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Kronzer VL, Sparks JA, Raychaudhuri S, Cerhan JR. Low-frequency and rare genetic variants associated with rheumatoid arthritis risk. Nat Rev Rheumatol 2024; 20:290-300. [PMID: 38538758 DOI: 10.1038/s41584-024-01096-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2024] [Indexed: 04/28/2024]
Abstract
Rheumatoid arthritis (RA) has an estimated heritability of nearly 50%, which is particularly high in seropositive RA. HLA alleles account for a large proportion of this heritability, in addition to many common single-nucleotide polymorphisms with smaller individual effects. Low-frequency and rare variants, such as those captured by next-generation sequencing, can also have a large role in heritability in some individuals. Rare variant discovery has informed the development of drugs such as inhibitors of PCSK9 and Janus kinases. Some 34 low-frequency and rare variants are currently associated with RA risk. One variant (19:10352442G>C in TYK2) was identified in five separate studies, and might therefore represent a promising therapeutic target. Following a set of best practices in future studies, including studying diverse populations, using large sample sizes, validating RA and serostatus, replicating findings, adjusting for other variants and performing functional assessment, could help to ensure the relevance of identified variants. Exciting opportunities are now on the horizon for genetics in RA, including larger datasets and consortia, whole-genome sequencing and direct applications of findings in the management, and especially treatment, of RA.
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Affiliation(s)
| | - Jeffrey A Sparks
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - James R Cerhan
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
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2
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Ferrer A, Duffy P, Olson RJ, Meiners MA, Schultz-Rogers L, Macke EL, Safgren S, Morales-Rosado JA, Cousin MA, Oliver GR, Rider D, Williams M, Pichurin PN, Deyle DR, Morava E, Gavrilova RH, Dhamija R, Wierenga KJ, Lanpher BC, Babovic-Vuksanovic D, Kaiwar C, Vitek CR, McAllister TM, Wick MJ, Schimmenti LA, Lazaridis KN, Vairo FPE, Klee EW. Semiautomated approach focused on new genomic information results in time and effort-efficient reannotation of negative exome data. Hum Genet 2024; 143:649-666. [PMID: 38538918 DOI: 10.1007/s00439-024-02664-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 02/25/2024] [Indexed: 05/18/2024]
Abstract
Most rare disease patients (75-50%) undergoing genomic sequencing remain unsolved, often due to lack of information about variants identified. Data review over time can leverage novel information regarding disease-causing variants and genes, increasing this diagnostic yield. However, time and resource constraints have limited reanalysis of genetic data in clinical laboratories setting. We developed RENEW, (REannotation of NEgative WES/WGS) an automated reannotation procedure that uses relevant new information in on-line genomic databases to enable rapid review of genomic findings. We tested RENEW in an unselected cohort of 1066 undiagnosed cases with a broad spectrum of phenotypes from the Mayo Clinic Center for Individualized Medicine using new information in ClinVar, HGMD and OMIM between the date of previous analysis/testing and April of 2022. 5741 variants prioritized by RENEW were rapidly reviewed by variant interpretation specialists. Mean analysis time was approximately 20 s per variant (32 h total time). Reviewed cases were classified as: 879 (93.0%) undiagnosed, 63 (6.6%) putatively diagnosed, and 4 (0.4%) definitively diagnosed. New strategies are needed to enable efficient review of genomic findings in unsolved cases. We report on a fast and practical approach to address this need and improve overall diagnostic success in patient testing through a recurrent reannotation process.
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Affiliation(s)
- Alejandro Ferrer
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Patrick Duffy
- Bioinformatics Systems, Information Technology, Mayo Clinic, Rochester, MN, USA
| | - Rory J Olson
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Michael A Meiners
- Bioinformatics Systems, Information Technology, Mayo Clinic, Rochester, MN, USA
| | - Laura Schultz-Rogers
- Department of Pathology and Lab Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Erica L Macke
- The Institute of Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | | | - Joel A Morales-Rosado
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Margot A Cousin
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Gavin R Oliver
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - David Rider
- Bioinformatics Systems, Information Technology, Mayo Clinic, Rochester, MN, USA
| | - Megan Williams
- Bioinformatics Systems, Information Technology, Mayo Clinic, Rochester, MN, USA
| | - Pavel N Pichurin
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - David R Deyle
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Eva Morava
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | - Radhika Dhamija
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Klass J Wierenga
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | | | | | - Carolyn R Vitek
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Myra J Wick
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Lisa A Schimmenti
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
- Departments of Otorhinolaryngology, Head and Neck Surgery, Ophthalmology, and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Konstantinos N Lazaridis
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Filippo Pinto E Vairo
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.
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3
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Huang H, Hu C, Na J, Hart SN, Gnanaolivu RD, Abozaid M, Rao T, Tecleab YA, Pesaran T, Lyra PCM, Karam R, Yadav S, Domchek SM, de la Hoya M, Robson M, Mehine M, Bandlamudi C, Mandelker D, Monteiro ANA, Boddicker N, Chen W, Richardson ME, Couch FJ. Saturation genome editing-based functional evaluation and clinical classification of BRCA2 single nucleotide variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.14.571597. [PMID: 38168194 PMCID: PMC10760149 DOI: 10.1101/2023.12.14.571597] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Germline BRCA2 loss-of function (LOF) variants identified by clinical genetic testing predispose to breast, ovarian, prostate and pancreatic cancer. However, variants of uncertain significance (VUS) (n>4000) limit the clinical use of testing results. Thus, there is an urgent need for functional characterization and clinical classification of all BRCA2 variants. Here we report on comprehensive saturation genome editing-based functional characterization of 97% of all possible single nucleotide variants (SNVs) in the BRCA2 DNA Binding Domain hotspot for pathogenic missense variants that is encoded by exons 15 to 26. The assay was based on deep sequence analysis of surviving endogenously targeted haploid cells. A total of 7013 SNVs were characterized as functionally abnormal (n=955), intermediate/uncertain, or functionally normal (n=5224) based on 95% agreement with ClinVar known pathogenic and benign standards. Results were validated relative to batches of nonsense and synonymous variants and variants evaluated using a homology directed repair (HDR) functional assay. Breast cancer case-control association studies showed that pooled SNVs encoding functionally abnormal missense variants were associated with increased risk of breast cancer (odds ratio (OR) 3.89, 95%CI: 2.77-5.51). In addition, 86% of tumors associated with abnormal missense SNVs displayed loss of heterozygosity (LOH), whereas 26% of tumors with normal variants had LOH. The functional data were added to other sources of information in a ClinGen/ACMG/AMP-like model and 700 functionally abnormal SNVs, including 220 missense SNVs, were classified as pathogenic or likely pathogenic, while 4862 functionally normal SNVs, including 3084 missense SNVs, were classified as benign or likely benign. These classified variants can now be used for risk assessment and clinical care of variant carriers and the remaining functional scores can be used directly for clinical classification and interpretation of many additional variants. Summary Germline BRCA2 loss-of function (LOF) variants identified by clinical genetic testing predispose to several types of cancer. However, variants of uncertain significance (VUS) limit the clinical use of testing results. Thus, there is an urgent need for functional characterization and clinical classification of all BRCA2 variants to facilitate current and future clinical management of individuals with these variants. Here we show the results from a saturation genome editing (SGE) and functional analysis of all possible single nucleotide variants (SNVs) from exons 15 to 26 that encode the BRCA2 DNA Binding Domain hotspot for pathogenic missense variants. The assay was based on deep sequence analysis of surviving endogenously targeted human haploid HAP1 cells. The assay was calibrated relative to ClinVar known pathogenic and benign missense standards and 95% prevalence thresholds for functionally abnormal and normal variants were identified. Thresholds were validated based on nonsense and synonymous variants. SNVs encoding functionally abnormal missense variants were associated with increased risks of breast and ovarian cancer. The functional assay results were integrated into a ClinGen/ACMG/AMP-like model for clinical classification of the majority of BRCA2 SNVs as pathogenic/likely pathogenic or benign/likely benign. The classified variants can be used for improved clinical management of variant carriers.
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Hughley RW, Matejcic M, Song Z, Sheng X, Wan P, Xia L, Hart SN, Hu C, Yadav S, Lubmawa A, Kiddu V, Asiimwe F, Amanya C, Mutema G, Job K, Ssebakumba MK, Ingles SA, Hamilton AS, Couch FJ, Watya S, Conti DV, Darst BF, Haiman CA. Polygenic Risk Score Modifies Prostate Cancer Risk of Pathogenic Variants in Men of African Ancestry. CANCER RESEARCH COMMUNICATIONS 2023; 3:2544-2550. [PMID: 38014910 PMCID: PMC10720390 DOI: 10.1158/2767-9764.crc-23-0022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/17/2023] [Accepted: 11/17/2023] [Indexed: 11/29/2023]
Abstract
Prostate cancer risk is influenced by rare and common germline variants. We examined the aggregate association of rare germline pathogenic/likely pathogenic/deleterious (P/LP/D) variants in ATM, BRCA2, PALB2, and NBN with a polygenic risk score (PRS) on prostate cancer risk among 1,796 prostate cancer cases (222 metastatic) and 1,424 controls of African ancestry. Relative to P/LP/D non-carriers at average genetic risk (33%-66% of PRS), men with low (0%-33%) and high (66%-100%) PRS had Odds Ratios (ORs) for overall prostate cancer of 2.08 [95% confidence interval (CI) = 0.58-7.49] and 18.06 (95% CI = 4.24-76.84) among P/LP/D carriers and 0.57 (95% CI = 0.46-0.71) and 3.02 (95% CI = 2.53-3.60) among non-carriers, respectively. The OR for metastatic prostate cancer was 2.73 (95% CI = 0.24-30.54) and 28.99 (95% CI = 4.39-191.43) among P/LP/D carriers and 0.54 (95% CI = 0.31-0.95) and 3.22 (95% CI = 2.20-4.73) among non-carriers, for men with low and high PRS, respectively. Lifetime absolute risks of overall prostate cancer increased with PRS (low to high) from 9.8% to 51.5% in P/LP/D carriers and 5.5% to 23.9% in non-carriers. Lifetime absolute risks of metastatic prostate cancer increased with PRS from 1.9% to 18.1% in P/LP/D carriers and 0.3% to 2.2% in non-carriers These findings suggest that assessment of prostate cancer risk for rare variant carriers should include PRS status. SIGNIFICANCE These findings highlight the importance of considering rare and common variants to comprehensively assess prostate cancer risk in men of African ancestry.
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Affiliation(s)
- Raymond W. Hughley
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Marco Matejcic
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Ziwei Song
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Xin Sheng
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Peggy Wan
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Lucy Xia
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Steven N. Hart
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Chunling Hu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | | | | | | | - Colline Amanya
- Makerere University College of Health Sciences, Kampala, Uganda
| | | | | | | | - Sue A. Ingles
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Ann S. Hamilton
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Fergus J. Couch
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Stephen Watya
- Uro Care, Kampala, Uganda
- Makerere University College of Health Sciences, Kampala, Uganda
| | - David V. Conti
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Burcu F. Darst
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
- Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Christopher A. Haiman
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
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Garcia Moreno AS, Guicciardi ME, Wixom AQ, Jessen E, Yang J, Ilyas SI, Bianchi JK, Pinto E Vairo F, Lazaridis KN, Gores GJ. IL-17 Signaling in Primary Sclerosing Cholangitis Patient-Derived Organoids. RESEARCH SQUARE 2023:rs.3.rs-3406046. [PMID: 37886596 PMCID: PMC10602181 DOI: 10.21203/rs.3.rs-3406046/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
The pathogenesis of primary sclerosing cholangitis (PSC) is unclear, although studies implicate IL-17A as an inflammatory mediator in this disease. However, a direct assessment of IL-17 signaling in PSC cholangiocytes is lacking. In this study we aimed to investigate the response of PSC extrahepatic cholangiocyte organoids (ECO) to IL-17A stimulation. Cholangiocytes obtained from PSC and non-PSC patients by endoscopic retrograde cholangiography (ERC) were cultured as ECO. The ECO were treated with vehicle or IL-17A and assessed by transcriptomics, secretome analysis, and genome sequencing (GS). Unsupervised clustering of all integrated scRNA-seq data identified 8 cholangiocyte clusters which did not differ between PSC and non-PSC ECO. However, PSC ECO cells demonstrated a robust response to IL-17 treatment, noted by an increased number of differentially expressed genes (DEG) by transcriptomics, and more abundant chemokine and cytokine expression and secretion. After rigorous filtering, GS identified candidate somatic variants shared among PSC ECO from unrelated individuals. However, no candidate rare variants in genes regulating the IL-17 pathway were identified, but rare variants regulating the MAPK signaling pathway were present in all PSC ECO. In conclusion, PSC and non-PSC patient derived ECO respond differently to IL-17 stimulation implicating this pathway in the pathogenesis of PSC.
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6
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Kotsopoulos J, Hathaway CA, Narod SA, Teras LR, Patel AV, Hu C, Yadav S, Couch FJ, Tworoger SS. Germline Mutations in 12 Genes and Risk of Ovarian Cancer in Three Population-Based Cohorts. Cancer Epidemiol Biomarkers Prev 2023; 32:1402-1410. [PMID: 37493628 PMCID: PMC10592229 DOI: 10.1158/1055-9965.epi-23-0041] [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: 05/12/2023] [Revised: 06/23/2023] [Accepted: 07/24/2023] [Indexed: 07/27/2023] Open
Abstract
BACKGROUND With the widespread use of multigene panel genetic testing, population-based studies are necessary to accurately assess penetrance in unselected individuals. We evaluated the prevalence of germline pathogenic or likely pathogenic variants (mutations) in 12 cancer-predisposition genes and associations with ovarian cancer risk in three population-based prospective studies [Nurses' Health Study (NHS), NHSII, Cancer Prevention Study II]. METHODS We included women with epithelial ovarian or peritoneal cancer (n = 776) and controls who were alive and had at least one intact ovary at the time of the matched case diagnosis (n = 1,509). Germline DNA was sequenced for mutations in 12 genes. Conditional logistic regression was used to estimate odds ratios (OR) and 95% confidence intervals (CI) for ovarian cancer risk by mutation status. RESULTS The mutation frequency across all 12 genes was 11.2% in cases and 3.3% in controls (P < 0.0001). BRCA1 and BRCA2 were the most frequently mutated (3.5% and 3.8% of cases and 0.3% and 0.5% of controls, respectively) and were associated with increased ovarian cancer risk [OR, BRCA1 = 12.38; 95% confidence interval (CI) = 4.72-32.45; OR, BRCA2 = 9.18; 95% CI = 3.98-21.15]. Mutation frequencies for the other genes were ≤1.0% and only PALB2 was significantly associated with risk (OR = 5.79; 95% CI = 1.09-30.83). There was no difference in survival for women with a BRCA germline mutation versus no mutation. CONCLUSIONS Further research is needed to better understand the role of other mutations in ovarian cancer among unselected populations. IMPACT Our data support guidelines for germline genetic testing for BRCA1 and BRCA2 among women diagnosed with epithelial ovarian cancer; testing for PALB2 may be warranted.
