G. Falusi, Abideen O. Oluwasola, Adewumi Adeoye, Abayomi Odetunde, Chinedum P. Babalola, Oladosu A. Ojengbede, Stella Odedina, Imaria Anetor, University of Ibadan; Clement A. Adebamowo, Centre for Bioethics and Research, Ibadan, Oyo, Nigeria, and University of Maryland School of Medicine, Baltimore, MD; and Gabriela E.S. Felix, Fundação Oswaldo Cruz and Universidade Federal da Bahia, Bahia, Brazil
| | - Adeyinka G. Falusi
- Yonglan Zheng, Shengfeng Wang, Dezheng Huo, Toshio F. Yoshimatsu, Jing Zhang, Gabriela E.S. Felix, and Olufunmilayo I. Olopade, The University of Chicago, Chicago, IL; Tom Walsh, Suleyman Gulsuner, Silvia Casadei, Ming K. Lee, and Mary-Claire King, University of Washington, Seattle, WA; Temidayo O. Ogundiran, Adeyinka Ademola, Adeyinka G. Falusi, Abideen O. Oluwasola, Adewumi Adeoye, Abayomi Odetunde, Chinedum P. Babalola, Oladosu A. Ojengbede, Stella Odedina, Imaria Anetor, University of Ibadan; Clement A. Adebamowo, Centre for Bioethics and Research, Ibadan, Oyo, Nigeria, and University of Maryland School of Medicine, Baltimore, MD; and Gabriela E.S. Felix, Fundação Oswaldo Cruz and Universidade Federal da Bahia, Bahia, Brazil
| | - Clement A. Adebamowo
- Yonglan Zheng, Shengfeng Wang, Dezheng Huo, Toshio F. Yoshimatsu, Jing Zhang, Gabriela E.S. Felix, and Olufunmilayo I. Olopade, The University of Chicago, Chicago, IL; Tom Walsh, Suleyman Gulsuner, Silvia Casadei, Ming K. Lee, and Mary-Claire King, University of Washington, Seattle, WA; Temidayo O. Ogundiran, Adeyinka Ademola, Adeyinka G. Falusi, Abideen O. Oluwasola, Adewumi Adeoye, Abayomi Odetunde, Chinedum P. Babalola, Oladosu A. Ojengbede, Stella Odedina, Imaria Anetor, University of Ibadan; Clement A. Adebamowo, Centre for Bioethics and Research, Ibadan, Oyo, Nigeria, and University of Maryland School of Medicine, Baltimore, MD; and Gabriela E.S. Felix, Fundação Oswaldo Cruz and Universidade Federal da Bahia, Bahia, Brazil
| | - Abideen O. Oluwasola
- Yonglan Zheng, Shengfeng Wang, Dezheng Huo, Toshio F. Yoshimatsu, Jing Zhang, Gabriela E.S. Felix, and Olufunmilayo I. Olopade, The University of Chicago, Chicago, IL; Tom Walsh, Suleyman Gulsuner, Silvia Casadei, Ming K. Lee, and Mary-Claire King, University of Washington, Seattle, WA; Temidayo O. Ogundiran, Adeyinka Ademola, Adeyinka G. Falusi, Abideen O. Oluwasola, Adewumi Adeoye, Abayomi Odetunde, Chinedum P. Babalola, Oladosu A. Ojengbede, Stella Odedina, Imaria Anetor, University of Ibadan; Clement A. Adebamowo, Centre for Bioethics and Research, Ibadan, Oyo, Nigeria, and University of Maryland School of Medicine, Baltimore, MD; and Gabriela E.S. Felix, Fundação Oswaldo Cruz and Universidade Federal da Bahia, Bahia, Brazil
| | - Adewumi Adeoye
- Yonglan Zheng, Shengfeng Wang, Dezheng Huo, Toshio F. Yoshimatsu, Jing Zhang, Gabriela E.S. Felix, and Olufunmilayo I. Olopade, The University of Chicago, Chicago, IL; Tom Walsh, Suleyman Gulsuner, Silvia Casadei, Ming K. Lee, and Mary-Claire King, University of Washington, Seattle, WA; Temidayo O. Ogundiran, Adeyinka Ademola, Adeyinka G. Falusi, Abideen O. Oluwasola, Adewumi Adeoye, Abayomi Odetunde, Chinedum P. Babalola, Oladosu A. Ojengbede, Stella Odedina, Imaria Anetor, University of Ibadan; Clement A. Adebamowo, Centre for Bioethics and Research, Ibadan, Oyo, Nigeria, and University of Maryland School of Medicine, Baltimore, MD; and Gabriela E.S. Felix, Fundação Oswaldo Cruz and Universidade Federal da Bahia, Bahia, Brazil
| | - Abayomi Odetunde
- Yonglan Zheng, Shengfeng Wang, Dezheng Huo, Toshio F. Yoshimatsu, Jing Zhang, Gabriela E.S. Felix, and Olufunmilayo I. Olopade, The University of Chicago, Chicago, IL; Tom Walsh, Suleyman Gulsuner, Silvia Casadei, Ming K. Lee, and Mary-Claire King, University of Washington, Seattle, WA; Temidayo O. Ogundiran, Adeyinka Ademola, Adeyinka G. Falusi, Abideen O. Oluwasola, Adewumi Adeoye, Abayomi Odetunde, Chinedum P. Babalola, Oladosu A. Ojengbede, Stella Odedina, Imaria Anetor, University of Ibadan; Clement A. Adebamowo, Centre for Bioethics and Research, Ibadan, Oyo, Nigeria, and University of Maryland School of Medicine, Baltimore, MD; and Gabriela E.S. Felix, Fundação Oswaldo Cruz and Universidade Federal da Bahia, Bahia, Brazil
| | - Chinedum P. Babalola
- Yonglan Zheng, Shengfeng Wang, Dezheng Huo, Toshio F. Yoshimatsu, Jing Zhang, Gabriela E.S. Felix, and Olufunmilayo I. Olopade, The University of Chicago, Chicago, IL; Tom Walsh, Suleyman Gulsuner, Silvia Casadei, Ming K. Lee, and Mary-Claire King, University of Washington, Seattle, WA; Temidayo O. Ogundiran, Adeyinka Ademola, Adeyinka G. Falusi, Abideen O. Oluwasola, Adewumi Adeoye, Abayomi Odetunde, Chinedum P. Babalola, Oladosu A. Ojengbede, Stella Odedina, Imaria Anetor, University of Ibadan; Clement A. Adebamowo, Centre for Bioethics and Research, Ibadan, Oyo, Nigeria, and University of Maryland School of Medicine, Baltimore, MD; and Gabriela E.S. Felix, Fundação Oswaldo Cruz and Universidade Federal da Bahia, Bahia, Brazil
| | - Oladosu A. Ojengbede
- Yonglan Zheng, Shengfeng Wang, Dezheng Huo, Toshio F. Yoshimatsu, Jing Zhang, Gabriela E.S. Felix, and Olufunmilayo I. Olopade, The University of Chicago, Chicago, IL; Tom Walsh, Suleyman Gulsuner, Silvia Casadei, Ming K. Lee, and Mary-Claire King, University of Washington, Seattle, WA; Temidayo O. Ogundiran, Adeyinka Ademola, Adeyinka G. Falusi, Abideen O. Oluwasola, Adewumi Adeoye, Abayomi Odetunde, Chinedum P. Babalola, Oladosu A. Ojengbede, Stella Odedina, Imaria Anetor, University of Ibadan; Clement A. Adebamowo, Centre for Bioethics and Research, Ibadan, Oyo, Nigeria, and University of Maryland School of Medicine, Baltimore, MD; and Gabriela E.S. Felix, Fundação Oswaldo Cruz and Universidade Federal da Bahia, Bahia, Brazil
| | - Stella Odedina
- Yonglan Zheng, Shengfeng Wang, Dezheng Huo, Toshio F. Yoshimatsu, Jing Zhang, Gabriela E.S. Felix, and Olufunmilayo I. Olopade, The University of Chicago, Chicago, IL; Tom Walsh, Suleyman Gulsuner, Silvia Casadei, Ming K. Lee, and Mary-Claire King, University of Washington, Seattle, WA; Temidayo O. Ogundiran, Adeyinka Ademola, Adeyinka G. Falusi, Abideen O. Oluwasola, Adewumi Adeoye, Abayomi Odetunde, Chinedum P. Babalola, Oladosu A. Ojengbede, Stella Odedina, Imaria Anetor, University of Ibadan; Clement A. Adebamowo, Centre for Bioethics and Research, Ibadan, Oyo, Nigeria, and University of Maryland School of Medicine, Baltimore, MD; and Gabriela E.S. Felix, Fundação Oswaldo Cruz and Universidade Federal da Bahia, Bahia, Brazil
| | - Imaria Anetor
- Yonglan Zheng, Shengfeng Wang, Dezheng Huo, Toshio F. Yoshimatsu, Jing Zhang, Gabriela E.S. Felix, and Olufunmilayo I. Olopade, The University of Chicago, Chicago, IL; Tom Walsh, Suleyman Gulsuner, Silvia Casadei, Ming K. Lee, and Mary-Claire King, University of Washington, Seattle, WA; Temidayo O. Ogundiran, Adeyinka Ademola, Adeyinka G. Falusi, Abideen O. Oluwasola, Adewumi Adeoye, Abayomi Odetunde, Chinedum P. Babalola, Oladosu A. Ojengbede, Stella Odedina, Imaria Anetor, University of Ibadan; Clement A. Adebamowo, Centre for Bioethics and Research, Ibadan, Oyo, Nigeria, and University of Maryland School of Medicine, Baltimore, MD; and Gabriela E.S. Felix, Fundação Oswaldo Cruz and Universidade Federal da Bahia, Bahia, Brazil
| | - Shengfeng Wang
- Yonglan Zheng, Shengfeng Wang, Dezheng Huo, Toshio F. Yoshimatsu, Jing Zhang, Gabriela E.S. Felix, and Olufunmilayo I. Olopade, The University of Chicago, Chicago, IL; Tom Walsh, Suleyman Gulsuner, Silvia Casadei, Ming K. Lee, and Mary-Claire King, University of Washington, Seattle, WA; Temidayo O. Ogundiran, Adeyinka Ademola, Adeyinka G. Falusi, Abideen O. Oluwasola, Adewumi Adeoye, Abayomi Odetunde, Chinedum P. Babalola, Oladosu A. Ojengbede, Stella Odedina, Imaria Anetor, University of Ibadan; Clement A. Adebamowo, Centre for Bioethics and Research, Ibadan, Oyo, Nigeria, and University of Maryland School of Medicine, Baltimore, MD; and Gabriela E.S. Felix, Fundação Oswaldo Cruz and Universidade Federal da Bahia, Bahia, Brazil
| | - Dezheng Huo
- Yonglan Zheng, Shengfeng Wang, Dezheng Huo, Toshio F. Yoshimatsu, Jing Zhang, Gabriela E.S. Felix, and Olufunmilayo I. Olopade, The University of Chicago, Chicago, IL; Tom Walsh, Suleyman Gulsuner, Silvia Casadei, Ming K. Lee, and Mary-Claire King, University of Washington, Seattle, WA; Temidayo O. Ogundiran, Adeyinka Ademola, Adeyinka G. Falusi, Abideen O. Oluwasola, Adewumi Adeoye, Abayomi Odetunde, Chinedum P. Babalola, Oladosu A. Ojengbede, Stella Odedina, Imaria Anetor, University of Ibadan; Clement A. Adebamowo, Centre for Bioethics and Research, Ibadan, Oyo, Nigeria, and University of Maryland School of Medicine, Baltimore, MD; and Gabriela E.S. Felix, Fundação Oswaldo Cruz and Universidade Federal da Bahia, Bahia, Brazil
| | - Toshio F. Yoshimatsu
- Yonglan Zheng, Shengfeng Wang, Dezheng Huo, Toshio F. Yoshimatsu, Jing Zhang, Gabriela E.S. Felix, and Olufunmilayo I. Olopade, The University of Chicago, Chicago, IL; Tom Walsh, Suleyman Gulsuner, Silvia Casadei, Ming K. Lee, and Mary-Claire King, University of Washington, Seattle, WA; Temidayo O. Ogundiran, Adeyinka Ademola, Adeyinka G. Falusi, Abideen O. Oluwasola, Adewumi Adeoye, Abayomi Odetunde, Chinedum P. Babalola, Oladosu A. Ojengbede, Stella Odedina, Imaria Anetor, University of Ibadan; Clement A. Adebamowo, Centre for Bioethics and Research, Ibadan, Oyo, Nigeria, and University of Maryland School of Medicine, Baltimore, MD; and Gabriela E.S. Felix, Fundação Oswaldo Cruz and Universidade Federal da Bahia, Bahia, Brazil
| | - Jing Zhang
