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Parsons BL, Beal MA, Dearfield KL, Douglas GR, Gi M, Gollapudi BB, Heflich RH, Horibata K, Kenyon M, Long AS, Lovell DP, Lynch AM, Myers MB, Pfuhler S, Vespa A, Zeller A, Johnson GE, White PA. Severity of effect considerations regarding the use of mutation as a toxicological endpoint for risk assessment: A report from the 8th International Workshop on Genotoxicity Testing (IWGT). ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2024. [PMID: 38828778 DOI: 10.1002/em.22599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/13/2024] [Accepted: 04/15/2024] [Indexed: 06/05/2024]
Abstract
Exposure levels without appreciable human health risk may be determined by dividing a point of departure on a dose-response curve (e.g., benchmark dose) by a composite adjustment factor (AF). An "effect severity" AF (ESAF) is employed in some regulatory contexts. An ESAF of 10 may be incorporated in the derivation of a health-based guidance value (HBGV) when a "severe" toxicological endpoint, such as teratogenicity, irreversible reproductive effects, neurotoxicity, or cancer was observed in the reference study. Although mutation data have been used historically for hazard identification, this endpoint is suitable for quantitative dose-response modeling and risk assessment. As part of the 8th International Workshops on Genotoxicity Testing, a sub-group of the Quantitative Analysis Work Group (WG) explored how the concept of effect severity could be applied to mutation. To approach this question, the WG reviewed the prevailing regulatory guidance on how an ESAF is incorporated into risk assessments, evaluated current knowledge of associations between germline or somatic mutation and severe disease risk, and mined available data on the fraction of human germline mutations expected to cause severe disease. Based on this review and given that mutations are irreversible and some cause severe human disease, in regulatory settings where an ESAF is used, a majority of the WG recommends applying an ESAF value between 2 and 10 when deriving a HBGV from mutation data. This recommendation may need to be revisited in the future if direct measurement of disease-causing mutations by error-corrected next generation sequencing clarifies selection of ESAF values.
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Affiliation(s)
- Barbara L Parsons
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Marc A Beal
- Bureau of Chemical Safety, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Kerry L Dearfield
- U.S. Environmental Protection Agency and U.S. Department of Agriculture, Washington, DC, USA
| | - George R Douglas
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Min Gi
- Department of Environmental Risk Assessment, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | | | - Robert H Heflich
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | | | - Michelle Kenyon
- Portfolio and Regulatory Strategy, Drug Safety Research and Development, Pfizer, Groton, Connecticut, USA
| | - Alexandra S Long
- Existing Substances Risk Assessment Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - David P Lovell
- Population Health Research Institute, St George's Medical School, University of London, London, UK
| | | | - Meagan B Myers
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | | | - Alisa Vespa
- Pharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Andreas Zeller
- Pharmaceutical Sciences, pRED Innovation Center Basel, Hoffmann-La Roche Ltd, Basel, Switzerland
| | - George E Johnson
- Swansea University Medical School, Swansea University, Swansea, Wales, UK
| | - Paul A White
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
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Parentelli AS, Boursier G, Cuisset L, Georgin-Lavialle S. [Genetic mosaicism in Systemic Auto-Inflammatory Diseases: A review of the literature]. Rev Med Interne 2024:S0248-8663(24)00566-6. [PMID: 38762439 DOI: 10.1016/j.revmed.2024.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 04/07/2024] [Accepted: 05/02/2024] [Indexed: 05/20/2024]
Abstract
Systemic auto-inflammatory diseases (SAIDs) are disorders associated with deregulation of innate immunity in which patients present classically with systemic inflammatory manifestations, in particular fever, skin-mucosal rashes, arthromyalgia and abdominal pain, with an increase in blood biomarkers of inflammation. At the time of their discovery, these diseases were associated with constitutional mutations in genes encoding proteins involved in innate immunity, and it was then considered that they had to begin in childhood. This dogma of constitutional mutations in SAIDs is no longer so unquestionable, since 2005 several cases of mosaicism have been reported in the literature, initially in cryopyrinopathies, but also in other SAIDs in patients with obvious clinical phenotypes and late onset of disease expression, in particular in the VEXAS syndrome (Vacuoles, E1 enzyme, X-linked, Autoinflammatory, Somatic Syndrome) and very recently in MEVF gene. Next-generation sequencing techniques are more sensitive than Sanger for detecting mosaicisms. So, when a clinical diagnosis seems obvious but no constitutional mutation is found by low-depth genetic analysis, it is useful to discuss with expert geneticists whether to consider another genetic approach in a child or an adult. This modifies the situations in which clinicians can evoke these diseases. This review provides an update on mosaicism in SAIDs.
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Affiliation(s)
- A-S Parentelli
- Service de pédiatrie, CHU Félix-Guyon, allée des Topazes, 97400 Saint-Denis, Réunion.
| | - G Boursier
- Service de génétique moléculaire et cytogénomique, laboratoire de génétique des maladies rares et auto-inflammatoires, CHU de Montpellier, université de Montpellier, 371, avenue du Doyen-Gaston-Giraud, 34295 Montpellier cedex 5, France; Centre de référence des maladies auto-inflammatoires rares et de l'amylose inflammatoire (CEREMAIA), hôpital Tenon, Assistance publique-Hôpitaux de Paris, 4, rue de la Chine, 75020 Paris, France
| | - L Cuisset
- Service de médecine génomique des maladies de système et d'organe, hôpital Cochin, Assistance publique-Hôpitaux de Paris, université Paris Cité, 27, rue du Faubourg-Saint-Jacques, 75014 Paris, France
| | - S Georgin-Lavialle
- Service de médecine interne, hôpital Tenon, Assistance publique-Hôpitaux de Paris, Sorbonne université, 4, rue de la Chine, 75020 Paris, France; Centre de référence des maladies auto-inflammatoires rares et de l'amylose inflammatoire (CEREMAIA), hôpital Tenon, Assistance publique-Hôpitaux de Paris, 4, rue de la Chine, 75020 Paris, France
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Fung WWS, Szeto CC, Chow KM, Cheng PMS, Kwong VWK, Lau SLF, Pang WF, Chu WCW, Ong ACM, Devuyst O, Li PKT. Clinical Characteristics and Kidney Outcomes in Chinese Patients with Autosomal Dominant Polycystic Kidney Disease. KIDNEY360 2024; 5:715-723. [PMID: 38556647 PMCID: PMC11146654 DOI: 10.34067/kid.0000000000000433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 03/26/2024] [Indexed: 04/02/2024]
Abstract
Key Points The Mayo clinic imaging classification allows more accurate risk stratification but is limited by the lack of data on non-White populations and on atypical imaging patterns. In this cohort of Chinese patients with autosomal dominant polycystic kidney disease, an atypical imaging pattern was observed in 17% of the cases, associated with later presentation and a milder disease course. There may be genotypic differences, especially among those with atypical imaging. Future genotyping studies will help to define the genetic basis for the phenotypic spectrum in Chinese patients. Background The management of autosomal dominant polycystic kidney disease (ADPKD) remains challenging with variable and uncertain genotype–phenotype correlations. The Mayo clinic imaging classification allows more accurate risk stratification but is limited by the atypical imaging patterns. We aim to assess the clinical characteristics and the morphology of the cystic kidneys in a cohort of Chinese patients with ADPKD. Methods Ninety-eight patients with ADPKD were recruited prospectively from August 2019 to December 2020 in Prince of Wales Hospital, Hong Kong. They were subsequently followed up every 6 months for a minimum of 2 years. We reviewed the clinical characteristics and magnetic resonance imaging patterns at baseline and the kidney outcome at the end of the follow-up. Atypical imaging patterns included unilateral, segmental, asymmetric, lopsided, and bilateral atrophy as defined by the Mayo Imaging Classification. Results The mean age was 51.5±14.3 years, and the mean eGFR 68.7±27.5 ml/min per 1.73 m2. The 98 patients included 36 male and 62 female. Seventy-six patients (77.6%) had a family history. Seventeen of the 98 (17.3%) patients had atypical imaging patterns. Compared with typical cases, atypical cases were older at the time of diagnosis (49.5±16.0 versus 33.0±13.0 years, P < 0.001) and at the time of starting antihypertensive medications (52.4±14.8 versus 39.7±11.0 years, P = 0.001) and were less likely to have a positive family history (58.8% versus 81.5%, P = 0.042). Patients with atypical patterns showed a lower eGFR decline compared with those with the typical pattern (−0.86±4.34 versus −3.44±4.07 ml/min per 1.73 m2 per year, P = 0.022). Conclusions In this cohort of Chinese patients with ADPKD, an atypical imaging pattern was observed in 17% of the cases, associated with later presentation and a milder disease course. Future genotyping studies will help to define the genetic architecture and the basis for the phenotypic spectrum in Chinese patients with ADPKD.
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Affiliation(s)
- Winston Wing-Shing Fung
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong, China
- CUHK Carol and Richard Yu Peritoneal Dialysis Research Centre, Hong Kong, China
| | - Cheuk-Chun Szeto
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong, China
- CUHK Carol and Richard Yu Peritoneal Dialysis Research Centre, Hong Kong, China
- Li Ka Shing Institute of Health Sciences (LiHS), The Chinese University of Hong Kong, Hong Kong, China
| | - Kai-Ming Chow
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong, China
- CUHK Carol and Richard Yu Peritoneal Dialysis Research Centre, Hong Kong, China
| | - Phyllis Mei-Shan Cheng
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong, China
- CUHK Carol and Richard Yu Peritoneal Dialysis Research Centre, Hong Kong, China
| | - Vickie Wai-Ki Kwong
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong, China
- CUHK Carol and Richard Yu Peritoneal Dialysis Research Centre, Hong Kong, China
| | - Sam Lik-Fung Lau
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong, China
- CUHK Carol and Richard Yu Peritoneal Dialysis Research Centre, Hong Kong, China
| | - Wing-Fai Pang
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong, China
- CUHK Carol and Richard Yu Peritoneal Dialysis Research Centre, Hong Kong, China
| | - Winnie Chiu-Wing Chu
- Department of Imaging and Interventional Radiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Albert Chee Meng Ong
- Academic Nephrology Unit, The University of Sheffield Medical School, Sheffield, United Kingdom
| | - Olivier Devuyst
- Institute of Physiology, University of Zurich, Zürich, Switzerland
- Division of Nephrology, UCLouvain Medical School, Brussels, Belgium
| | - Philip Kam-Tao Li
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong, China
- CUHK Carol and Richard Yu Peritoneal Dialysis Research Centre, Hong Kong, China
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Waldvogel SM, Posey JE, Goodell MA. Human embryonic genetic mosaicism and its effects on development and disease. Nat Rev Genet 2024:10.1038/s41576-024-00715-z. [PMID: 38605218 DOI: 10.1038/s41576-024-00715-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2024] [Indexed: 04/13/2024]
Abstract
Nearly every mammalian cell division is accompanied by a mutational event that becomes fixed in a daughter cell. When carried forward to additional cell progeny, a clone of variant cells can emerge. As a result, mammals are complex mosaics of clones that are genetically distinct from one another. Recent high-throughput sequencing studies have revealed that mosaicism is common, clone sizes often increase with age and specific variants can affect tissue function and disease development. Variants that are acquired during early embryogenesis are shared by multiple cell types and can affect numerous tissues. Within tissues, variant clones compete, which can result in their expansion or elimination. Embryonic mosaicism has clinical implications for genetic disease severity and transmission but is likely an under-recognized phenomenon. To better understand its implications for mosaic individuals, it is essential to leverage research tools that can elucidate the mechanisms by which expanded embryonic variants influence development and disease.
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Affiliation(s)
- Sarah M Waldvogel
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
- Graduate Program in Cancer and Cell Biology, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Margaret A Goodell
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
- Graduate Program in Cancer and Cell Biology, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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Mansoorshahi S, Scurlock C, Research Registry SABOTTSSOTUS, Prakash SK. Methodological advances in patient-centered rare disease research: the UTHealth Houston Turner Syndrome Society of the United States research registry. Orphanet J Rare Dis 2024; 19:112. [PMID: 38468317 DOI: 10.1186/s13023-024-03120-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 03/03/2024] [Indexed: 03/13/2024] Open
Abstract
BACKGROUND Many different clinical specialists provide care to patients with Turner syndrome (TS), who have highly variable clinical manifestations. Therefore, a national TS registry is essential to inform a cohesive approach to healthcare and research. In 2015, the Turner Syndrome Society of the United States (TSSUS) created the Turner Syndrome Research Registry (TSRR) to engage directly with community participants who voluntarily provide longitudinal data about their experiences with TS. TSRR projects are collaborative partnerships between people with TS, TSSUS, and researchers. RESULTS To ensure that registry workflows conform to the data privacy choices of participants, TSSUS collaborated with UTHealth Houston in 2021 to create a new version of the TSRR that completely separates participant health data (stored at UTHealth) and personal identifiers (maintained at TSSUS). We developed an innovative Visual Basic (VB) script that, when embedded into Microsoft Outlook, redirects REDCap surveys through TSSUS to participants by matching registry IDs to participant email addresses. Additionally, the utilization of REDCap allows for portability of data as it is an open source platform. CONCLUSION In this report, we will highlight three recent changes that more closely align the TSRR with this mission: a unique and equal collaborative partnership between UTHealth and TSSUS, an open-source platform, REDCap, that ensures data portability and compatibility across institutions, and an innovative survey routing system that retains participant confidentiality without sacrificing REDCap survey distribution capabilities to connect researchers with thousands of participants.
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Affiliation(s)
- Sara Mansoorshahi
- Department of Internal Medicine, John P. and Katherine G. McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin Street, MSB 6.116, Houston, TX, 77030, USA
| | - Cindy Scurlock
- Turner Syndrome Society of the United States, 11250 West Rd, Suite G, Houston, TX, 77065, USA
| | | | - Siddharth K Prakash
- Department of Internal Medicine, John P. and Katherine G. McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin Street, MSB 6.116, Houston, TX, 77030, USA.
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6
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De Mazancourt P, Mazoyer E, Hormi M, Hanss M. Absence of Missense Variant Detection in Inherited Dysfibrinogenemia May Result from a Poor Raw Data Analysis Algorithm or Mosaicism. Int J Mol Sci 2023; 24:16551. [PMID: 38068874 PMCID: PMC10706790 DOI: 10.3390/ijms242316551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/18/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Variant identification underlying inherited dysfibrinogenemia quite exceptionally fails. We report on two dysfibrinogenemia cases whose underlying DNA variant could not be identified by Sanger analysis. These failures result from two distinct mechanisms. The first case involved raw signal overcorrection by a built-in software, and the second constituted the first description of mosaicism for one of the fibrinogen genes. This mosaicism was subsequently identified by next-generation sequencing reanalysis of the sample.