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Affiliation(s)
- Joanne Kotsopoulos
- Women’s College Research Institute, Women’s College Hospital, 76 Grenville St, 6 Floor, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, 155 College Street Health Science Building, 6 Floor, Toronto, ON, Canada
| | | | - Steven A. Narod
- Women’s College Research Institute, Women’s College Hospital, 76 Grenville St, 6 Floor, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, 155 College Street Health Science Building, 6 Floor, Toronto, ON, Canada
| | - Lauren R. Teras
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Alpa V. Patel
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Chunling Hu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Fergus J. Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
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7
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Ravindran A, Dasari S, Ruan GJ, Artymiuk CJ, He R, Viswanatha DS, Abeykoon JP, Zanwar S, Young JR, Goyal G, Go RS, Rech KL. Malignant Histiocytosis Comprises a Phenotypic Spectrum That Parallels the Lineage Differentiation of Monocytes, Macrophages, Dendritic Cells, and Langerhans Cells. Mod Pathol 2023; 36:100268. [PMID: 37406859 DOI: 10.1016/j.modpat.2023.100268] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 06/22/2023] [Accepted: 06/27/2023] [Indexed: 07/07/2023]
Abstract
Malignant histiocytoses (MHs), or the 'M group' of the Histiocyte Society classification, are characterized by neoplastic histiocytes with large pleomorphic nuclei. MH encompasses the diagnoses of histiocytic sarcoma, interdigitating dendritic cell sarcoma, and Langerhans cell sarcoma. We aimed to define the phenotypic spectrum of MH and examine the genotypic features across this spectrum. Using immunohistochemistry, we arranged the 22 cases into 4 subtypes that correspond to the lines of differentiation from monocytic and dendritic cell precursors as follows: (1) macrophage (n = 5): CD68+, CD163+, CD14+, and Factor 13a+; (2) monocyte-macrophage (n = 5): CD68+, CD163+, CD14+, S100+, and OCT2+; (3) dendritic cell (n = 6): CD68+, CD11c+, S100+, lysozyme+, ZBTB46+, and CD1a/langerin < 5%; and (4) Langerhans cell (n = 6): CD68+, CD11c+, S100+, ZBTB46+, CD1a+, and langerin+. The phenotypic subtypes align with those seen in low-grade histiocytic neoplasms as follows: MH-macrophage type correlates with Erdheim-Chester disease phenotype; MH-monocyte-macrophage type with Rosai-Dorfman disease phenotype, and MH-Langerhans cell type with Langerhans cell histiocytosis. Activating mutations in MAPK-pathway genes were identified in 80% of MH cases; 29% had mutations in the PI3k-AKT-mTOR pathway and 59% had mutations in epigenetic modulating genes. Strong expression of cyclin D1 was present in all cases, whereas p-ERK and p-AKT were not uniformly expressed. Eight of 22 (36%) MH cases were proven to be clonally related to a prior B-cell lymphoma. Defining the phenotypic spectrum of MH provides a guide to diagnosis and allows further exploration into the potential biological and clinical significance.
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Affiliation(s)
- Aishwarya Ravindran
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota; Division of Laboratory Medicine-Hematopathology, Department of Pathology, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Surendra Dasari
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Gordon J Ruan
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Cody J Artymiuk
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Rong He
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - David S Viswanatha
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Jithma P Abeykoon
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Saurabh Zanwar
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Jason R Young
- Department of Radiology, Mayo Clinic, Jacksonville, Florida
| | - Gaurav Goyal
- Division of Hematology-Medical Oncology, The University of Alabama at Birmingham, Birmingham, Alabama; Research Collaborator (limited tenure), Mayo Clinic, Rochester, Minnesota
| | - Ronald S Go
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Karen L Rech
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.
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8
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Fares MB, Alijevic O, Johne S, Overk C, Hashimoto M, Kondylis A, Adame A, Dulize R, Peric D, Nury C, Battey J, Guedj E, Sierro N, Mc Hugh D, Rockenstein E, Kim C, Rissman RA, Hoeng J, Peitsch MC, Masliah E, Mathis C. Nicotine-mediated effects in neuronal and mouse models of synucleinopathy. Front Neurosci 2023; 17:1239009. [PMID: 37719154 PMCID: PMC10501483 DOI: 10.3389/fnins.2023.1239009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/08/2023] [Indexed: 09/19/2023] Open
Abstract
Introduction Alpha-synuclein (α-Syn) aggregation, transmission, and contribution to neurotoxicity represent central mechanisms underlying Parkinson's disease. The plant alkaloid "nicotine" was reported to attenuate α-Syn aggregation in different models, but its precise mode of action remains unclear. Methods In this study, we investigated the effect of 2-week chronic nicotine treatment on α-Syn aggregation, neuroinflammation, neurodegeneration, and motor deficits in D-line α-Syn transgenic mice. We also established a novel humanized neuronal model of α-Syn aggregation and toxicity based on treatment of dopaminergic neurons derived from human induced pluripotent stem cells (iPSC) with α-Syn preformed fibrils (PFF) and applied this model to investigate the effects of nicotine and other compounds and their modes of action. Results and discussion Overall, our results showed that nicotine attenuated α-Syn-provoked neuropathology in both models. Moreover, when investigating the role of nicotinic acetylcholine receptor (nAChR) signaling in nicotine's neuroprotective effects in iPSC-derived dopaminergic neurons, we observed that while α4-specific antagonists reduced the nicotine-induced calcium response, α4 agonists (e.g., AZD1446 and anatabine) mediated similar neuroprotective responses against α-Syn PFF-provoked neurodegeneration. Our results show that nicotine attenuates α-Syn-provoked neuropathology in vivo and in a humanized neuronal model of synucleinopathy and that activation of α4β2 nicotinic receptors might mediate these neuroprotective effects.
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Affiliation(s)
| | - Omar Alijevic
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Stephanie Johne
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Cassia Overk
- Department of Neurosciences, University of California, San Diego, San Diego, CA, United States
| | - Makoto Hashimoto
- Department of Neurosciences, University of California, San Diego, San Diego, CA, United States
| | | | - Anthony Adame
- Department of Neurosciences, University of California, San Diego, San Diego, CA, United States
| | - Remi Dulize
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Dariusz Peric
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Catherine Nury
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - James Battey
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Emmanuel Guedj
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Nicolas Sierro
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Damian Mc Hugh
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Edward Rockenstein
- Department of Neurosciences, University of California, San Diego, San Diego, CA, United States
| | - Changyoun Kim
- Department of Neurosciences, University of California, San Diego, San Diego, CA, United States
| | - Robert A. Rissman
- Department of Neurosciences, University of California, San Diego, San Diego, CA, United States
| | - Julia Hoeng
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | | | - Eliezer Masliah
- Department of Neurosciences, University of California, San Diego, San Diego, CA, United States
| | - Carole Mathis
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
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9
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Xiang Y, Luettich K, Martin F, Battey JND, Trivedi K, Neau L, Wong ET, Guedj E, Dulize R, Peric D, Bornand D, Ouadi S, Sierro N, Büttner A, Ivanov NV, Vanscheeuwijck P, Hoeng J, Peitsch MC. Discriminating Spontaneous From Cigarette Smoke and THS 2.2 Aerosol Exposure-Related Proliferative Lung Lesions in A/J Mice by Using Gene Expression and Mutation Spectrum Data. FRONTIERS IN TOXICOLOGY 2022; 3:634035. [PMID: 35295134 PMCID: PMC8915865 DOI: 10.3389/ftox.2021.634035] [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: 11/26/2020] [Accepted: 02/19/2021] [Indexed: 11/25/2022] Open
Abstract
Mice, especially A/J mice, have been widely employed to elucidate the underlying mechanisms of lung tumor formation and progression and to derive human-relevant modes of action. Cigarette smoke (CS) exposure induces tumors in the lungs; but, non-exposed A/J mice will also develop lung tumors spontaneously with age, which raises the question of discriminating CS-related lung tumors from spontaneous ones. However, the challenge is that spontaneous tumors are histologically indistinguishable from the tumors occurring in CS-exposed mice. We conducted an 18-month inhalation study in A/J mice to assess the impact of lifetime exposure to Tobacco Heating System (THS) 2.2 aerosol relative to exposure to 3R4F cigarette smoke (CS) on toxicity and carcinogenicity endpoints. To tackle the above challenge, a 13-gene gene signature was developed based on an independent A/J mouse CS exposure study, following by a one-class classifier development based on the current study. Identifying gene signature in one data set and building classifier in another data set addresses the feature/gene selection bias which is a well-known problem in literature. Applied to data from this study, this gene signature classifier distinguished tumors in CS-exposed animals from spontaneous tumors. Lung tumors from THS 2.2 aerosol-exposed mice were significantly different from those of CS-exposed mice but not from spontaneous tumors. The signature was also applied to human lung adenocarcinoma gene expression data (from The Cancer Genome Atlas) and discriminated cancers in never-smokers from those in ever-smokers, suggesting translatability of our signature genes from mice to humans. A possible application of this gene signature is to discriminate lung cancer patients who may benefit from specific treatments (i.e., EGFR tyrosine kinase inhibitors). Mutational spectra from a subset of samples were also utilized for tumor classification, yielding similar results. “Landscaping” the molecular features of A/J mouse lung tumors highlighted, for the first time, a number of events that are also known to play a role in human lung tumorigenesis, such as Lrp1b mutation and Ros1 overexpression. This study shows that omics and computational tools provide useful means of tumor classification where histopathological evaluation alone may be unsatisfactory to distinguish between age- and exposure-related lung tumors.
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Affiliation(s)
- Yang Xiang
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Karsta Luettich
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Florian Martin
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - James N D Battey
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Keyur Trivedi
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Laurent Neau
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Ee Tsin Wong
- Philip Morris International R&D, Philip Morris International Research Laboratories Pte. Ltd., Singapore, Singapore
| | - Emmanuel Guedj
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Remi Dulize
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Dariusz Peric
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - David Bornand
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Sonia Ouadi
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Nicolas Sierro
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | | | - Nikolai V Ivanov
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | | | - Julia Hoeng
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Manuel C Peitsch
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
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10
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Lopes GS, Lopes JL, Bielinski SJ, Armasu SM, Zhu Y, Cavanaugh DC, Moyer AM, Jacobson DJ, Wang L, Jiang R, St. Sauver JL, Larson NB. Identification of sex-specific genetic associations in response to opioid analgesics in a White, non-Hispanic cohort from Southeast Minnesota. THE PHARMACOGENOMICS JOURNAL 2022; 22:117-123. [PMID: 35102242 PMCID: PMC8975736 DOI: 10.1038/s41397-022-00265-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 01/10/2022] [Indexed: 11/27/2022]
Abstract
The study of sex-specific genetic associations with opioid response may improve the understanding of inter-individual variability in pain treatments. We investigated sex-specific associations between genetic variation and opioid response. We identified participants in the RIGHT Study prescribed codeine, tramadol, hydrocodone, and oxycodone between 01/01/2005 and 12/31/2017. Prescriptions were collapsed into codeine/tramadol and hydrocodone/oxycodone. Outcomes included poor pain control and adverse reactions within six weeks after prescription date. We performed gene-level and single-variant association analyses stratified by sex. We included 7169 non-Hispanic white participants and a total of 1940 common and low-frequency variants (MAF > 0.01). Common variants in MACROD2 (rs76026520), CYP1B1 (rs1056837, rs1056836), and CYP2D6 (rs35742686) were associated with outcomes. At the gene level, FAAH, SCN1A, and TYMS had associations for men and women, and NAT2, CYP3A4, CYP1A2, and SLC22A2 had associations for men only. Our findings highlight the importance of considering sex in association studies on opioid response.
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11
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Liu Y, Raimondo M, Wallace MB, Mody K, Stauffer JA, Zhang L, Ji B, Bi Y. Exome Sequencing of Pancreatic Acinar Carcinoma Identified Distinctive Mutation Patterns. Pancreas 2021; 50:1007-1013. [PMID: 34629449 PMCID: PMC8516064 DOI: 10.1097/mpa.0000000000001870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVES Pancreatic acinar cell carcinoma (ACC) is a rare pancreatic cancer. The advancement of treatment is hampered because of the limited knowledge of its molecular mechanism. METHODS Whole-exome sequencing was performed on DNA extracted from 11 pure ACC surgical samples. Potential germline variants were removed on the basis of polymorphic databases, alternative allele frequency, coverage depth, and Catalogue of Somatic Mutations in Cancer (COSMIC) annotations after variant calling procedure. Mutation profiles and signatures were assessed through the Mutational Patterns package. RESULTS A median of 34 somatic mutations were detected (range, 19-60). Three novel recurrent small deletions were identified. Common pancreatic ductal adenocarcinoma mutations or neuroendocrine tumor mutants were not found. FAT atypical cadherin 4, mucin 5B, titin, and zinc finger homeobox 3 were consistently mutated across 4 independent ACC studies. A high contribution of COSMIC mutational signature 1 was seen in ACC, indicating deamination of 5-methylcytosine. The majority of the patients had COSMIC signatures 6, 15, or 20, relating to defective DNA mismatch repair. Six patients showed COSMIC mutational signature 10 because of the altered activity of DNA polymerase epsilon. CONCLUSIONS Distinct mutational signatures pathways were found in ACC and targeting them may improve clinical outcome.
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Affiliation(s)
- Yuanhang Liu
- From the Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN
| | | | | | - Kabir Mody
- Division of Hematology and Medical Oncology
| | | | - Lizhi Zhang
- Department of Pathology, Mayo Clinic, Rochester, MN
| | - Baoan Ji
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL
| | - Yan Bi
- Division of Gastroenterology and Hepatology
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12
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Winham SJ, Wang C, Heinzen EP, Bhagwate A, Liu Y, McDonough SJ, Stallings-Mann ML, Frost MH, Vierkant RA, Denison LA, Carter JM, Sherman ME, Radisky DC, Degnim AC, Cunningham JM. Somatic mutations in benign breast disease tissues and association with breast cancer risk. BMC Med Genomics 2021; 14:185. [PMID: 34261476 PMCID: PMC8278587 DOI: 10.1186/s12920-021-01032-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 07/06/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Benign breast disease (BBD) is a risk factor for breast cancer (BC); however, little is known about the genetic alterations present at the time of BBD diagnosis and how these relate to risk of incident BC. METHODS A subset of a long-term BBD cohort was selected to examine DNA variation across three BBD groups (42 future estrogen receptor-positive (ER+) BC, 36 future estrogen receptor-negative (ER-) BC, and 42 controls cancer-free for at least 16 years post-BBD). DNA extracted from archival formalin fixed, paraffin-embedded (FFPE) tissue blocks was analyzed for presence of DNA alterations using a targeted panel of 93 BC-associated genes. To address artifacts frequently observed in FFPE tissues (e.g., C>T changes), we applied three filtering strategies based on alternative allele frequencies and nucleotide substitution context. Gene-level associations were performed using two types of burden tests and adjusted for clinical and technical covariates. RESULTS After filtering, the variant frequency of SNPs in our sample was highly consistent with population allele frequencies reported in 1 KG/ExAC (0.986, p < 1e-16). The top ten genes found to be nominally associated with later cancer status by four of 12 association methods(p < 0.05) were MED12, MSH2, BRIP1, PMS1, GATA3, MUC16, FAM175A, EXT2, MLH1 and TGFB1, although these were not statistically significant in permutation testing. However, all 10 gene-level associations had OR < 1 with lower mutation burden in controls compared to cases, which was marginally statistically significant in permutation testing (p = 0.04). Comparing between the three case groups, BBD ER+ cases were closer to controls in mutation profile, while BBD ER- cases were distinct. Notably, the variant burden was significantly higher in controls than in either ER+ or ER- cases. CD45 expression was associated with mutational burden (p < 0.001). CONCLUSIONS Somatic mutations were more frequent in benign breast tissue from women who did not develop cancer, opening questions of clonal diversity or immune-mediated restraint on future cancer development. CD45 expression was positively associated with mutational burden, most strongly in controls. Further studies in both normal and premalignant tissues are needed to better understand the role of somatic gene mutations and their contribution to future cancer development.