- Yonglan Zheng, Shengfeng Wang, Dezheng Huo, Toshio F. Yoshimatsu, Jing Zhang, Gabriela E.S. Felix, and Olufunmilayo I. Olopade, The University of Chicago, Chicago, IL; Tom Walsh, Suleyman Gulsuner, Silvia Casadei, Ming K. Lee, and Mary-Claire King, University of Washington, Seattle, WA; Temidayo O. Ogundiran, Adeyinka Ademola, Adeyinka G. Falusi, Abideen O. Oluwasola, Adewumi Adeoye, Abayomi Odetunde, Chinedum P. Babalola, Oladosu A. Ojengbede, Stella Odedina, Imaria Anetor, University of Ibadan; Clement A. Adebamowo, Centre for Bioethics and Research, Ibadan, Oyo, Nigeria, and University of Maryland School of Medicine, Baltimore, MD; and Gabriela E.S. Felix, Fundação Oswaldo Cruz and Universidade Federal da Bahia, Bahia, Brazil
| | - Gabriela E.S. Felix
- Yonglan Zheng, Shengfeng Wang, Dezheng Huo, Toshio F. Yoshimatsu, Jing Zhang, Gabriela E.S. Felix, and Olufunmilayo I. Olopade, The University of Chicago, Chicago, IL; Tom Walsh, Suleyman Gulsuner, Silvia Casadei, Ming K. Lee, and Mary-Claire King, University of Washington, Seattle, WA; Temidayo O. Ogundiran, Adeyinka Ademola, Adeyinka G. Falusi, Abideen O. Oluwasola, Adewumi Adeoye, Abayomi Odetunde, Chinedum P. Babalola, Oladosu A. Ojengbede, Stella Odedina, Imaria Anetor, University of Ibadan; Clement A. Adebamowo, Centre for Bioethics and Research, Ibadan, Oyo, Nigeria, and University of Maryland School of Medicine, Baltimore, MD; and Gabriela E.S. Felix, Fundação Oswaldo Cruz and Universidade Federal da Bahia, Bahia, Brazil
| | - Mary-Claire King
- Yonglan Zheng, Shengfeng Wang, Dezheng Huo, Toshio F. Yoshimatsu, Jing Zhang, Gabriela E.S. Felix, and Olufunmilayo I. Olopade, The University of Chicago, Chicago, IL; Tom Walsh, Suleyman Gulsuner, Silvia Casadei, Ming K. Lee, and Mary-Claire King, University of Washington, Seattle, WA; Temidayo O. Ogundiran, Adeyinka Ademola, Adeyinka G. Falusi, Abideen O. Oluwasola, Adewumi Adeoye, Abayomi Odetunde, Chinedum P. Babalola, Oladosu A. Ojengbede, Stella Odedina, Imaria Anetor, University of Ibadan; Clement A. Adebamowo, Centre for Bioethics and Research, Ibadan, Oyo, Nigeria, and University of Maryland School of Medicine, Baltimore, MD; and Gabriela E.S. Felix, Fundação Oswaldo Cruz and Universidade Federal da Bahia, Bahia, Brazil
| | - Olufunmilayo I. Olopade
- Yonglan Zheng, Shengfeng Wang, Dezheng Huo, Toshio F. Yoshimatsu, Jing Zhang, Gabriela E.S. Felix, and Olufunmilayo I. Olopade, The University of Chicago, Chicago, IL; Tom Walsh, Suleyman Gulsuner, Silvia Casadei, Ming K. Lee, and Mary-Claire King, University of Washington, Seattle, WA; Temidayo O. Ogundiran, Adeyinka Ademola, Adeyinka G. Falusi, Abideen O. Oluwasola, Adewumi Adeoye, Abayomi Odetunde, Chinedum P. Babalola, Oladosu A. Ojengbede, Stella Odedina, Imaria Anetor, University of Ibadan; Clement A. Adebamowo, Centre for Bioethics and Research, Ibadan, Oyo, Nigeria, and University of Maryland School of Medicine, Baltimore, MD; and Gabriela E.S. Felix, Fundação Oswaldo Cruz and Universidade Federal da Bahia, Bahia, Brazil
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Weinberg-Shukron A, Rachmiel M, Renbaum P, Gulsuner S, Walsh T, Lobel O, Dreifuss A, Ben-Moshe A, Zeligson S, Segel R, Shore T, Kalifa R, Goldberg M, King MC, Gerlitz O, Levy-Lahad E, Zangen D. Essential Role of BRCA2 in Ovarian Development and Function. N Engl J Med 2018; 379:1042-1049. [PMID: 30207912 PMCID: PMC6230262 DOI: 10.1056/nejmoa1800024] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The causes of ovarian dysgenesis remain incompletely understood. Two sisters with XX ovarian dysgenesis carried compound heterozygous truncating mutations in the BRCA2 gene that led to reduced BRCA2 protein levels and an impaired response to DNA damage, which resulted in chromosomal breakage and the failure of RAD51 to be recruited to double-stranded DNA breaks. The sisters also had microcephaly, and one sister was in long-term remission from leukemia, which had been diagnosed when she was 5 years old. Drosophila mutants that were null for an orthologue of BRCA2 were sterile, and gonadal dysgenesis was present in both sexes. These results revealed a new role for BRCA2 and highlight the importance to ovarian development of genes that are critical for recombination during meiosis. (Funded by the Israel Science Foundation and others.).
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Affiliation(s)
- Ariella Weinberg-Shukron
- From the Medical Genetics Institute, Shaare Zedek Medical Center (A.W.-S., P.R., O.L., S.Z., R.S., E.L.-L.), the Faculty of Medicine, Hebrew University of Jerusalem, Hadassah Medical School (A.W.-S., E.L.-L., D.Z.), the Department of Developmental Biology and Cancer Research, IMRIC (Institute for Medical Research, Israel-Canada), Faculty of Medicine, Hebrew University of Jerusalem (A.D., T.S., R.K., O.G.), the Department of Genetics, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem (A.B.-M., M.G.), and the Division of Pediatric Endocrinology, Hadassah Hebrew University Medical Center (D.Z.), Jerusalem, and the Pediatric Endocrinology Clinic, Assaf Harofeh Medical Center, Zerifin, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv (M.R.) - all in Israel; and the Division of Medical Genetics, Department of Medicine and the Department of Genome Sciences, University of Washington, Seattle (S.G., T.W., M.-C.K.)
| | - Mariana Rachmiel
- From the Medical Genetics Institute, Shaare Zedek Medical Center (A.W.-S., P.R., O.L., S.Z., R.S., E.L.-L.), the Faculty of Medicine, Hebrew University of Jerusalem, Hadassah Medical School (A.W.-S., E.L.-L., D.Z.), the Department of Developmental Biology and Cancer Research, IMRIC (Institute for Medical Research, Israel-Canada), Faculty of Medicine, Hebrew University of Jerusalem (A.D., T.S., R.K., O.G.), the Department of Genetics, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem (A.B.-M., M.G.), and the Division of Pediatric Endocrinology, Hadassah Hebrew University Medical Center (D.Z.), Jerusalem, and the Pediatric Endocrinology Clinic, Assaf Harofeh Medical Center, Zerifin, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv (M.R.) - all in Israel; and the Division of Medical Genetics, Department of Medicine and the Department of Genome Sciences, University of Washington, Seattle (S.G., T.W., M.-C.K.)
| | - Paul Renbaum
- From the Medical Genetics Institute, Shaare Zedek Medical Center (A.W.-S., P.R., O.L., S.Z., R.S., E.L.-L.), the Faculty of Medicine, Hebrew University of Jerusalem, Hadassah Medical School (A.W.-S., E.L.-L., D.Z.), the Department of Developmental Biology and Cancer Research, IMRIC (Institute for Medical Research, Israel-Canada), Faculty of Medicine, Hebrew University of Jerusalem (A.D., T.S., R.K., O.G.), the Department of Genetics, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem (A.B.-M., M.G.), and the Division of Pediatric Endocrinology, Hadassah Hebrew University Medical Center (D.Z.), Jerusalem, and the Pediatric Endocrinology Clinic, Assaf Harofeh Medical Center, Zerifin, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv (M.R.) - all in Israel; and the Division of Medical Genetics, Department of Medicine and the Department of Genome Sciences, University of Washington, Seattle (S.G., T.W., M.-C.K.)
| | - Suleyman Gulsuner
- From the Medical Genetics Institute, Shaare Zedek Medical Center (A.W.-S., P.R., O.L., S.Z., R.S., E.L.-L.), the Faculty of Medicine, Hebrew University of Jerusalem, Hadassah Medical School (A.W.-S., E.L.-L., D.Z.), the Department of Developmental Biology and Cancer Research, IMRIC (Institute for Medical Research, Israel-Canada), Faculty of Medicine, Hebrew University of Jerusalem (A.D., T.S., R.K., O.G.), the Department of Genetics, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem (A.B.-M., M.G.), and the Division of Pediatric Endocrinology, Hadassah Hebrew University Medical Center (D.Z.), Jerusalem, and the Pediatric Endocrinology Clinic, Assaf Harofeh Medical Center, Zerifin, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv (M.R.) - all in Israel; and the Division of Medical Genetics, Department of Medicine and the Department of Genome Sciences, University of Washington, Seattle (S.G., T.W., M.-C.K.)
| | - Tom Walsh
- From the Medical Genetics Institute, Shaare Zedek Medical Center (A.W.-S., P.R., O.L., S.Z., R.S., E.L.-L.), the Faculty of Medicine, Hebrew University of Jerusalem, Hadassah Medical School (A.W.-S., E.L.-L., D.Z.), the Department of Developmental Biology and Cancer Research, IMRIC (Institute for Medical Research, Israel-Canada), Faculty of Medicine, Hebrew University of Jerusalem (A.D., T.S., R.K., O.G.), the Department of Genetics, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem (A.B.-M., M.G.), and the Division of Pediatric Endocrinology, Hadassah Hebrew University Medical Center (D.Z.), Jerusalem, and the Pediatric Endocrinology Clinic, Assaf Harofeh Medical Center, Zerifin, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv (M.R.) - all in Israel; and the Division of Medical Genetics, Department of Medicine and the Department of Genome Sciences, University of Washington, Seattle (S.G., T.W., M.-C.K.)
| | - Orit Lobel
- From the Medical Genetics Institute, Shaare Zedek Medical Center (A.W.-S., P.R., O.L., S.Z., R.S., E.L.-L.), the Faculty of Medicine, Hebrew University of Jerusalem, Hadassah Medical School (A.W.-S., E.L.-L., D.Z.), the Department of Developmental Biology and Cancer Research, IMRIC (Institute for Medical Research, Israel-Canada), Faculty of Medicine, Hebrew University of Jerusalem (A.D., T.S., R.K., O.G.), the Department of Genetics, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem (A.B.-M., M.G.), and the Division of Pediatric Endocrinology, Hadassah Hebrew University Medical Center (D.Z.), Jerusalem, and the Pediatric Endocrinology Clinic, Assaf Harofeh Medical Center, Zerifin, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv (M.R.) - all in Israel; and the Division of Medical Genetics, Department of Medicine and the Department of Genome Sciences, University of Washington, Seattle (S.G., T.W., M.-C.K.)