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Affiliation(s)
- Philippe De Mazancourt
- UMR1179, Université de Versailles-Saint-Quentin, 1 Rue de la Source de la Bièvre, 78180 Montigny le Bretonneux, France
- Laboratoire de Biologie Moléculaire, Hôpital A. Paré, GHU APHP Paris-Saclay, 9 Avenue Charles de Gaulle, 92100 Boulogne-Billancourt, France
- Département d’Hématologie, Hôpital Européen Georges Pompidou, GHU AP-HP Centre—Université Paris Cité, 20 Rue Leblanc, 75015 Paris, France
| | - Elisabeth Mazoyer
- Service d’Hématologie Biologique, GHU APHP Paris-Seine-St-Denis, Site Avicenne, 125 Rue de Stalingrad, 93000 Bobigny, France; (E.M.); (M.H.)
| | - Myriam Hormi
- Service d’Hématologie Biologique, GHU APHP Paris-Seine-St-Denis, Site Avicenne, 125 Rue de Stalingrad, 93000 Bobigny, France; (E.M.); (M.H.)
| | - Michel Hanss
- Laboratoire d’Hématologie, Centre de Biologie et Pathologie Est, CHU de Lyon HCL—GH Est, 59 Boulevard Pinel, 69677 Bron, France;
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Ahmad M, Ríos-Anillo MR, Acosta-López JE, Cervantes-Henríquez ML, Martínez-Banfi M, Pineda-Alhucema W, Puentes-Rozo P, Sánchez-Barros C, Pinzón A, Patel HR, Vélez JI, Villarreal-Camacho JL, Pineda DA, Arcos-Burgos M, Sánchez-Rojas M. Uncovering the Genetic and Molecular Features of Huntington's Disease in Northern Colombia. Int J Mol Sci 2023; 24:16154. [PMID: 38003344 PMCID: PMC10671691 DOI: 10.3390/ijms242216154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
Huntington's disease (HD) is a genetic disorder caused by a CAG trinucleotide expansion in the huntingtin (HTT) gene. Juan de Acosta, Atlántico, a city located on the Caribbean coast of Colombia, is home to the world's second-largest HD pedigree. Here, we include 291 descendants of this pedigree with at least one family member with HD. Blood samples were collected, and genomic DNA was extracted. We quantified the HTT CAG expansion using an amplicon sequencing protocol. The genetic heterogeneity was measured as the ratio of the mosaicism allele's read peak and the slippage ratio of the allele's read peak from our sequence data. The statistical and bioinformatic analyses were performed with a significance threshold of p < 0.05. We found that the average HTT CAG repeat length in all participants was 21.91 (SD = 8.92). Of the 291 participants, 33 (11.3%, 18 females) had a positive molecular diagnosis for HD. Most affected individuals were adults, and the most common primary and secondary alleles were 17/7 (CAG/CCG) and 17/10 (CAG/CCG), respectively. The mosaicism increased with age in the participants with HD, while the slippage analyses revealed differences by the HD allele type only for the secondary allele. The slippage tended to increase with the HTT CAG repeat length in the participants with HD, but the increase was not statistically significant. This study analyzed the genetic and molecular features of 291 participants, including 33 with HD. We found that the mosaicism increased with age in the participants with HD, particularly for the secondary allele. The most common haplotype was 17/7_17/10. The slippage for the secondary allele varied by the HD allele type, but there was no significant difference in the slippage by sex. Our findings offer valuable insights into HD and could have implications for future research and clinical management.
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Affiliation(s)
- Mostapha Ahmad
- Facultad de Ciencias de la Salud, Universidad Simón Bolívar, Barranquilla 080002, Colombia
- Life Science Research Center, Universidad Simón Bolívar, Barranquilla 080002, Colombia
| | - Margarita R Ríos-Anillo
- Facultad de Ciencias de la Salud, Universidad Simón Bolívar, Barranquilla 080002, Colombia
- Life Science Research Center, Universidad Simón Bolívar, Barranquilla 080002, Colombia
- Médica Residente de Neurología, Universidad Simón Bolívar, Barranquilla 080002, Colombia
| | - Johan E Acosta-López
- Life Science Research Center, Universidad Simón Bolívar, Barranquilla 080002, Colombia
- Facultad de Ciencias Jurídicas y Sociales, Universidad Simón Bolívar, Barranquilla 080002, Colombia
| | - Martha L Cervantes-Henríquez
- Life Science Research Center, Universidad Simón Bolívar, Barranquilla 080002, Colombia
- Facultad de Ciencias Jurídicas y Sociales, Universidad Simón Bolívar, Barranquilla 080002, Colombia
| | - Martha Martínez-Banfi
- Life Science Research Center, Universidad Simón Bolívar, Barranquilla 080002, Colombia
- Facultad de Ciencias Jurídicas y Sociales, Universidad Simón Bolívar, Barranquilla 080002, Colombia
| | - Wilmar Pineda-Alhucema
- Life Science Research Center, Universidad Simón Bolívar, Barranquilla 080002, Colombia
- Facultad de Ciencias Jurídicas y Sociales, Universidad Simón Bolívar, Barranquilla 080002, Colombia
| | - Pedro Puentes-Rozo
- Facultad de Ciencias de la Salud, Universidad Simón Bolívar, Barranquilla 080002, Colombia
- Life Science Research Center, Universidad Simón Bolívar, Barranquilla 080002, Colombia
- Grupo de Neurociencias del Caribe, Universidad del Atlántico, Barranquilla 080001, Colombia
| | - Cristian Sánchez-Barros
- Facultad de Ciencias de la Salud, Universidad Simón Bolívar, Barranquilla 080002, Colombia
- Life Science Research Center, Universidad Simón Bolívar, Barranquilla 080002, Colombia
- Departamento de Neurofisiología Clínica Palma de Mallorca, Hospital Juaneda Miramar, Islas Baleares, 07011 Palma, Spain
| | - Andrés Pinzón
- Bioinformatics and Systems Biology Laboratory, Institute for Genetics, Universidad Nacional de Colombia, Bogota 111321, Colombia
| | - Hardip R Patel
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
| | - Jorge I Vélez
- Department of Industrial Engineering, Universidad del Norte, Barranquilla 081007, Colombia
| | - José Luis Villarreal-Camacho
- Programa de Medicina, Facultad de Ciencias de la Salud, Universidad Libre Seccional Barranquilla, Barranquilla 081007, Colombia
| | - David A Pineda
- Grupo de Investigación en Neuropsicología y Conducta, Universidad de San Buenaventura, Medellin 050010, Colombia
- Grupo de Neurociencias de Antioquia, Universidad de Antioquia, Medellin 050010, Colombia
| | - Mauricio Arcos-Burgos
- Grupo de Investigación en Psiquiatría (GIPSI), Departamento de Psiquiatría, Instituto de Investigaciones Médicas, Facultad de Medicina, Universidad de Antioquia, Medellin 050010, Colombia
| | - Manuel Sánchez-Rojas
- Facultad de Ciencias de la Salud, Universidad Simón Bolívar, Barranquilla 080002, Colombia
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Kerwin AJ, Lop AL, Vicente K, Weiler T, Kana SL. Testing With Intent in Mosaic Conditions: A Case-Based Review. Cureus 2023; 15:e49644. [PMID: 38161893 PMCID: PMC10755638 DOI: 10.7759/cureus.49644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 11/29/2023] [Indexed: 01/03/2024] Open
Abstract
Recent advancements in genetic testing have revealed cases of mosaicism, demonstrating the phenomenon may be more common than once thought. Broadly defined, mosaicism describes the presence of two genotypically different cell lineages within the same organism. This can arise from small mutations or errors in chromosome segregation, as early as in gametes, before or after fertilization. Mosaicism is directly responsible for many conditions that present in a wide range of tissues, with the presence of the mutation or genetic abnormality following a tissue-dependent pattern. This makes it possible for patients to test negative for a condition using a standard tissue sample while harboring the variant in a different tissue. Understanding the timing and mechanisms of mosaic conditions will aid in targeted testing that is more appropriate to identify a pathogenic variant. This targeted testing should reduce the length of a patient's diagnostic odyssey and provide a better understanding of the chances of passing on their variant to their offspring, thereby allowing for more accurate genetic counseling. We illustrate this phenomenon with two cases: one of Pallister-Killian syndrome and the other of tuberous sclerosis complex. Both patients had increased time to diagnosis because of difficulties in identifying genetic variants in tested tissues. Beyond just increased time to diagnosis, we illustrate that mosaic conditions can present as less severe and more variable than the germline condition and how specific germ layers may be affected by the variant. Knowing which germ layers may be affected by the variant can give clinicians a clue as to which tissues may need to be tested to yield the most accurate result.
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Affiliation(s)
- Andrew J Kerwin
- Department of Genetics, Florida International University, Herbert Wertheim College of Medicine, Miami, USA
| | - Ana L Lop
- Department of Genetics, Florida International University, Herbert Wertheim College of Medicine, Miami, USA
| | - Kristyn Vicente
- Department of Genetics, New York Medical College, Valhalla, USA
| | - Tracey Weiler
- Department of Medical Education, Florida International University, Herbert Wertheim College of Medicine, Miami, USA
| | - Sajel L Kana
- Division of Clinical Genetics, Genomics, and Metabolism, Nicklaus Children's Hospital, Miami, USA
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9
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Lee M, Lui ACY, Chan JCK, Doong PHL, Kwong AKY, Mak CCY, Li RHW, Kan ASY, Chung BHY. Revealing parental mosaicism: the hidden answer to the recurrence of apparent de novo variants. Hum Genomics 2023; 17:91. [PMID: 37798624 PMCID: PMC10557286 DOI: 10.1186/s40246-023-00535-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 09/18/2023] [Indexed: 10/07/2023] Open
Abstract
Mosaicism refers to the presence of two or more populations of genetically distinct cells within an individual, all of which originate from a single zygote. Previous literature estimated the percentage of parental mosaicism ranged from 0.33 to 25.9%. In this study, parents whose children had previously been diagnosed with developmental disorders with an apparent de novo variant were recruited. Peripheral blood, buccal and semen samples were collected from these parents if available for the detection of potential parental mosaicism using droplet digital PCR, complemented with the method of blocker displacement amplification. Among the 20 families being analyzed, we report four families with parental mosaicism (4/20, 20%). Two families have maternal gonosomal mosaicism (EYA1 and EBF3) and one family has paternal gonadal mosaicism (CHD7) with a pathogenic/ likely pathogenic variant. One family has a paternal gonosomal mosaicism with a variant of uncertain significance (FLNC) with high clinical relevance. The detectable variant allele frequency in our cohort ranged from 8.7-35.9%, limit of detection 0.08-0.16% based on our in-house EBF3 assay. Detecting parental mosaicism not only informs family with a more accurate recurrence risk, but also facilitates medical teams to create appropriate plans for pregnancy and delivery, offering the most suitable care.
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Affiliation(s)
- Mianne Lee
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Adrian C Y Lui
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Joshua C K Chan
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Phoenix H L Doong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Anna K Y Kwong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Christopher C Y Mak
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Raymond H W Li
- Department of Obstetrics and Gynaecology, Queen Mary Hospital, Pok Fu Lam, Hong Kong SAR, China
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Anita S Y Kan
- Department of Obstetrics and Gynaecology, Queen Mary Hospital, Pok Fu Lam, Hong Kong SAR, China
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
- Prenatal Diagnostic Laboratory, Department of Obstetrics and Gynaecology, Tsan Yuk Hospital, Sai Wan Ho, Hong Kong SAR, China
| | - Brian H Y Chung
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China.
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Ngau Tau Kok, Hong Kong SAR, China.
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10
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Ben Jdila M, Kammoun F, Abdelmaksoud-Dammak R, Triki C, Fakhfakh F. Mutation in the β-tubulin gene TUBB4A results in epileptic encephalopathy associated with hypomyelinated leucodystrophy: Unexpected findings reveal genetic mosaicism. Int J Dev Neurosci 2023; 83:532-545. [PMID: 37529938 DOI: 10.1002/jdn.10284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 05/10/2023] [Accepted: 06/15/2023] [Indexed: 08/03/2023] Open
Abstract
INTRODUCTION Epileptic encephalopathies (EEs) are a group of heterogeneous epileptic syndromes characterized by early-onset refractory seizures, specific EEG abnormalities, developmental delay or regression and intellectual disability. The genetic spectrum of EE is very wide with mutations in a number of genes having various functions, such as those encoding AMPA ionotropic and glutamate receptors as well as voltage-gated ion channels. However, the list of EE-responsible genes could certainly be enlarged by next-generation sequencing. PATIENTS AND METHODS The present study reports a clinical investigation and a molecular analysis by the whole exome sequencing (WES) and pyrosequencing of a patient's family affected by epileptic spasms and severe psychomotor delay. RESULTS Clinical and radiological investigations revealed that the patient presented clinical features of severe and drug-resistant EE-type infantile epileptic spasm syndrome that evolved to Lennox Gastaut syndrome with radiological findings of hypomyelinated leukodystrophy. The results of WES revealed the presence of a novel heterozygous c.466C>T mutation in exon 4 of the TUBB4A gene in the patient. This transition led to the replacement of arginine by cysteine at position 156 (p.R156C) of the conserved helix 4 among the N-terminal domain of the TUBB4A protein. Bioinformatic tools predicted its deleterious effects on the structural arrangement and stability of the protein. The presence of the mutation in the asymptomatic father suggested the hypothesis of somatic mosaicism that was tested by pyrosequencing of DNA from two tissues of the patient and her father. The obtained results showed a lower rate of mutated alleles in the asymptomatic father compared with the affected daughter in both lymphocytes and buccal mucosa cells, confirming the occurrence of paternal mosaicism. The phenotypic features of the patient were also compared with those of previously described patients presenting TUBB4A mutations. CONCLUSIONS Our study is the first to report a disease-causing variant in the TUBB4A gene in a patient with EE associated with hypomyelinated leucodystrophy. In addition, we expanded the phenotypic spectrum associated with the TUBB4A gene.