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Affiliation(s)
- Stacey J Winham
- Biomedical Statistics and Informatics, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
| | - Chen Wang
- Biomedical Statistics and Informatics, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Ethan P Heinzen
- Biomedical Statistics and Informatics, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Aditya Bhagwate
- Biomedical Statistics and Informatics, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Yuanhang Liu
- Biomedical Statistics and Informatics, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Samantha J McDonough
- Medical Genome Facility, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | | | - Marlene H Frost
- Women's Cancer Program, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Robert A Vierkant
- Biomedical Statistics and Informatics, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Lori A Denison
- Information Technology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Jodi M Carter
- Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Mark E Sherman
- Epidemiology and Laboratory Medicine and Pathology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, 32224, USA
| | - Derek C Radisky
- Cancer Biology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, 32224, USA
| | - Amy C Degnim
- Breast, Endocrine, Metabolic and GI Surgery, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Julie M Cunningham
- Experimental Pathology and Laboratory Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
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13
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DeVoe E, Oliver GR, Zenka R, Blackburn PR, Cousin MA, Boczek NJ, Kocher JPA, Urrutia R, Klee EW, Zimmermann MT. P 2T 2: Protein Panoramic annoTation Tool for the interpretation of protein coding genetic variants. JAMIA Open 2021; 4:ooab065. [PMID: 34377961 PMCID: PMC8346652 DOI: 10.1093/jamiaopen/ooab065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/06/2021] [Accepted: 07/17/2021] [Indexed: 11/29/2022] Open
Abstract
MOTIVATION Genomic data are prevalent, leading to frequent encounters with uninterpreted variants or mutations with unknown mechanisms of effect. Researchers must manually aggregate data from multiple sources and across related proteins, mentally translating effects between the genome and proteome, to attempt to understand mechanisms. MATERIALS AND METHODS P2T2 presents diverse data and annotation types in a unified protein-centric view, facilitating the interpretation of coding variants and hypothesis generation. Information from primary sequence, domain, motif, and structural levels are presented and also organized into the first Paralog Annotation Analysis across the human proteome. RESULTS Our tool assists research efforts to interpret genomic variation by aggregating diverse, relevant, and proteome-wide information into a unified interactive web-based interface. Additionally, we provide a REST API enabling automated data queries, or repurposing data for other studies. CONCLUSION The unified protein-centric interface presented in P2T2 will help researchers interpret novel variants identified through next-generation sequencing. Code and server link available at github.com/GenomicInterpretation/p2t2.
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Affiliation(s)
- Elias DeVoe
- Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - Gavin R Oliver
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Roman Zenka
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
| | - Patrick R Blackburn
- Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
- Center for Individualized Medicine, Mayo Clinic, Jacksonville, Florida, USA
| | - Margot A Cousin
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Nicole J Boczek
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Jean-Pierre A Kocher
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Raul Urrutia
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
- Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, 53226, USA
| | - Eric W Klee
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Michael T Zimmermann
- Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
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14
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Chen I, Chen MY, Goedegebuure SP, Gillanders WE. Challenges targeting cancer neoantigens in 2021: a systematic literature review. Expert Rev Vaccines 2021; 20:827-837. [PMID: 34047245 DOI: 10.1080/14760584.2021.1935248] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Cancer neoantigens represent important targets of cancer immunotherapy. The goal of cancer neoantigen vaccines is to induce neoantigen-specific immune responses and antitumor immunity while minimizing the potential for autoimmune toxicity. Advances in sequencing technologies, neoantigen prediction algorithms, and other technologies have dramatically improved the ability to identify and prioritize cancer neoantigens. Unfortunately, results from preclinical studies and early phase clinical trials highlight important challenges to the successful clinical translation of neoantigen cancer vaccines.Areas covered: In this review, we provide an overview of current strategies for the identification and prioritization of cancer neoantigens with a particular emphasis on the two most common strategies used for neoantigen identification: (1) direct identification of peptide ligands eluted from peptide-MHC complexes, and (2) next-generation sequencing combined with neoantigen prediction algorithms. We highlight the limitations of current neoantigen prediction pipelines, and discuss broader challenges associated with cancer neoantigen vaccines including tumor purity/heterogeneity and the immunosuppressive tumor microenvironment.Expert opinion: Despite current limitations, neoantigen prediction is likely to improve rapidly based on advances in sequencing, machine learning, and information sharing. The successful development of robust cancer neoantigen prediction strategies is likely to have a significant impact, with the potential to facilitate cancer neoantigen vaccine design.
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Affiliation(s)
- Ina Chen
- Department of Surgery, Washington University and Siteman Cancer Center in St. Louis, St Louis, Missouri, USA
| | - Michael Y Chen
- Department of Surgery, Washington University and Siteman Cancer Center in St. Louis, St Louis, Missouri, USA
| | - S Peter Goedegebuure
- Department of Surgery, Washington University and Siteman Cancer Center in St. Louis, St Louis, Missouri, USA.,The Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine, St Louis, MO, USA
| | - William E Gillanders
- Department of Surgery, Washington University and Siteman Cancer Center in St. Louis, St Louis, Missouri, USA.,The Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine, St Louis, MO, USA
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15
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Topka S, Steinsnyder Z, Ravichandran V, Tkachuk K, Kemel Y, Bandlamudi C, Winkel Madsen M, Furberg H, Ouerfelli O, Rudin CM, Iyer G, Lipkin SM, Mukherjee S, Solit DB, Berger MF, Bajorin DF, Rosenberg JE, Taylor BS, de Stanchina E, Vijai J, Offit K. Targeting Germline- and Tumor-Associated Nucleotide Excision Repair Defects in Cancer. Clin Cancer Res 2021; 27:1997-2010. [PMID: 33199492 DOI: 10.1158/1078-0432.ccr-20-3322] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/19/2020] [Accepted: 11/12/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Nucleotide excision repair (NER) gene alterations constitute potential cancer therapeutic targets. We explored the prevalence of NER gene alterations across cancers and putative therapeutic strategies targeting these vulnerabilities. EXPERIMENTAL DESIGN We interrogated our institutional dataset with mutational data from more than 40,000 patients with cancer to assess the frequency of putative deleterious alterations in four key NER genes. Gene-edited isogenic pairs of wild-type and mutant ERCC2 or ERCC3 cell lines were created and used to assess response to several candidate drugs. RESULTS We found that putative damaging germline and somatic alterations in NER genes were present with frequencies up to 10% across multiple cancer types. Both in vitro and in vivo studies showed significantly enhanced sensitivity to the sesquiterpene irofulven in cells harboring specific clinically observed heterozygous mutations in ERCC2 or ERCC3. Sensitivity of NER mutants to irofulven was greater than to a current standard-of-care agent, cisplatin. Hypomorphic ERCC2/3-mutant cells had impaired ability to repair irofulven-induced DNA damage. Transcriptomic profiling of tumor tissues suggested codependencies between DNA repair pathways, indicating a potential benefit of combination therapies, which were confirmed by in vitro studies. CONCLUSIONS These findings provide novel insights into a synthetic lethal relationship between clinically observed NER gene deficiencies and sensitivity to irofulven and its potential synergistic combination with other drugs.See related commentary by Jiang and Greenberg, p. 1833.
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Affiliation(s)
- Sabine Topka
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York. .,Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Zoe Steinsnyder
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Vignesh Ravichandran
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kaitlyn Tkachuk
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering, New York, New York
| | - Yelena Kemel
- Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Chaitanya Bandlamudi
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Helena Furberg
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ouathek Ouerfelli
- Chemical Synthesis Core, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Charles M Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gopa Iyer
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Steven M Lipkin
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Semanti Mukherjee
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David B Solit
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.,Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dean F Bajorin
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Jonathan E Rosenberg
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Barry S Taylor
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elisa de Stanchina
- Antitumor Assessment Core Facility, Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Joseph Vijai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York. .,Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York.,Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York. .,Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York.,Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
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16
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Inflation of tumor mutation burden by tumor-only sequencing in under-represented groups. NPJ Precis Oncol 2021; 5:22. [PMID: 33742076 PMCID: PMC7979755 DOI: 10.1038/s41698-021-00164-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 02/18/2021] [Indexed: 12/15/2022] Open
Abstract
With the recent FDA approval of tumor mutational burden-high (TMB-H) status as a biomarker for treatment with a PD-1 inhibitor regardless of tumor type, accurate assessment of patient-specific TMB is more critical now more than ever. Using paired tumor and germline exome sequencing data from 701 patients newly diagnosed with multiple myeloma, including 575 self-reported White patients and 126 self-reported Black patients, we observed that compared to the gold standard of filtering germline variants with patient-paired germline sequencing data, TMB estimates were significantly higher in both Black and White patients when using public databases for filtering non-somatic mutations; however, TMB was more significantly inflated in Black patients compared to White patients. TMB as a biomarker for patient selection to receive immune checkpoint inhibitors (ICIs) therapy without patient-paired germline sequencing may introduce racial bias due to the under-representation of minority groups in public databases.
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17
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Variant Calling in Next Generation Sequencing Data. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11285-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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18
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Yadav S, Kasi PM, Bamlet WR, Ho TP, Polley EC, Hu C, Hart SN, Rabe KG, Boddicker NJ, Gnanaolivu RD, Lee KY, Lindstrom TH, Petersen GM, Couch FJ, McWilliams RR. Effect of Germline Mutations in Homologous Recombination Repair Genes on Overall Survival of Patients with Pancreatic Adenocarcinoma. Clin Cancer Res 2020; 26:6505-6512. [PMID: 33028596 PMCID: PMC9063708 DOI: 10.1158/1078-0432.ccr-20-1788] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/20/2020] [Accepted: 09/28/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE To compare the clinical characteristics and overall survival (OS) of germline mutation carriers in homologous recombination repair (HRR) genes and noncarriers with pancreatic ductal adenocarcinoma (PDAC). EXPERIMENTAL DESIGN Germline DNA from 3,078 patients with PDAC enrolled in a prospective registry at Mayo Clinic between 2000 and 2017 was analyzed for mutations in 37 cancer predisposition genes. Characteristics and OS of patients with mutations in eight genes (ATM, BARD1, BRCA1, BRCA2, BRIP1, PALB2, RAD51C, and RAD51D) involved in HRR were compared with patients testing negative for mutations in all 37 genes. RESULTS The 175 HRR mutation carriers and 2,730 noncarriers in the study had a median duration of follow-up of 9.9 years. HRR mutation carriers were younger (median age at diagnosis: 63 vs. 66 years, P < 0.001) and more likely to have metastatic disease at diagnosis (46% vs. 36%, P = 0.004). In a multivariable model adjusting for sex, age at diagnosis, and tumor staging, patients with germline HRR mutations had a significantly longer OS compared with noncarriers [HR, 0.83; 95% confidence interval (CI), 0.70-0.97; P = 0.02]. Further gene-level analysis demonstrated that germline ATM mutation carriers had longer OS compared with patients without germline mutations in any of the 37 genes (HR, 0.72; 95% CI, 0.55-0.94; P = 0.01). CONCLUSIONS This study demonstrates that germline mutation carrier status in PDAC is associated with longer OS compared with noncarriers. Further research into tumor biology and response to platinum-based chemotherapy in germline mutation carriers with PDAC are needed to better understand the association with longer OS.
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Affiliation(s)
| | - Pashtoon M Kasi
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa
| | - William R Bamlet
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Thanh P Ho
- Department of Oncology, Mayo Clinic, Rochester, Minnesota
| | - Eric C Polley
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Chunling Hu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Steven N Hart
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Kari G Rabe
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | | | - Rohan D Gnanaolivu
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Kun Y Lee
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Tricia H Lindstrom
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Gloria M Petersen
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
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19
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Palmer JR, Polley EC, Hu C, John EM, Haiman C, Hart SN, Gaudet M, Pal T, Anton-Culver H, Trentham-Dietz A, Bernstein L, Ambrosone CB, Bandera EV, Bertrand KA, Bethea TN, Gao C, Gnanaolivu RD, Huang H, Lee KY, LeMarchand L, Na J, Sandler DP, Shah PD, Yadav S, Yang W, Weitzel JN, Domchek SM, Goldgar DE, Nathanson KL, Kraft P, Yao S, Couch FJ. Contribution of Germline Predisposition Gene Mutations to Breast Cancer Risk in African American Women. J Natl Cancer Inst 2020; 112:1213-1221. [PMID: 32427313 PMCID: PMC7735769 DOI: 10.1093/jnci/djaa040] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 01/27/2020] [Accepted: 03/23/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The risks of breast cancer in African American (AA) women associated with inherited mutations in breast cancer predisposition genes are not well defined. Thus, whether multigene germline hereditary cancer testing panels are applicable to this population is unknown. We assessed associations between mutations in panel-based genes and breast cancer risk in 5054 AA women with breast cancer and 4993 unaffected AA women drawn from 10 epidemiologic studies. METHODS Germline DNA samples were sequenced for mutations in 23 cancer predisposition genes using a QIAseq multiplex amplicon panel. Prevalence of mutations and odds ratios (ORs) for associations with breast cancer risk were estimated with adjustment for study design, age, and family history of breast cancer. RESULTS Pathogenic mutations were identified in 10.3% of women with estrogen receptor (ER)-negative breast cancer, 5.2% of women with ER-positive breast cancer, and 2.3% of unaffected women. Mutations in BRCA1, BRCA2, and PALB2 were associated with high risks of breast cancer (OR = 47.55, 95% confidence interval [CI] = 10.43 to >100; OR = 7.25, 95% CI = 4.07 to 14.12; OR = 8.54, 95% CI = 3.67 to 24.95, respectively). RAD51D mutations were associated with high risk of ER-negative disease (OR = 7.82, 95% CI = 1.61 to 57.42). Moderate risks were observed for CHEK2, ATM, ERCC3, and FANCC mutations with ER-positive cancer, and RECQL mutations with all breast cancer. CONCLUSIONS The study identifies genes that predispose to breast cancer in the AA population, demonstrates the validity of current breast cancer testing panels for use in AA women, and provides a basis for increased referral of AA patients for cancer genetic testing.