| | - Amatzia Dreifuss
- From the Medical Genetics Institute, Shaare Zedek Medical Center (A.W.-S., P.R., O.L., S.Z., R.S., E.L.-L.), the Faculty of Medicine, Hebrew University of Jerusalem, Hadassah Medical School (A.W.-S., E.L.-L., D.Z.), the Department of Developmental Biology and Cancer Research, IMRIC (Institute for Medical Research, Israel-Canada), Faculty of Medicine, Hebrew University of Jerusalem (A.D., T.S., R.K., O.G.), the Department of Genetics, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem (A.B.-M., M.G.), and the Division of Pediatric Endocrinology, Hadassah Hebrew University Medical Center (D.Z.), Jerusalem, and the Pediatric Endocrinology Clinic, Assaf Harofeh Medical Center, Zerifin, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv (M.R.) - all in Israel; and the Division of Medical Genetics, Department of Medicine and the Department of Genome Sciences, University of Washington, Seattle (S.G., T.W., M.-C.K.)
| | - Avital Ben-Moshe
- From the Medical Genetics Institute, Shaare Zedek Medical Center (A.W.-S., P.R., O.L., S.Z., R.S., E.L.-L.), the Faculty of Medicine, Hebrew University of Jerusalem, Hadassah Medical School (A.W.-S., E.L.-L., D.Z.), the Department of Developmental Biology and Cancer Research, IMRIC (Institute for Medical Research, Israel-Canada), Faculty of Medicine, Hebrew University of Jerusalem (A.D., T.S., R.K., O.G.), the Department of Genetics, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem (A.B.-M., M.G.), and the Division of Pediatric Endocrinology, Hadassah Hebrew University Medical Center (D.Z.), Jerusalem, and the Pediatric Endocrinology Clinic, Assaf Harofeh Medical Center, Zerifin, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv (M.R.) - all in Israel; and the Division of Medical Genetics, Department of Medicine and the Department of Genome Sciences, University of Washington, Seattle (S.G., T.W., M.-C.K.)
| | - Sharon Zeligson
- From the Medical Genetics Institute, Shaare Zedek Medical Center (A.W.-S., P.R., O.L., S.Z., R.S., E.L.-L.), the Faculty of Medicine, Hebrew University of Jerusalem, Hadassah Medical School (A.W.-S., E.L.-L., D.Z.), the Department of Developmental Biology and Cancer Research, IMRIC (Institute for Medical Research, Israel-Canada), Faculty of Medicine, Hebrew University of Jerusalem (A.D., T.S., R.K., O.G.), the Department of Genetics, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem (A.B.-M., M.G.), and the Division of Pediatric Endocrinology, Hadassah Hebrew University Medical Center (D.Z.), Jerusalem, and the Pediatric Endocrinology Clinic, Assaf Harofeh Medical Center, Zerifin, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv (M.R.) - all in Israel; and the Division of Medical Genetics, Department of Medicine and the Department of Genome Sciences, University of Washington, Seattle (S.G., T.W., M.-C.K.)
| | - Reeval Segel
- From the Medical Genetics Institute, Shaare Zedek Medical Center (A.W.-S., P.R., O.L., S.Z., R.S., E.L.-L.), the Faculty of Medicine, Hebrew University of Jerusalem, Hadassah Medical School (A.W.-S., E.L.-L., D.Z.), the Department of Developmental Biology and Cancer Research, IMRIC (Institute for Medical Research, Israel-Canada), Faculty of Medicine, Hebrew University of Jerusalem (A.D., T.S., R.K., O.G.), the Department of Genetics, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem (A.B.-M., M.G.), and the Division of Pediatric Endocrinology, Hadassah Hebrew University Medical Center (D.Z.), Jerusalem, and the Pediatric Endocrinology Clinic, Assaf Harofeh Medical Center, Zerifin, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv (M.R.) - all in Israel; and the Division of Medical Genetics, Department of Medicine and the Department of Genome Sciences, University of Washington, Seattle (S.G., T.W., M.-C.K.)
| | - Tikva Shore
- From the Medical Genetics Institute, Shaare Zedek Medical Center (A.W.-S., P.R., O.L., S.Z., R.S., E.L.-L.), the Faculty of Medicine, Hebrew University of Jerusalem, Hadassah Medical School (A.W.-S., E.L.-L., D.Z.), the Department of Developmental Biology and Cancer Research, IMRIC (Institute for Medical Research, Israel-Canada), Faculty of Medicine, Hebrew University of Jerusalem (A.D., T.S., R.K., O.G.), the Department of Genetics, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem (A.B.-M., M.G.), and the Division of Pediatric Endocrinology, Hadassah Hebrew University Medical Center (D.Z.), Jerusalem, and the Pediatric Endocrinology Clinic, Assaf Harofeh Medical Center, Zerifin, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv (M.R.) - all in Israel; and the Division of Medical Genetics, Department of Medicine and the Department of Genome Sciences, University of Washington, Seattle (S.G., T.W., M.-C.K.)
| | - Rachel Kalifa
- From the Medical Genetics Institute, Shaare Zedek Medical Center (A.W.-S., P.R., O.L., S.Z., R.S., E.L.-L.), the Faculty of Medicine, Hebrew University of Jerusalem, Hadassah Medical School (A.W.-S., E.L.-L., D.Z.), the Department of Developmental Biology and Cancer Research, IMRIC (Institute for Medical Research, Israel-Canada), Faculty of Medicine, Hebrew University of Jerusalem (A.D., T.S., R.K., O.G.), the Department of Genetics, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem (A.B.-M., M.G.), and the Division of Pediatric Endocrinology, Hadassah Hebrew University Medical Center (D.Z.), Jerusalem, and the Pediatric Endocrinology Clinic, Assaf Harofeh Medical Center, Zerifin, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv (M.R.) - all in Israel; and the Division of Medical Genetics, Department of Medicine and the Department of Genome Sciences, University of Washington, Seattle (S.G., T.W., M.-C.K.)
| | - Michal Goldberg
- From the Medical Genetics Institute, Shaare Zedek Medical Center (A.W.-S., P.R., O.L., S.Z., R.S., E.L.-L.), the Faculty of Medicine, Hebrew University of Jerusalem, Hadassah Medical School (A.W.-S., E.L.-L., D.Z.), the Department of Developmental Biology and Cancer Research, IMRIC (Institute for Medical Research, Israel-Canada), Faculty of Medicine, Hebrew University of Jerusalem (A.D., T.S., R.K., O.G.), the Department of Genetics, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem (A.B.-M., M.G.), and the Division of Pediatric Endocrinology, Hadassah Hebrew University Medical Center (D.Z.), Jerusalem, and the Pediatric Endocrinology Clinic, Assaf Harofeh Medical Center, Zerifin, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv (M.R.) - all in Israel; and the Division of Medical Genetics, Department of Medicine and the Department of Genome Sciences, University of Washington, Seattle (S.G., T.W., M.-C.K.)
| | - Mary-Claire King
- From the Medical Genetics Institute, Shaare Zedek Medical Center (A.W.-S., P.R., O.L., S.Z., R.S., E.L.-L.), the Faculty of Medicine, Hebrew University of Jerusalem, Hadassah Medical School (A.W.-S., E.L.-L., D.Z.), the Department of Developmental Biology and Cancer Research, IMRIC (Institute for Medical Research, Israel-Canada), Faculty of Medicine, Hebrew University of Jerusalem (A.D., T.S., R.K., O.G.), the Department of Genetics, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem (A.B.-M., M.G.), and the Division of Pediatric Endocrinology, Hadassah Hebrew University Medical Center (D.Z.), Jerusalem, and the Pediatric Endocrinology Clinic, Assaf Harofeh Medical Center, Zerifin, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv (M.R.) - all in Israel; and the Division of Medical Genetics, Department of Medicine and the Department of Genome Sciences, University of Washington, Seattle (S.G., T.W., M.-C.K.)
| | - Offer Gerlitz
- From the Medical Genetics Institute, Shaare Zedek Medical Center (A.W.-S., P.R., O.L., S.Z., R.S., E.L.-L.), the Faculty of Medicine, Hebrew University of Jerusalem, Hadassah Medical School (A.W.-S., E.L.-L., D.Z.), the Department of Developmental Biology and Cancer Research, IMRIC (Institute for Medical Research, Israel-Canada), Faculty of Medicine, Hebrew University of Jerusalem (A.D., T.S., R.K., O.G.), the Department of Genetics, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem (A.B.-M., M.G.), and the Division of Pediatric Endocrinology, Hadassah Hebrew University Medical Center (D.Z.), Jerusalem, and the Pediatric Endocrinology Clinic, Assaf Harofeh Medical Center, Zerifin, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv (M.R.) - all in Israel; and the Division of Medical Genetics, Department of Medicine and the Department of Genome Sciences, University of Washington, Seattle (S.G., T.W., M.-C.K.)
| | - Ephrat Levy-Lahad
- From the Medical Genetics Institute, Shaare Zedek Medical Center (A.W.-S., P.R., O.L., S.Z., R.S., E.L.-L.), the Faculty of Medicine, Hebrew University of Jerusalem, Hadassah Medical School (A.W.-S., E.L.-L., D.Z.), the Department of Developmental Biology and Cancer Research, IMRIC (Institute for Medical Research, Israel-Canada), Faculty of Medicine, Hebrew University of Jerusalem (A.D., T.S., R.K., O.G.), the Department of Genetics, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem (A.B.-M., M.G.), and the Division of Pediatric Endocrinology, Hadassah Hebrew University Medical Center (D.Z.), Jerusalem, and the Pediatric Endocrinology Clinic, Assaf Harofeh Medical Center, Zerifin, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv (M.R.) - all in Israel; and the Division of Medical Genetics, Department of Medicine and the Department of Genome Sciences, University of Washington, Seattle (S.G., T.W., M.-C.K.)
| | - David Zangen
- From the Medical Genetics Institute, Shaare Zedek Medical Center (A.W.-S., P.R., O.L., S.Z., R.S., E.L.-L.), the Faculty of Medicine, Hebrew University of Jerusalem, Hadassah Medical School (A.W.-S., E.L.-L., D.Z.), the Department of Developmental Biology and Cancer Research, IMRIC (Institute for Medical Research, Israel-Canada), Faculty of Medicine, Hebrew University of Jerusalem (A.D., T.S., R.K., O.G.), the Department of Genetics, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem (A.B.-M., M.G.), and the Division of Pediatric Endocrinology, Hadassah Hebrew University Medical Center (D.Z.), Jerusalem, and the Pediatric Endocrinology Clinic, Assaf Harofeh Medical Center, Zerifin, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv (M.R.) - all in Israel; and the Division of Medical Genetics, Department of Medicine and the Department of Genome Sciences, University of Washington, Seattle (S.G., T.W., M.-C.K.)