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Affiliation(s)
- Marwa Ben Jdila
- Research Laboratory 'NeuroPédiatrie' (LR19ES15), Sfax Medical School, Sfax University, Sfax, Tunisia
- Laboratory of Molecular and Functional Genetics, Faculty of Science of Sfax, Sfax University, Sfax, Tunisia
| | - Fatma Kammoun
- Research Laboratory 'NeuroPédiatrie' (LR19ES15), Sfax Medical School, Sfax University, Sfax, Tunisia
- Child Neurology Department, Hedi Chaker University Hospital of Sfax, Sfax, Tunisia
| | - Rania Abdelmaksoud-Dammak
- Center of Biotechnology of Sfax, Laboratory of Eucaryotes Molecular Biotechnology, University of Sfax, Sfax, Tunisia
| | - Chahnez Triki
- Research Laboratory 'NeuroPédiatrie' (LR19ES15), Sfax Medical School, Sfax University, Sfax, Tunisia
- Child Neurology Department, Hedi Chaker University Hospital of Sfax, Sfax, Tunisia
| | - Faiza Fakhfakh
- Laboratory of Molecular and Functional Genetics, Faculty of Science of Sfax, Sfax University, Sfax, Tunisia
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11
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Tinker RJ, Bastarache L, Ezell K, Kobren SN, Esteves C, Rosenfeld JA, Macnamara EF, Hamid R, Cogan JD, Rinker D, Mukharjee S, Glass I, Dipple K, Phillips JA. The contribution of mosaicism to genetic diseases and de novo pathogenic variants. Am J Med Genet A 2023; 191:2482-2492. [PMID: 37246601 DOI: 10.1002/ajmg.a.63309] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/29/2023] [Accepted: 05/03/2023] [Indexed: 05/30/2023]
Abstract
The contribution of mosaicism to diagnosed genetic disease and presumed de novo variants (DNV) is under investigated. We determined the contribution of mosaic genetic disease (MGD) and diagnosed parental mosaicism (PM) in parents of offspring with reported DNV (in the same variant) in the (1) Undiagnosed Diseases Network (UDN) (N = 1946) and (2) in 12,472 individuals electronic health records (EHR) who underwent genetic testing at an academic medical center. In the UDN, we found 4.51% of diagnosed probands had MGD, and 2.86% of parents of those with DNV exhibited PM. In the EHR, we found 6.03% and 2.99% and (of diagnosed probands) had MGD detected on chromosomal microarray and exome/genome sequencing, respectively. We found 2.34% (of those with a presumed pathogenic DNV) had a parent with PM for the variant. We detected mosaicism (regardless of pathogenicity) in 4.49% of genetic tests performed. We found a broad phenotypic spectrum of MGD with previously unknown phenotypic phenomena. MGD is highly heterogeneous and provides a significant contribution to genetic diseases. Further work is required to improve the diagnosis of MGD and investigate how PM contributes to DNV risk.
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Affiliation(s)
- Rory J Tinker
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kimberly Ezell
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | - Cecilia Esteves
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Jill A Rosenfeld
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Ellen F Macnamara
- Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Rizwan Hamid
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Joy D Cogan
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - David Rinker
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Souhrid Mukharjee
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Ian Glass
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Katrina Dipple
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - John A Phillips
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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12
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Belosevic A, Minder AE, Gueuning M, van Breemen F, Thun GA, Mattle-Greminger MP, Meyer S, Baumer A, Minder EI, Schneider-Yin X, Barman-Aksözen J. First Report of a Low-Frequency Mosaic Mutation in the Hydroxymethylbilane Synthase Gene Causing Acute Intermittent Porphyria. Life (Basel) 2023; 13:1889. [PMID: 37763293 PMCID: PMC10533070 DOI: 10.3390/life13091889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Acute porphyrias are a group of monogenetic inborn errors of heme biosynthesis, characterized by acute and potentially life-threatening neurovisceral attacks upon exposure to certain triggering factors. Biochemical analyses can determine the type of acute porphyria, and subsequent genetic analysis allows for the identification of pathogenic variants in the specific gene, which provides information for family counselling. In 2017, a male Swiss patient was diagnosed with an acute porphyria while suffering from an acute attack. The pattern of porphyrin metabolite excretion in urine, faeces, and plasma was typical for an acute intermittent porphyria (AIP), which is caused by inherited autosomal dominant mutations in the gene for hydroxymethylbilane synthase (HMBS), the third enzyme in the heme biosynthetic pathway. However, the measurement of HMBS enzymatic activity in the erythrocytes was within the normal range and Sanger sequencing of the HMBS gene failed to detect any pathogenic variants. To explore the molecular basis of the apparent AIP in this patient, we performed third-generation long-read single-molecule sequencing (nanopore sequencing) on a PCR product spanning the entire HMBS gene, including the intronic sequences. We identified a known pathogenic variant, c.77G>A, p.(Arg26His), in exon 3 at an allelic frequency of ~22% in the patient's blood. The absence of the pathogenic variant in the DNA of the parents and the results of additional confirmatory studies supported the presence of a de novo mosaic mutation. To our knowledge, such a mutation has not been previously described in any acute porphyria. Therefore, de novo mosaic mutations should be considered as potential causes of acute porphyrias when no pathogenic genetic variant can be identified through routine molecular diagnostics.
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Affiliation(s)
- Adrian Belosevic
- Institute of Laboratory Medicine, Stadtspital Zürich, Triemli, 8063 Zurich, Switzerland
| | - Anna-Elisabeth Minder
- Division of Endocrinology, Diabetology, Porphyria and Clinical Nutrition, Stadtspital Zürich, Triemli, 8063 Zurich, Switzerland
- Swiss Reference Centre for Porphyrias, Stadtspital Zürich, Triemli, 8063 Zurich, Switzerland
| | - Morgan Gueuning
- Department of Research and Development, Blood Transfusion Service Zurich, Swiss Red Cross, 8952 Schlieren, Switzerland
| | - Franziska van Breemen
- Institute of Laboratory Medicine, Stadtspital Zürich, Triemli, 8063 Zurich, Switzerland
- Swiss Reference Centre for Porphyrias, Stadtspital Zürich, Triemli, 8063 Zurich, Switzerland
| | - Gian Andri Thun
- Department of Research and Development, Blood Transfusion Service Zurich, Swiss Red Cross, 8952 Schlieren, Switzerland
| | - Maja P. Mattle-Greminger
- Department of Research and Development, Blood Transfusion Service Zurich, Swiss Red Cross, 8952 Schlieren, Switzerland
| | - Stefan Meyer
- Department of Molecular Diagnostics and Cytometry, Blood Transfusion Service Zurich, Swiss Red Cross, 8952 Schlieren, Switzerland
| | - Alessandra Baumer
- Institute of Medical Genetics, University of Zürich, 8952 Schlieren, Switzerland
| | - Elisabeth I. Minder
- Division of Endocrinology, Diabetology, Porphyria and Clinical Nutrition, Stadtspital Zürich, Triemli, 8063 Zurich, Switzerland
- Swiss Reference Centre for Porphyrias, Stadtspital Zürich, Triemli, 8063 Zurich, Switzerland
| | - Xiaoye Schneider-Yin
- Institute of Laboratory Medicine, Stadtspital Zürich, Triemli, 8063 Zurich, Switzerland
- Swiss Reference Centre for Porphyrias, Stadtspital Zürich, Triemli, 8063 Zurich, Switzerland
| | - Jasmin Barman-Aksözen
- Institute of Laboratory Medicine, Stadtspital Zürich, Triemli, 8063 Zurich, Switzerland
- Swiss Reference Centre for Porphyrias, Stadtspital Zürich, Triemli, 8063 Zurich, Switzerland
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13
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Chen D, Xu Y, Fu Y, Wang Y, Liu Y, Ding C, Cai B, Pan J, Wang J, Li R, Guo J, Zhang H, Zeng Y, Shen X, Zhou C. Clinical application of next generation sequencing-based haplotype linkage analysis in the preimplantation genetic testing for germline mosaicisms. Orphanet J Rare Dis 2023; 18:137. [PMID: 37270548 DOI: 10.1186/s13023-023-02736-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/18/2023] [Indexed: 06/05/2023] Open
Abstract
BACKGROUND Preimplantation genetic testing (PGT) for monogenic disorders (PGT-M) for germline mosaicism was previously highly dependent on polymerase chain reaction (PCR)-based directed mutation detection combined with linkage analysis of short tandem repeats (STRs). However, the number of STRs is usually limited. In addition, designing suitable probes and optimizing the reaction conditions for multiplex PCR are time-consuming and laborious. Here, we evaluated the effectiveness of next generation sequencing (NGS)-based haplotype linkage analysis in PGT of germline mosaicism. METHODS PGT-M with NGS-based haplotype linkage analysis was performed for two families with maternal germline mosaicism for an X-linked Duchenne muscular dystrophy (DMD) mutation (del exon 45-50) or an autosomal TSC1 mutation (c.2074C > T). Trophectoderm biopsy and multiple displacement amplification (MDA) were performed for a total of nine blastocysts. NGS and Sanger sequencing were performed in genomic DNA of family members and embryonic MDA products to detect DMD deletion and TSC1 mutation, respectively. Single nucleotide polymorphism (SNP) sites closely linked to pathogenic mutations were detected with NGS and served in haplotype linkage analysis. NGS-based aneuploidy screening was performed for all embryos to reduce the risk of pregnancy loss. RESULTS All nine blastocytes showed conclusive PGT results. Each family underwent one or two frozen-thawed embryo transfer cycles to obtain a clinical pregnancy, and the prenatal diagnosis showed that the fetus was genotypically normal and euploid for both families. CONCLUSIONS NGS-SNP could effectively realize PGT for germline mosaicism. Compared with PCR-based methods, the NGS-SNP method with increased polymorphic informative markers can achieve a greater diagnostic accuracy. Further studies are warranted to verify the effectiveness of NGS-based PGT of germline mosaicism cases in the absence of surviving offsprings.
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Affiliation(s)
- Dongjia Chen
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, 510080, China
| | - Yan Xu
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, 510080, China
| | - Yu Fu
- The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, 570102, China
| | - Yali Wang
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, 510080, China
| | - Yuliang Liu
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, 510080, China
| | - Chenhui Ding
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, 510080, China
| | - Bing Cai
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, 510080, China
| | - Jiafu Pan
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, 510080, China
| | - Jing Wang
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, 510080, China
| | - Rong Li
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, 510080, China
| | - Jing Guo
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, 510080, China
| | - Han Zhang
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, 510080, China
| | - Yanhong Zeng
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, 510080, China
| | - Xiaoting Shen
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China.
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, 510080, China.
- Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Canquan Zhou
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China.
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, 510080, China.
- Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China.
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14
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Chang YH, Kang EYC, Liu L, Jenny LA, Khang R, Seo GH, Lee H, Chen KJ, Wu WC, Hsiao MC, Wang NK. Maternal mosaicism in SSBP1 causing optic atrophy with retinal degeneration: implications for genetic counseling. Orphanet J Rare Dis 2023; 18:131. [PMID: 37259171 PMCID: PMC10233871 DOI: 10.1186/s13023-023-02748-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/18/2023] [Indexed: 06/02/2023] Open
Abstract
BACKGROUND Optic atrophy-13 with retinal and foveal abnormalities (OPA13) (MIM #165510) is a mitochondrial disease in which apparent bilateral optic atrophy is present and sometimes followed by retinal pigmentary changes or photoreceptors degeneration. OPA13 is caused by heterozygous mutation in the SSBP1 gene, associated with variable mitochondrial dysfunctions. RESULTS We have previously reported a 16-year-old Taiwanese male diagnosed with OPA13 and SSBP1 variant c.320G>A (p.Arg107Gln) was identified by whole exon sequence (WES). This variant was assumed to be de novo since his parents were clinically unaffected. However, WES and Sanger sequencing further revealed the proband's unaffected mother carrying the same SSBP1 variant with a 13% variant allele frequency (VAF) in her peripheral blood. That finding strongly indicates the maternal gonosomal mosaicism contributing to OPA13, which has not been reported before. CONCLUSIONS In summary, we described the first case of OPA13 caused by maternal gonosomal mosaicism in SSBP1. Parental mosaicism could be a serious issue in OPA13 diagnosis, and appropriate genetic counseling should be considered.
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Affiliation(s)
- Yin-Hsi Chang
- Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Eugene Yu-Chuan Kang
- Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Laura Liu
- Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Laura A Jenny
- Department of Ophthalmology, Edward S. Harkness Eye Institute, Columbia University Irving Medical Center, Columbia University, 635 West 165th Street, New York, NY, 10032, USA
| | - Rin Khang
- Division of Medical Genetics, 3Billion Inc., Seoul, South Korea
| | - Go Hun Seo
- Division of Medical Genetics, 3Billion Inc., Seoul, South Korea
| | - Hane Lee
- Division of Medical Genetics, 3Billion Inc., Seoul, South Korea
| | - Kuan-Jen Chen
- Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Wei-Chi Wu
- Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Meng-Chang Hsiao
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Nan-Kai Wang
- Department of Ophthalmology, Edward S. Harkness Eye Institute, Columbia University Irving Medical Center, Columbia University, 635 West 165th Street, New York, NY, 10032, USA.
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15
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Simon B, Mangano FG, Pál A, Simon I, Pellei D, Shahbazi A, Vág J. Palatal asymmetry assessed by intraoral scans: effects of sex, orthodontic treatment, and twinning. A retrospective cohort study. BMC Oral Health 2023; 23:305. [PMID: 37202781 DOI: 10.1186/s12903-023-02993-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 04/27/2023] [Indexed: 05/20/2023] Open
Abstract
BACKGROUND Symmetry is critical in perceived attractiveness, especially in female faces. The palate determines the teeth' alignment and supports facial soft tissues. Therefore, the study aimed to assess the effects of sex, orthodontic treatment, age, and heritability on the directional, anti-, and fluctuational asymmetry in the digital palatal model. METHODS The palate of 113 twins, 86 female and 27 male subjects, with and without previous orthodontic treatment, were scanned by the Emerald (Planmeca) intraoral scanner. Three lines were constructed horizontally in the digital model, one between the right and left first upper molars and two between the first molars and incisive papilla. Two observers calculated the left and right angles between the mid-sagittal plane and molar-papilla lines. The intraclass correlation coefficient was used to assess the inter-observer absolute agreement. The directional symmetry was determined by comparing the mean left and right angles. The antisymmetry was estimated from the distribution curve of the signed side difference. The fluctuating asymmetry was approximated from the magnitude of the absolute side difference. Finally, the genetic background was assessed by correlating the absolute side difference between monozygotic twin siblings. RESULTS The right angle (31.1 degrees) was not significantly different from the left one (31.6 degrees). The signed side difference followed a normal distribution with a mean of -0.48 degrees. The absolute side difference (2.29 degrees, p < 0.001) was significantly different from zero and negatively correlated (r=-0.46, p < 0.05) between siblings. None of the asymmetries was affected by sex, orthodontic treatment or age. CONCLUSIONS The palate illustrates neither directional asymmetry nor antisymmetry, indicating that most people's palates are symmetric. However, the significant fluctuating asymmetry suggests that some subject has considerable asymmetry but is not influenced by sex, orthodontic treatment, age, and genetics. The proposed digital method is a reliable and non-invasive tool that could facilitate achieving a more symmetrical structure during orthodontic and aesthetic rehabilitation. TRIAL REGISTRATION The Clinicatrial.gov registration number is NCT05349942 (27/04/2022).