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Affiliation(s)
- Julie R Palmer
- Department of Medicine, Boston University School of Medicine, and Slone Epidemiology Center, Boston, MA 02118, USA
| | - Eric C Polley
- Departments of Health Sciences Research, Laboratory Medicine and Pathology, and Oncology, Mayo Clinic, Rochester, MN 55902, USA
| | - Chunling Hu
- Departments of Health Sciences Research, Laboratory Medicine and Pathology, and Oncology, Mayo Clinic, Rochester, MN 55902, USA
| | - Esther M John
- Department of Health Research & Policy, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Christopher Haiman
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Steven N Hart
- Departments of Health Sciences Research, Laboratory Medicine and Pathology, and Oncology, Mayo Clinic, Rochester, MN 55902, USA
| | - Mia Gaudet
- Epidemiology Research, American Cancer Society, Atlanta, GA 30303, USA
| | - Tuya Pal
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | - Amy Trentham-Dietz
- Department of Population Health Sciences and Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Leslie Bernstein
- Department of Population Sciences, City of Hope, Duarte, CA 91010, USA
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14203, USA
| | - Elisa V Bandera
- Cancer Epidemiology and Health Outcomes, Rutgers Cancer Institute of New, New Brunswick, NJ 08903, USA
| | - Kimberly A Bertrand
- Department of Medicine, Boston University School of Medicine, and Slone Epidemiology Center, Boston, MA 02118, USA
| | - Traci N Bethea
- Department of Medicine, Boston University School of Medicine, and Slone Epidemiology Center, Boston, MA 02118, USA
| | - Chi Gao
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Rohan D Gnanaolivu
- Departments of Health Sciences Research, Laboratory Medicine and Pathology, and Oncology, Mayo Clinic, Rochester, MN 55902, USA
| | - Hongyan Huang
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Kun Y Lee
- Departments of Health Sciences Research, Laboratory Medicine and Pathology, and Oncology, Mayo Clinic, Rochester, MN 55902, USA
| | - Loic LeMarchand
- Population Sciences in the Pacific Program (Cancer Epidemiology), University of Hawaii Cancer Center Honolulu, HI 96813, USA
| | - Jie Na
- Departments of Health Sciences Research, Laboratory Medicine and Pathology, and Oncology, Mayo Clinic, Rochester, MN 55902, USA
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Payal D Shah
- Abramson Cancer Center and Basser Center for BRCA, University of Pennsylvania, Philadelphia, PA 19104, USA; and 16Department of Dermatology, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Siddhartha Yadav
- Departments of Health Sciences Research, Laboratory Medicine and Pathology, and Oncology, Mayo Clinic, Rochester, MN 55902, USA
| | - William Yang
- Departments of Health Sciences Research, Laboratory Medicine and Pathology, and Oncology, Mayo Clinic, Rochester, MN 55902, USA
| | - Jeffrey N Weitzel
- Department of Population Sciences, City of Hope, Duarte, CA 91010, USA
| | - Susan M Domchek
- Abramson Cancer Center and Basser Center for BRCA, University of Pennsylvania, Philadelphia, PA 19104, USA; and 16Department of Dermatology, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - David E Goldgar
- Department of Medicine, Boston University School of Medicine, and Slone Epidemiology Center, Boston, MA 02118, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Katherine L Nathanson
- Abramson Cancer Center and Basser Center for BRCA, University of Pennsylvania, Philadelphia, PA 19104, USA; and 16Department of Dermatology, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Peter Kraft
- Departments of Health Sciences Research, Laboratory Medicine and Pathology, and Oncology, Mayo Clinic, Rochester, MN 55902, USA
| | - Song Yao
- Departments of Health Sciences Research, Laboratory Medicine and Pathology, and Oncology, Mayo Clinic, Rochester, MN 55902, USA
| | - Fergus J Couch
- Departments of Health Sciences Research, Laboratory Medicine and Pathology, and Oncology, Mayo Clinic, Rochester, MN 55902, USA
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20
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Theis JL, Vogler G, Missinato MA, Li X, Nielsen T, Zeng XXI, Martinez-Fernandez A, Walls SM, Kervadec A, Kezos JN, Birker K, Evans JM, O'Byrne MM, Fogarty ZC, Terzic A, Grossfeld P, Ocorr K, Nelson TJ, Olson TM, Colas AR, Bodmer R. Patient-specific genomics and cross-species functional analysis implicate LRP2 in hypoplastic left heart syndrome. eLife 2020; 9:e59554. [PMID: 33006316 PMCID: PMC7581429 DOI: 10.7554/elife.59554] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 09/29/2020] [Indexed: 12/12/2022] Open
Abstract
Congenital heart diseases (CHDs), including hypoplastic left heart syndrome (HLHS), are genetically complex and poorly understood. Here, a multidisciplinary platform was established to functionally evaluate novel CHD gene candidates, based on whole-genome and iPSC RNA sequencing of a HLHS family-trio. Filtering for rare variants and altered expression in proband iPSCs prioritized 10 candidates. siRNA/RNAi-mediated knockdown in healthy human iPSC-derived cardiomyocytes (hiPSC-CM) and in developing Drosophila and zebrafish hearts revealed that LDL receptor-related protein LRP2 is required for cardiomyocyte proliferation and differentiation. Consistent with hypoplastic heart defects, compared to patents the proband's iPSC-CMs exhibited reduced proliferation. Interestingly, rare, predicted-damaging LRP2 variants were enriched in a HLHS cohort; however, understanding their contribution to HLHS requires further investigation. Collectively, we have established a multi-species high-throughput platform to rapidly evaluate candidate genes and their interactions during heart development, which are crucial first steps toward deciphering oligogenic underpinnings of CHDs, including hypoplastic left hearts.
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Affiliation(s)
- Jeanne L Theis
- Cardiovascular Genetics Research LaboratoryRochesterUnited States
| | - Georg Vogler
- Development, Aging and Regeneration, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
| | - Maria A Missinato
- Development, Aging and Regeneration, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
| | - Xing Li
- Division of Biomedical Statistics and Informatics, Mayo ClinicRochesterUnited States
| | - Tanja Nielsen
- Development, Aging and Regeneration, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
- Doctoral Degrees and Habilitations, Department of Biology, Chemistry, and Pharmacy, Freie Universität BerlinBerlinGermany
| | - Xin-Xin I Zeng
- Development, Aging and Regeneration, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
| | | | - Stanley M Walls
- Development, Aging and Regeneration, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
| | - Anaïs Kervadec
- Development, Aging and Regeneration, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
| | - James N Kezos
- Development, Aging and Regeneration, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
| | - Katja Birker
- Development, Aging and Regeneration, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
| | - Jared M Evans
- Division of Biomedical Statistics and Informatics, Mayo ClinicRochesterUnited States
| | - Megan M O'Byrne
- Division of Biomedical Statistics and Informatics, Mayo ClinicRochesterUnited States
| | - Zachary C Fogarty
- Division of Biomedical Statistics and Informatics, Mayo ClinicRochesterUnited States
| | - André Terzic
- Department of Cardiovascular Medicine, Mayo ClinicRochesterUnited States
- Department of Molecular and Pharmacology and Experimental Therapeutics, Mayo ClinicLa JollaUnited States
- Center for Regenerative Medicine, Mayo ClinicRochesterUnited States
- Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo ClinicRochesterUnited States
| | - Paul Grossfeld
- University of California San Diego, Rady’s HospitalSan DiegoUnited States
- Division of General Internal Medicine, Mayo ClinicRochesterUnited States
| | - Karen Ocorr
- Development, Aging and Regeneration, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
| | - Timothy J Nelson
- Department of Molecular and Pharmacology and Experimental Therapeutics, Mayo ClinicLa JollaUnited States
- Center for Regenerative Medicine, Mayo ClinicRochesterUnited States
- Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo ClinicRochesterUnited States
| | - Timothy M Olson
- Department of Cardiovascular Medicine, Mayo ClinicRochesterUnited States
- Department of Molecular and Pharmacology and Experimental Therapeutics, Mayo ClinicLa JollaUnited States
- Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo ClinicRochesterUnited States
| | - Alexandre R Colas
- Development, Aging and Regeneration, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
| | - Rolf Bodmer
- Development, Aging and Regeneration, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
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21
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Squeo GM, Augello B, Massa V, Milani D, Colombo EA, Mazza T, Castellana S, Piccione M, Maitz S, Petracca A, Prontera P, Accadia M, Della Monica M, Di Giacomo MC, Melis D, Selicorni A, Giglio S, Fischetto R, Di Fede E, Malerba N, Russo M, Castori M, Gervasini C, Merla G. Customised next-generation sequencing multigene panel to screen a large cohort of individuals with chromatin-related disorder. J Med Genet 2020; 57:760-768. [PMID: 32170002 DOI: 10.1136/jmedgenet-2019-106724] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/11/2020] [Accepted: 02/19/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND The regulation of the chromatin state by epigenetic mechanisms plays a central role in gene expression, cell function, and maintenance of cell identity. Hereditary disorders of chromatin regulation are a group of conditions caused by abnormalities of the various components of the epigenetic machinery, namely writers, erasers, readers, and chromatin remodelers. Although neurological dysfunction is almost ubiquitous in these disorders, the constellation of additional features characterizing many of these genes and the emerging clinical overlap among them indicate the existence of a community of syndromes. The introduction of high-throughput next generation sequencing (NGS) methods for testing multiple genes simultaneously is a logical step for the implementation of diagnostics of these disorders. METHODS We screened a heterogeneous cohort of 263 index patients by an NGS-targeted panel, containing 68 genes associated with more than 40 OMIM entries affecting chromatin function. RESULTS This strategy allowed us to identify clinically relevant variants in 87 patients (32%), including 30 for which an alternative clinical diagnosis was proposed after sequencing analysis and clinical re-evaluation. CONCLUSION Our findings indicate that this approach is effective not only in disorders with locus heterogeneity, but also in order to anticipate unexpected misdiagnoses due to clinical overlap among cognate disorders. Finally, this work highlights the utility of a prompt diagnosis in such a clinically and genetically heterogeneous group of disorders that we propose to group under the umbrella term of chromatinopathies.
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Affiliation(s)
- Gabriella Maria Squeo
- Division of Medical Genetics, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Bartolomeo Augello
- Division of Medical Genetics, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Valentina Massa
- Dipartimento di Scienze della Salute, Universita degli Studi di Milano Dipartimento di Scienze della Salute, Milano, Italy
| | - Donatella Milani
- UOSD Pediatria ad alta intensità di cura, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Elisa Adele Colombo
- Dipartimento di Scienze della Salute, Universita degli Studi di Milano Dipartimento di Scienze della Salute, Milano, Italy
| | - Tommaso Mazza
- Bioinformatics Unit, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Stefano Castellana
- Bioinformatics Unit, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Maria Piccione
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Silvia Maitz
- Clinical Pediatric Genetics Unit, Pediatrics Clinics, MBBM Foundation, Hospital San Gerardo, Monza, Italy
| | - Antonio Petracca
- Division of Medical Genetics, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Paolo Prontera
- Medical Genetics Unit, University of Perugia Hospital SM della Misericordia, Perugia, Italy
| | - Maria Accadia
- Medical Genetics Service, Hospital "Cardinale G. Panico", Tricase, Italy
| | - Matteo Della Monica
- Medical Genetics Unit, Cardarelli Hospital, Largo A Cardarelli, Napoli, Italy
| | | | - Daniela Melis
- Department of Translational Medical Science, Section of Pediatrics, University of Naples Federico II, Napoli, Italy
| | - Angelo Selicorni
- Pediatric Department, ASST Lariana, Sant'Anna General Hospital, Como, Italy
| | - Sabrina Giglio
- Department of Biomedical, Experimental and Clinical Sciences 'Mario Serio', Medical Genetics Unit, University Hospital Meyer, Firenze, Italy
| | - Rita Fischetto
- Metabolic Diseases, Clinical Genetics and Diabetology Unit, Paediatric Hospital Giovanni XXIII, Bari, Italy
| | - Elisabetta Di Fede
- Dipartimento di Scienze della Salute, Universita degli Studi di Milano Dipartimento di Scienze della Salute, Milano, Italy
| | - Natascia Malerba
- Division of Medical Genetics, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Matteo Russo
- Division of Medical Genetics, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Marco Castori
- Division of Medical Genetics, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Cristina Gervasini
- Dipartimento di Scienze della Salute, Universita degli Studi di Milano Dipartimento di Scienze della Salute, Milano, Italy
| | - Giuseppe Merla
- Division of Medical Genetics, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
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22
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Matejcic M, Patel Y, Lilyquist J, Hu C, Lee KY, Gnanaolivu RD, Hart SN, Polley EC, Yadav S, Boddicker NJ, Samara R, Xia L, Sheng X, Lubmawa A, Kiddu V, Masaba B, Namuguzi D, Mutema G, Job K, Dabanja HM, Ingles SA, Wilkens L, Le Marchand L, Watya S, Couch FJ, Conti DV, Haiman CA. Pathogenic Variants in Cancer Predisposition Genes and Prostate Cancer Risk in Men of African Ancestry. JCO Precis Oncol 2020; 4:32-43. [PMID: 32832836 PMCID: PMC7442213 DOI: 10.1200/po.19.00179] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2019] [Indexed: 01/07/2023] Open
Abstract
PURPOSE In studies of men of European ancestry, rare pathogenic variants in DNA repair pathway genes have been shown to be associated with risk of aggressive prostate cancer. The contribution of rare coding variation to prostate cancer risk in men of African ancestry has not been established. METHODS We sequenced a panel of 19 DNA repair and cancer predisposition genes in 2,453 African American and 1,151 Ugandan prostate cancer cases and controls. Rare variants were classified as pathogenic or putatively functionally disruptive and examined in association with prostate cancer risk and disease aggressiveness in gene and pathway-level association analyses. RESULTS Pathogenic variants were found in 75 out of 2,098 cases (3.6%) and 31 out of 1,481 controls (2.1%) (OR=1.82, 95% CI=1.19 to 2.79, P=0.0044) with the association being stronger for more aggressive disease phenotypes (OR=3.10, 95% CI=1.54 to 6.23, P=0.0022). The highest risks for aggressive disease were observed with pathogenic variants in the ATM, BRCA2, PALB2 and NBN genes, with odds ratios ranging from ~4 to 15 in the combined study sample of African American and Ugandan men. Rare, non-pathogenic, non-synonymous variants did not have a major impact on risk of overall prostate cancer or disease aggressiveness. CONCLUSIONS Rare pathogenic variants in DNA repair genes have appreciable effects on risk of aggressive prostate cancer in men of African ancestry. These findings have potential implications for panel testing and risk stratification in this high-risk population.
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Affiliation(s)
- Marco Matejcic
- Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Yesha Patel
- Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Jenna Lilyquist
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Chunling Hu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Kun Y. Lee
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | | | - Steven N. Hart
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Eric C. Polley
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | | | | | | | - Lucy Xia
- Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Xin Sheng
- Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | | | | | | | - Dan Namuguzi
- Makerere University College of Health Sciences, Kampala, Uganda
| | | | | | | | - Sue A. Ingles
- Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Lynne Wilkens
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI
| | - Stephen Watya
- Uro Care, Kampala, Uganda
- Makerere University College of Health Sciences, Kampala, Uganda
| | - Fergus J. Couch
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - David V. Conti
- Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Christopher A. Haiman
- Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA
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23
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Yadav S, Hart SN, Hu C, Hillman D, Lee KY, Gnanaolivu R, Na J, Polley EC, Couch FJ, Kohli M. Contribution of Inherited DNA-Repair Gene Mutations to Hormone-Sensitive and Castrate-Resistant Metastatic Prostate Cancer and Implications for Clinical Outcome. JCO Precis Oncol 2019; 3:PO.19.00067. [PMID: 32923857 PMCID: PMC7446380 DOI: 10.1200/po.19.00067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2019] [Indexed: 12/30/2022] Open
Abstract
PURPOSE To compare the prevalence of germline mutations in metastatic hormone-sensitive prostate cancer (mHSPC) and metastatic castrate-resistant prostate cancer (mCRPC) and assess the impact of mutations on progression to castration resistance and overall survival. METHODS Targeted sequencing of germline DNA from 704 men (221 at the time of mHSPC and 483 at the time of mCRPC) enrolled in two advanced prostate cancer registries at Mayo Clinic between 2003 and 2013 was performed for 21 predisposition genes. Frequencies of pathogenic mutations were compared in patients and reference controls to identify genes enriched in metastatic prostate cancer. Multivariable Cox proportional hazards regression was used to identify predictors of progression to mCRPC and overall survival. RESULTS Sixty-eight germline mutations in 12 genes were identified in 66 men (9.4%). Mutations in ATM, BRCA2, CHEK2, FANCM, and TP53 were significantly enriched (odds ratio greater than 2.0) in the metastatic cohorts compared with reference controls. The frequency of germline mutations was similar for patients with mHSPC and mCRPC (11.8% v 8.3%; P = .16). The median time to progression from mHSPC to mCRPC was 23.1 and 32.5 months for patients with and without mutations, respectively (P = .96). Although older age at diagnosis, Gleason score greater than 7, elevated alkaline phosphatase level, and high volume of disease were associated with shorter duration of progression to mCRPC and poor overall survival, mutation status was not (progression to mCRPC hazard ratio, 0.81; 95% CI, 0.61 to 1.09; P = .17; overall survival hazard ratio, 1.00; 95% CI, 0.75 to 1.34; P = .98). CONCLUSION Similarly elevated rates of germline predisposition gene mutations in mHSPC and mCRPC suggest that germline genetic testing may help to guide medical management for all patients with advanced metastatic prostate cancer. Mutation status was not associated with shorter progression to mCRPC or poor overall survival.
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Affiliation(s)
| | | | | | | | | | | | - Jie Na
- Mayo Clinic, Rochester, MN
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24
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Deep sequencing across germline genome-wide association study signals relating to breast cancer events in women receiving aromatase inhibitors for adjuvant therapy of early breast cancer. Pharmacogenet Genomics 2019; 29:183-191. [PMID: 31211741 DOI: 10.1097/fpc.0000000000000382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVE To identify additional genetic variants beyond those observed in a previous genome-wide association study (GWAS) in women treated on the MA.27 clinical trial in which women were randomized to 5 years of adjuvant therapy with anastrozole or exemestane. PATIENTS AND METHODS We performed a matched case-control study in 234 women who had a recurrence of breast cancer (cases) and 649 women who had not (controls). The analysis was restricted to White women with an estrogen receptor-positive breast cancer. Multiplex PCR-based targeted deep sequencing was performed of the MIR2052HG region on chromosome 8 between positions 75.4 and 75.7, a span of 300 kb, in an attempt to identify additional functional single nucleotide polymorphisms (SNPs). RESULTS A total of 4677 unique variants were identified that had not been identified in the previous GWAS. Clinical Annotation of Variants analysis revealed 10 variants, including eight SNPs and two insertion-deletion mutations with moderate or high impact. However, none of the common and variant regions was significant after adjustment for the most significant SNP (rs13260300) identified in our previous GWAS. We performed haplotype analysis that revealed two regions in which the haplotypes lost significance when adjusted for this prior GWAS SNP and one region with two significant haplotypes (P = 0.046 and 0.031) after adjusting for the GWAS SNP. CONCLUSION We were unable to identify common or rare variant regions that added value to the findings from our previous GWAS. We did find two haplotypes that were significant after adjusting for our top GWAS SNP but these were considered to be of marginal value.