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Danial-Farran N, Brownstein Z, Gulsuner S, Tammer L, Khayat M, Aleme O, Chervinsky E, Zoubi OA, Walsh T, Ast G, King MC, Avraham KB, Shalev SA. Genetics of hearing loss in the Arab population of Northern Israel. Eur J Hum Genet 2018; 26:1840-1847. [PMID: 30139988 PMCID: PMC6244407 DOI: 10.1038/s41431-018-0218-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 06/18/2018] [Accepted: 06/26/2018] [Indexed: 01/04/2023] Open
Abstract
For multiple generations, much of the Arab population of Northern Israel has lived in communities with consanguineous marriages and large families. These communities have been particularly cooperative and informative for understanding the genetics of recessive traits. We studied the genetics of hearing loss in this population, evaluating 168 families from 46 different villages. All families were screened for founder variants by Sanger sequencing and 13 families were further evaluated by sequencing all known genes for hearing loss using our targeted gene panel HEar-Seq. Deafness in 34 of 168 families (20%) was explained by founder variants in GJB2, SLC26A4, or OTOF. In 6 of 13 families (46%) evaluated using HEar-Seq, deafness was explained by damaging alleles of SLC26A4, MYO15A, OTOG, LOXHD1, and TBC1D24. In some genes critical to hearing, it is particularly difficult to interpret variants that might affect splicing, because the genes are not expressed in accessible tissue. To address this problem for possible splice-altering variants of MYO15A, we evaluated minigenes transfected into HEK293 cells. Results revealed exon skipping in the message of MYO15A c.9083+6T>A, and intron retention in the message of MYO15A c.8340G>A, in each case leading to a premature stop and consistent with co-segregation of homozygosity for each variant with hearing loss. The profile of genetics of hearing loss in this population reflects the genetic heterogeneity of hearing loss and the usefulness of synthetic technologies to evaluate potentially causal variants in genes not expressed in accessible tissues.
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Affiliation(s)
- Nada Danial-Farran
- Genetics Institute, Emek Medical Center, Afula, Israel.,Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel.,Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Zippora Brownstein
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Suleyman Gulsuner
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | - Luna Tammer
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Morad Khayat
- Genetics Institute, Emek Medical Center, Afula, Israel
| | - Ola Aleme
- Genetics Institute, Emek Medical Center, Afula, Israel
| | | | | | - Tom Walsh
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | - Gil Ast
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Mary-Claire King
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
| | - Stavit A Shalev
- Genetics Institute, Emek Medical Center, Afula, Israel. .,Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel.
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Shirts BH, Konnick EQ, Upham S, Walsh T, Ranola JMO, Jacobson AL, King MC, Pearlman R, Hampel H, Pritchard CC. Using Somatic Mutations from Tumors to Classify Variants in Mismatch Repair Genes. Am J Hum Genet 2018; 103:19-29. [PMID: 29887214 DOI: 10.1016/j.ajhg.2018.05.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 05/01/2018] [Indexed: 01/28/2023] Open
Abstract
Present guidelines for classification of constitutional variants do not incorporate inferences from mutations seen in tumors, even when these are associated with a specific molecular phenotype. When somatic mutations and constitutional mutations lead to the same molecular phenotype, as for the mismatch repair genes, information from somatic mutations may enable interpretation of previously unclassified variants. To test this idea, we first estimated likelihoods that somatic variants in MLH1, MSH2, MSH6, and PMS2 drive microsatellite instability and characteristic IHC staining patterns by calculating likelihoods of high versus low normalized variant read fractions of 153 mutations known to be pathogenic versus those of 760 intronic passenger mutations from 174 paired tumor-normal samples. Mutations that explained the tumor mismatch repair phenotype had likelihood ratio for high variant read fraction of 1.56 (95% CI 1.42-1.71) at sites with no loss of heterozygosity and of 26.5 (95% CI 13.2-53.0) at sites with loss of heterozygosity. Next, we applied these ratios to 165 missense, synonymous, and splice variants observed in tumors, combining in a Bayesian analysis the likelihood ratio corresponding with the adjusted variant read fraction with pretest probabilities derived from published analyses and public databases. We suggest classifications for 86 of 165 variants: 7 benign, 31 likely benign, 22 likely pathogenic, and 26 pathogenic. These results illustrate that for mismatch repair genes, characterization of tumor mutations permits tumor mutation data to inform constitutional variant classification. We suggest modifications to incorporate molecular phenotype in future variant classification guidelines.
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Affiliation(s)
- Brian H Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA.
| | - Eric Q Konnick
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Sarah Upham
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Tom Walsh
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | | | - Angela L Jacobson
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Mary-Claire King
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Rachel Pearlman
- Department of Internal Medicine, Division of Human Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43221, USA
| | - Heather Hampel
- Department of Internal Medicine, Division of Human Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43221, USA
| | - Colin C Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
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King MC, Walsh T. Testing Ashkenazi Jewish Women for Mutations Predisposing to Breast Cancer in Genes Other Than BRCA1 and BRCA2-Reply. JAMA Oncol 2018; 4:1012-1013. [PMID: 29800948 DOI: 10.1001/jamaoncol.2018.0616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Mary-Claire King
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle.,Department of Genome Sciences, University of Washington, Seattle
| | - Tom Walsh
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle.,Department of Genome Sciences, University of Washington, Seattle
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Hassan R, Morrow B, Walsh T, Lee MK, Gao J, Mian I, Khan J, Raffeld M, Patel S, Xi L, Wei JS, Schrump D, Hesdorffer M, Zhang J, Calzone K, Padiernos E, Alewine C, Steinberg SM, Thomas A, King MC. Inherited predisposition to malignant mesothelioma (MM) due to mutations in DNA repair genes. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.8504] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Raffit Hassan
- Thoracic and Gastrointestinal Oncology Branch, National Cancer Institute, Bethesda, MD
| | | | - Tom Walsh
- University of Washington, Seattle, WA
| | | | - James Gao
- National Cancer Institute, Bethesda, MD
| | | | - Javed Khan
- Genetics Branch, National Cancer Institute, Bethesda, MD
| | | | | | | | | | | | | | | | | | - Emerson Padiernos
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
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Langer Y, Aran A, Gulsuner S, Abu Libdeh B, Renbaum P, Brunetti D, Teixeira PF, Walsh T, Zeligson S, Ruotolo R, Beeri R, Dweikat I, Shahrour M, Weinberg-Shukron A, Zahdeh F, Baruffini E, Glaser E, King MC, Levy-Lahad E, Zeviani M, Segel R. Mitochondrial PITRM1 peptidase loss-of-function in childhood cerebellar atrophy. J Med Genet 2018; 55:599-606. [PMID: 29764912 DOI: 10.1136/jmedgenet-2018-105330] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 03/28/2018] [Accepted: 04/10/2018] [Indexed: 12/28/2022]
Abstract
OBJECTIVE To identify the genetic basis of a childhood-onset syndrome of variable severity characterised by progressive spinocerebellar ataxia, mental retardation, psychotic episodes and cerebellar atrophy. METHODS Identification of the underlying mutations by whole exome and whole genome sequencing. Consequences were examined in patients' cells and in yeast. RESULTS Two brothers from a consanguineous Palestinian family presented with progressive spinocerebellar ataxia, mental retardation and psychotic episodes. Serial brain imaging showed severe progressive cerebellar atrophy. Whole exome sequencing revealed a novel mutation: pitrilysin metallopeptidase 1 (PITRM1) c.2795C>T, p.T931M, homozygous in the affected children and resulting in 95% reduction in PITRM1 protein. Whole genome sequencing revealed a chromosome X structural rearrangement that also segregated with the disease. Independently, two siblings from a second Palestinian family presented with similar, somewhat milder symptoms and the same PITRM1 mutation on a shared haplotype. PITRM1T931M carrier frequency was 0.027 (3/110) in the village of the first family evaluated, and 0/300 among Palestinians from other locales. PITRM1 is a mitochondrial matrix enzyme that degrades 10-65 amino acid oligopeptides, including the mitochondrial fraction of amyloid-beta peptide. Analysis of peptide cleavage activity by the PITRM1T931M protein revealed a significant decrease in the degradation capacity specifically of peptides ≥40 amino acids. CONCLUSION PITRM1T931M results in childhood-onset recessive cerebellar pathology. Severity of PITRM1-related disease may be affected by the degree of impairment in cleavage of mitochondrial long peptides. Disruption and deletion of X linked regulatory segments may also contribute to severity.
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Affiliation(s)
- Yeshaya Langer
- Department of Pediatrics, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Adi Aran
- Department of Pediatrics, Neuropediatrics Unit, Shaare Zedek Medical Center and Hebrew University-Hadassah School of Medicine, Jerusalem, Israel
| | - Suleyman Gulsuner
- Departments of Medicine and Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Bassam Abu Libdeh
- Departments of Pediatrics and Genetics, Makassed Hospital, Al-Quds University, Jerusalem, Israel
| | - Paul Renbaum
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Dario Brunetti
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - Pedro-Filipe Teixeira
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Tom Walsh
- Departments of Medicine and Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Sharon Zeligson
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Roberta Ruotolo
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Rachel Beeri
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Imad Dweikat
- Departments of Pediatrics and Genetics, Makassed Hospital, Al-Quds University, Jerusalem, Israel
| | - Maher Shahrour
- Departments of Pediatrics and Genetics, Makassed Hospital, Al-Quds University, Jerusalem, Israel
| | | | - Fouad Zahdeh
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Enrico Baruffini
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Elzbieta Glaser
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Mary-Claire King
- Departments of Medicine and Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Ephrat Levy-Lahad
- Medical Genetics Institute, Shaare Zedek Medical Center, Hebrew University-Hadassah School of Medicine, Jerusalem, Israel
| | - Massimo Zeviani
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Reeval Segel
- Department of Pediatrics, Medical Genetics Institute, Shaare Zedek Medical Center, Hebrew University-Hadassah School of Medicine, Jerusalem, Israel
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Jarvik GP, King MC. Arno G. Motulsky (1923–2018): A Founder of Medical Genetics, Creator of Pharmacogenetics, and Former ASHG President. Am J Hum Genet 2018. [DOI: 10.1016/j.ajhg.2018.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Affiliation(s)
- Sarah K Baxter
- Department of Medicine, University of Washington, Seattle.,Department of Genome Sciences, University of Washington, Seattle.,Department of Rheumatology, Seattle Children's Hospital, Seattle, Washington
| | - Mary-Claire King
- Department of Medicine, University of Washington, Seattle.,Department of Genome Sciences, University of Washington, Seattle
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Greider C, Hopkins N, Steitz J, Amon A, Asai D, Barres B, Bass B, Bassler B, Birgeneau R, Bjorkman P, Botchan M, Brugge J, Cech T, Colwell R, Craig N, deLange T, Eisen M, Gottesman S, Green R, Handelsman J, Kimble J, King MC, Lehmann R, Marder E, Mullins D, O'Shea E, Schmid S, Seydoux G, Spradling A, Storz G, Szostak J, Telesnitsky A, Tilghman S, Tjian R, Vale R, Wolberger C, Zakian V. Not just Salk. Science 2017; 357:1105-1106. [DOI: 10.1126/science.aao6221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Carol Greider
- Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nancy Hopkins
- Massacusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Angelika Amon
- Massacusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David Asai
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Ben Barres
- Stanford University, Stanford, CA 94305, USA
| | - Brenda Bass
- University of Utah, Salt Lake City, UT 84112, USA
| | | | | | | | | | - Joan Brugge
- Harvard Medical School, Boston, MA 02115, USA
| | - Tom Cech
- University of Colorado Boulder, Boulder, CO 80309, USA
| | - Rita Colwell
- University of Maryland, College Park, MD 20742, USA
| | - Nancy Craig
- Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Michael Eisen
- University of California Berkeley, Berkeley, CA 94720, USA
| | | | - Rachel Green
- Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | | | | | | | - Eve Marder
- Brandeis University, Waltham, MA 01454, USA
| | - Dyche Mullins
- University of California San Francisco, San Francisco, CA 94158, USA
| | - Erin O'Shea
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Sandra Schmid
- University of Texas Southwestern Medical School, Dallas, TX 75390, USA
| | - Geraldine Seydoux
- Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Allan Spradling
- Carnegie Institution of Washington, Baltimore, MD 21218, USA
| | | | | | | | | | - Robert Tjian
- University of California Berkeley, Berkeley, CA 94720, USA
| | - Ronald Vale
- University of California San Francisco, San Francisco, CA 94158, USA
| | - Cynthia Wolberger
- Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Hamameh SL, Renbaum P, Kamal L, Dweik D, Salahat M, Jaraysa T, Rayyan AA, Casadei S, Mandell JB, Gulsuner S, Lee MK, Walsh T, King MC, Levy-Lahad E, Kanaan M. Genomic analysis of inherited breast cancer among Palestinian women: Genetic heterogeneity and a founder mutation in TP53. Int J Cancer 2017; 141:750-756. [PMID: 28486781 PMCID: PMC5526459 DOI: 10.1002/ijc.30771] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 03/24/2017] [Accepted: 04/25/2017] [Indexed: 02/01/2023]
Abstract
Breast cancer among Palestinian women has lower incidence than in Europe or North America, yet is very frequently familial. We studied genetic causes of this familial clustering in a consecutive hospital-based series of 875 Palestinian patients with invasive breast cancer, including 453 women with diagnosis by age 40, or with breast or ovarian cancer in a mother, sister, grandmother or aunt ("discovery series"); and 422 women diagnosed after age 40 and with negative family history ("older-onset sporadic patient series"). Genomic DNA from women in the discovery series was sequenced for all known breast cancer genes, revealing a pathogenic mutation in 13% (61/453) of patients. These mutations were screened in all patients and in 300 Palestinian female controls, revealing 1.0% (4/422) carriers among older, nonfamilial patients and two carriers among controls. The mutational spectrum was highly heterogeneous, including pathogenic mutations in 11 different genes: BRCA1, BRCA2, TP53, ATM, CHEK2, BARD1, BRIP1, PALB2, MRE11A, PTEN and XRCC2. BRCA1 carriers were significantly more likely than other patients to have triple negative tumors (p = 0.03). The single most frequent mutation was TP53 p.R181C, which was significantly enriched in the discovery series compared to controls (p = 0.01) and was responsible for 15% of breast cancers among young onset or familial patients. TP53 p.R181C predisposed specifically to breast cancer with incomplete penetrance, and not to other Li-Fraumeni cancers. Palestinian women with young onset or familial breast cancer and their families would benefit from genetic analysis and counseling.