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Affiliation(s)
- Botond Simon
- Department of Restorative Dentistry and Endodontics, Semmelweis University, Budapest, Hungary.
| | - Francesco Guido Mangano
- Department of Pediatric, Preventive Dentistry and Orthodontics, Sechenov First State Medical University, Moscow, Russia
| | - Adrienn Pál
- Department of Prosthodontics, Semmelweis University, Budapest, Hungary
| | - István Simon
- Department of Paediatric Dentistry and Orthodontics, Semmelweis University, Budapest, Hungary
| | - Dalma Pellei
- Department of Restorative Dentistry and Endodontics, Semmelweis University, Budapest, Hungary
| | - Arvin Shahbazi
- Department of Restorative Dentistry and Endodontics, Semmelweis University, Budapest, Hungary
- Department of Anatomy, Histology and Embryology (Oral Morphology Group), Semmelweis University, Budapest, Hungary
- Department of Periodontology, Semmelweis University, Budapest, Hungary
| | - János Vág
- Department of Restorative Dentistry and Endodontics, Semmelweis University, Budapest, Hungary
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Aluri J, Cooper MA. Somatic mosaicism in inborn errors of immunity: Current knowledge, challenges, and future perspectives. Semin Immunol 2023; 67:101761. [PMID: 37062181 DOI: 10.1016/j.smim.2023.101761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 04/03/2023] [Accepted: 04/05/2023] [Indexed: 04/18/2023]
Abstract
Inborn errors of immunity (IEI) are a diverse group of monogenic disorders of the immune system due to germline variants in genes important for the immune response. Over the past decade there has been increasing recognition that acquired somatic variants present in a subset of cells can also lead to immune disorders or 'phenocopies' of IEI. Discovery of somatic mosaicism causing IEI has largely arisen from investigation of seemingly sporadic cases of IEI with predominant symptoms of autoinflammation and/or autoimmunity in which germline disease-causing variants are not detected. Disease-causing somatic mosaicism has been identified in genes that also cause germline IEI, such as FAS, and in genes without significant corresponding germline disease, such as UBA1 and TLR8. There are challenges in detecting low-level somatic variants, and it is likely that the extent of the somatic mosaicism causing IEI is largely uncharted. Here we review the field of somatic mosaicism leading to IEI and discuss challenges and methods for somatic variant detection, including diagnostic approaches for molecular diagnoses of patients.
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Affiliation(s)
- Jahnavi Aluri
- Department of Pediatrics, Division of Rheumatology/Immunology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Megan A Cooper
- Department of Pediatrics, Division of Rheumatology/Immunology, Washington University in St. Louis, St. Louis, MO 63110, USA.
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17
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Truty R, Rojahn S, Ouyang K, Kautzer C, Kennemer M, Pineda-Alvarez D, Johnson B, Stafford A, Basel-Salmon L, Saitta S, Slavotinek A, Chandrasekharappa SC, Suarez CJ, Burnett L, Nussbaum RL, Aradhya S. Patterns of mosaicism for sequence and copy-number variants discovered through clinical deep sequencing of disease-related genes in one million individuals. Am J Hum Genet 2023; 110:551-564. [PMID: 36933558 PMCID: PMC10119133 DOI: 10.1016/j.ajhg.2023.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 02/23/2023] [Indexed: 03/19/2023] Open
Abstract
DNA variants that arise after conception can show mosaicism, varying in presence and extent among tissues. Mosaic variants have been reported in Mendelian diseases, but further investigation is necessary to broadly understand their incidence, transmission, and clinical impact. A mosaic pathogenic variant in a disease-related gene may cause an atypical phenotype in terms of severity, clinical features, or timing of disease onset. Using high-depth sequencing, we studied results from one million unrelated individuals referred for genetic testing for almost 1,900 disease-related genes. We observed 5,939 mosaic sequence or intragenic copy number variants distributed across 509 genes in nearly 5,700 individuals, constituting approximately 2% of molecular diagnoses in the cohort. Cancer-related genes had the most mosaic variants and showed age-specific enrichment, in part reflecting clonal hematopoiesis in older individuals. We also observed many mosaic variants in genes related to early-onset conditions. Additional mosaic variants were observed in genes analyzed for reproductive carrier screening or associated with dominant disorders with low penetrance, posing challenges for interpreting their clinical significance. When we controlled for the potential involvement of clonal hematopoiesis, most mosaic variants were enriched in younger individuals and were present at higher levels than in older individuals. Furthermore, individuals with mosaicism showed later disease onset or milder phenotypes than individuals with non-mosaic variants in the same genes. Collectively, the large compendium of variants, disease correlations, and age-specific results identified in this study expand our understanding of the implications of mosaic DNA variation for diagnosis and genetic counseling.
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Affiliation(s)
- Rebecca Truty
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
| | - Susan Rojahn
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
| | - Karen Ouyang
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
| | | | | | | | - Britt Johnson
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
| | | | - Lina Basel-Salmon
- Rabin Medical Center-Beilinson Hospital and Schneider Children's Medical Center of Israel, Petach Tikva, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Sulagna Saitta
- Division of Clinical Genetics, Departments of Pediatrics and Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Anne Slavotinek
- Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Settara C Chandrasekharappa
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Carlos Jose Suarez
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94301, USA
| | | | - Robert L Nussbaum
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA; School of Medicine, University of California - San Francisco, San Francisco, CA, USA
| | - Swaroop Aradhya
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94301, USA.
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18
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Kim H, Suyama M. Genome-wide identification of copy neutral loss of heterozygosity reveals its possible association with spatial positioning of chromosomes. Hum Mol Genet 2023; 32:1175-1183. [PMID: 36349694 PMCID: PMC10026252 DOI: 10.1093/hmg/ddac278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/17/2022] [Accepted: 11/02/2022] [Indexed: 11/10/2022] Open
Abstract
Loss of heterozygosity (LOH) is a genetic alteration that results from the loss of one allele at a heterozygous locus. In particular, copy neutral LOH (CN-LOH) events are generated, for example, by mitotic homologous recombination after monoallelic defection or gene conversion, resulting in novel homozygous locus having two copies of the normal counterpart allele. This phenomenon can serve as a source of genome diversity and is associated with various diseases. To clarify the nature of the CN-LOH such as the frequency, genomic distribution and inheritance pattern, we made use of whole-genome sequencing data of the three-generation CEPH/Utah family cohort, with the pedigree consisting of grandparents, parents and offspring. We identified an average of 40.7 CN-LOH events per individual taking advantage of 285 healthy individuals from 33 families in the cohort. On average 65% of them were classified as gonosomal-mosaicism-associated CN-LOH, which exists in both germline and somatic cells. We also confirmed that the incidence of the CN-LOH has little to do with the parents' age and sex. Furthermore, through the analysis of the genomic region including the CN-LOH, we found that the chance of the occurrence of the CN-LOH tends to increase at the GC-rich locus and/or on the chromosome having a relatively close inter-homolog distance. We expect that these results provide significant insights into the association between genetic alteration and spatial position of chromosomes as well as the intrinsic genetic property of the CN-LOH.
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Affiliation(s)
- Hyeonjeong Kim
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Mikita Suyama
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
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19
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Chang YH, Kang EYC, Liu L, Jenny LA, Khang R, Seo GH, Lee H, Chen KJ, Wu WC, Hsiao MC, Wang NK. Maternal Mosaicism in SSBP1 Causing Optic Atrophy with Retinal Degeneration: Implications for Genetic Counseling. RESEARCH SQUARE 2023:rs.3.rs-2554402. [PMID: 36993412 PMCID: PMC10055506 DOI: 10.21203/rs.3.rs-2554402/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
Background: Optic atrophy-13 with retinal and foveal abnormalities (OPA13) (MIM #165510) is a mitochondrial disease in which apparent bilateral optic atrophy is present and sometimes followed by retinal pigmentary changes or photoreceptors degeneration. OPA13 is caused by heterozygous mutation in the SSBP1 gene, associated with variable mitochondrial dysfunctions. Results: We have previously reported a 16-year-old Taiwanese male diagnosed with OPA13 and SSBP1 variant c.320G>A (p.Arg107Gln) was identified by whole exon sequence (WES). This variant was assumed to be de novo since his parents were clinically unaffected. However, WES and Sanger sequencing further revealed the proband’s unaffected mother carrying the same SSBP1 variant with a 13% variant allele frequency (VAF) in her peripheral blood. That finding strongly indicates the maternal gonosomal mosaicism contributing to OPA13, which has not been reported before. Conclusions: In summary, we described the first case of OPA13 caused by maternal gonosomal mosaicism in SSBP1 . Parental mosaicism could be a serious issue in OPA13 diagnosis, and appropriate genetic counseling should be considered.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Meng-Chang Hsiao
- Columbia University Medical Center: Columbia University Irving Medical Center
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20
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Hidalgo Mayoral I, Almeida Santiago A, Sánchez-Zapardiel JM, Hidalgo Calero B, de la Hoya M, Gómez-Sanz A, de Miguel Reyes M, Robles L. Unexpected Findings in Hereditary Breast and Ovarian Cancer Syndrome: Low-Level Constitutional Mosaicism in BRCA2. Genes (Basel) 2023; 14:502. [PMID: 36833429 PMCID: PMC9957471 DOI: 10.3390/genes14020502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023] Open
Abstract
Hereditary breast and ovarian cancer syndrome (HBOC) is a clinical entity characterized by an increased risk of developing breast and ovarian cancer. The genetic diagnosis is based on the identification of heterozygous germinal variants in HBOC susceptibility genes. However, it has recently been described that constitutional mosaic variants can contribute to the aetiology of HBOC. In constitutional mosaicism, individuals have at least two genotypically distinct populations of cells that arise from an early post-zygote event. The mutational event occurs early enough in development to affect several tissues. It is detected in germinal genetic studies as low variant allele frequency (VAF) variants (<30%) that are generally overlooked during the prioritization process. Constitutional mosaic variants can affect both somatic and germinal cells, and thus can be passed to the offspring and have important consequences for genetic counselling. In this work, we report the c.9648+1G>A mosaic variant in the BRCA2 gene and propose a diagnostic algorithm to deal with potential mosaic findings identified by Next Generation Sequencing (NGS).
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Affiliation(s)
- Irene Hidalgo Mayoral
- Hereditary Cancer Laboratory, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
| | - Ainhoa Almeida Santiago
- Hereditary Cancer Laboratory, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
| | | | | | - Miguel de la Hoya
- Molecular Oncology Laboratory, Instituto de Investigacion Sanitaria San Carlos, Hospital Universitario Clínico San Carlos, 28040 Madrid, Spain
| | - Alicia Gómez-Sanz
- Molecular Oncology Laboratory, Instituto de Investigacion Sanitaria San Carlos, Hospital Universitario Clínico San Carlos, 28040 Madrid, Spain
| | | | - Luis Robles
- Medical Oncology Service, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
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21
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Bodoano Sánchez I, Mata Agudo A, Guerrero-Jiménez M, Girela Serrano B, Álvarez Gil P, Carrillo de Albornoz Calahorro CM, Gutiérrez-Rojas L. Treatment of post-psychotic depression in first-episode psychosis. A systematic review. Nord J Psychiatry 2023; 77:109-117. [PMID: 35507756 DOI: 10.1080/08039488.2022.2067225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND Post-psychotic depression (PPD) after a FEP (first-episode psychosis) differs from other depressive symptoms in chronic schizophrenia in its aetiology, symptomatology, and prognostic implications. The objective was to search if any pharmacological or non-pharmacological interventions have proven to be effective on depressive symptoms after a FEP. METHODS for this systematic review we systematically searched and screened PubMed for articles published from August 1975 to October 15, 2020, with the terms: treatment AND first-episode psychosis OR post-psychotic OR post-schizophrenic AND depression. RESULTS we identified 139 articles of which 20 met the inclusion criteria. These interventions were then categorized into four subgroups (antipsychotics, antidepressants, psychological and miscellaneous). LIMITATIONS this review has several limitations. The reviewed studies were heterogeneous as to assessments, interventions, and samples; furthermore, only one study had PPD in FEP as its primary outcome. CONCLUSIONS to our knowledge, this is the first review of PPD in a FEP's treatment. PPD continues to be a diagnostic and therapeutic challenge. The available evidence for the use of treatment whether pharmacological or non-pharmacological is limited. However, certain approaches such as online therapy and treatment with n-3 polyunsaturated fatty acids (PUFA) show promising results. It could be of interest for future studies to focus not only on the treatment of PPD but also on the diagnostic heterogeneity of the sample and the adaptation of the content of the intervention to the individual.
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Affiliation(s)
| | - Alba Mata Agudo
- Psychiatry Service, Virgen de las Nieves University Hospital, Granada, Spain
| | | | | | - Paula Álvarez Gil
- Psychiatry Service, Virgen de las Nieves University Hospital, Granada, Spain
| | | | - Luis Gutiérrez-Rojas
- Psychiatry and Neurosciences Research Group (CTS-549), Institute of Neurosciences, University of Granada, Granada, Spain.,Psychiatry Service, San Cecilio University Hospital, Granada, Spain.,Psychiatry Department, University of Granada, Granada, Spain
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22
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Iourov IY, Gerasimov AP, Zelenova MA, Ivanova NE, Kurinnaia OS, Zabrodskaya YM, Demidova IA, Barantsevich ER, Vasin KS, Kolotii AD, Ushanov VV, Sitovskaya DA, Lobzhanidze TBA, Iuditskaia ME, Iakushev NS, Zhumatov MM, Vorsanova SG, Samochernyh KA. Cytogenomic epileptology. Mol Cytogenet 2023; 16:1. [PMID: 36600272 PMCID: PMC9814426 DOI: 10.1186/s13039-022-00634-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023] Open
Abstract
Molecular cytogenetic and cytogenomic studies have made a contribution to genetics of epilepsy. However, current genomic research of this devastative condition is generally focused on the molecular genetic aspects (i.e. gene hunting, detecting mutations in known epilepsy-associated genes, searching monogenic causes of epilepsy). Nonetheless, chromosomal abnormalities and copy number variants (CNVs) represent an important part of genetic defects causing epilepsy. Moreover, somatic chromosomal mosaicism and genome/chromosome instability seem to be a possible mechanism for a wide spectrum of epileptic conditions. This idea becomes even more attracting taking into account the potential of molecular neurocytogenetic (neurocytogenomic) studies of the epileptic brain. Unfortunately, analyses of chromosome numbers and structure in the affected brain or epileptogenic brain foci are rarely performed. Therefore, one may conclude that cytogenomic area of genomic epileptology is poorly researched. Accordingly, molecular cytogenetic and cytogenomic studies of the clinical cohorts and molecular neurocytogenetic analyses of the epileptic brain appear to be required. Here, we have performed a theoretical analysis to define the targets of the aforementioned studies and to highlight future directions for molecular cytogenetic and cytogenomic research of epileptic disorders in the widest sense. To succeed, we have formed a consortium, which is planned to perform at least a part of suggested research. Taking into account the nature of the communication, "cytogenomic epileptology" has been introduced to cover the research efforts in this field of medical genomics and epileptology. Additionally, initial results of studying cytogenomic variations in the Russian neurodevelopmental cohort are reviewed with special attention to epilepsy. In total, we have concluded that (i) epilepsy-associated cytogenomic variations require more profound research; (ii) ontological analyses of epilepsy genes affected by chromosomal rearrangements and/or CNVs with unraveling pathways implicating epilepsy-associated genes are beneficial for epileptology; (iii) molecular neurocytogenetic (neurocytogenomic) analysis of postoperative samples are warranted in patients suffering from epileptic disorders.