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25
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Wilhite TJ, Youland RS, Tian S, Finley RR, Sarkaria JN, Corbin KS. Pathogenic Germ Line Variants in a Patient With Severe Toxicity From Breast Radiotherapy. Clin Breast Cancer 2019; 19:e400-e405. [PMID: 31031124 DOI: 10.1016/j.clbc.2019.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/15/2019] [Accepted: 03/12/2019] [Indexed: 11/18/2022]
Affiliation(s)
- Tyler J Wilhite
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN
| | - Ryan S Youland
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN
| | - Shulan Tian
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Randi R Finley
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN
| | - Jann N Sarkaria
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN
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Targeted massively parallel sequencing characterises the mutation spectrum of PALB2 in breast and ovarian cancer cases from Poland and Ukraine. Fam Cancer 2019; 17:345-349. [PMID: 29052111 PMCID: PMC5999175 DOI: 10.1007/s10689-017-0050-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Loss-of-function germline mutations in the PALB2 gene are associated with an increase of breast cancer risk. The purpose of this study was to characterise the spectrum of PALB2 mutations in women affected with breast or ovarian cancer from South-West Poland and West Ukraine. We applied Hi-Plex, an amplicon-based enrichment method for targeted massively parallel sequencing, to screen the coding exons and proximal intron–exon junctions of PALB2 in germline DNA from unrelated women affected with breast cancer (n = 338) and ovarian cancer (n = 89) from Poland (n = 304) and Ukraine (n = 123). These women were at high-risk of carrying a genetic predisposition to breast and/or ovarian cancer due to a family history and/or early-onset disease. Targeted-sequencing identified two frameshift deletions: PALB2:c.509_510del; p.R170Ifs in three women affected with breast cancer and PALB2:c.172_175del;p.Q60Rfs in one woman affected with ovarian cancer. A number of other previously described missense (some predicted to be damaging by PolyPhen-2 and CADD) and synonymous mutations were also identified in this population. This study is consistent with previous reports that PALB2:c.509_510del and PALB2:c.172_175del are recurrent mutations associated with breast cancer predisposition in Polish women with a family history of the disease. Our study contributes to the accumulating evidence indicating that PALB2 should be included in genetic testing for breast cancer susceptibility in these populations to enhance risk assessment and management of women at high-risk of developing breast cancer. This data could also contribute to ongoing work that is assessing the possible association between ovarian cancer risk and PALB2 mutations for which there is currently no evidence.
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Yost S, Münz M, Mahamdallie S, Renwick A, Ruark E, Rahman N. Clinical Annotation Reference Templates: a resource for consistent variant annotation. Wellcome Open Res 2018. [DOI: 10.12688/wellcomeopenres.14924.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Annotating the impact of a variant on a gene is a vital component of genetic medicine and genetic research. Different gene annotations for the same genomic variant are possible, because different structures and sequences for the same gene are available. The clinical community typically use RefSeq NMs to annotate gene variation, which do not always match the reference genome. The scientific community typically use Ensembl ENSTs to annotate gene variation. These match the reference genome, but often do not match the equivalent NM. Often the transcripts used to annotate gene variation are not provided, impeding interoperability and consistency. Here we introduce the concept of the Clinical Annotation Reference Template (CART). CARTs are analogous to the reference genome; they provide a universal standard template so reference genomic coordinates are consistently annotated at the protein level. Naturally, there are many situations where annotations using a specific transcript, or multiple transcripts are useful. The aim of the CARTs is not to impede this practice. Rather, the CART annotation serves as an anchor to ensure interoperability between different annotation systems and variant frequency accuracy. Annotations using other explicitly-named transcripts should also be provided, wherever useful. We have integrated transcript data to generate CARTs for over 18,000 genes, for both GRCh37 and GRCh38, based on the associated NM and ENST identified through the CART selection process. Each CART has a unique ID and can be used individually or as a stable set of templates; CART37A for GRCh37 and CART38A for GRCh38. We have made the CARTs available on the UCSC browser and in different file formats on the Open Science Framework: https://osf.io/tcvbq/. We have also made the CARTtools software we used to generate the CARTs available on GitHub. We hope the CARTs will be useful in helping to drive transparent, stable, consistent, interoperable variant annotation.
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28
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Pawliczek P, Patel RY, Ashmore LR, Jackson AR, Bizon C, Nelson T, Powell B, Freimuth RR, Strande N, Shah N, Paithankar S, Wright MW, Dwight S, Zhen J, Landrum M, McGarvey P, Babb L, Plon SE, Milosavljevic A. ClinGen Allele Registry links information about genetic variants. Hum Mutat 2018; 39:1690-1701. [PMID: 30311374 PMCID: PMC6519371 DOI: 10.1002/humu.23637] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/01/2018] [Accepted: 08/28/2018] [Indexed: 11/18/2022]
Abstract
Effective exchange of information about genetic variants is currently hampered by the lack of readily available globally unique variant identifiers that would enable aggregation of information from different sources. The ClinGen Allele Registry addresses this problem by providing (1) globally unique "canonical" variant identifiers (CAids) on demand, either individually or in large batches; (2) access to variant-identifying information in a searchable Registry; (3) links to allele-related records in many commonly used databases; and (4) services for adding links to information about registered variants in external sources. A core element of the Registry is a canonicalization service, implemented using in-memory sequence alignment-based index, which groups variant identifiers denoting the same nucleotide variant and assigns unique and dereferenceable CAids. More than 650 million distinct variants are currently registered, including those from gnomAD, ExAC, dbSNP, and ClinVar, including a small number of variants registered by Registry users. The Registry is accessible both via a web interface and programmatically via well-documented Hypertext Transfer Protocol (HTTP) Representational State Transfer Application Programming Interface (REST-APIs). For programmatic interoperability, the Registry content is accessible in the JavaScript Object Notation for Linked Data (JSON-LD) format. We present several use cases and demonstrate how the linked information may provide raw material for reasoning about variant's pathogenicity.
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Affiliation(s)
- Piotr Pawliczek
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas
| | - Ronak Y. Patel
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas
| | - Lillian R. Ashmore
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas
| | - Andrew R. Jackson
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas
| | - Chris Bizon
- Renaissance Computing InstituteUniversity of North CarolinaChapel HillNorth Carolina
| | - Tristan Nelson
- Geisinger's Autism and Developmental MedicineLewisburgPennsylvania
| | - Bradford Powell
- Department of GeneticsUniversity of North CarolinaChapel HillNorth Carolina
| | | | - Natasha Strande
- Department of GeneticsUniversity of North CarolinaChapel HillNorth Carolina
| | - Neethu Shah
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas
| | - Sameer Paithankar
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas
| | - Matt W. Wright
- Department of Biomedical Data SciencesStanford University School of MedicinePalo AltoCalifornia
| | - Selina Dwight
- Department of Biomedical Data SciencesStanford University School of MedicinePalo AltoCalifornia
| | - Jimmy Zhen
- Department of Biomedical Data SciencesStanford University School of MedicinePalo AltoCalifornia
| | - Melissa Landrum
- National Center for Biotechnology InformationNational Institutes of HealthBethesdaMaryland
| | - Peter McGarvey
- Innovation Center for Biomedical InformaticsGeorgetown University Medical CenterWashingtonDistrict of Columbia
| | - Larry Babb
- Sunquest Information Systems CompanyBostonMassachusetts
| | - Sharon E. Plon
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas
- Department of PediatricsBaylor College of Medicine HoustonTexas
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29
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Ruark E, Holt E, Renwick A, Münz M, Wakeling M, Ellard S, Mahamdallie S, Yost S, Rahman N. ICR142 Benchmarker: evaluating, optimising and benchmarking variant calling performance using the ICR142 NGS validation series. Wellcome Open Res 2018; 3:108. [PMID: 30483600 PMCID: PMC6234721 DOI: 10.12688/wellcomeopenres.14754.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2018] [Indexed: 11/20/2022] Open
Abstract
Evaluating, optimising and benchmarking of next generation sequencing (NGS) variant calling performance are essential requirements for clinical, commercial and academic NGS pipelines. Such assessments should be performed in a consistent, transparent and reproducible fashion, using independently, orthogonally generated data. Here we present ICR142 Benchmarker, a tool to generate outputs for assessing germline base substitution and indel calling performance using the ICR142 NGS validation series, a dataset of Illumina platform-based exome sequence data from 142 samples together with Sanger sequence data at 704 sites. ICR142 Benchmarker provides summary and detailed information on the sensitivity, specificity and false detection rates of variant callers. ICR142 Benchmarker also automatically generates a single page report highlighting key performance metrics and how performance compares to widely-used open-source tools. We used ICR142 Benchmarker with VCF files outputted by GATK, OpEx and DeepVariant to create a benchmark for variant calling performance. This evaluation revealed pipeline-specific differences and shared challenges in variant calling, for example in detecting indels in short repeating sequence motifs. We next used ICR142 Benchmarker to perform regression testing with DeepVariant versions 0.5.2 and 0.6.1. This showed that v0.6.1 improves variant calling performance, but there was evidence of minor changes in indel calling behaviour that may benefit from attention. The data also allowed us to evaluate filters to optimise DeepVariant calling, and we recommend using 30 as the QUAL threshold for base substitution calls when using DeepVariant v0.6.1. Finally, we used ICR142 Benchmarker with VCF files from two commercial variant calling providers to facilitate optimisation of their in-house pipelines and to provide transparent benchmarking of their performance. ICR142 Benchmarker consistently and transparently analyses variant calling performance based on the ICR142 NGS validation series, using the standard VCF input and outputting informative metrics to enable user understanding of pipeline performance. ICR142 Benchmarker is freely available at https://github.com/RahmanTeamDevelopment/ICR142_Benchmarker/releases.
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Affiliation(s)
- Elise Ruark
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Esty Holt
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Anthony Renwick
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Márton Münz
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Matthew Wakeling
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, EX2 5DW, UK
| | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, EX2 5DW, UK
| | - Shazia Mahamdallie
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Shawn Yost
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Nazneen Rahman
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, SM2 5PT, UK
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30
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Ruark E, Holt E, Renwick A, Münz M, Wakeling M, Ellard S, Mahamdallie S, Yost S, Rahman N. ICR142 Benchmarker: evaluating, optimising and benchmarking variant calling using the ICR142 NGS validation series. Wellcome Open Res 2018; 3:108. [PMID: 30483600 PMCID: PMC6234721 DOI: 10.12688/wellcomeopenres.14754.1] [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] [Accepted: 08/23/2018] [Indexed: 10/05/2023] Open
Abstract
Evaluating, optimising and benchmarking of next generation sequencing (NGS) variant calling performance are essential requirements for clinical, commercial and academic NGS pipelines. Such assessments should be performed in a consistent, transparent and reproducible fashion, using independently, orthogonally generated data. Here we present ICR142 Benchmarker, a tool to generate outputs for assessing variant calling performance using the ICR142 NGS validation series, a dataset of exome sequence data from 142 samples together with Sanger sequence data at 704 sites. ICR142 Benchmarker provides summary and detailed information on the sensitivity, specificity and false detection rates of variant callers. ICR142 Benchmarker also automatically generates a single page report highlighting key performance metrics and how performance compares to widely-used open-source tools. We used ICR142 Benchmarker with VCF files outputted by GATK, OpEx and DeepVariant to create a benchmark for variant calling performance. This evaluation revealed pipeline-specific differences and shared challenges in variant calling, for example in detecting indels in short repeating sequence motifs. We next used ICR142 Benchmarker to perform regression testing with versions 0.5.2 and 0.6.1 of DeepVariant. This showed that v0.6.1 improves variant calling performance, but there was evidence of some minor changes in indel calling behaviour that may benefit from attention in future updates. The data also allowed us to evaluate filters to optimise DeepVariant calling, and we recommend using 30 as the QUAL threshold for base substitution calls when using DeepVariant v0.6.1. Finally, we used ICR142 Benchmarker with VCF files from two commercial variant calling providers to facilitate optimisation of their in-house pipelines and to provide transparent benchmarking of their performance. ICR142 Benchmarker consistently and transparently analyses variant calling performance based on the ICR142 NGS validation series, using the standard VCF input and outputting informative metrics to enable user understanding of pipeline performance. ICR142 Benchmarker is freely available at https://github.com/RahmanTeamDevelopment/ICR142_Benchmarker/releases.
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Affiliation(s)
- Elise Ruark
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Esty Holt
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Anthony Renwick
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Márton Münz
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Matthew Wakeling
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, EX2 5DW, UK
| | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, EX2 5DW, UK
| | - Shazia Mahamdallie
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Shawn Yost
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Nazneen Rahman
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, SM2 5PT, UK
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31
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Zimmermann MT, Urrutia R, Cousin MA, Oliver GR, Klee EW. Assessing Human Genetic Variations in Glucose Transporter SLC2A10 and Their Role in Altering Structural and Functional Properties. Front Genet 2018; 9:276. [PMID: 30090112 PMCID: PMC6068234 DOI: 10.3389/fgene.2018.00276] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 07/05/2018] [Indexed: 11/13/2022] Open
Abstract
Purpose: Demand is increasing for clinical genomic sequencing to provide diagnoses for patients presenting phenotypes indicative of genetic diseases, but for whom routine genetic testing failed to yield a diagnosis. DNA-based testing using high-throughput technologies often identifies variants with insufficient evidence to determine whether they are disease-causal or benign, leading to categorization as variants of uncertain significance (VUS). Methods: We used molecular modeling and simulation to generate specific hypotheses for the molecular effects of variants in the human glucose transporter, GLUT10 (SLC2A10). Similar to many disease-relevant membrane proteins, no experimentally derived 3D structure exists. An atomic model was generated and used to evaluate multiple variants, including pathogenic, benign, and VUS. Results: These analyses yielded detailed mechanistic data, not currently predictable from sequence, including altered protein stability, charge distribution of ligand binding surfaces, and shifts toward or away from transport-competent conformations. Consideration of the two major conformations of GLUT10 was important as variants have conformation-specific effects. We generated detailed molecular hypotheses for the functional impact of variants in GLUT10 and propose means to determine their pathogenicity. Conclusion: The type of workflow we present here is valuable for increasing the throughput and resolution with which VUS effects can be assessed and interpreted.