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Affiliation(s)
- Suhair Lolas Hamameh
- Hereditary Research Laboratory and Department of Life Sciences, Bethlehem University, Bethlehem, PALESTINE
- Medical Genetics Institute, Share Zedek Medical Center, and Faculty of Medicine, Hebrew University, Jerusalem, ISRAEL
| | - Paul Renbaum
- Medical Genetics Institute, Share Zedek Medical Center, and Faculty of Medicine, Hebrew University, Jerusalem, ISRAEL
| | - Lara Kamal
- Hereditary Research Laboratory and Department of Life Sciences, Bethlehem University, Bethlehem, PALESTINE
| | - Dima Dweik
- Hereditary Research Laboratory and Department of Life Sciences, Bethlehem University, Bethlehem, PALESTINE
| | - Mohammad Salahat
- Hereditary Research Laboratory and Department of Life Sciences, Bethlehem University, Bethlehem, PALESTINE
| | - Tamara Jaraysa
- Hereditary Research Laboratory and Department of Life Sciences, Bethlehem University, Bethlehem, PALESTINE
| | - Amal Abu Rayyan
- Hereditary Research Laboratory and Department of Life Sciences, Bethlehem University, Bethlehem, PALESTINE
| | - Silvia Casadei
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle WA, USA
| | - Jessica B. Mandell
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle WA, USA
| | - Suleyman Gulsuner
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle WA, USA
| | - Ming K. Lee
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle WA, USA
| | - Tom Walsh
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle WA, USA
| | - Mary-Claire King
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle WA, USA
| | - Ephrat Levy-Lahad
- Medical Genetics Institute, Share Zedek Medical Center, and Faculty of Medicine, Hebrew University, Jerusalem, ISRAEL
| | - Moein Kanaan
- Hereditary Research Laboratory and Department of Life Sciences, Bethlehem University, Bethlehem, PALESTINE
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Lieberman S, Walsh T, Schechter M, Adar T, Goldin E, Beeri R, Sharon N, Baris H, Ben Avi L, Half E, Lerer I, Shirts BH, Pritchard CC, Tomlinson I, King MC, Levy-Lahad E, Peretz T, Goldberg Y. Features of Patients With Hereditary Mixed Polyposis Syndrome Caused by Duplication of GREM1 and Implications for Screening and Surveillance. Gastroenterology 2017; 152:1876-1880.e1. [PMID: 28242209 DOI: 10.1053/j.gastro.2017.02.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 02/04/2017] [Accepted: 02/16/2017] [Indexed: 12/02/2022]
Abstract
Hereditary mixed polyposis syndrome is a rare colon cancer predisposition syndrome caused by a duplication of a noncoding sequence near the gremlin 1, DAN family BMP antagonist gene (GREM1) originally described in Ashkenazi Jews. Few families with GREM1 duplications have been described, so there are many questions about detection and management. We report 4 extended families with the duplication near GREM1 previously found in Ashkenazi Jews; 3 families were identified at cancer genetic clinics in Israel and 1 family was identified in a cohort of patients with familial colorectal cancer. Their clinical features include extracolonic tumors, onset of polyps in adolescence, and rapid progression of some polyps to advanced adenomas. One family met diagnostic criteria for Lynch syndrome. Expansion of the hereditary mixed polyposis syndrome phenotype can inform surveillance strategies for carriers of GREM1 duplications.
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Affiliation(s)
- Sari Lieberman
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Tom Walsh
- Department of Medicine, Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Menachem Schechter
- Gastroenterology Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Tomer Adar
- Gastroenterology Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Eran Goldin
- Gastroenterology Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Rachel Beeri
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Nitzan Sharon
- Genetics Institute, Rambam Medical Center, Jerusalem, Israel
| | - Hagit Baris
- Genetics Institute, Rambam Medical Center, Jerusalem, Israel
| | - Liat Ben Avi
- Department of Human Genetics and Metabolic Diseases, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Elizabeth Half
- Gastroenterology Institute, Rambam Medical Center, Jerusalem, Israel
| | - Israela Lerer
- Department of Human Genetics and Metabolic Diseases, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Brian H Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Colin C Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Ian Tomlinson
- Oxford Centre for Cancer Gene Research and Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Mary-Claire King
- Department of Medicine, Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Ephrat Levy-Lahad
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel; Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tamar Peretz
- Sharett Institute of Oncology, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Yael Goldberg
- Sharett Institute of Oncology, Hebrew University-Hadassah Medical Center, Jerusalem, Israel.
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Felix GES, Zheng Y, Guindalini RSC, Machado-Lopes TMB, Zhang J, Côrtes J, Oliveira PC, Santos IS, Bomfim T, Garicochea B, Toralles MB, Abe-Sandes K, Nascimento ILO, King MC, Walsh T, Olopade OI. BROCA gene panel testing in African descendants from northeastern Brazil: Genetic susceptibility profile of an admixed population. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.1572] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
1572 Background: The rising global burden of breast cancer (BC) in developing countries demands innovative interventions to accelerate progress in cancer control and prevention. Given the high rates of aggressive young onset breast cancer in Brazil, we sought to examine genetic susceptibility to the disease in the State of Bahia in the Northeast of Brazil, which has the largest population of African descendants. Methods: We screened cases, high-risk breast cancer patients with and without family history of breast cancer, and controls (cancer-free women) for twenty-eight breast cancer susceptibility genes using a validated targeted capture and multiplex sequencing approach – the BROCA panel. Each participant gave informed consent under IRB approved protocols and provided clinical-pathological and epidemiological data. Results: A total of 292 consecutive and unrelated individuals (173 cases and 119 controls) were included. Nearly 2/3rds of the cases (116/173) and about 90% of the controls (108/119) self-reported as African-descendant. Mutations considered pathogenic were identified in 37 (21.4%) cases and in one control (0.84%, RAD51C c.266insA), OR = 27.75 and p = 0.008. The mutated genes in cases were BRCA1 (in 12 patients), BRCA2 (10), ATM (3), PALB2 (3), BRIP1 (3), BRCA2/ BARD1 (1), FAM175A (1), FANCM (1), NBN (1), SLX4 (1) and TP53 (1). Three recurrent mutations accounted for 12.4% (9/37) of the total: 3 BRCA1 c.3331_3334delCAAG (known European mutation), 3 BRCA1 c.211A > G (known Galician mutation), and 3 PALB2c.1671_1674delTATT (novel mutation). Conclusions: Mutations in BRCA1 and BRCA2 (64.85%) or another breast cancer gene (35.15%) occur in one in five high-risk breast cancer patients in the largest study of Northeastern Brazil to date, and a significant proportion were recurrent mutations of European origin, which can be explained by the admixture pattern of the Brazilian population. This result underscores the importance of using multigene panel in cancer genetic epidemiologic research of understudied populations where unexpected findings, such as the recurrent and novel variant in PALB2 c.1671_1674delTATT, can be detected.
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Affiliation(s)
| | - Yonglan Zheng
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, IL
| | | | | | | | | | | | | | | | | | | | | | | | | | - Tom Walsh
- University of Washington, Seattle, WA
| | - Olufunmilayo I. Olopade
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, IL
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Aran A, Segel R, Kaneshige K, Gulsuner S, Renbaum P, Oliphant S, Meirson T, Weinberg-Shukron A, Hershkovitz Y, Zeligson S, Lee MK, Samson AO, Parsons SM, King MC, Levy-Lahad E, Walsh T. Vesicular acetylcholine transporter defect underlies devastating congenital myasthenia syndrome. Neurology 2017; 88:1021-1028. [PMID: 28188302 DOI: 10.1212/wnl.0000000000003720] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 12/21/2016] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE To identify the genetic basis of a recessive congenital neurologic syndrome characterized by severe hypotonia, arthrogryposis, and respiratory failure. METHODS Identification of the responsible gene by exome sequencing and assessment of the effect of the mutation on protein stability in transfected rat neuronal-like PC12A123.7 cells. RESULTS Two brothers from a nonconsanguineous Yemeni Jewish family manifested at birth with severe hypotonia and arthrogryposis. The older brother died of respiratory failure at 5 days of age. The proband, now 4.5 years old, has been mechanically ventilated since birth with virtually no milestones achievement. Whole exome sequencing revealed homozygosity of SLC18A3 c.1078G>C, p.Gly360Arg in the affected brothers but not in other family members. SLC18A3 p.Gly360Arg is not reported in world populations but is present at a carrier frequency of 1:30 in healthy Yemeni Jews. SLC18A3 encodes the vesicular acetylcholine transporter (VAChT), which loads newly synthesized acetylcholine from the neuronal cytoplasm into synaptic vesicles. Mice that are VAChT-null have been shown to die at birth of respiratory failure. In human VAChT, residue 360 is located in a conserved region and substitution of arginine for glycine is predicted to disrupt proper protein folding and membrane embedding. Stable transfection of wild-type and mutant human VAChT into neuronal-like PC12A123.7 cells revealed similar mRNA levels, but undetectable levels of the mutant protein, suggesting post-translational degradation of mutant VAChT. CONCLUSION Loss of function of VAChT underlies severe arthrogryposis and respiratory failure. While most congenital myasthenic syndromes are caused by defects in postsynaptic proteins, VAChT deficiency is a presynaptic myasthenic syndrome.