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Affiliation(s)
- Ivan Y. Iourov
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia ,grid.445984.00000 0001 2224 0652Department of Medical Biological Disciplines, Belgorod State University, Belgorod, Russia
| | - Alexandr P. Gerasimov
- grid.452417.1Research Laboratory of Pediatric Neurosurgery, Polenov Neurosurgical Institute, Almazov National Medical Research Centre, Saint Petersburg, Russia
| | - Maria A. Zelenova
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Natalya E. Ivanova
- grid.452417.1Scientific Department of Polenov Neurosurgical Institute, Almazov National Medical Research Centre, Saint Petersburg, Russia
| | - Oksana S. Kurinnaia
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Yulia M. Zabrodskaya
- grid.452417.1Research Laboratory of Pathomorphology of the Nervous System, Almazov National Medical Research Centre, Saint Petersburg, Russia
| | - Irina A. Demidova
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Evgeny R. Barantsevich
- grid.412460.5Postgraduate Neurology and Manual Medicine Department, Pavlov First Saint-Petersburg State Medical University, Saint Petersburg, Russia
| | - Kirill S. Vasin
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Alexey D. Kolotii
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Vseslav V. Ushanov
- grid.452417.1Department of Neurosurgery, Almazov National Medical Research Centre, Saint Petersburg, Russia
| | - Darya A. Sitovskaya
- grid.452417.1Research Laboratory of Pathomorphology of the Nervous System, Almazov National Medical Research Centre, Saint Petersburg, Russia
| | - Timur B.-A. Lobzhanidze
- grid.445931.e0000 0004 0471 4078Saint Petersburg State Pediatric Medical University, Saint Petersburg, Russia
| | - Maria E. Iuditskaia
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Nikita S. Iakushev
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Muslim M. Zhumatov
- grid.445931.e0000 0004 0471 4078Saint Petersburg State Pediatric Medical University, Saint Petersburg, Russia
| | - Svetlana G. Vorsanova
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Konstantin A. Samochernyh
- grid.452417.1Polenov Neurosurgical Institute, Almazov National Medical Research Centre, Saint Petersburg, Russia
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23
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Zhou L, Chen X, Xiong J, Lei L. A mosaic mutation in the CLCNKB gene causing Bartter syndrome: A case report. Front Pediatr 2023; 11:1034923. [PMID: 37138571 PMCID: PMC10149701 DOI: 10.3389/fped.2023.1034923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 03/10/2023] [Indexed: 05/05/2023] Open
Abstract
Background Type III Bartter syndrome (BS) is an autosomal recessive disease caused by mutations in the CLCNKB (chloride voltage-gated channel Kb) gene that encodes CLC-Kb. CLC-Kb is mainly located in the thick ascending limb of Henle's loop and regulates chloride efflux from tubular epithelial cells to the interstitium. Type III BS is characterized by metabolic alkalosis, renal salt wasting, hyperreninemia, and hyperaldosteronism with normal blood pressure. Case presentation We reported the case of a 3-day-old girl whose initial symptom we diagnosed as jaundice, but we accidentally found metabolic alkalosis. She showed recurrent metabolic alkalosis, hypokalemia, and hypochloremia and also had hyperreninemia and hyperaldosteronism with normal blood pressure. Both oral potassium supplements and potassium infusion therapy were unable to entirely restore the electrolyte imbalance. She was suspected of Bartter syndrome and genetic tests were performed on her and her parents. Next-generation sequencing identified CLCNKB gene mutation including heterozygous mutation c.1257delC (p.M421Cfs*58) and a low-level mutation c.595G > T (p.E199*); both mutations were also verified in the parents. Conclusion We reported the case of a classic Bartter syndrome in a newborn with a heterozygous frameshift mutation and a mosaic non-sense mutation in the CLCNKB gene.
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Affiliation(s)
- Lan Zhou
- Department of Obstetrics and Gynecology, Chongqing Health Center for Women and Children, Chongqing, China
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaohui Chen
- Department of Obstetrics and Gynecology, Chongqing Health Center for Women and Children, Chongqing, China
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Jiaojiao Xiong
- Department of Obstetrics and Gynecology, Chongqing Health Center for Women and Children, Chongqing, China
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Ling Lei
- Department of Obstetrics and Gynecology, Chongqing Health Center for Women and Children, Chongqing, China
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
- Correspondence: Ling Lei
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24
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Evans MA, Walsh K. Clonal hematopoiesis, somatic mosaicism, and age-associated disease. Physiol Rev 2023; 103:649-716. [PMID: 36049115 PMCID: PMC9639777 DOI: 10.1152/physrev.00004.2022] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 07/19/2022] [Accepted: 08/02/2022] [Indexed: 12/15/2022] Open
Abstract
Somatic mosaicism, the occurrence of multiple genetically distinct cell clones within the same tissue, is an evitable consequence of human aging. The hematopoietic system is no exception to this, where studies have revealed the presence of expanded blood cell clones carrying mutations in preleukemic driver genes and/or genetic alterations in chromosomes. This phenomenon is referred to as clonal hematopoiesis and is remarkably prevalent in elderly individuals. While clonal hematopoiesis represents an early step toward a hematological malignancy, most individuals will never develop blood cancer. Somewhat unexpectedly, epidemiological studies have found that clonal hematopoiesis is associated with an increase in the risk of all-cause mortality and age-related disease, particularly in the cardiovascular system. Studies using murine models of clonal hematopoiesis have begun to shed light on this relationship, suggesting that driver mutations in mature blood cells can causally contribute to aging and disease by augmenting inflammatory processes. Here we provide an up-to-date review of clonal hematopoiesis within the context of somatic mosaicism and aging and describe recent epidemiological studies that have reported associations with age-related disease. We will also discuss the experimental studies that have provided important mechanistic insight into how driver mutations promote age-related disease and how this knowledge could be leveraged to treat individuals with clonal hematopoiesis.
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Affiliation(s)
- Megan A Evans
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Kenneth Walsh
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia
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25
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Zhang Y, Wei WB, Zhao J, Xu X, Wang F. Spectrum and tissue distribution of RB1 pathogenic alleles in mosaic retinoblastoma patients. Ophthalmic Genet 2022; 43:795-805. [PMID: 35938543 DOI: 10.1080/13816810.2022.2098985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
To characterize the spectrum of mosaic RB1 pathogenic alleles and map the distribution of mutant cells in available tissues from mosaic patients. Next-generation sequencing was performed on blood samples from 263 retinoblastoma families to identify mosaic RB1 variant alleles. A variety of available tissues were sampled to determine tissue distribution and fraction of mutant cells in five mosaic patients who consented to participate in mosaic pathogenic allele research. Twelve identified mosaic RB1 variants were all "null" pathogenic alleles and displayed reduced expressivity. The use of next-generation deep sequencing increased the sensitivity of mosaicism detection to 0.03% in the case of tissue DNA. In the five mosaic participants, we observed coherent but uneven, bilateral asymmetrical distribution of mutant cells across various tissues. They all carried early-embryonic mosaic pathogenic alleles and had significantly higher variant fractions in blood than in other tissues. Variant fractions of ipsilateral tissue samples were not concordant higher or lower compared with the contralateral side. Only ipsilateral conjunctival and oral epithelial cells showed concordance in mosaicism levels. No associations were observed between the laterality of affected eyes and variant fractions of any tissue type. NGS allows the detection of low-level mosaicism. Mosaic RB1 pathogenic alleles are prone to occur at very early stages of human embryonic development. With respect to genetic counseling, risk prediction should take into account unrecognized mosaicism. The underlying tissue distribution patterns of mosaic RB1 variant alleles remain to be determined.
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Affiliation(s)
- Yan Zhang
- Department of Ophthalmology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Wen-Bin Wei
- Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Junyang Zhao
- Department of Ophthalmology, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Xiaolin Xu
- Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Fufeng Wang
- Nanjing Geneseeq Technology Inc, Nanjing, China
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26
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Francis DI, Stark Z, Scheffer IE, Tan TY, Murali K, Gallacher L, Amor DJ, Goel H, Downie L, Stutterd CA, Krzesinski EI, Vasudevan A, Oertel R, Petrovic V, Boys A, Wei V, Burgess T, Dun K, Oliver KL, Baxter A, Hackett A, Ayres S, Lunke S, Kalitsis P, Wall M. Comparing saliva and blood for the detection of mosaic genomic abnormalities that cause syndromic intellectual disability. Eur J Hum Genet 2022; 31:521-525. [PMID: 36446895 PMCID: PMC10172398 DOI: 10.1038/s41431-022-01232-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/23/2022] [Accepted: 10/31/2022] [Indexed: 11/30/2022] Open
Abstract
AbstractWe aimed to determine whether SNP-microarray genomic testing of saliva had a greater diagnostic yield than blood for pathogenic copy number variants (CNVs). We selected patients who underwent CMA testing of both blood and saliva from 23,289 blood and 21,857 saliva samples. Our cohort comprised 370 individuals who had testing of both, 224 with syndromic intellectual disability (ID) and 146 with isolated ID. Mosaic pathogenic CNVs or aneuploidy were detected in saliva but not in blood in 20/370 (4.4%). All 20 individuals had syndromic ID, accounting for 9.1% of the syndromic ID sub-cohort. Pathogenic CNVs were large in size (median of 46 Mb), and terminal in nature, with median mosaicism of 27.5% (not exceeding 40%). By contrast, non-mosaic pathogenic CNVs were 100% concordant between blood and saliva, considerably smaller in size (median of 0.65 Mb), and predominantly interstitial in location. Given that salivary microarray testing has increased diagnostic utility over blood in individuals with syndromic ID, we recommend it as a first-tier testing in this group.
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Chen M, Shen MC, Chang SP, Ma GC, Huang YC, Lin CY. Origin and timing of de novo variants implicated in type 2 von Willebrand disease. J Cell Mol Med 2022; 26:5403-5413. [PMID: 36226571 PMCID: PMC9639050 DOI: 10.1111/jcmm.17563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/30/2022] [Accepted: 09/11/2022] [Indexed: 12/03/2022] Open
Abstract
Very few studies have shown the real origin and timing of de novo variants (DNV) implicated in von Willebrand disease (VWD). We investigated four families with type 2 VWD. First, we conducted linkage analysis using single nucleotide variant genotyping to recognize the possible provenance of DNV. Second, we performed amplification refractory mutation system‐quantitative polymerase chain reaction to confirm the real origin of variant (~0% mutant cells) or presence of a genetic mosaic variant (0%–50% mutant cells) in three embryonic germ layer‐derived tissues and sperm cells. Then, three possible timings of DNV were categorized based on the relative likelihood of occurrence according to the number of cell divisions during embryogenesis. Two each with type 2B VWD (proband 1 p.Arg1308Cys, proband 4 p.Arg1306Trp) and type 2A VWD (proband 2 p.Leu1276Arg, proband 3 p.Ser1506Leu) were identified. Variant origins were identified for families 1, 2 and 3 and confirmed to originate from the mother, father and father, respectively. However, the father of family 4 was confirmed to have isolated germline mosaicism with 2.2% mutant sperm cells. Further investigation confirmed the paternal grandfather to be the origin of variant. Thus, we proposed that DNV originating from the two fathers most likely occurred at the single sperm cell, the one originating from the mother occurred at the zygote during the first few cellular divisions; alternatively, in family 4, the DNV most likely occurred at the early postzygotic development in the father. Our findings are essential for understanding genetic pathogenesis and providing accurate genetic counselling.
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Affiliation(s)
- Ming Chen
- Department of Genomic Medicine, Changhua Christian Hospital, Changhua, Taiwan.,Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei, Taiwan
| | - Ming-Ching Shen
- Department of Internal Medicine, Changhua Christian Hospital, Changhua, Taiwan.,Department of Laboratory Medicine and Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Shun-Ping Chang
- Department of Genomic Medicine, Changhua Christian Hospital, Changhua, Taiwan
| | - Gwo-Chin Ma
- Department of Genomic Medicine, Changhua Christian Hospital, Changhua, Taiwan
| | - Ying-Chih Huang
- Department of Internal Medicine, Changhua Christian Hospital, Changhua, Taiwan
| | - Ching-Yeh Lin
- Department of Internal Medicine, Changhua Christian Hospital, Changhua, Taiwan
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28
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Iourov IY, Heng HH. Editorial: Somatic genomic mosaicism & human disease. Front Genet 2022; 13:1045559. [PMID: 36276972 PMCID: PMC9585291 DOI: 10.3389/fgene.2022.1045559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 09/21/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Ivan Y. Iourov
- Yurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia
- Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
- Department of Medical Biological Disciplines, Belgorod State University, Belgorod, Russia
- *Correspondence: Ivan Y. Iourov,
| | - Henry H. Heng
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, United States
- Department of Pathology, Wayne State University School of Medicine, Detroit, United States
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29
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Mohiuddin M, Kooy RF, Pearson CE. De novo mutations, genetic mosaicism and human disease. Front Genet 2022; 13:983668. [PMID: 36226191 PMCID: PMC9550265 DOI: 10.3389/fgene.2022.983668] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/08/2022] [Indexed: 11/23/2022] Open
Abstract
Mosaicism—the existence of genetically distinct populations of cells in a particular organism—is an important cause of genetic disease. Mosaicism can appear as de novo DNA mutations, epigenetic alterations of DNA, and chromosomal abnormalities. Neurodevelopmental or neuropsychiatric diseases, including autism—often arise by de novo mutations that usually not present in either of the parents. De novo mutations might occur as early as in the parental germline, during embryonic, fetal development, and/or post-natally, through ageing and life. Mutation timing could lead to mutation burden of less than heterozygosity to approaching homozygosity. Developmental timing of somatic mutation attainment will affect the mutation load and distribution throughout the body. In this review, we discuss the timing of de novo mutations, spanning from mutations in the germ lineage (all ages), to post-zygotic, embryonic, fetal, and post-natal events, through aging to death. These factors can determine the tissue specific distribution and load of de novo mutations, which can affect disease. The disease threshold burden of somatic de novo mutations of a particular gene in any tissue will be important to define.