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Affiliation(s)
- Michael T Zimmermann
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, United States.,Bioinformatics Research and Development Laboratory, Genomics Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Raul Urrutia
- Bioinformatics Research and Development Laboratory, Genomics Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States.,Laboratory of Epigenetics and Chromatin Dynamics, Department of Biochemistry and Molecular Biology, Epigenomics Translational Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States
| | - Margot A Cousin
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States
| | - Gavin R Oliver
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, United States.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States
| | - Eric W Klee
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, United States.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States
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32
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Hu C, Hart SN, Polley EC, Gnanaolivu R, Shimelis H, Lee KY, Lilyquist J, Na J, Moore R, Antwi SO, Bamlet WR, Chaffee KG, DiCarlo J, Wu Z, Samara R, Kasi PM, McWilliams RR, Petersen GM, Couch FJ. Association Between Inherited Germline Mutations in Cancer Predisposition Genes and Risk of Pancreatic Cancer. JAMA 2018; 319:2401-2409. [PMID: 29922827 PMCID: PMC6092184 DOI: 10.1001/jama.2018.6228] [Citation(s) in RCA: 352] [Impact Index Per Article: 58.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
IMPORTANCE Individuals genetically predisposed to pancreatic cancer may benefit from early detection. Genes that predispose to pancreatic cancer and the risks of pancreatic cancer associated with mutations in these genes are not well defined. OBJECTIVE To determine whether inherited germline mutations in cancer predisposition genes are associated with increased risks of pancreatic cancer. DESIGN, SETTING, AND PARTICIPANTS Case-control analysis to identify pancreatic cancer predisposition genes; longitudinal analysis of patients with pancreatic cancer for prognosis. The study included 3030 adults diagnosed as having pancreatic cancer and enrolled in a Mayo Clinic registry between October 12, 2000, and March 31, 2016, with last follow-up on June 22, 2017. Reference controls were 123 136 individuals with exome sequence data in the public Genome Aggregation Database and 53 105 in the Exome Aggregation Consortium database. EXPOSURES Individuals were classified based on carrying a deleterious mutation in cancer predisposition genes and having a personal or family history of cancer. MAIN OUTCOMES AND MEASURES Germline mutations in coding regions of 21 cancer predisposition genes were identified by sequencing of products from a custom multiplex polymerase chain reaction-based panel; associations of genes with pancreatic cancer were assessed by comparing frequency of mutations in genes of pancreatic cancer patients with those of reference controls. RESULTS Comparing 3030 case patients with pancreatic cancer (43.2% female; 95.6% non-Hispanic white; mean age at diagnosis, 65.3 [SD, 10.7] years) with reference controls, significant associations were observed between pancreatic cancer and mutations in CDKN2A (0.3% of cases and 0.02% of controls; odds ratio [OR], 12.33; 95% CI, 5.43-25.61); TP53 (0.2% of cases and 0.02% of controls; OR, 6.70; 95% CI, 2.52-14.95); MLH1 (0.13% of cases and 0.02% of controls; OR, 6.66; 95% CI, 1.94-17.53); BRCA2 (1.9% of cases and 0.3% of controls; OR, 6.20; 95% CI, 4.62-8.17); ATM (2.3% of cases and 0.37% of controls; OR, 5.71; 95% CI, 4.38-7.33); and BRCA1 (0.6% of cases and 0.2% of controls; OR, 2.58; 95% CI, 1.54-4.05). CONCLUSIONS AND RELEVANCE In this case-control study, mutations in 6 genes associated with pancreatic cancer were found in 5.5% of all pancreatic cancer patients, including 7.9% of patients with a family history of pancreatic cancer and 5.2% of patients without a family history of pancreatic cancer. Further research is needed for replication in other populations.
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Affiliation(s)
- Chunling Hu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Steven N Hart
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Eric C Polley
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Rohan Gnanaolivu
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Hermela Shimelis
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Kun Y Lee
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Jenna Lilyquist
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Jie Na
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Raymond Moore
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Samuel O Antwi
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, Florida
| | - William R Bamlet
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Kari G Chaffee
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - John DiCarlo
- Qiagen Sciences Research and Development, Qiagen Inc, Hilden, Germany
| | - Zhong Wu
- Qiagen Sciences Research and Development, Qiagen Inc, Hilden, Germany
| | - Raed Samara
- Qiagen Sciences Research and Development, Qiagen Inc, Hilden, Germany
| | | | | | - Gloria M Petersen
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
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33
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Mahamdallie S, Ruark E, Holt E, Poyastro-Pearson E, Renwick A, Strydom A, Seal S, Rahman N. The ICR639 CPG NGS validation series: A resource to assess analytical sensitivity of cancer predisposition gene testing. Wellcome Open Res 2018; 3:68. [PMID: 30175241 PMCID: PMC6081973 DOI: 10.12688/wellcomeopenres.14594.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2018] [Indexed: 11/20/2022] Open
Abstract
The analytical sensitivity of a next generation sequencing (NGS) test reflects the ability of the test to detect real sequence variation. The evaluation of analytical sensitivity relies on the availability of gold-standard, validated, benchmarking datasets. For NGS analysis the availability of suitable datasets has been limited. Most laboratories undertake small scale evaluations using in-house data, and/or rely on in silico generated datasets to evaluate the performance of NGS variant detection pipelines. Cancer predisposition genes (CPGs), such as BRCA1 and BRCA2, are amongst the most widely tested genes in clinical practice today. Hundreds of providers across the world are now offering CPG testing using NGS methods. Validating and comparing the analytical sensitivity of CPG tests has proved difficult, due to the absence of comprehensive, orthogonally validated, benchmarking datasets of CPG pathogenic variants. To address this we present the ICR639 CPG NGS validation series. This dataset comprises data from 639 individuals. Each individual has sequencing data generated using the TruSight Cancer Panel (TSCP), a targeted NGS assay for the analysis of CPGs, together with orthogonally generated data showing the presence of at least one CPG pathogenic variant per individual. The set consists of 645 pathogenic variants in total. There is strong representation of the most challenging types of variants to detect, with 339 indels, including 16 complex indels and 24 with length greater than five base pairs and 74 exon copy number variations (CNVs) including 23 single exon CNVs. The series includes pathogenic variants in 31 CPGs, including 502 pathogenic variants in BRCA1 or BRCA2, making this an important comprehensive validation dataset for providers of BRCA1 and BRCA2 NGS testing. We have deposited the TSCP FASTQ files of the ICR639 series in the European Genome-phenome Archive (EGA) under accession number EGAD00001004134.
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Affiliation(s)
- Shazia Mahamdallie
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Elise Ruark
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Esty Holt
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Emma Poyastro-Pearson
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Anthony Renwick
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Ann Strydom
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Sheila Seal
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Nazneen Rahman
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK.,Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, SM2 5PT, UK
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34
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Fasching PA, Loibl S, Hu C, Hart SN, Shimelis H, Moore R, Schem C, Tesch H, Untch M, Hilfrich J, Rezai M, Gerber B, Costa SD, Blohmer JU, Fehm T, Huober J, Liedtke C, Weinshilboum RM, Wang L, Ingle JN, Müller V, Nekljudova V, Weber KE, Rack B, Rübner M, von Minckwitz G, Couch FJ. BRCA1/2 Mutations and Bevacizumab in the Neoadjuvant Treatment of Breast Cancer: Response and Prognosis Results in Patients With Triple-Negative Breast Cancer From the GeparQuinto Study. J Clin Oncol 2018; 36:2281-2287. [PMID: 29791287 DOI: 10.1200/jco.2017.77.2285] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Purpose BRCA1/2 mutations are frequent in patients with triple-negative breast cancer (TNBC). These patients are often treated with primary systemic chemotherapy. The aim of this study was to analyze the effects of BRCA1/2 mutations on pathologic complete response (pCR) and disease-free survival (DFS) in a cohort of patients with TNBC treated with anthracycline and taxane-containing chemotherapy, with or without bevacizumab. Patients and Methods Germline DNA was sequenced to identify mutations in BRCA1 and BRCA2 in 493 patients with TNBC from the GeparQuinto study. The pCR rates were compared in patients with and without mutation, as well as in patients treated with and without bevacizumab. In addition, the influence of BRCA1/2 mutation status and pCR status on DFS was evaluated relative to treatment. Results BRCA1/2 mutations were detected in 18.3% of patients with TNBC. Overall, patients with mutations had a pCR rate of 50%, compared with 31.5% in patients without a mutation (odds ratio [OR], 2.17; 95% CI, 1.37 to 3.46; P = .001). The pCR rate among patients treated with bevacizumab was 61.5% for BRCA1/2 mutation carriers and 35.6% for those without mutations (OR, 2.90; 95% CI, 1.43 to 5.89; P = .004). pCR was a strong predictor of DFS for patients without BRCA1/2 mutations (hazard ratio, 0.18; 95% CI, 0.11 to 0.31) but not for patients with BRCA1/2 mutations (hazard ratio, 0.74; 95% CI, 0.32 to 1.69). Conclusion The addition of bevacizumab may increase the pCR after standard neoadjuvant chemotherapy for patients with TNBC with BRCA1/2 mutations. In patients treated with anthracycline and taxane-based chemotherapy (with or without bevacizumab), pCR was a weaker predictor of DFS for BRCA1/2 mutation carriers than for patients without mutations.
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Affiliation(s)
- Peter A Fasching
- Peter A. Fasching and Matthias Rübner, Erlangen University Hospital, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen; Sibylle Loibl, Valentina Nekljudova, Karsten E. Weber, and Gunter von Minckwitz, German Breast Group Forschungs, Neu-Isenburg; Christian Schem, University Medical Center Schleswig-Holstein, Kiel; Hans Tesch, Centrum für Hämatologie und Onkologie Bethanien, Frankfurt; Michael Untch, Helios-Klinikum, Berlin-Buch; Jörn Hilfrich, Eilenriede-Klinik, Hannover; Mahdi Rezai, Luisenkrankenhaus; Tanja Fehm, Düsseldorf University Hospital, Heinrich-Heine University of Düsseldorf, Düsseldorf; Bernd Gerber, University of Rostock, Rostock; Serban Dan Costa, Magdeburg University Hospital, Magdeburg; Jens-Uwe Blohmer and Cornelia Liedtke, Charité University Hospital Campus Charité-Mitte, Berlin; Jens Huober, University of Ulm; Brigitte Rack, University Hospital Ulm, Ulm; Volkmar Müller, Hamburg University Hospital, Hamburg, Germany; Chunling Hu, Steven N. Hart, Hermela Shimelis, Raymond Moore, James N. Ingle, and Fergus J. Couch, Mayo Clinic; and Richard M. Weinshilboum and Liewei Wang, Mayo Clinic College of Medicine, Mayo Foundation, Rochester, MN
| | - Sibylle Loibl
- Peter A. Fasching and Matthias Rübner, Erlangen University Hospital, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen; Sibylle Loibl, Valentina Nekljudova, Karsten E. Weber, and Gunter von Minckwitz, German Breast Group Forschungs, Neu-Isenburg; Christian Schem, University Medical Center Schleswig-Holstein, Kiel; Hans Tesch, Centrum für Hämatologie und Onkologie Bethanien, Frankfurt; Michael Untch, Helios-Klinikum, Berlin-Buch; Jörn Hilfrich, Eilenriede-Klinik, Hannover; Mahdi Rezai, Luisenkrankenhaus; Tanja Fehm, Düsseldorf University Hospital, Heinrich-Heine University of Düsseldorf, Düsseldorf; Bernd Gerber, University of Rostock, Rostock; Serban Dan Costa, Magdeburg University Hospital, Magdeburg; Jens-Uwe Blohmer and Cornelia Liedtke, Charité University Hospital Campus Charité-Mitte, Berlin; Jens Huober, University of Ulm; Brigitte Rack, University Hospital Ulm, Ulm; Volkmar Müller, Hamburg University Hospital, Hamburg, Germany; Chunling Hu, Steven N. Hart, Hermela Shimelis, Raymond Moore, James N. Ingle, and Fergus J. Couch, Mayo Clinic; and Richard M. Weinshilboum and Liewei Wang, Mayo Clinic College of Medicine, Mayo Foundation, Rochester, MN
| | - Chunling Hu
- Peter A. Fasching and Matthias Rübner, Erlangen University Hospital, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen; Sibylle Loibl, Valentina Nekljudova, Karsten E. Weber, and Gunter von Minckwitz, German Breast Group Forschungs, Neu-Isenburg; Christian Schem, University Medical Center Schleswig-Holstein, Kiel; Hans Tesch, Centrum für Hämatologie und Onkologie Bethanien, Frankfurt; Michael Untch, Helios-Klinikum, Berlin-Buch; Jörn Hilfrich, Eilenriede-Klinik, Hannover; Mahdi Rezai, Luisenkrankenhaus; Tanja Fehm, Düsseldorf University Hospital, Heinrich-Heine University of Düsseldorf, Düsseldorf; Bernd Gerber, University of Rostock, Rostock; Serban Dan Costa, Magdeburg University Hospital, Magdeburg; Jens-Uwe Blohmer and Cornelia Liedtke, Charité University Hospital Campus Charité-Mitte, Berlin; Jens Huober, University of Ulm; Brigitte Rack, University Hospital Ulm, Ulm; Volkmar Müller, Hamburg University Hospital, Hamburg, Germany; Chunling Hu, Steven N. Hart, Hermela Shimelis, Raymond Moore, James N. Ingle, and Fergus J. Couch, Mayo Clinic; and Richard M. Weinshilboum and Liewei Wang, Mayo Clinic College of Medicine, Mayo Foundation, Rochester, MN
| | - Steven N Hart