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Affiliation(s)
- Adi Aran
- From the Neuropediatric Unit (A.A.) and Medical Genetics (R.S., P.R., A.W.-S., S.Z., E.L.-L.), Shaare Zedek Medical Center; Hebrew University-Hadassah School of Medicine (A.A., R.S., A.W.-S., E.L.-L.), Jerusalem, Israel; Department of Chemistry and Biochemistry (K.K., S.O., S.M.P.), University of California, Santa Barbara; Faculty of Medicine (T.M., Y.H., A.O.S.), Bar Ilan University, Safed, Israel; and Departments of Medicine and Genome Sciences (S.G., M.K.L., M.-C.K., T.W.), University of Washington, Seattle
| | - Reeval Segel
- From the Neuropediatric Unit (A.A.) and Medical Genetics (R.S., P.R., A.W.-S., S.Z., E.L.-L.), Shaare Zedek Medical Center; Hebrew University-Hadassah School of Medicine (A.A., R.S., A.W.-S., E.L.-L.), Jerusalem, Israel; Department of Chemistry and Biochemistry (K.K., S.O., S.M.P.), University of California, Santa Barbara; Faculty of Medicine (T.M., Y.H., A.O.S.), Bar Ilan University, Safed, Israel; and Departments of Medicine and Genome Sciences (S.G., M.K.L., M.-C.K., T.W.), University of Washington, Seattle
| | - Kota Kaneshige
- From the Neuropediatric Unit (A.A.) and Medical Genetics (R.S., P.R., A.W.-S., S.Z., E.L.-L.), Shaare Zedek Medical Center; Hebrew University-Hadassah School of Medicine (A.A., R.S., A.W.-S., E.L.-L.), Jerusalem, Israel; Department of Chemistry and Biochemistry (K.K., S.O., S.M.P.), University of California, Santa Barbara; Faculty of Medicine (T.M., Y.H., A.O.S.), Bar Ilan University, Safed, Israel; and Departments of Medicine and Genome Sciences (S.G., M.K.L., M.-C.K., T.W.), University of Washington, Seattle
| | - Suleyman Gulsuner
- From the Neuropediatric Unit (A.A.) and Medical Genetics (R.S., P.R., A.W.-S., S.Z., E.L.-L.), Shaare Zedek Medical Center; Hebrew University-Hadassah School of Medicine (A.A., R.S., A.W.-S., E.L.-L.), Jerusalem, Israel; Department of Chemistry and Biochemistry (K.K., S.O., S.M.P.), University of California, Santa Barbara; Faculty of Medicine (T.M., Y.H., A.O.S.), Bar Ilan University, Safed, Israel; and Departments of Medicine and Genome Sciences (S.G., M.K.L., M.-C.K., T.W.), University of Washington, Seattle
| | - Paul Renbaum
- From the Neuropediatric Unit (A.A.) and Medical Genetics (R.S., P.R., A.W.-S., S.Z., E.L.-L.), Shaare Zedek Medical Center; Hebrew University-Hadassah School of Medicine (A.A., R.S., A.W.-S., E.L.-L.), Jerusalem, Israel; Department of Chemistry and Biochemistry (K.K., S.O., S.M.P.), University of California, Santa Barbara; Faculty of Medicine (T.M., Y.H., A.O.S.), Bar Ilan University, Safed, Israel; and Departments of Medicine and Genome Sciences (S.G., M.K.L., M.-C.K., T.W.), University of Washington, Seattle
| | - Scott Oliphant
- From the Neuropediatric Unit (A.A.) and Medical Genetics (R.S., P.R., A.W.-S., S.Z., E.L.-L.), Shaare Zedek Medical Center; Hebrew University-Hadassah School of Medicine (A.A., R.S., A.W.-S., E.L.-L.), Jerusalem, Israel; Department of Chemistry and Biochemistry (K.K., S.O., S.M.P.), University of California, Santa Barbara; Faculty of Medicine (T.M., Y.H., A.O.S.), Bar Ilan University, Safed, Israel; and Departments of Medicine and Genome Sciences (S.G., M.K.L., M.-C.K., T.W.), University of Washington, Seattle
| | - Tomer Meirson
- From the Neuropediatric Unit (A.A.) and Medical Genetics (R.S., P.R., A.W.-S., S.Z., E.L.-L.), Shaare Zedek Medical Center; Hebrew University-Hadassah School of Medicine (A.A., R.S., A.W.-S., E.L.-L.), Jerusalem, Israel; Department of Chemistry and Biochemistry (K.K., S.O., S.M.P.), University of California, Santa Barbara; Faculty of Medicine (T.M., Y.H., A.O.S.), Bar Ilan University, Safed, Israel; and Departments of Medicine and Genome Sciences (S.G., M.K.L., M.-C.K., T.W.), University of Washington, Seattle
| | - Ariella Weinberg-Shukron
- From the Neuropediatric Unit (A.A.) and Medical Genetics (R.S., P.R., A.W.-S., S.Z., E.L.-L.), Shaare Zedek Medical Center; Hebrew University-Hadassah School of Medicine (A.A., R.S., A.W.-S., E.L.-L.), Jerusalem, Israel; Department of Chemistry and Biochemistry (K.K., S.O., S.M.P.), University of California, Santa Barbara; Faculty of Medicine (T.M., Y.H., A.O.S.), Bar Ilan University, Safed, Israel; and Departments of Medicine and Genome Sciences (S.G., M.K.L., M.-C.K., T.W.), University of Washington, Seattle
| | - Yair Hershkovitz
- From the Neuropediatric Unit (A.A.) and Medical Genetics (R.S., P.R., A.W.-S., S.Z., E.L.-L.), Shaare Zedek Medical Center; Hebrew University-Hadassah School of Medicine (A.A., R.S., A.W.-S., E.L.-L.), Jerusalem, Israel; Department of Chemistry and Biochemistry (K.K., S.O., S.M.P.), University of California, Santa Barbara; Faculty of Medicine (T.M., Y.H., A.O.S.), Bar Ilan University, Safed, Israel; and Departments of Medicine and Genome Sciences (S.G., M.K.L., M.-C.K., T.W.), University of Washington, Seattle
| | - Sharon Zeligson
- From the Neuropediatric Unit (A.A.) and Medical Genetics (R.S., P.R., A.W.-S., S.Z., E.L.-L.), Shaare Zedek Medical Center; Hebrew University-Hadassah School of Medicine (A.A., R.S., A.W.-S., E.L.-L.), Jerusalem, Israel; Department of Chemistry and Biochemistry (K.K., S.O., S.M.P.), University of California, Santa Barbara; Faculty of Medicine (T.M., Y.H., A.O.S.), Bar Ilan University, Safed, Israel; and Departments of Medicine and Genome Sciences (S.G., M.K.L., M.-C.K., T.W.), University of Washington, Seattle
| | - Ming K Lee
- From the Neuropediatric Unit (A.A.) and Medical Genetics (R.S., P.R., A.W.-S., S.Z., E.L.-L.), Shaare Zedek Medical Center; Hebrew University-Hadassah School of Medicine (A.A., R.S., A.W.-S., E.L.-L.), Jerusalem, Israel; Department of Chemistry and Biochemistry (K.K., S.O., S.M.P.), University of California, Santa Barbara; Faculty of Medicine (T.M., Y.H., A.O.S.), Bar Ilan University, Safed, Israel; and Departments of Medicine and Genome Sciences (S.G., M.K.L., M.-C.K., T.W.), University of Washington, Seattle
| | - Abraham O Samson
- From the Neuropediatric Unit (A.A.) and Medical Genetics (R.S., P.R., A.W.-S., S.Z., E.L.-L.), Shaare Zedek Medical Center; Hebrew University-Hadassah School of Medicine (A.A., R.S., A.W.-S., E.L.-L.), Jerusalem, Israel; Department of Chemistry and Biochemistry (K.K., S.O., S.M.P.), University of California, Santa Barbara; Faculty of Medicine (T.M., Y.H., A.O.S.), Bar Ilan University, Safed, Israel; and Departments of Medicine and Genome Sciences (S.G., M.K.L., M.-C.K., T.W.), University of Washington, Seattle
| | - Stanley M Parsons
- From the Neuropediatric Unit (A.A.) and Medical Genetics (R.S., P.R., A.W.-S., S.Z., E.L.-L.), Shaare Zedek Medical Center; Hebrew University-Hadassah School of Medicine (A.A., R.S., A.W.-S., E.L.-L.), Jerusalem, Israel; Department of Chemistry and Biochemistry (K.K., S.O., S.M.P.), University of California, Santa Barbara; Faculty of Medicine (T.M., Y.H., A.O.S.), Bar Ilan University, Safed, Israel; and Departments of Medicine and Genome Sciences (S.G., M.K.L., M.-C.K., T.W.), University of Washington, Seattle
| | - Mary-Claire King
- From the Neuropediatric Unit (A.A.) and Medical Genetics (R.S., P.R., A.W.-S., S.Z., E.L.-L.), Shaare Zedek Medical Center; Hebrew University-Hadassah School of Medicine (A.A., R.S., A.W.-S., E.L.-L.), Jerusalem, Israel; Department of Chemistry and Biochemistry (K.K., S.O., S.M.P.), University of California, Santa Barbara; Faculty of Medicine (T.M., Y.H., A.O.S.), Bar Ilan University, Safed, Israel; and Departments of Medicine and Genome Sciences (S.G., M.K.L., M.-C.K., T.W.), University of Washington, Seattle
| | - Ephrat Levy-Lahad
- From the Neuropediatric Unit (A.A.) and Medical Genetics (R.S., P.R., A.W.-S., S.Z., E.L.-L.), Shaare Zedek Medical Center; Hebrew University-Hadassah School of Medicine (A.A., R.S., A.W.-S., E.L.-L.), Jerusalem, Israel; Department of Chemistry and Biochemistry (K.K., S.O., S.M.P.), University of California, Santa Barbara; Faculty of Medicine (T.M., Y.H., A.O.S.), Bar Ilan University, Safed, Israel; and Departments of Medicine and Genome Sciences (S.G., M.K.L., M.-C.K., T.W.), University of Washington, Seattle.
| | - Tom Walsh
- From the Neuropediatric Unit (A.A.) and Medical Genetics (R.S., P.R., A.W.-S., S.Z., E.L.-L.), Shaare Zedek Medical Center; Hebrew University-Hadassah School of Medicine (A.A., R.S., A.W.-S., E.L.-L.), Jerusalem, Israel; Department of Chemistry and Biochemistry (K.K., S.O., S.M.P.), University of California, Santa Barbara; Faculty of Medicine (T.M., Y.H., A.O.S.), Bar Ilan University, Safed, Israel; and Departments of Medicine and Genome Sciences (S.G., M.K.L., M.-C.K., T.W.), University of Washington, Seattle
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Catucci I, Casadei S, Ding YC, Volorio S, Ficarazzi F, Falanga A, Marchetti M, Tondini C, Franchi M, Adamson A, Mandell J, Walsh T, Olopade OI, Manoukian S, Radice P, Ricker C, Weitzel J, King MC, Peterlongo P, Neuhausen SL. Haplotype analyses of the c.1027C>T and c.2167_2168delAT recurrent truncating mutations in the breast cancer-predisposing gene PALB2. Breast Cancer Res Treat 2016; 160:121-129. [PMID: 27624329 DOI: 10.1007/s10549-016-3981-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 09/07/2016] [Indexed: 12/19/2022]
Abstract
PURPOSE Breast cancer-predisposing mutations PALB2 c.1027C>T (p.Gln343*) and PALB2 c.2167_2168delAT have each been observed multiple times in breast cancer families of Italian ancestry. More recently, the c2167_2168delAT mutation was identified in unrelated breast cancer cases of various ancestries. For each mutation, we investigated whether the origin was multiple mutational events (a "hot-spot") or a single event (a founder allele). METHODS We genotyped and reconstructed haplotypes for 36 participants of Italian, Italian-American, Hispanic, and Nigerian ancestries, using seven short tandem repeat (STR) markers that covered 3 Megabases within and flanking PALB2 on chromosome 16. RESULTS For PALB2 c.1027C>T, a shared haplotype with a minimum size of 150 kb was shared by all 19 carriers investigated, all of Italian ancestry. This result suggests that this allele arose as a single event in a shared ancestor. For PALB2 c.2167_2168delAT, all 12 carriers from American-Italian and Italian families shared a 1-Mb haplotype, the 3 Hispanic carriers shared a different haplotype of size 2 Mb, and the Nigerian carrier had different alleles at all 7 STR markers. These results suggest that PALB2 c.2167_2168delAT arose multiple times, but that within each population, PALB2 c.2167_2168delAT likely represents a single mutational event. CONCLUSION We identified two PALB2 mutations that are founder alleles in Italian families, one of which is, independently, also a founder mutation in American-Hispanic breast cancers.