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Affiliation(s)
- Mohiuddin Mohiuddin
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- *Correspondence: Mohiuddin Mohiuddin, ; Christopher E. Pearson,
| | - R. Frank Kooy
- Department of Medical Genetics, University of Antwerp, Edegem, Belgium
| | - Christopher E. Pearson
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- *Correspondence: Mohiuddin Mohiuddin, ; Christopher E. Pearson,
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30
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Hereditary Transthyretin-Related Amyloidosis: Genetic Heterogeneity and Early Personalized Gene Therapy. Biomedicines 2022; 10:biomedicines10102394. [PMID: 36289657 PMCID: PMC9598525 DOI: 10.3390/biomedicines10102394] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/14/2022] [Accepted: 09/23/2022] [Indexed: 12/02/2022] Open
Abstract
Point mutations of the transthyretin (TTR) gene are related with hereditary amyloidosis (hATTR). The number of people affected by this rare disease is only partially estimated. The real impact of somatic mosaicism and other genetic factors on expressivity, complexity, progression, and transmission of the disease should be better investigated. The relevance of this rare disease is increasing and many efforts have been made to improve the time to diagnosis and to estimate the real number of cases in endemic and non-endemic areas. In this context, somatic mosaicism should be better investigated to explain the complexity of the heterogeneity of the hATTR clinical features, to better estimate the number of new cases, and to focus on early and personalized gene therapy. Gene therapy can potentially improve the living conditions of affected individuals and is one of the central goals in research on amyloidosis related to the TTR gene, with the advantage of overcoming liver transplantation as the sole treatment for hATTR disease.
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31
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Shi S, Wang Q, Shang Y, Bu C, Lu M, Jiang M, Zhang H, Yu S, Zeng J, Zhang Z, Du Z, Xiao J. TSomVar: a tumor-only somatic and germline variant identification method with random forest. Brief Bioinform 2022; 23:6695269. [DOI: 10.1093/bib/bbac381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
Somatic variants act as critical players during cancer occurrence and development. Thus, an accurate and robust method to identify them is the foundation of cutting-edge cancer genome research. However, due to low accessibility and high individual-/sample-specificity of the somatic variants in tumor samples, the detection is, to date, still crammed with challenges, particularly when lacking paired normal samples as control. To solve this burning issue, we developed a tumor-only somatic and germline variant identification method (TSomVar) using the random forest algorithm established on sample-specific variant datasets derived from genotype imputation, reads-mapping level annotation and functional annotation. We trained TSomVar by using genomic variant datasets of three major cancer types: colorectal cancer, hepatocellular carcinoma and skin cutaneous melanoma. Compared with existing tumor-only somatic variant identification tools, TSomVar shows excellent performances in somatic variant detection with higher accuracy and better capability of recalling for test datasets from colorectal cancer and skin cutaneous melanoma. In addition, TSomVar is equipped with the competence of accurately identifying germline variants in tumor samples. Taken together, TSomVar will undoubtedly facilitate and revolutionize somatic variant explorations in cancer research.
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Affiliation(s)
- Shuo Shi
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- University of Chinese Academy of Sciences , Beijing 100049, China
- Burning Rock Biotech Ltd , Shanghai 201114, China
| | - Qi Wang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- University of Chinese Academy of Sciences , Beijing 100049, China
- Qujiang Culture Finance Holding (Group) Co., Ltd , Xian 710061, China
| | - Yunfei Shang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Congfan Bu
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
| | - Mingming Lu
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Meiye Jiang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Hao Zhang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Shuhuan Yu
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Jingyao Zeng
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
| | - Zaichao Zhang
- Department of Biology, The University of Western Ontario , London, Ontario N6A 5B7, Canada
| | - Zhenglin Du
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
| | - Jingfa Xiao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- University of Chinese Academy of Sciences , Beijing 100049, China
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Chen JL, Miller DT, Schmidt LS, Malkin D, Korf BR, Eng C, Kwiatkowski DJ, Giannikou K. Mosaicism in Tumor Suppressor Gene Syndromes: Prevalence, Diagnostic Strategies, and Transmission Risk. Annu Rev Genomics Hum Genet 2022; 23:331-361. [PMID: 36044908 DOI: 10.1146/annurev-genom-120121-105450] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A mosaic state arises when pathogenic variants are acquired in certain cell lineages during postzygotic development, and mosaic individuals may present with a generalized or localized phenotype. Here, we review the current state of knowledge regarding mosaicism for eight common tumor suppressor genes-NF1, NF2, TSC1, TSC2, PTEN, VHL, RB1, and TP53-and their related genetic syndromes/entities. We compare and discuss approaches for comprehensive diagnostic genetic testing, the spectrum of variant allele frequency, and disease severity. We also review affected individuals who have no mutation identified after conventional genetic analysis, as well as genotype-phenotype correlations and transmission risk for each tumor suppressor gene in full heterozygous and mosaic patients. This review provides new insight into similarities as well as marked differences regarding the appreciation of mosaicism in these tumor suppressor syndromes.
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Affiliation(s)
- Jillian L Chen
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine and Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA; .,Boston University School of Medicine, Boston, Massachusetts, USA
| | - David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Laura S Schmidt
- Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA.,Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - David Malkin
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.,Germline High Risk Cancer Focus Group, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, USA
| | - David J Kwiatkowski
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine and Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA;
| | - Krinio Giannikou
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine and Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA; .,Division of Hematology and Oncology, Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, California, USA;
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33
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Prevalence of pathogenic germline variants in the circulating tumor DNA testing. Int J Clin Oncol 2022; 27:1554-1561. [PMID: 35870019 PMCID: PMC9510107 DOI: 10.1007/s10147-022-02220-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/06/2022] [Indexed: 11/05/2022]
Abstract
Abstract
Background
Somatic and germline variants are not distinguishable by circulating tumor DNA (ctDNA) testing without analyzing non-tumor samples. Although confirmatory germline testing is clinically relevant, the criteria for selecting presumed germline variants have not been established in ctDNA testing. In the present study, we aimed to evaluate the prevalence of pathogenic germline variants in clinical ctDNA testing through their variant allele fractions (VAFs).
Methods
A total of consecutive 106 patients with advanced solid tumors who underwent ctDNA testing (Guardant360®) between January 2018 and March 2020 were eligible for this study. To verify the origin of pathogenic variants reported in ctDNA testing, germline sequencing was performed using peripheral blood DNA samples archived in the Clinical Bioresource Center in Kyoto University Hospital (Kyoto, Japan) under clinical research settings.
Results
Among 223 pathogenic variants reported in ctDNA testing, the median VAF was 0.9% (0.02–81.8%), and 88 variants with ≥ 1% VAFs were analyzed in germline sequencing. Among 25 variants with ≥ 30% VAFs, seven were found in peripheral blood DNA (BRCA2: n = 6, JAK2: n = 1). In contrast, among the 63 variants with VAFs ranging from 1 to < 30%, only one variant was found in peripheral blood DNA (TP53: n = 1). Eventually, this variant with 15.6% VAF was defined to be an acquired variant, because its allelic distribution did not completely link to those of neighboring germline polymorphisms.
Conclusion
Our current study demonstrated that VAFs values are helpful for selecting presumed germline variants in clinical ctDNA testing.
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Manders F, van Boxtel R, Middelkamp S. The Dynamics of Somatic Mutagenesis During Life in Humans. FRONTIERS IN AGING 2022; 2:802407. [PMID: 35822044 PMCID: PMC9261377 DOI: 10.3389/fragi.2021.802407] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 11/30/2021] [Indexed: 12/12/2022]
Abstract
From conception to death, human cells accumulate somatic mutations in their genomes. These mutations can contribute to the development of cancer and non-malignant diseases and have also been associated with aging. Rapid technological developments in sequencing approaches in the last few years and their application to normal tissues have greatly advanced our knowledge about the accumulation of these mutations during healthy aging. Whole genome sequencing studies have revealed that there are significant differences in mutation burden and patterns across tissues, but also that the mutation rates within tissues are surprisingly constant during adult life. In contrast, recent lineage-tracing studies based on whole-genome sequencing have shown that the rate of mutation accumulation is strongly increased early in life before birth. These early mutations, which can be shared by many cells in the body, may have a large impact on development and the origin of somatic diseases. For example, cancer driver mutations can arise early in life, decades before the detection of the malignancy. Here, we review the recent insights in mutation accumulation and mutagenic processes in normal tissues. We compare mutagenesis early and later in life and discuss how mutation rates and patterns evolve during aging. Additionally, we outline the potential impact of these mutations on development, aging and disease.
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Affiliation(s)
- Freek Manders
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Utrecht, Netherlands
| | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Utrecht, Netherlands
| | - Sjors Middelkamp
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Utrecht, Netherlands
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35
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Zemet R, Van den Veyver IB, Stankiewicz P. Parental mosaicism for apparent de novo genetic variants: Scope, detection, and counseling challenges. Prenat Diagn 2022; 42:811-821. [PMID: 35394072 PMCID: PMC9995893 DOI: 10.1002/pd.6144] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 04/04/2022] [Accepted: 04/04/2022] [Indexed: 11/07/2022]
Abstract
The disease burden of de novo mutations (DNMs) has been evidenced only recently when the common application of next-generation sequencing technologies enabled their reliable and affordable detection through family-based clinical exome or genome sequencing. Implementation of exome sequencing into prenatal diagnostics revealed that up to 63% of pathogenic or likely pathogenic variants associated with fetal structural anomalies are apparently de novo, primarily for autosomal dominant disorders. Apparent DNMs have been considered to primarily occur as germline or zygotic events, with consequently negligible recurrence risks. However, there is now evidence that a considerable proportion of them are in fact inherited from a parent mosaic for the variant. Here, we review the burden of DNMs in prenatal diagnostics and the influence of parental mosaicism on the interpretation of apparent DNMs and discuss the challenges with detecting and quantifying parental mosaicism and its effect on recurrence risk. We also describe new bioinformatic and technological tools developed to assess mosaicism and discuss how they improve the accuracy of reproductive risk counseling when parental mosaicism is detected.
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Affiliation(s)
- Roni Zemet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Ignatia B Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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36
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Spielmann M, Kircher M. Computational and experimental methods for classifying variants of unknown clinical significance. Cold Spring Harb Mol Case Stud 2022; 8:mcs.a006196. [PMID: 35483875 PMCID: PMC9059783 DOI: 10.1101/mcs.a006196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The increase in sequencing capacity, reduction in costs, and national and international coordinated efforts have led to the widespread introduction of next-generation sequencing (NGS) technologies in patient care. More generally, human genetics and genomic medicine are gaining importance for more and more patients. Some communities are already discussing the prospect of sequencing each individual's genome at time of birth. Together with digital health records, this shall enable individualized treatments and preventive measures, so-called precision medicine. A central step in this process is the identification of disease causal mutations or variant combinations that make us more susceptible for diseases. Although various technological advances have improved the identification of genetic alterations, the interpretation and ranking of the identified variants remains a major challenge. Based on our knowledge of molecular processes or previously identified disease variants, we can identify potentially functional genetic variants and, using different lines of evidence, we are sometimes able to demonstrate their pathogenicity directly. However, the vast majority of variants are classified as variants of uncertain clinical significance (VUSs) with not enough experimental evidence to determine their pathogenicity. In these cases, computational methods may be used to improve the prioritization and an increasing toolbox of experimental methods is emerging that can be used to assay the molecular effects of VUSs. Here, we discuss how computational and experimental methods can be used to create catalogs of variant effects for a variety of molecular and cellular phenotypes. We discuss the prospects of integrating large-scale functional data with machine learning and clinical knowledge for the development of accurate pathogenicity predictions for clinical applications.
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Affiliation(s)
- Malte Spielmann
- Institute of Human Genetics, University of Lübeck, 23562 Lübeck, Germany;,Institute of Human Genetics, Christian-Albrechts-Universität, 24105 Kiel, Germany;,Human Molecular Genomics Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany;,DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Lübeck/Kiel, 23562 Lübeck, Germany
| | - Martin Kircher
- Institute of Human Genetics, University of Lübeck, 23562 Lübeck, Germany;,Berlin Institute of Health at Charité—Universitätsmedizin Berlin, 10117 Berlin, Germany;,DZHK (German Centre for Cardiovascular Research), partner site Berlin, 10115 Berlin, Germany
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37
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Bakloushinskaya I. Chromosome Changes in Soma and Germ Line: Heritability and Evolutionary Outcome. Genes (Basel) 2022; 13:genes13040602. [PMID: 35456408 PMCID: PMC9029507 DOI: 10.3390/genes13040602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/25/2022] [Accepted: 03/26/2022] [Indexed: 12/13/2022] Open
Abstract
The origin and inheritance of chromosome changes provide the essential foundation for natural selection and evolution. The evolutionary fate of chromosome changes depends on the place and time of their emergence and is controlled by checkpoints in mitosis and meiosis. Estimating whether the altered genome can be passed to subsequent generations should be central when we consider a particular genome rearrangement. Through comparative analysis of chromosome rearrangements in soma and germ line, the potential impact of macromutations such as chromothripsis or chromoplexy appears to be fascinating. What happens with chromosomes during the early development, and which alterations lead to mosaicism are other poorly studied but undoubtedly essential issues. The evolutionary impact can be gained most effectively through chromosome rearrangements arising in male meiosis I and in female meiosis II, which are the last divisions following fertilization. The diversity of genome organization has unique features in distinct animals; the chromosome changes, their internal relations, and some factors safeguarding genome maintenance in generations under natural selection were considered for mammals.