- Peter A. Fasching and Matthias Rübner, Erlangen University Hospital, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen; Sibylle Loibl, Valentina Nekljudova, Karsten E. Weber, and Gunter von Minckwitz, German Breast Group Forschungs, Neu-Isenburg; Christian Schem, University Medical Center Schleswig-Holstein, Kiel; Hans Tesch, Centrum für Hämatologie und Onkologie Bethanien, Frankfurt; Michael Untch, Helios-Klinikum, Berlin-Buch; Jörn Hilfrich, Eilenriede-Klinik, Hannover; Mahdi Rezai, Luisenkrankenhaus; Tanja Fehm, Düsseldorf University Hospital, Heinrich-Heine University of Düsseldorf, Düsseldorf; Bernd Gerber, University of Rostock, Rostock; Serban Dan Costa, Magdeburg University Hospital, Magdeburg; Jens-Uwe Blohmer and Cornelia Liedtke, Charité University Hospital Campus Charité-Mitte, Berlin; Jens Huober, University of Ulm; Brigitte Rack, University Hospital Ulm, Ulm; Volkmar Müller, Hamburg University Hospital, Hamburg, Germany; Chunling Hu, Steven N. Hart, Hermela Shimelis, Raymond Moore, James N. Ingle, and Fergus J. Couch, Mayo Clinic; and Richard M. Weinshilboum and Liewei Wang, Mayo Clinic College of Medicine, Mayo Foundation, Rochester, MN
| | - Hermela Shimelis
- Peter A. Fasching and Matthias Rübner, Erlangen University Hospital, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen; Sibylle Loibl, Valentina Nekljudova, Karsten E. Weber, and Gunter von Minckwitz, German Breast Group Forschungs, Neu-Isenburg; Christian Schem, University Medical Center Schleswig-Holstein, Kiel; Hans Tesch, Centrum für Hämatologie und Onkologie Bethanien, Frankfurt; Michael Untch, Helios-Klinikum, Berlin-Buch; Jörn Hilfrich, Eilenriede-Klinik, Hannover; Mahdi Rezai, Luisenkrankenhaus; Tanja Fehm, Düsseldorf University Hospital, Heinrich-Heine University of Düsseldorf, Düsseldorf; Bernd Gerber, University of Rostock, Rostock; Serban Dan Costa, Magdeburg University Hospital, Magdeburg; Jens-Uwe Blohmer and Cornelia Liedtke, Charité University Hospital Campus Charité-Mitte, Berlin; Jens Huober, University of Ulm; Brigitte Rack, University Hospital Ulm, Ulm; Volkmar Müller, Hamburg University Hospital, Hamburg, Germany; Chunling Hu, Steven N. Hart, Hermela Shimelis, Raymond Moore, James N. Ingle, and Fergus J. Couch, Mayo Clinic; and Richard M. Weinshilboum and Liewei Wang, Mayo Clinic College of Medicine, Mayo Foundation, Rochester, MN
| | - Raymond Moore
- Peter A. Fasching and Matthias Rübner, Erlangen University Hospital, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen; Sibylle Loibl, Valentina Nekljudova, Karsten E. Weber, and Gunter von Minckwitz, German Breast Group Forschungs, Neu-Isenburg; Christian Schem, University Medical Center Schleswig-Holstein, Kiel; Hans Tesch, Centrum für Hämatologie und Onkologie Bethanien, Frankfurt; Michael Untch, Helios-Klinikum, Berlin-Buch; Jörn Hilfrich, Eilenriede-Klinik, Hannover; Mahdi Rezai, Luisenkrankenhaus; Tanja Fehm, Düsseldorf University Hospital, Heinrich-Heine University of Düsseldorf, Düsseldorf; Bernd Gerber, University of Rostock, Rostock; Serban Dan Costa, Magdeburg University Hospital, Magdeburg; Jens-Uwe Blohmer and Cornelia Liedtke, Charité University Hospital Campus Charité-Mitte, Berlin; Jens Huober, University of Ulm; Brigitte Rack, University Hospital Ulm, Ulm; Volkmar Müller, Hamburg University Hospital, Hamburg, Germany; Chunling Hu, Steven N. Hart, Hermela Shimelis, Raymond Moore, James N. Ingle, and Fergus J. Couch, Mayo Clinic; and Richard M. Weinshilboum and Liewei Wang, Mayo Clinic College of Medicine, Mayo Foundation, Rochester, MN
| | - Christian Schem
- Peter A. Fasching and Matthias Rübner, Erlangen University Hospital, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen; Sibylle Loibl, Valentina Nekljudova, Karsten E. Weber, and Gunter von Minckwitz, German Breast Group Forschungs, Neu-Isenburg; Christian Schem, University Medical Center Schleswig-Holstein, Kiel; Hans Tesch, Centrum für Hämatologie und Onkologie Bethanien, Frankfurt; Michael Untch, Helios-Klinikum, Berlin-Buch; Jörn Hilfrich, Eilenriede-Klinik, Hannover; Mahdi Rezai, Luisenkrankenhaus; Tanja Fehm, Düsseldorf University Hospital, Heinrich-Heine University of Düsseldorf, Düsseldorf; Bernd Gerber, University of Rostock, Rostock; Serban Dan Costa, Magdeburg University Hospital, Magdeburg; Jens-Uwe Blohmer and Cornelia Liedtke, Charité University Hospital Campus Charité-Mitte, Berlin; Jens Huober, University of Ulm; Brigitte Rack, University Hospital Ulm, Ulm; Volkmar Müller, Hamburg University Hospital, Hamburg, Germany; Chunling Hu, Steven N. Hart, Hermela Shimelis, Raymond Moore, James N. Ingle, and Fergus J. Couch, Mayo Clinic; and Richard M. Weinshilboum and Liewei Wang, Mayo Clinic College of Medicine, Mayo Foundation, Rochester, MN
| | - Hans Tesch
- Peter A. Fasching and Matthias Rübner, Erlangen University Hospital, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen; Sibylle Loibl, Valentina Nekljudova, Karsten E. Weber, and Gunter von Minckwitz, German Breast Group Forschungs, Neu-Isenburg; Christian Schem, University Medical Center Schleswig-Holstein, Kiel; Hans Tesch, Centrum für Hämatologie und Onkologie Bethanien, Frankfurt; Michael Untch, Helios-Klinikum, Berlin-Buch; Jörn Hilfrich, Eilenriede-Klinik, Hannover; Mahdi Rezai, Luisenkrankenhaus; Tanja Fehm, Düsseldorf University Hospital, Heinrich-Heine University of Düsseldorf, Düsseldorf; Bernd Gerber, University of Rostock, Rostock; Serban Dan Costa, Magdeburg University Hospital, Magdeburg; Jens-Uwe Blohmer and Cornelia Liedtke, Charité University Hospital Campus Charité-Mitte, Berlin; Jens Huober, University of Ulm; Brigitte Rack, University Hospital Ulm, Ulm; Volkmar Müller, Hamburg University Hospital, Hamburg, Germany; Chunling Hu, Steven N. Hart, Hermela Shimelis, Raymond Moore, James N. Ingle, and Fergus J. Couch, Mayo Clinic; and Richard M. Weinshilboum and Liewei Wang, Mayo Clinic College of Medicine, Mayo Foundation, Rochester, MN
| | - Michael Untch
- Peter A. Fasching and Matthias Rübner, Erlangen University Hospital, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen; Sibylle Loibl, Valentina Nekljudova, Karsten E. Weber, and Gunter von Minckwitz, German Breast Group Forschungs, Neu-Isenburg; Christian Schem, University Medical Center Schleswig-Holstein, Kiel; Hans Tesch, Centrum für Hämatologie und Onkologie Bethanien, Frankfurt; Michael Untch, Helios-Klinikum, Berlin-Buch; Jörn Hilfrich, Eilenriede-Klinik, Hannover; Mahdi Rezai, Luisenkrankenhaus; Tanja Fehm, Düsseldorf University Hospital, Heinrich-Heine University of Düsseldorf, Düsseldorf; Bernd Gerber, University of Rostock, Rostock; Serban Dan Costa, Magdeburg University Hospital, Magdeburg; Jens-Uwe Blohmer and Cornelia Liedtke, Charité University Hospital Campus Charité-Mitte, Berlin; Jens Huober, University of Ulm; Brigitte Rack, University Hospital Ulm, Ulm; Volkmar Müller, Hamburg University Hospital, Hamburg, Germany; Chunling Hu, Steven N. Hart, Hermela Shimelis, Raymond Moore, James N. Ingle, and Fergus J. Couch, Mayo Clinic; and Richard M. Weinshilboum and Liewei Wang, Mayo Clinic College of Medicine, Mayo Foundation, Rochester, MN
| | - Jörn Hilfrich
- Peter A. Fasching and Matthias Rübner, Erlangen University Hospital, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen; Sibylle Loibl, Valentina Nekljudova, Karsten E. Weber, and Gunter von Minckwitz, German Breast Group Forschungs, Neu-Isenburg; Christian Schem, University Medical Center Schleswig-Holstein, Kiel; Hans Tesch, Centrum für Hämatologie und Onkologie Bethanien, Frankfurt; Michael Untch, Helios-Klinikum, Berlin-Buch; Jörn Hilfrich, Eilenriede-Klinik, Hannover; Mahdi Rezai, Luisenkrankenhaus; Tanja Fehm, Düsseldorf University Hospital, Heinrich-Heine University of Düsseldorf, Düsseldorf; Bernd Gerber, University of Rostock, Rostock; Serban Dan Costa, Magdeburg University Hospital, Magdeburg; Jens-Uwe Blohmer and Cornelia Liedtke, Charité University Hospital Campus Charité-Mitte, Berlin; Jens Huober, University of Ulm; Brigitte Rack, University Hospital Ulm, Ulm; Volkmar Müller, Hamburg University Hospital, Hamburg, Germany; Chunling Hu, Steven N. Hart, Hermela Shimelis, Raymond Moore, James N. Ingle, and Fergus J. Couch, Mayo Clinic; and Richard M. Weinshilboum and Liewei Wang, Mayo Clinic College of Medicine, Mayo Foundation, Rochester, MN
| | - Mahdi Rezai
- Peter A. Fasching and Matthias Rübner, Erlangen University Hospital, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen; Sibylle Loibl, Valentina Nekljudova, Karsten E. Weber, and Gunter von Minckwitz, German Breast Group Forschungs, Neu-Isenburg; Christian Schem, University Medical Center Schleswig-Holstein, Kiel; Hans Tesch, Centrum für Hämatologie und Onkologie Bethanien, Frankfurt; Michael Untch, Helios-Klinikum, Berlin-Buch; Jörn Hilfrich, Eilenriede-Klinik, Hannover; Mahdi Rezai, Luisenkrankenhaus; Tanja Fehm, Düsseldorf University Hospital, Heinrich-Heine University of Düsseldorf, Düsseldorf; Bernd Gerber, University of Rostock, Rostock; Serban Dan Costa, Magdeburg University Hospital, Magdeburg; Jens-Uwe Blohmer and Cornelia Liedtke, Charité University Hospital Campus Charité-Mitte, Berlin; Jens Huober, University of Ulm; Brigitte Rack, University Hospital Ulm, Ulm; Volkmar Müller, Hamburg University Hospital, Hamburg, Germany; Chunling Hu, Steven N. Hart, Hermela Shimelis, Raymond Moore, James N. Ingle, and Fergus J. Couch, Mayo Clinic; and Richard M. Weinshilboum and Liewei Wang, Mayo Clinic College of Medicine, Mayo Foundation, Rochester, MN
| | - Bernd Gerber
- Peter A. Fasching and Matthias Rübner, Erlangen University Hospital, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen; Sibylle Loibl, Valentina Nekljudova, Karsten E. Weber, and Gunter von Minckwitz, German Breast Group Forschungs, Neu-Isenburg; Christian Schem, University Medical Center Schleswig-Holstein, Kiel; Hans Tesch, Centrum für Hämatologie und Onkologie Bethanien, Frankfurt; Michael Untch, Helios-Klinikum, Berlin-Buch; Jörn Hilfrich, Eilenriede-Klinik, Hannover; Mahdi Rezai, Luisenkrankenhaus; Tanja Fehm, Düsseldorf University Hospital, Heinrich-Heine University of Düsseldorf, Düsseldorf; Bernd Gerber, University of Rostock, Rostock; Serban Dan Costa, Magdeburg University Hospital, Magdeburg; Jens-Uwe Blohmer and Cornelia Liedtke, Charité University Hospital Campus Charité-Mitte, Berlin; Jens Huober, University of Ulm; Brigitte Rack, University Hospital Ulm, Ulm; Volkmar Müller, Hamburg University Hospital, Hamburg, Germany; Chunling Hu, Steven N. Hart, Hermela Shimelis, Raymond Moore, James N. Ingle, and Fergus J. Couch, Mayo Clinic; and Richard M. Weinshilboum and Liewei Wang, Mayo Clinic College of Medicine, Mayo Foundation, Rochester, MN
| | - Serban Dan Costa
- Peter A. Fasching and Matthias Rübner, Erlangen University Hospital, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen; Sibylle Loibl, Valentina Nekljudova, Karsten E. Weber, and Gunter von Minckwitz, German Breast Group Forschungs, Neu-Isenburg; Christian Schem, University Medical Center Schleswig-Holstein, Kiel; Hans Tesch, Centrum für Hämatologie und Onkologie Bethanien, Frankfurt; Michael Untch, Helios-Klinikum, Berlin-Buch; Jörn Hilfrich, Eilenriede-Klinik, Hannover; Mahdi Rezai, Luisenkrankenhaus; Tanja Fehm, Düsseldorf University Hospital, Heinrich-Heine University of Düsseldorf, Düsseldorf; Bernd Gerber, University of Rostock, Rostock; Serban Dan Costa, Magdeburg University Hospital, Magdeburg; Jens-Uwe Blohmer and Cornelia Liedtke, Charité University Hospital Campus Charité-Mitte, Berlin; Jens Huober, University of Ulm; Brigitte Rack, University Hospital Ulm, Ulm; Volkmar Müller, Hamburg University Hospital, Hamburg, Germany; Chunling Hu, Steven N. Hart, Hermela Shimelis, Raymond Moore, James N. Ingle, and Fergus J. Couch, Mayo Clinic; and Richard M. Weinshilboum and Liewei Wang, Mayo Clinic College of Medicine, Mayo Foundation, Rochester, MN
| | - Jens-Uwe Blohmer
- Peter A. Fasching and Matthias Rübner, Erlangen University Hospital, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen; Sibylle Loibl, Valentina Nekljudova, Karsten E. Weber, and Gunter von Minckwitz, German Breast Group Forschungs, Neu-Isenburg; Christian Schem, University Medical Center Schleswig-Holstein, Kiel; Hans Tesch, Centrum für Hämatologie und Onkologie Bethanien, Frankfurt; Michael Untch, Helios-Klinikum, Berlin-Buch; Jörn Hilfrich, Eilenriede-Klinik, Hannover; Mahdi Rezai, Luisenkrankenhaus; Tanja Fehm, Düsseldorf University Hospital, Heinrich-Heine University of Düsseldorf, Düsseldorf; Bernd Gerber, University of Rostock, Rostock; Serban Dan Costa, Magdeburg University Hospital, Magdeburg; Jens-Uwe Blohmer and Cornelia Liedtke, Charité University Hospital Campus Charité-Mitte, Berlin; Jens Huober, University of Ulm; Brigitte Rack, University Hospital Ulm, Ulm; Volkmar Müller, Hamburg University Hospital, Hamburg, Germany; Chunling Hu, Steven N. Hart, Hermela Shimelis, Raymond Moore, James N. Ingle, and Fergus J. Couch, Mayo Clinic; and Richard M. Weinshilboum and Liewei Wang, Mayo Clinic College of Medicine, Mayo Foundation, Rochester, MN
| | - Tanja Fehm
- Peter A. Fasching and Matthias Rübner, Erlangen University Hospital, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen; Sibylle Loibl, Valentina Nekljudova, Karsten E. Weber, and Gunter von Minckwitz, German Breast Group Forschungs, Neu-Isenburg; Christian Schem, University Medical Center Schleswig-Holstein, Kiel; Hans Tesch, Centrum für Hämatologie und Onkologie Bethanien, Frankfurt; Michael Untch, Helios-Klinikum, Berlin-Buch; Jörn Hilfrich, Eilenriede-Klinik, Hannover; Mahdi Rezai, Luisenkrankenhaus; Tanja Fehm, Düsseldorf University Hospital, Heinrich-Heine University of Düsseldorf, Düsseldorf; Bernd Gerber, University of Rostock, Rostock; Serban Dan Costa, Magdeburg University Hospital, Magdeburg; Jens-Uwe Blohmer and Cornelia Liedtke, Charité University Hospital Campus Charité-Mitte, Berlin; Jens Huober, University of Ulm; Brigitte Rack, University Hospital Ulm, Ulm; Volkmar Müller, Hamburg University Hospital, Hamburg, Germany; Chunling Hu, Steven N. Hart, Hermela Shimelis, Raymond Moore, James N. Ingle, and Fergus J. Couch, Mayo Clinic; and Richard M. Weinshilboum and Liewei Wang, Mayo Clinic College of Medicine, Mayo Foundation, Rochester, MN
| | - Jens Huober
- Peter A. Fasching and Matthias Rübner, Erlangen University Hospital, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen; Sibylle Loibl, Valentina Nekljudova, Karsten E. Weber, and Gunter von Minckwitz, German Breast Group Forschungs, Neu-Isenburg; Christian Schem, University Medical Center Schleswig-Holstein, Kiel; Hans Tesch, Centrum für Hämatologie und Onkologie Bethanien, Frankfurt; Michael Untch, Helios-Klinikum, Berlin-Buch; Jörn Hilfrich, Eilenriede-Klinik, Hannover; Mahdi Rezai, Luisenkrankenhaus; Tanja Fehm, Düsseldorf University Hospital, Heinrich-Heine University of Düsseldorf, Düsseldorf; Bernd Gerber, University of Rostock, Rostock; Serban Dan Costa, Magdeburg University Hospital, Magdeburg; Jens-Uwe Blohmer and Cornelia Liedtke, Charité University Hospital Campus Charité-Mitte, Berlin; Jens Huober, University of Ulm; Brigitte Rack, University Hospital Ulm, Ulm; Volkmar Müller, Hamburg University Hospital, Hamburg, Germany; Chunling Hu, Steven N. Hart, Hermela Shimelis, Raymond Moore, James N. Ingle, and Fergus J. Couch, Mayo Clinic; and Richard M. Weinshilboum and Liewei Wang, Mayo Clinic College of Medicine, Mayo Foundation, Rochester, MN