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Affiliation(s)
- Irene Catucci
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Silvia Casadei
- Departments of Medicine and Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Yuan Chun Ding
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Sara Volorio
- Cogentech, Cancer Genetic Test Laboratory, Milan, Italy
| | | | - Anna Falanga
- Department of Immunohematology and Transfusion Medicine, Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - Marina Marchetti
- Department of Immunohematology and Transfusion Medicine, Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - Carlo Tondini
- Unit of Oncology, Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - Michela Franchi
- Unit of Oncology, Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - Aaron Adamson
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Jessica Mandell
- Departments of Medicine and Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Tom Walsh
- Departments of Medicine and Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Olufunmilayo I Olopade
- Department of Medicine, Center for Clinical Cancer Genetics and Global Health, University of Chicago, Chicago, IL, USA
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Charite Ricker
- Department Medicine, Keck School of Medicine at University of Southern California, Los Angeles, CA, USA
| | - Jeffrey Weitzel
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Mary-Claire King
- Departments of Medicine and Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA.
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Abstract
It is my great pleasure to have been asked by the Editorial Committee of the Annual Review of Genomics and Human Genetics to write a short autobiography of my life in genetics over the past 70 years. It has been a great adventure. I came both to America and to human genetics by a circuitous and ultimately very fortunate route. I hope the next generation of geneticists will enjoy reading about it.
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Affiliation(s)
- Arno G. Motulsky
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington 98195
| | - Mary-Claire King
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington 98195
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Pierce SB, Gulsuner S, Stapleton GA, Walsh T, Lee MK, Mandell JB, Morales A, Klevit RE, King MC, Rogers RC. Infantile onset spinocerebellar ataxia caused by compound heterozygosity for Twinkle mutations and modeling of Twinkle mutations causing recessive disease. Cold Spring Harb Mol Case Stud 2016; 2:a001107. [PMID: 27551684 PMCID: PMC4990813 DOI: 10.1101/mcs.a001107] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Mutations in nuclear genes required for the replication and maintenance of mitochondrial DNA cause progressive multisystemic neuromuscular disorders with overlapping phenotypes. Biallelic mutations in C10orf2, encoding the Twinkle mitochondrial DNA helicase, lead to infantile-onset cerebellar ataxia (IOSCA), as well as milder and more severe phenotypes. We present a 13-year-old girl with ataxia, severe hearing loss, optic atrophy, peripheral neuropathy, and hypergonadotropic hypogonadism. Whole-exome sequencing revealed that the patient is compound heterozygous for previously unreported variants in the C10orf2 gene: a paternally inherited frameshift variant (c.333delT; p.L112Sfs*3) and a maternally inherited missense variant (c.904C>T; p.R302W). The identification of novel C10orf2 mutations extends the spectrum of mutations in the Twinkle helicase causing recessive disease, in particular the intermediate IOSCA phenotype. Structural modeling suggests that the p.R302W mutation and many other recessively inherited Twinkle mutations impact the position or interactions of the linker region, which is critical for the oligomeric ring structure and activity of the helicase. This study emphasizes the utility of whole-exome sequencing for the genetic diagnosis of a complex multisystemic disorder.
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Affiliation(s)
- Sarah B Pierce
- Department of Medicine (Medical Genetics), University of Washington, Seattle, Washington 98195, USA
| | - Suleyman Gulsuner
- Department of Medicine (Medical Genetics), University of Washington, Seattle, Washington 98195, USA
| | | | - Tom Walsh
- Department of Medicine (Medical Genetics), University of Washington, Seattle, Washington 98195, USA
| | - Ming K Lee
- Department of Medicine (Medical Genetics), University of Washington, Seattle, Washington 98195, USA
| | - Jessica B Mandell
- Department of Medicine (Medical Genetics), University of Washington, Seattle, Washington 98195, USA
| | - Augusto Morales
- Pediatric Neurology, Greenville Health System, Greenville, South Carolina 29615, USA
| | - Rachel E Klevit
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Mary-Claire King
- Department of Medicine (Medical Genetics), University of Washington, Seattle, Washington 98195, USA;; Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - R Curtis Rogers
- Greenwood Genetic Center, Greenville, South Carolina 29605, USA
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Rojek K, Nickels E, Neistadt B, Marquez R, Wickrema A, Artz A, van Besien K, Larson RA, Lee MK, Segal JP, King MC, Walsh T, Shimamura A, Keel SB, Churpek JE, Godley LA. Identifying Inherited and Acquired Genetic Factors Involved in Poor Stem Cell Mobilization and Donor-Derived Malignancy. Biol Blood Marrow Transplant 2016; 22:2100-2103. [PMID: 27497531 DOI: 10.1016/j.bbmt.2016.08.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 08/01/2016] [Indexed: 11/16/2022]
Abstract
Analysis of the clinical characteristics of hematopoietic stem cell transplant (HSCT) donors has proven beneficial for identifying cases of heritable hematopoietic disorders. This study examines poor peripheral blood hematopoietic stem cell mobilization after granulocyte colony-stimulating factor administration among 328 donors as a potential marker for suspected familial predisposition to myeloid malignancies. Here, we present data comparing the clinical characteristics of poor-mobilizing versus nonpoor-mobilizing donors and the results of panel-based sequencing of hematopoietic genes in poor-mobilizing donors. From this analysis, we identified a novel case of a donor-derived myelodysplastic syndrome in an HSCT recipient that is consistent with clonal evolution of TET2-mutated clonal hematopoiesis of indeterminate potential (CHIP) within the donor. This study demonstrates the potential risk of using hematopoietic stem cells from a donor with CHIP and raises the question of whether there should be increased screening measures to identify such donors.
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Affiliation(s)
- Katarzyna Rojek
- Section of Hematology/Oncology, Department of Medicine, and The University of Chicago Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois
| | - Eric Nickels
- Section of Hematology/Oncology, Department of Medicine, and The University of Chicago Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois
| | - Barbara Neistadt
- Section of Hematology/Oncology, Department of Medicine, and The University of Chicago Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois
| | - Rafael Marquez
- Section of Hematology/Oncology, Department of Medicine, and The University of Chicago Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois
| | - Amittha Wickrema
- Section of Hematology/Oncology, Department of Medicine, and The University of Chicago Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois
| | - Andrew Artz
- Section of Hematology/Oncology, Department of Medicine, and The University of Chicago Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois
| | - Koen van Besien
- Section of Hematology/Oncology, Department of Medicine, and The University of Chicago Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois
| | - Richard A Larson
- Section of Hematology/Oncology, Department of Medicine, and The University of Chicago Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois
| | - Ming K Lee
- Department of Medicine, Division of Medical Genetics, and Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Jeremy P Segal
- Division of Genomic and Molecular Pathology, Department of Pathology, University of Chicago, Chicago, Illinois
| | - Mary-Claire King
- Department of Medicine, Division of Medical Genetics, and Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Tom Walsh
- Department of Medicine, Division of Medical Genetics, and Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Akiko Shimamura
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Pediatric Hematology/Oncology, Seattle Children's Hospital, and Department of Pediatrics, University of Washington, Seattle, Washington
| | - Sioban B Keel
- Department of Medicine, Division of Hematology, University of Washington, Seattle, Washington
| | - Jane E Churpek
- Section of Hematology/Oncology, Department of Medicine, and The University of Chicago Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois; Center for Clinical Cancer Genetics, The University of Chicago, Chicago, Illinois
| | - Lucy A Godley
- Section of Hematology/Oncology, Department of Medicine, and The University of Chicago Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois; Center for Clinical Cancer Genetics, The University of Chicago, Chicago, Illinois.
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45
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Keel SB, Scott A, Sanchez-Bonilla M, Ho PA, Gulsuner S, Pritchard CC, Abkowitz JL, King MC, Walsh T, Shimamura A. Genetic features of myelodysplastic syndrome and aplastic anemia in pediatric and young adult patients. Haematologica 2016; 101:1343-1350. [PMID: 27418648 DOI: 10.3324/haematol.2016.149476] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 07/13/2016] [Indexed: 11/09/2022] Open
Abstract
The clinical and histopathological distinctions between inherited versus acquired bone marrow failure and myelodysplastic syndromes are challenging. The identification of inherited bone marrow failure/myelodysplastic syndromes is critical to inform appropriate clinical management. To investigate whether a subset of pediatric and young adults undergoing transplant for aplastic anemia or myelodysplastic syndrome have germline mutations in bone marrow failure/myelodysplastic syndrome genes, we performed a targeted genetic screen of samples obtained between 1990-2012 from children and young adults with aplastic anemia or myelodysplastic syndrome transplanted at the Fred Hutchinson Cancer Research Center. Mutations in inherited bone marrow failure/myelodysplastic syndrome genes were found in 5.1% (5/98) of aplastic anemia patients and 13.6% (15/110) of myelodysplastic syndrome patients. While the majority of mutations were constitutional, a RUNX1 mutation present in the peripheral blood at a 51% variant allele fraction was confirmed to be somatically acquired in one myelodysplastic syndrome patient. This highlights the importance of distinguishing germline versus somatic mutations by sequencing DNA from a second tissue or from parents. Pathological mutations were present in DKC1, MPL, and TP53 among the aplastic anemia cohort, and in FANCA, GATA2, MPL, RTEL1, RUNX1, SBDS, TERT, TINF2, and TP53 among the myelodysplastic syndrome cohort. Family history or physical examination failed to reliably predict the presence of germline mutations. This study shows that while any single specific bone marrow failure/myelodysplastic syndrome genetic disorder is rare, screening for these disorders in aggregate identifies a significant subset of patients with inherited bone marrow failure/myelodysplastic syndrome.
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Affiliation(s)
- Siobán B Keel
- Department of Medicine, Division of Hematology, University of Washington, Seattle, WA, USA
| | - Angela Scott
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Pediatric Hematology/Oncology, Seattle Children's Hospital, WA, USA.,Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Marilyn Sanchez-Bonilla
- Boston Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, MA, USA
| | - Phoenix A Ho
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Pediatric Hematology/Oncology, Seattle Children's Hospital, WA, USA.,Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Suleyman Gulsuner
- Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Colin C Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Janis L Abkowitz
- Department of Medicine, Division of Hematology, University of Washington, Seattle, WA, USA
| | - Mary-Claire King
- Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Tom Walsh
- Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Akiko Shimamura
- Boston Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, MA, USA
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46
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Grati M, Yan D, Raval MH, Walsh T, Ma Q, Chakchouk I, Kannan-Sundhari A, Mittal R, Masmoudi S, Blanton SH, Tekin M, King MC, Yengo CM, Liu XZ. MYO3A Causes Human Dominant Deafness and Interacts with Protocadherin 15-CD2 Isoform. Hum Mutat 2016; 37:481-7. [PMID: 26841241 DOI: 10.1002/humu.22961] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 01/15/2016] [Indexed: 01/10/2023]
Abstract
Hereditary hearing loss (HL) is characterized by both allelic and locus genetic heterogeneity. Both recessive and dominant forms of HL may be caused by different mutations in the same deafness gene. In a family with post-lingual progressive non-syndromic deafness, whole-exome sequencing of genomic DNA from five hearing-impaired relatives revealed a single variant, p.Gly488Glu (rs145970949:G>A) in MYO3A, co-segregating with HL as an autosomal dominant trait. This amino acid change, predicted to be pathogenic, alters a highly conserved residue in the motor domain of MYO3A. The mutation severely alters the ATPase activity and motility of the protein in vitro, and the mutant protein fails to accumulate in the filopodia tips in COS7 cells. However, the mutant MYO3A was able to reach the tips of organotypic inner ear culture hair cell stereocilia, raising the possibility of a local effect on positioning of the mechanoelectrical transduction (MET) complex at the stereocilia tips. To address this hypothesis, we investigated the interaction of MYO3A with the cytosolic tail of the integral tip-link protein protocadherin 15 (PCDH15), a core component of MET complex. Interestingly, we uncovered a novel interaction between MYO3A and PCDH15 shedding new light on the function of myosin IIIA at stereocilia tips.