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Affiliation(s)
- Irina Bakloushinskaya
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
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38
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Moosavi SA, Hasannejad-Asl B, Kourosh Arami M, Nasuti M, Oguz MC, Naseri AH. Confirmatory test versus screening test analyses for fetal mosaic variations; a large scale study. ALEXANDRIA JOURNAL OF MEDICINE 2022. [DOI: 10.1080/20905068.2021.2010450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Seyed Akbar Moosavi
- Department of Medical Laboratory Sciences, Iran University of Medical Sciences, Tehran, Iran
- Neuroscience Research Center, Iran University of Medical Science, Tehran, Iran
- Tehran Women Hospital, AST Genetic Lab, Tehran, Iran
| | - Behnam Hasannejad-Asl
- Biotechnology Department, School of Advaned Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoumeh Kourosh Arami
- Neuroscience Research Center, Iran University of Medical Science, Tehran, Iran
- Department of Basic Sciences, Allied Medicine College, Iran University of Medical Sciences, Tehran, Iran
| | - Mahsa Nasuti
- Department of Microbiology, Islamic Azad University of Karaj, Karaj, Iran
| | - Mehmet Cemal Oguz
- Health Service, Vocational College of Mardin Artuklu University, Mardin, Turkey
| | - Abdol-Hossain Naseri
- Department of Medical Laboratory Sciences, Iran University of Medical Sciences, Tehran, Iran
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40
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Rydzanicz M, Glinkowski W, Walczak A, Koppolu A, Kostrzewa G, Gasperowicz P, Pollak A, Stawiński P, Płoski R. Postzygotic mosaicism of a novel PTPN11 mutation in monozygotic twins discordant for metachondromatosis. Am J Med Genet A 2022; 188:1482-1487. [PMID: 35112464 DOI: 10.1002/ajmg.a.62670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 12/16/2021] [Accepted: 01/11/2022] [Indexed: 01/05/2023]
Abstract
Genetic mosaicism caused by postzygotic mutations is of a great interest due to its role in human disease. Monozygotic twins arising from a single zygote are considered as genetically identical, and any differences likely to be caused by postzygotic events. Thus, phenotypically discordant monozygotic twins offer a unique opportunity to study genotype-phenotype correlation. Here, we present a three-generation family starting from a pair of monozygotic twins discordant for metachondromatosis due to postzygotic p.(Gln175His) variant in the PTPN11 gene. Both phenotypically discordant monozygotic twins harbor p.(Gln175His), however significant differences in mosaic ratio is observed not only between twins, but also within different tissue types within one individual. Phenotypic manifestation of p.(Gln175His) in examined family clearly depends on allele variant fraction (VAF). Individuals harboring constitutional mutation (VAF 50%) present typical metachondromatosis. Milder phenotype is observed in twin harboring high-level mosaicism in the tissue of ectodermal origin (VAF 45%), but not in a blood (VAF 5%). Finally, her twin sister harboring low-level mosaicism in blood (VAF 2%) and nonblood (VAF 12%) tissues is phenotypically normal. Our results provide insights into biological role of mosaicism in disease and further support the usefulness of nonblood tissues as an optimal source of DNA for the identification of postzygotic mutations in phenotypically discordant monozygotic twins.
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Affiliation(s)
| | - Wojciech Glinkowski
- Center of Excellence "TeleOrto" for Telediagnostics and Treatment of Disorders and Injuries of the Locomotor System, Department of Medical Informatics and Telemedicine, Medical University of Warsaw, Warsaw, Poland
| | - Anna Walczak
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Koppolu
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Grażyna Kostrzewa
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Piotr Gasperowicz
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Pollak
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Piotr Stawiński
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
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41
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Li JF, Tian GL, Pan H, Zhang WT, Li DC, Liu JD, Zhao L, Li HL. An Analysis of the Pathogenic Genes and Mutation Sites of Macrodactyly. Pharmgenomics Pers Med 2022; 15:55-64. [PMID: 35125881 PMCID: PMC8809672 DOI: 10.2147/pgpm.s346373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/20/2022] [Indexed: 11/23/2022] Open
Abstract
Objective This study aimed to explore the pathogenic genes and mutation sites of macrodactyly. Methods Whole-exome sequencing was performed on the pathological tissue and peripheral blood of 12 patients with macrodactyly who were operated in our hospital between June 2018 and May 2020. In order to conduct comprehensive bioinformatics analysis and screen the pathogenic genes of macrodactyly, the patients were divided into four groups: macrodactyly of finger group, macrodactyly of foot group, macrodactyly and syndactyly of finger group, and macrodactyly and syndactyly of foot group. The results of the whole-exome sequencing were verified using Sanger sequencing in order to clarify the pathogenic genes and mutation sites of macrodactyly, and immunohistochemical analysis of the protein signaling pathways encoded by the pathogenic genes was performed to observe the protein expression and further verify the mutant genes. Results In the comprehensive bioinformatics analysis and Sanger verification of the whole-exome sequencing, the PIK3CA gene mutation was screened as the pathogenic gene of macrodactyly. The mutation sites were identified as the p.E542K (c.G1624A) and p.E545K (c.G1633A) sites of exon10 and the p.H1047R (c.A3140G) and p.G1049R (c.G3145C) sites of exon21. Among these, the p.G1049R (c.G3145C) locus was found in macrodactyly for the first time. The mutation of the PIK3CA gene was also found to lead to increased expression of serine-threonine kinase (AKT) in adipocytes in the PI3K-AKT-mTOR signaling pathway. Conclusion Mutation of the PIK3CA gene leads to the enhancement of the PI3K-AKT-mTOR signaling pathway, which is the cause of macrodactyly. There is also some diversity in PIK3CA gene mutation sites.
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Affiliation(s)
- Jian-Feng Li
- Department of Hand Surgery, Beijing Shunyi District Hospital; Shunyi Teaching Hospital of Capital Medical University, Beijing, 101300, People’s Republic of China
- Correspondence: Jian-Feng Li, Department of Hand Surgery, Beijing Shunyi District Hospital; Shunyi Teaching Hospital of Capital Medical University, No. 3 Guangming South Street, Shunyi District, Beijing, 101300, People’s Republic of China, Tel +86 10 69423220, Email
| | - Guang-Lei Tian
- Department of Hand Surgery, Beijing Jishuitan Hospital; Peking University Fourth School of Clinical Medicine, Beijing, 100035, People’s Republic of China
| | - Hui Pan
- Department of Pathology, Beijing Shunyi District Hospital; Shunyi Teaching Hospital of Capital Medical University, Beijing, 101300, People’s Republic of China
| | - Wen-Tong Zhang
- Department of Hand Surgery, Beijing Shunyi District Hospital; Shunyi Teaching Hospital of Capital Medical University, Beijing, 101300, People’s Republic of China
| | - Da-Cun Li
- Department of Hand Surgery, Beijing Shunyi District Hospital; Shunyi Teaching Hospital of Capital Medical University, Beijing, 101300, People’s Republic of China
| | - Jing-Da Liu
- Department of Hand Surgery, Beijing Shunyi District Hospital; Shunyi Teaching Hospital of Capital Medical University, Beijing, 101300, People’s Republic of China
| | - Liang Zhao
- Department of Hand Surgery, Beijing Shunyi District Hospital; Shunyi Teaching Hospital of Capital Medical University, Beijing, 101300, People’s Republic of China
| | - Hai-Lei Li
- Department of Hand Surgery, Beijing Shunyi District Hospital; Shunyi Teaching Hospital of Capital Medical University, Beijing, 101300, People’s Republic of China
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42
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Mei Y, Zhang H, Zhang Z. Comparing Clinical and Genetic Characteristics of De Novo and Inherited COL1A1/COL1A2 Variants in a Large Chinese Cohort of Osteogenesis Imperfecta. Front Endocrinol (Lausanne) 2022; 13:935905. [PMID: 35909573 PMCID: PMC9329653 DOI: 10.3389/fendo.2022.935905] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/17/2022] [Indexed: 01/07/2023] Open
Abstract
PURPOSE Nearly 85%-90% of osteogenesis imperfecta (OI) cases are caused by autosome dominant mutations of COL1A1 and COL1A2 genes, of which de novo mutations cover a large proportion, whereas their characteristics remain to be elucidated. This study aims to compare the differences in clinical and genetic characteristics of de novo and inherited COL1A1/COL1A2 mutations of OI, assess the average paternal and maternal age at conception in de novo mutations, and research the rate of nonpenetrance in inherited mutations. MATERIALS AND METHODS A retrospective comparison between de novo and inherited mutations was performed among 135 OI probands with COL1A1/COL1A2 mutations. Mutational analyses of all probands and their family members were completed by Sanger sequencing. A new clinical scoring system was developed to assess the clinical severity of OI quantitatively. RESULTS A total of 51 probands (37.78%) with de novo mutations and 84 probands (62.22%) with inherited mutations were grouped by the results of the parental gene verification. The proportion of clinical type III (P<0.001) and clinical scores (P<0.001) were significantly higher in de novo mutations. Missense mutations covered a slightly higher proportion of de novo COL1A1 mutations (46.34%) compared with inherited COL1A1 mutations (33.33%), however, lacking a significant difference (P=0.1923). The mean BMD Z/T-score at the lumbar spine in de novo mutations was -2.3 ± 1.5, lower than inherited mutations (-1.7 ± 1.8), but lacking statistical significance (P=0.0742). There was no significant difference between the two groups in OI-related phenotypes (like fracture frequency, blue sclera, and hearing loss) and biochemical indexes. In de novo mutations, the average paternal and maternal age at conception was 29.2 (P<0.05) and 26.8 (P<0.0001), respectively, which were significantly younger than the average gestational age of the population. Additionally, 98.04% of pedigrees (50/51) with de novo mutations were spontaneous conception. The rate of nonpenetrance of parents with pathogenic variants in the inherited mutation group was 25.64% (20/78). CONCLUSIONS Our data revealed that the proportion of clinical type III and clinical scores were significantly higher in de novo mutations than in inherited mutations, demonstrating that de novo mutations are more damaging because they have not undergone purifying selection.
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Affiliation(s)
| | - Hao Zhang
- *Correspondence: Zhenlin Zhang, ; Hao Zhang,
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43
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Huang TX, Ma GC, Chen M, Li WF, Shaw SW. Difficulties of Prenatal Genetic Counseling for a Subsequent Child in a Family With Multiple Genetic Variations. Front Genet 2022; 12:612100. [PMID: 34970295 PMCID: PMC8712678 DOI: 10.3389/fgene.2021.612100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
Many parents with a disabled child caused by a genetic condition appreciate the option of prenatal genetic diagnosis to understand the chance of recurrence in a future pregnancy. Genome-wide tests, such as chromosomal microarray analysis and whole-exome sequencing, have been increasingly used for prenatal diagnosis, but prenatal counseling can be challenging due to the complexity of genomic data. This situation is further complicated by incidental findings of additional genetic variations in subsequent pregnancies. Here, we report the prenatal identification of a baby with a MECP2 missense variant and 15q11.2 microduplication in a family that has had a child with developmental and epileptic encephalopathy caused by a de novo KCNQ2 variant. An extended segregation analysis including extended relatives, in addition to the parents, was carried out to provide further information for genetic counseling. This case illustrates the challenges of prenatal counseling and highlights the need to understand the clinical and ethical implications of genome-wide tests.
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Affiliation(s)
- Ting-Xuan Huang
- Department of Obstetrics and Gynecology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Gwo-Chin Ma
- Department of Genomic Medicine and Center for Medical Genetics, Changhua Christian Hospital, Changhua, Taiwan
| | - Ming Chen
- Department of Genomic Medicine and Center for Medical Genetics, Changhua Christian Hospital, Changhua, Taiwan.,Department of Obstetrics and Gynecology, Changhua Christian Hospital, Changhua, Taiwan.,Department of Molecular Biotechnology, Da-Yeh University, Changhua, Taiwan.,Department of Obstetrics and Gynecology, College of Medicine, National Taiwan University, Taipei, Taiwan.,Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan.,Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Wen-Fang Li
- Department of Obstetrics and Gynecology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Steven W Shaw
- Department of Obstetrics and Gynecology, Taipei Chang Gung Memorial Hospital, Taipei, Taiwan.,College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Prenatal Cell and Gene Therapy Group, Institute for Women's Health University College London, London, United Kingdom
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44
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Grossi A, Morelli F, Di Duca M, Caroli F, Moroni I, Tonduti D, Bachetti T, Ceccherini I. Parental Somatic Mosaicism Uncovers Inheritance of an Apparently De Novo GFAP Mutation. Front Genet 2021; 12:744068. [PMID: 34950187 PMCID: PMC8688950 DOI: 10.3389/fgene.2021.744068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/02/2021] [Indexed: 12/02/2022] Open
Abstract
Alexander disease is a leukodystrophy caused by heterozygous mutations of GFAP gene. Recurrence in siblings from healthy parents provides a confirmation to the transmission of variants through germinal mosaicism. With the use of DNA isolated from peripheral blood, next-generation sequencing (NGS) of GFAP locus was performed with deep coverage (≥500×) in 11 probands and their parents (trios) with probands heterozygous for apparently de novo GFAP mutations. Indeed, one parent had somatic mosaicism, estimated in the range of 8.9%–16%, for the mutant allele transmitted to the affected sibling. Parental germline mosaicism deserves attention, as it is critical in assessing the risk of recurrence in families with Alexander disease.
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Affiliation(s)
- Alice Grossi
- UOSD Laboratory of Genetics and Genomics of Rare Diseases, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Federico Morelli
- UOSD Laboratory of Genetics and Genomics of Rare Diseases, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Marco Di Duca
- Laboratory of Molecular Nephrology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Francesco Caroli
- UOSD Laboratory of Genetics and Genomics of Rare Diseases, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Isabella Moroni
- Department of Pediatric Neurosciences, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Davide Tonduti
- Unit of Pediatric Neurology - C.O.A.L.A (Center for Diagnosis and Treatment of Leukodystrophies), V. Buzzi Children's Hospital, Milan, Italy
| | - Tiziana Bachetti
- UOSD Laboratory of Genetics and Genomics of Rare Diseases, IRCCS Istituto Giannina Gaslini, Genoa, Italy.,Laboratory of Developmental Neuro-Biology, DISTAV, University of Genoa, Genoa, Italy
| | - Isabella Ceccherini
- UOSD Laboratory of Genetics and Genomics of Rare Diseases, IRCCS Istituto Giannina Gaslini, Genoa, Italy
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Domogala DD, Gambin T, Zemet R, Wu CW, Schulze KV, Yang Y, Wilson TA, Machol I, Liu P, Stankiewicz P. Detection of low-level parental somatic mosaicism for clinically relevant SNVs and indels identified in a large exome sequencing dataset. Hum Genomics 2021; 15:72. [PMID: 34930489 PMCID: PMC8686574 DOI: 10.1186/s40246-021-00369-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 11/27/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Due to the limitations of the current routine diagnostic methods, low-level somatic mosaicism with variant allele fraction (VAF) < 10% is often undetected in clinical settings. To date, only a few studies have attempted to analyze tissue distribution of low-level parental mosaicism in a large clinical exome sequencing (ES) cohort. METHODS Using a customized bioinformatics pipeline, we analyzed apparent de novo single-nucleotide variants or indels identified in the affected probands in ES trio data at Baylor Genetics clinical laboratories. Clinically relevant variants with VAFs between 30 and 70% in probands and lower than 10% in one parent were studied. DNA samples extracted from saliva, buccal cells, redrawn peripheral blood, urine, hair follicles, and nail, representing all three germ layers, were tested using PCR amplicon next-generation sequencing (amplicon NGS) and droplet digital PCR (ddPCR). RESULTS In a cohort of 592 clinical ES trios, we found 61 trios, each with one parent suspected of low-level mosaicism. In 21 parents, the variants were validated using amplicon NGS and seven of them by ddPCR in peripheral blood DNA samples. The parental VAFs in blood samples varied between 0.08 and 9%. The distribution of VAFs in additional tissues ranged from 0.03% in hair follicles to 9% in re-drawn peripheral blood. CONCLUSIONS Our study illustrates the importance of analyzing ES data using sensitive computational and molecular methods for low-level parental somatic mosaicism for clinically relevant variants previously diagnosed in routine clinical diagnostics as apparent de novo.
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Affiliation(s)
- Daniel D Domogala
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Graduate Program in Diagnostic Genetics, School of Health Professions, University of Texas at MD Anderson, Houston, TX, USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Roni Zemet
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Chung Wah Wu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Baylor Genetics, Houston, TX, USA
| | - Katharina V Schulze
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Baylor Genetics, Houston, TX, USA
| | - Yaping Yang
- AiLife Diagnostics, 1920 Country Place Pkwy Suite 100, Pearland, TX, USA
| | - Theresa A Wilson
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | | | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Baylor Genetics, Houston, TX, USA
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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Lupski JR. Clan genomics: From OMIM phenotypic traits to genes and biology. Am J Med Genet A 2021; 185:3294-3313. [PMID: 34405553 PMCID: PMC8530976 DOI: 10.1002/ajmg.a.62434] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/29/2021] [Accepted: 07/04/2021] [Indexed: 12/20/2022]
Abstract
Clinical characterization of a patient phenotype has been the quintessential approach for elucidating a differential diagnosis and a hypothesis to explore a potential clinical diagnosis. This has resulted in a language of medicine and a semantic ontology, with both specialty- and subspecialty-specific lexicons, that can be challenging to translate and interpret. There is no 'Rosetta Stone' of clinical medicine such as the genetic code that can assist translation and interpretation of the language of genetics. Nevertheless, the information content embodied within a clinical diagnosis can guide management, therapeutic intervention, and potentially prognostic outlook of disease enabling anticipatory guidance for patients and families. Clinical genomics is now established firmly in medical practice. The granularity and informative content of a personal genome is immense. Yet, we are limited in our utility of much of that personal genome information by the lack of functional characterization of the overwhelming majority of computationally annotated genes in the haploid human reference genome sequence. Whereas DNA and the genetic code have provided a 'Rosetta Stone' to translate genetic variant information, clinical medicine, and clinical genomics provide the context to understand human biology and disease. A path forward will integrate deep phenotyping, such as available in a clinical synopsis in the Online Mendelian Inheritance in Man (OMIM) entries, with personal genome analyses.
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Affiliation(s)
- James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
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47
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Potocki-Lupski Syndrome Dup17p11.2 in a Girl with Hypotonia and Early Behavioural Disturbances. Pril (Makedon Akad Nauk Umet Odd Med Nauki) 2021; 42:91-94. [PMID: 34699703 DOI: 10.2478/prilozi-2021-0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Potocki-Lupski syndrome (PTLS) is a contiguous gene syndrome caused by duplication of chromosome 17p11.2. PTLS is characterized by hypotonia, failure to thrive, congenital anomalies (particularly of the cardiovascular system), intellectual disability, and behavioural disturbances. The patient was a full-term baby girl, 2,750 grams at birth, delivered via an uncomplicated vaginal delivery with pronounced hypotonia at birth. Nevertheless, there was failure to thrive (weight 7.6 kg; 2.8 SD). Micrognathia, epicanthal skin folds, and megalocornea were noticeable. There was a harsh continuous systolic murmur, and the ultrasound of the heart revealed a persistent arteriosus duct which was surgically closed. At the age of 18 months, the girl could not sit without support, and she could not utter simple words. The girl is often moody, angry, and aggressive. She is hyperactive and unable to establish contacts with family members. A 17p12-p11.2 microduplication was identified via MLPA. Muscle hypotonia, congenital heart malformation, failure to thrive, developmental delay, behavioural disturbances (or autism spectrum disorder), and intellectual disability are early signs of PTLS. The presence of PTLS was proven by an MLPA analysis.
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48
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Schreuder WH, van der Wal JE, de Lange J, van den Berg H. Multiple versus solitary giant cell lesions of the jaw: Similar or distinct entities? Bone 2021; 149:115935. [PMID: 33771761 DOI: 10.1016/j.bone.2021.115935] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 02/27/2021] [Accepted: 03/17/2021] [Indexed: 02/06/2023]
Abstract
The majority of giant cell lesions of the jaw present as a solitary focus of disease in bones of the maxillofacial skeleton. Less frequently they occur as multifocal lesions. This raises the clinical dilemma if these should be considered distinct entities and therefore each need a specific therapeutic approach. Solitary giant cell lesions of the jaw present with a great diversity of symptoms. Recent molecular analysis revealed that these are associated with somatic gain-of-function mutations in KRAS, FGFR1 or TRPV4 in a large component of the mononuclear stromal cells which all act on the RAS/MAPK pathway. For multifocal lesions, a small group of neoplastic multifocal giant cell lesions of the jaw remain after ruling out hyperparathyroidism. Strikingly, most of these patients are diagnosed with jaw lesions before the age of 20 years, thus before the completion of dental and jaw development. These multifocal lesions are often accompanied by a diagnosis or strong clinical suspicion of a syndrome. Many of the frequently reported syndromes belong to the so-called RASopathies, with germline or mosaic mutations leading to downstream upregulation of the RAS/MAPK pathway. The other frequently reported syndrome is cherubism, with gain-of-function mutations in the SH3BP2 gene leading through assumed and unknown signaling to an autoinflammatory bone disorder with hyperactive osteoclasts and defective osteoblastogenesis. Based on this extensive literature review, a RAS/MAPK pathway activation is hypothesized in all giant cell lesions of the jaw. The different interaction between and contribution of deregulated signaling in individual cell lineages and crosstalk with other pathways among the different germline- and non-germline-based alterations causing giant cell lesions of the jaw can be explanatory for the characteristic clinical features. As such, this might also aid in the understanding of the age-dependent symptomatology of syndrome associated giant cell lesions of the jaw; hopefully guiding ideal timing when installing treatment strategies in the future.
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Affiliation(s)
- Willem H Schreuder
- Department of Oral and Maxillofacial Surgery, Amsterdam UMC and Academic Center for Dentistry Amsterdam, University of Amsterdam, Amsterdam, the Netherlands; Department of Head and Neck Surgery and Oncology, Antoni van Leeuwenhoek / Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Jacqueline E van der Wal
- Department of Pathology, Antoni van Leeuwenhoek / Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Jan de Lange
- Department of Oral and Maxillofacial Surgery, Amsterdam UMC and Academic Center for Dentistry Amsterdam, University of Amsterdam, Amsterdam, the Netherlands
| | - Henk van den Berg
- Department of Pediatrics / Oncology, Amsterdam UMC, University of Amsterdam, Emma Children's Hospital, Amsterdam, the Netherlands
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49
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Latorre-Pellicer A, Gil-Salvador M, Parenti I, Lucia-Campos C, Trujillano L, Marcos-Alcalde I, Arnedo M, Ascaso Á, Ayerza-Casas A, Antoñanzas-Pérez R, Gervasini C, Piccione M, Mariani M, Weber A, Kanber D, Kuechler A, Munteanu M, Khuller K, Bueno-Lozano G, Puisac B, Gómez-Puertas P, Selicorni A, Kaiser FJ, Ramos FJ, Pié J. Clinical relevance of postzygotic mosaicism in Cornelia de Lange syndrome and purifying selection of NIPBL variants in blood. Sci Rep 2021; 11:15459. [PMID: 34326454 PMCID: PMC8322329 DOI: 10.1038/s41598-021-94958-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/19/2021] [Indexed: 11/09/2022] Open
Abstract
Postzygotic mosaicism (PZM) in NIPBL is a strong source of causality for Cornelia de Lange syndrome (CdLS) that can have major clinical implications. Here, we further delineate the role of somatic mosaicism in CdLS by describing a series of 11 unreported patients with mosaic disease-causing variants in NIPBL and performing a retrospective cohort study from a Spanish CdLS diagnostic center. By reviewing the literature and combining our findings with previously published data, we demonstrate a negative selection against somatic deleterious NIPBL variants in blood. Furthermore, the analysis of all reported cases indicates an unusual high prevalence of mosaicism in CdLS, occurring in 13.1% of patients with a positive molecular diagnosis. It is worth noting that most of the affected individuals with mosaicism have a clinical phenotype at least as severe as those with constitutive pathogenic variants. However, the type of genetic change does not vary between germline and somatic events and, even in the presence of mosaicism, missense substitutions are located preferentially within the HEAT repeat domain of NIPBL. In conclusion, the high prevalence of mosaicism in CdLS as well as the disparity in tissue distribution provide a novel orientation for the clinical management and genetic counselling of families.
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Affiliation(s)
- Ana Latorre-Pellicer
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Marta Gil-Salvador
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Ilaria Parenti
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Cristina Lucia-Campos
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Laura Trujillano
- Unit of Clinical Genetics, Service of Paediatrics, Hospital Clínico Universitario Lozano Blesa, Department of Paediatrics, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Iñigo Marcos-Alcalde
- Molecular Modelling Group, Centro de Biología Molecular Severo Ochoa, CBMSO (CSIC-UAM), 28049, Madrid, Spain
- Biosciences Research Institute, School of Experimental Sciences, Universidad Francisco de Vitoria, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - María Arnedo
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Ángela Ascaso
- Unit of Clinical Genetics, Service of Paediatrics, Hospital Clínico Universitario Lozano Blesa, Department of Paediatrics, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Ariadna Ayerza-Casas
- Unit of Paediatric Cardiology, Service of Paediatrics, Hospital Universitario Miguel Servet, 50009, Zaragoza, Spain
| | - Rebeca Antoñanzas-Pérez
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Cristina Gervasini
- Genetica Medica, Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milano, Italy
| | - Maria Piccione
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Milena Mariani
- Centro Fondazione Mariani per il Bambino Fragile, Department of Pediatrics, ASST-Lariana Sant'Anna Hospital, San Fermo della Battaglia (Como), Italy
| | - Axel Weber
- Institute of Human Genetics, Justus-Liebig-University, Giessen, Germany
| | - Deniz Kanber
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Alma Kuechler
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Martin Munteanu
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Katharina Khuller
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Gloria Bueno-Lozano
- Unit of Clinical Genetics, Service of Paediatrics, Hospital Clínico Universitario Lozano Blesa, Department of Paediatrics, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Beatriz Puisac
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Paulino Gómez-Puertas
- Molecular Modelling Group, Centro de Biología Molecular Severo Ochoa, CBMSO (CSIC-UAM), 28049, Madrid, Spain
| | - Angelo Selicorni
- Centro Fondazione Mariani per il Bambino Fragile, Department of Pediatrics, ASST-Lariana Sant'Anna Hospital, San Fermo della Battaglia (Como), Italy
| | - Frank J Kaiser
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
- Essener Zentrum für Seltene Erkrankungen (EZSE), Universitätsmedizin Essen, Universitätsklinikum Essen, Essen, Germany
| | - Feliciano J Ramos
- Unit of Clinical Genetics, Service of Paediatrics, Hospital Clínico Universitario Lozano Blesa, Department of Paediatrics, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain.
| | - Juan Pié
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain.
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50
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Maani N, Panabaker K, McCuaig JM, Buckley K, Semotiuk K, Farncombe KM, Ainsworth P, Panchal S, Sadikovic B, Armel SR, Lin H, Kim RH. Incidental findings from cancer next generation sequencing panels. NPJ Genom Med 2021; 6:63. [PMID: 34282142 PMCID: PMC8289933 DOI: 10.1038/s41525-021-00224-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 06/09/2021] [Indexed: 11/09/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have facilitated multi-gene panel (MGP) testing to detect germline DNA variants in hereditary cancer patients. This sensitive technique can uncover unexpected, non-germline incidental findings indicative of mosaicism, clonal hematopoiesis (CH), or hematologic malignancies. A retrospective chart review was conducted to identify cases of incidental findings from NGS-MGP testing. Inclusion criteria included: 1) multiple pathogenic variants in the same patient; 2) pathogenic variants at a low allele fraction; and/or 3) the presence of pathogenic variants not consistent with family history. Secondary tissue analysis, complete blood count (CBC) and medical record review were conducted to further delineate the etiology of the pathogenic variants. Of 6060 NGS-MGP tests, 24 cases fulfilling our inclusion criteria were identified. Pathogenic variants were detected in TP53, ATM, CHEK2, BRCA1 and APC. 18/24 (75.0%) patients were classified as CH, 3/24 (12.5%) as mosaic, 2/24 (8.3%) related to a hematologic malignancy, and 1/24 (4.2%) as true germline. We describe a case-specific workflow to identify and interpret the nature of incidental findings on NGS-MGP. This workflow will provide oncology and genetic clinics a practical guide for the management and counselling of patients with unexpected NGS-MGP findings.
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Affiliation(s)
- Nika Maani
- Program for Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Karen Panabaker
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, ON, Canada
| | - Jeanna M McCuaig
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Familial Cancer Clinic, Princess Margaret Hospital Cancer Centre, Toronto, ON, Canada
| | | | - Kara Semotiuk
- Zane Cohen Centre for Digestive Diseases, Familial Gastrointestinal Cancer Registry, Mount Sinai Hospital, Toronto, ON, Canada
| | - Kirsten M Farncombe
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Peter Ainsworth
- Molecular Genetics Laboratory, Division of Molecular Diagnostics, London Health Sciences Centre, London, ON, Canada
| | - Seema Panchal
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Familial Breast Cancer Clinic, Mount Sinai Hospital, Toronto, ON, Canada
| | - Bekim Sadikovic
- Molecular Genetics Laboratory, Division of Molecular Diagnostics, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Susan Randall Armel
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Familial Cancer Clinic, Princess Margaret Hospital Cancer Centre, Toronto, ON, Canada
| | - Hanxin Lin
- Molecular Genetics Laboratory, Division of Molecular Diagnostics, London Health Sciences Centre, London, ON, Canada. .,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.
| | - Raymond H Kim
- Familial Cancer Clinic, Princess Margaret Hospital Cancer Centre, Toronto, ON, Canada. .,Department of Medicine, University of Toronto, Toronto, ON, Canada.
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