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Affiliation(s)
- M'hamed Grati
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida
| | - Denise Yan
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida
| | - Manmeet H Raval
- Department of Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Tom Walsh
- Departments of Medicine and Genome Sciences, University of Washington, Seattle, Washington
| | - Qi Ma
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida
| | - Imen Chakchouk
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida.,Laboratoire Procédés de Criblage Moléculaire et Cellulaire, Centre de Biotechnologie de Sfax, Université de Sfax, Sfax, Tunisie
| | | | - Rahul Mittal
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida
| | - Saber Masmoudi
- Laboratoire Procédés de Criblage Moléculaire et Cellulaire, Centre de Biotechnologie de Sfax, Université de Sfax, Sfax, Tunisie
| | - Susan H Blanton
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida.,Dr. John T. Macdonald Foundation, Department of Human Genetics, and John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida
| | - Mustafa Tekin
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida.,Dr. John T. Macdonald Foundation, Department of Human Genetics, and John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida
| | - Mary-Claire King
- Departments of Medicine and Genome Sciences, University of Washington, Seattle, Washington
| | - Christopher M Yengo
- Department of Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Xue Zhong Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida.,Dr. John T. Macdonald Foundation, Department of Human Genetics, and John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida.,Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, Hunan, China
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47
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Shirts BH, Casadei S, Jacobson AL, Lee MK, Gulsuner S, Bennett RL, Miller M, Hall SA, Hampel H, Hisama FM, Naylor LV, Goetsch C, Leppig K, Tait JF, Scroggins SM, Turner EH, Livingston R, Salipante SJ, King MC, Walsh T, Pritchard CC. Improving performance of multigene panels for genomic analysis of cancer predisposition. Genet Med 2016; 18:974-81. [PMID: 26845104 DOI: 10.1038/gim.2015.212] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 12/11/2015] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Screening multiple genes for inherited cancer predisposition expands opportunities for cancer prevention; however, reports of variants of uncertain significance (VUS) may limit clinical usefulness. We used an expert-driven approach, exploiting all available information, to evaluate multigene panels for inherited cancer predisposition in a clinical series that included multiple cancer types and complex family histories. METHODS For 1,462 sequential patients referred for testing by BROCA or ColoSeq multigene panels, genomic DNA was sequenced and variants were interpreted by multiple experts using International Agency for Research on Cancer guidelines and incorporating evolutionary conservation, known and predicted variant consequences, and personal and family cancer history. Diagnostic yield was evaluated for various presenting conditions and family-history profiles. RESULTS Of 1,462 patients, 12% carried damaging mutations in established cancer genes. Diagnostic yield varied by clinical presentation. Actionable results were identified for 13% of breast and colorectal cancer patients and for 4% of cancer-free subjects, based on their family histories of cancer. Incidental findings explaining cancer in neither the patient nor the family were present in 1.7% of subjects. Less than 1% of patients carried VUS in BRCA1 or BRCA2. For all genes combined, initial reports contained VUS for 10.5% of patients, which declined to 7.5% of patients after reclassification based on additional information. CONCLUSIONS Individualized interpretation of gene panels is a complex medical activity. Interpretation by multiple experts in the context of personal and family histories maximizes actionable results and minimizes reports of VUS.Genet Med 18 10, 974-981.
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Affiliation(s)
- Brian H Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Silvia Casadei
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Angela L Jacobson
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Ming K Lee
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Suleyman Gulsuner
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Robin L Bennett
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA
| | | | - Sarah A Hall
- Kadlec Regional Medical Center, Richland, Washington, USA
| | - Heather Hampel
- Division of Human Genetics, Department of Internal Medicine, Ohio State University, Columbus, Ohio, USA
| | - Fuki M Hisama
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Lorraine V Naylor
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA
| | | | - Kathleen Leppig
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA.,Clinical Genetics, Group Health Cooperative, Seattle, Washington, USA
| | - Jonathan F Tait
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Sheena M Scroggins
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Emily H Turner
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Robert Livingston
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Stephen J Salipante
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Mary-Claire King
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA.,Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Tom Walsh
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Colin C Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
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48
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Churpek JE, Marquez R, Neistadt B, Claussen K, Lee MK, Churpek MM, Huo D, Weiner H, Bannerjee M, Godley LA, Le Beau MM, Pritchard CC, Walsh T, King MC, Olopade OI, Larson RA. Inherited mutations in cancer susceptibility genes are common among survivors of breast cancer who develop therapy-related leukemia. Cancer 2015; 122:304-11. [PMID: 26641009 DOI: 10.1002/cncr.29615] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 04/09/2015] [Indexed: 12/12/2022]
Abstract
BACKGROUND Risk factors for the development of therapy-related leukemia (TRL), an often lethal late complication of cytotoxic therapy, remain poorly understood and may differ for survivors of different malignancies. Survivors of breast cancer (BC) now account for the majority of TRL cases, making the study of TRL risk factors in this population a priority. METHODS Subjects with TRL after cytotoxic therapy for a primary BC were identified from the TRL registry at The University of Chicago. Those with an available germline DNA sample were screened with a comprehensive gene panel covering known inherited BC susceptibility genes. Clinical and TRL characteristics of all subjects and those with identified germline mutations were described. RESULTS Nineteen of 88 survivors of BC with TRL (22%) had an additional primary cancer and 40 of the 70 survivors with an available family history (57%) had a close relative with breast, ovarian, or pancreatic cancer. Of the 47 subjects with available DNA, 10 (21%) were found to carry a deleterious inherited mutation in BRCA1 (3 subjects; 6%), BRCA2 (2 subjects; 4%), TP53 (tumor protein p53) (3 subjects; 6%), CHEK2 (checkpoint kinase 2) (1 subject; 2%), and PALB2 (partner and localizer of BRCA2) (1 subject; 2%). CONCLUSIONS Survivors of BC with TRL have personal and family histories suggestive of inherited cancer susceptibility and frequently carry germline mutations in BC susceptibility genes. The data from the current study support the role of these genes in TRL risk and suggest that long-term follow-up studies of women with germline mutations who are treated for BC and functional studies of the effects of heterozygous mutations in these genes on bone marrow function after cytotoxic exposures are warranted. Cancer 2016;122:304-311. © 2015 American Cancer Society.
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Affiliation(s)
- Jane E Churpek
- Center for Clinical Cancer Genetics, The University of Chicago, Chicago, Illinois.,Department of Medicine, The University of Chicago, Chicago, Illinois.,Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois
| | - Rafael Marquez
- Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Barbara Neistadt
- Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Kimberly Claussen
- Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Ming K Lee
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, Washington
| | - Matthew M Churpek
- Department of Medicine, The University of Chicago, Chicago, Illinois.,Department of Health Studies, The University of Chicago, Chicago, Illinois
| | - Dezheng Huo
- Department of Health Studies, The University of Chicago, Chicago, Illinois
| | - Howard Weiner
- Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Mekhala Bannerjee
- Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Lucy A Godley
- Center for Clinical Cancer Genetics, The University of Chicago, Chicago, Illinois.,Department of Medicine, The University of Chicago, Chicago, Illinois.,Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois
| | - Michelle M Le Beau
- Department of Medicine, The University of Chicago, Chicago, Illinois.,Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois
| | - Colin C Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Tom Walsh
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, Washington
| | - Mary-Claire King
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, Washington
| | - Olufunmilayo I Olopade
- Center for Clinical Cancer Genetics, The University of Chicago, Chicago, Illinois.,Department of Medicine, The University of Chicago, Chicago, Illinois.,Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois
| | - Richard A Larson
- Department of Medicine, The University of Chicago, Chicago, Illinois.,Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois
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49
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Miller K, Tong Y, Jones DR, Walsh T, Danso MA, Ma CX, Silverman P, King MC, Badve SS, Perkins SM. Cisplatin with or without rucaparib after preoperative chemotherapy in patients with triple negative breast cancer: Final efficacy results of Hoosier Oncology Group BRE09-146. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.15_suppl.1082] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Kathy Miller
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN
| | - Yan Tong
- Indiana University School of Medicine, Indianapolis, IN
| | - David R Jones
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN
| | - Tom Walsh
- University of Washington, Seattle, WA
| | | | | | | | | | | | - Susan M. Perkins
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN
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50
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Bayram Y, Gulsuner S, Guran T, Abaci A, Yesil G, Gulsuner HU, Atay Z, Pierce SB, Gambin T, Lee M, Turan S, Bober E, Atik MM, Walsh T, Karaca E, Pehlivan D, Jhangiani SN, Muzny D, Bereket A, Buyukgebiz A, Boerwinkle E, Gibbs RA, King MC, Lupski JR. Homozygous loss-of-function mutations in SOHLH1 in patients with nonsyndromic hypergonadotropic hypogonadism. J Clin Endocrinol Metab 2015; 100:E808-14. [PMID: 25774885 PMCID: PMC4422898 DOI: 10.1210/jc.2015-1150] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CONTEXT Hypergonadotropic hypogonadism presents in females with delayed or arrested puberty, primary or secondary amenorrhea due to gonadal dysfunction, and is further characterized by elevated gonadotropins and low sex steroids. Chromosomal aberrations and various specific gene defects can lead to hypergonadotropic hypogonadism. Responsible genes include those with roles in gonadal development or maintenance, sex steroid synthesis, or end-organ resistance to gonadotropins. Identification of novel causative genes in this disorder will contribute to our understanding of the regulation of human reproductive function. OBJECTIVES The aim of this study was to identify and report the gene responsible for autosomal-recessive hypergonadotropic hypogonadism in two unrelated families. DESIGN AND PARTICIPANTS Clinical evaluation and whole-exome sequencing were performed in two pairs of sisters with nonsyndromic hypergonadotropic hypogonadism from two unrelated families. RESULTS Exome sequencing analysis revealed two different truncating mutations in the same gene: SOHLH1 c.705delT (p.Pro235fs*4) and SOHLH1 c.27C>G (p.Tyr9stop). Both mutations were unique to the families and segregation was consistent with Mendelian expectations for an autosomal-recessive mode of inheritance. CONCLUSIONS Sohlh1 was known from previous mouse studies to be a transcriptional regulator that functions in the maintenance and survival of primordial ovarian follicles, but loss-of-function mutations in human females have not been reported. Our results provide evidence that homozygous-truncating mutations in SOHLH1 cause female nonsyndromic hypergonadotropic hypogonadism.
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Affiliation(s)
- Yavuz Bayram
- Department of Molecular and Human Genetics (Y.B., T.Ga., M.M.A., E.K., D.P., J.R.L.), Baylor College of Medicine, Houston, Texas 77030; Department of Medicine, Division of Medical Genetics (S.G., H.U.G., S.B.P., M.L., T.W., M.-C.K.), University of Washington, Seattle, Washington 98195; Department of Pediatric Endocrinology and Diabetes (T.Gu., Z.A., S.T., A.Be.), Marmara University Hospital, Istanbul, Turkey 34899; Department of Pediatric Endocrinology (A.Ab., E.Bob., A.Bu.), Dokuz Eylül University Faculty of Medicine, Izmir, Turkey 35340; Department of Medical Genetics (G.Y.), Bezmialem University, Istanbul, Turkey 34093; Human Genome Sequencing Center (S.N.J., D.M., E.Boe., R.A.G.), Baylor College of Medicine, Houston, Texas 77030; Human Genetics Center (E.Boe.), University of Texas Health Science Center at Houston, Houston, Texas 77030; Department of Pediatrics (J.R.L.), Baylor College of Medicine, Houston, Texas 77030; and Texas Children's Hospital (J.R.L.), Houston, Texas 77030
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