| | - Cornelia Liedtke
- Peter A. Fasching and Matthias Rübner, Erlangen University Hospital, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen; Sibylle Loibl, Valentina Nekljudova, Karsten E. Weber, and Gunter von Minckwitz, German Breast Group Forschungs, Neu-Isenburg; Christian Schem, University Medical Center Schleswig-Holstein, Kiel; Hans Tesch, Centrum für Hämatologie und Onkologie Bethanien, Frankfurt; Michael Untch, Helios-Klinikum, Berlin-Buch; Jörn Hilfrich, Eilenriede-Klinik, Hannover; Mahdi Rezai, Luisenkrankenhaus; Tanja Fehm, Düsseldorf University Hospital, Heinrich-Heine University of Düsseldorf, Düsseldorf; Bernd Gerber, University of Rostock, Rostock; Serban Dan Costa, Magdeburg University Hospital, Magdeburg; Jens-Uwe Blohmer and Cornelia Liedtke, Charité University Hospital Campus Charité-Mitte, Berlin; Jens Huober, University of Ulm; Brigitte Rack, University Hospital Ulm, Ulm; Volkmar Müller, Hamburg University Hospital, Hamburg, Germany; Chunling Hu, Steven N. Hart, Hermela Shimelis, Raymond Moore, James N. Ingle, and Fergus J. Couch, Mayo Clinic; and Richard M. Weinshilboum and Liewei Wang, Mayo Clinic College of Medicine, Mayo Foundation, Rochester, MN
| | - Richard M Weinshilboum
- Peter A. Fasching and Matthias Rübner, Erlangen University Hospital, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen; Sibylle Loibl, Valentina Nekljudova, Karsten E. Weber, and Gunter von Minckwitz, German Breast Group Forschungs, Neu-Isenburg; Christian Schem, University Medical Center Schleswig-Holstein, Kiel; Hans Tesch, Centrum für Hämatologie und Onkologie Bethanien, Frankfurt; Michael Untch, Helios-Klinikum, Berlin-Buch; Jörn Hilfrich, Eilenriede-Klinik, Hannover; Mahdi Rezai, Luisenkrankenhaus; Tanja Fehm, Düsseldorf University Hospital, Heinrich-Heine University of Düsseldorf, Düsseldorf; Bernd Gerber, University of Rostock, Rostock; Serban Dan Costa, Magdeburg University Hospital, Magdeburg; Jens-Uwe Blohmer and Cornelia Liedtke, Charité University Hospital Campus Charité-Mitte, Berlin; Jens Huober, University of Ulm; Brigitte Rack, University Hospital Ulm, Ulm; Volkmar Müller, Hamburg University Hospital, Hamburg, Germany; Chunling Hu, Steven N. Hart, Hermela Shimelis, Raymond Moore, James N. Ingle, and Fergus J. Couch, Mayo Clinic; and Richard M. Weinshilboum and Liewei Wang, Mayo Clinic College of Medicine, Mayo Foundation, Rochester, MN
| | - Liewei Wang
- Peter A. Fasching and Matthias Rübner, Erlangen University Hospital, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen; Sibylle Loibl, Valentina Nekljudova, Karsten E. Weber, and Gunter von Minckwitz, German Breast Group Forschungs, Neu-Isenburg; Christian Schem, University Medical Center Schleswig-Holstein, Kiel; Hans Tesch, Centrum für Hämatologie und Onkologie Bethanien, Frankfurt; Michael Untch, Helios-Klinikum, Berlin-Buch; Jörn Hilfrich, Eilenriede-Klinik, Hannover; Mahdi Rezai, Luisenkrankenhaus; Tanja Fehm, Düsseldorf University Hospital, Heinrich-Heine University of Düsseldorf, Düsseldorf; Bernd Gerber, University of Rostock, Rostock; Serban Dan Costa, Magdeburg University Hospital, Magdeburg; Jens-Uwe Blohmer and Cornelia Liedtke, Charité University Hospital Campus Charité-Mitte, Berlin; Jens Huober, University of Ulm; Brigitte Rack, University Hospital Ulm, Ulm; Volkmar Müller, Hamburg University Hospital, Hamburg, Germany; Chunling Hu, Steven N. Hart, Hermela Shimelis, Raymond Moore, James N. Ingle, and Fergus J. Couch, Mayo Clinic; and Richard M. Weinshilboum and Liewei Wang, Mayo Clinic College of Medicine, Mayo Foundation, Rochester, MN
| | - James N Ingle
- Peter A. Fasching and Matthias Rübner, Erlangen University Hospital, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen; Sibylle Loibl, Valentina Nekljudova, Karsten E. Weber, and Gunter von Minckwitz, German Breast Group Forschungs, Neu-Isenburg; Christian Schem, University Medical Center Schleswig-Holstein, Kiel; Hans Tesch, Centrum für Hämatologie und Onkologie Bethanien, Frankfurt; Michael Untch, Helios-Klinikum, Berlin-Buch; Jörn Hilfrich, Eilenriede-Klinik, Hannover; Mahdi Rezai, Luisenkrankenhaus; Tanja Fehm, Düsseldorf University Hospital, Heinrich-Heine University of Düsseldorf, Düsseldorf; Bernd Gerber, University of Rostock, Rostock; Serban Dan Costa, Magdeburg University Hospital, Magdeburg; Jens-Uwe Blohmer and Cornelia Liedtke, Charité University Hospital Campus Charité-Mitte, Berlin; Jens Huober, University of Ulm; Brigitte Rack, University Hospital Ulm, Ulm; Volkmar Müller, Hamburg University Hospital, Hamburg, Germany; Chunling Hu, Steven N. Hart, Hermela Shimelis, Raymond Moore, James N. Ingle, and Fergus J. Couch, Mayo Clinic; and Richard M. Weinshilboum and Liewei Wang, Mayo Clinic College of Medicine, Mayo Foundation, Rochester, MN
| | - Volkmar Müller
- Peter A. Fasching and Matthias Rübner, Erlangen University Hospital, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen; Sibylle Loibl, Valentina Nekljudova, Karsten E. Weber, and Gunter von Minckwitz, German Breast Group Forschungs, Neu-Isenburg; Christian Schem, University Medical Center Schleswig-Holstein, Kiel; Hans Tesch, Centrum für Hämatologie und Onkologie Bethanien, Frankfurt; Michael Untch, Helios-Klinikum, Berlin-Buch; Jörn Hilfrich, Eilenriede-Klinik, Hannover; Mahdi Rezai, Luisenkrankenhaus; Tanja Fehm, Düsseldorf University Hospital, Heinrich-Heine University of Düsseldorf, Düsseldorf; Bernd Gerber, University of Rostock, Rostock; Serban Dan Costa, Magdeburg University Hospital, Magdeburg; Jens-Uwe Blohmer and Cornelia Liedtke, Charité University Hospital Campus Charité-Mitte, Berlin; Jens Huober, University of Ulm; Brigitte Rack, University Hospital Ulm, Ulm; Volkmar Müller, Hamburg University Hospital, Hamburg, Germany; Chunling Hu, Steven N. Hart, Hermela Shimelis, Raymond Moore, James N. Ingle, and Fergus J. Couch, Mayo Clinic; and Richard M. Weinshilboum and Liewei Wang, Mayo Clinic College of Medicine, Mayo Foundation, Rochester, MN
| | - Valentina Nekljudova
- Peter A. Fasching and Matthias Rübner, Erlangen University Hospital, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen; Sibylle Loibl, Valentina Nekljudova, Karsten E. Weber, and Gunter von Minckwitz, German Breast Group Forschungs, Neu-Isenburg; Christian Schem, University Medical Center Schleswig-Holstein, Kiel; Hans Tesch, Centrum für Hämatologie und Onkologie Bethanien, Frankfurt; Michael Untch, Helios-Klinikum, Berlin-Buch; Jörn Hilfrich, Eilenriede-Klinik, Hannover; Mahdi Rezai, Luisenkrankenhaus; Tanja Fehm, Düsseldorf University Hospital, Heinrich-Heine University of Düsseldorf, Düsseldorf; Bernd Gerber, University of Rostock, Rostock; Serban Dan Costa, Magdeburg University Hospital, Magdeburg; Jens-Uwe Blohmer and Cornelia Liedtke, Charité University Hospital Campus Charité-Mitte, Berlin; Jens Huober, University of Ulm; Brigitte Rack, University Hospital Ulm, Ulm; Volkmar Müller, Hamburg University Hospital, Hamburg, Germany; Chunling Hu, Steven N. Hart, Hermela Shimelis, Raymond Moore, James N. Ingle, and Fergus J. Couch, Mayo Clinic; and Richard M. Weinshilboum and Liewei Wang, Mayo Clinic College of Medicine, Mayo Foundation, Rochester, MN
| | - Karsten E Weber
- Peter A. Fasching and Matthias Rübner, Erlangen University Hospital, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen; Sibylle Loibl, Valentina Nekljudova, Karsten E. Weber, and Gunter von Minckwitz, German Breast Group Forschungs, Neu-Isenburg; Christian Schem, University Medical Center Schleswig-Holstein, Kiel; Hans Tesch, Centrum für Hämatologie und Onkologie Bethanien, Frankfurt; Michael Untch, Helios-Klinikum, Berlin-Buch; Jörn Hilfrich, Eilenriede-Klinik, Hannover; Mahdi Rezai, Luisenkrankenhaus; Tanja Fehm, Düsseldorf University Hospital, Heinrich-Heine University of Düsseldorf, Düsseldorf; Bernd Gerber, University of Rostock, Rostock; Serban Dan Costa, Magdeburg University Hospital, Magdeburg; Jens-Uwe Blohmer and Cornelia Liedtke, Charité University Hospital Campus Charité-Mitte, Berlin; Jens Huober, University of Ulm; Brigitte Rack, University Hospital Ulm, Ulm; Volkmar Müller, Hamburg University Hospital, Hamburg, Germany; Chunling Hu, Steven N. Hart, Hermela Shimelis, Raymond Moore, James N. Ingle, and Fergus J. Couch, Mayo Clinic; and Richard M. Weinshilboum and Liewei Wang, Mayo Clinic College of Medicine, Mayo Foundation, Rochester, MN
| | - Brigitte Rack
- Peter A. Fasching and Matthias Rübner, Erlangen University Hospital, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen; Sibylle Loibl, Valentina Nekljudova, Karsten E. Weber, and Gunter von Minckwitz, German Breast Group Forschungs, Neu-Isenburg; Christian Schem, University Medical Center Schleswig-Holstein, Kiel; Hans Tesch, Centrum für Hämatologie und Onkologie Bethanien, Frankfurt; Michael Untch, Helios-Klinikum, Berlin-Buch; Jörn Hilfrich, Eilenriede-Klinik, Hannover; Mahdi Rezai, Luisenkrankenhaus; Tanja Fehm, Düsseldorf University Hospital, Heinrich-Heine University of Düsseldorf, Düsseldorf; Bernd Gerber, University of Rostock, Rostock; Serban Dan Costa, Magdeburg University Hospital, Magdeburg; Jens-Uwe Blohmer and Cornelia Liedtke, Charité University Hospital Campus Charité-Mitte, Berlin; Jens Huober, University of Ulm; Brigitte Rack, University Hospital Ulm, Ulm; Volkmar Müller, Hamburg University Hospital, Hamburg, Germany; Chunling Hu, Steven N. Hart, Hermela Shimelis, Raymond Moore, James N. Ingle, and Fergus J. Couch, Mayo Clinic; and Richard M. Weinshilboum and Liewei Wang, Mayo Clinic College of Medicine, Mayo Foundation, Rochester, MN
| | - Matthias Rübner
- Peter A. Fasching and Matthias Rübner, Erlangen University Hospital, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen; Sibylle Loibl, Valentina Nekljudova, Karsten E. Weber, and Gunter von Minckwitz, German Breast Group Forschungs, Neu-Isenburg; Christian Schem, University Medical Center Schleswig-Holstein, Kiel; Hans Tesch, Centrum für Hämatologie und Onkologie Bethanien, Frankfurt; Michael Untch, Helios-Klinikum, Berlin-Buch; Jörn Hilfrich, Eilenriede-Klinik, Hannover; Mahdi Rezai, Luisenkrankenhaus; Tanja Fehm, Düsseldorf University Hospital, Heinrich-Heine University of Düsseldorf, Düsseldorf; Bernd Gerber, University of Rostock, Rostock; Serban Dan Costa, Magdeburg University Hospital, Magdeburg; Jens-Uwe Blohmer and Cornelia Liedtke, Charité University Hospital Campus Charité-Mitte, Berlin; Jens Huober, University of Ulm; Brigitte Rack, University Hospital Ulm, Ulm; Volkmar Müller, Hamburg University Hospital, Hamburg, Germany; Chunling Hu, Steven N. Hart, Hermela Shimelis, Raymond Moore, James N. Ingle, and Fergus J. Couch, Mayo Clinic; and Richard M. Weinshilboum and Liewei Wang, Mayo Clinic College of Medicine, Mayo Foundation, Rochester, MN
| | - Gunter von Minckwitz
- Peter A. Fasching and Matthias Rübner, Erlangen University Hospital, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen; Sibylle Loibl, Valentina Nekljudova, Karsten E. Weber, and Gunter von Minckwitz, German Breast Group Forschungs, Neu-Isenburg; Christian Schem, University Medical Center Schleswig-Holstein, Kiel; Hans Tesch, Centrum für Hämatologie und Onkologie Bethanien, Frankfurt; Michael Untch, Helios-Klinikum, Berlin-Buch; Jörn Hilfrich, Eilenriede-Klinik, Hannover; Mahdi Rezai, Luisenkrankenhaus; Tanja Fehm, Düsseldorf University Hospital, Heinrich-Heine University of Düsseldorf, Düsseldorf; Bernd Gerber, University of Rostock, Rostock; Serban Dan Costa, Magdeburg University Hospital, Magdeburg; Jens-Uwe Blohmer and Cornelia Liedtke, Charité University Hospital Campus Charité-Mitte, Berlin; Jens Huober, University of Ulm; Brigitte Rack, University Hospital Ulm, Ulm; Volkmar Müller, Hamburg University Hospital, Hamburg, Germany; Chunling Hu, Steven N. Hart, Hermela Shimelis, Raymond Moore, James N. Ingle, and Fergus J. Couch, Mayo Clinic; and Richard M. Weinshilboum and Liewei Wang, Mayo Clinic College of Medicine, Mayo Foundation, Rochester, MN
| | - Fergus J Couch
- Peter A. Fasching and Matthias Rübner, Erlangen University Hospital, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen; Sibylle Loibl, Valentina Nekljudova, Karsten E. Weber, and Gunter von Minckwitz, German Breast Group Forschungs, Neu-Isenburg; Christian Schem, University Medical Center Schleswig-Holstein, Kiel; Hans Tesch, Centrum für Hämatologie und Onkologie Bethanien, Frankfurt; Michael Untch, Helios-Klinikum, Berlin-Buch; Jörn Hilfrich, Eilenriede-Klinik, Hannover; Mahdi Rezai, Luisenkrankenhaus; Tanja Fehm, Düsseldorf University Hospital, Heinrich-Heine University of Düsseldorf, Düsseldorf; Bernd Gerber, University of Rostock, Rostock; Serban Dan Costa, Magdeburg University Hospital, Magdeburg; Jens-Uwe Blohmer and Cornelia Liedtke, Charité University Hospital Campus Charité-Mitte, Berlin; Jens Huober, University of Ulm; Brigitte Rack, University Hospital Ulm, Ulm; Volkmar Müller, Hamburg University Hospital, Hamburg, Germany; Chunling Hu, Steven N. Hart, Hermela Shimelis, Raymond Moore, James N. Ingle, and Fergus J. Couch, Mayo Clinic; and Richard M. Weinshilboum and Liewei Wang, Mayo Clinic College of Medicine, Mayo Foundation, Rochester, MN
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Münz M, Mahamdallie S, Yost S, Rimmer A, Poyastro-Pearson E, Strydom A, Seal S, Ruark E, Rahman N. CoverView: a sequence quality evaluation tool for next generation sequencing data. Wellcome Open Res 2018; 3:36. [PMID: 29881786 PMCID: PMC5964631 DOI: 10.12688/wellcomeopenres.14306.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2018] [Indexed: 01/05/2023] Open
Abstract
Quality assurance and quality control are essential for robust next generation sequencing (NGS). Here we present CoverView, a fast, flexible, user-friendly quality evaluation tool for NGS data. CoverView processes mapped sequencing reads and user-specified regions to report depth of coverage, base and mapping quality metrics with increasing levels of detail from a chromosome-level summary to per-base profiles. CoverView can flag regions that do not fulfil user-specified quality requirements, allowing suboptimal data to be systematically and automatically presented for review. It also provides an interactive graphical user interface (GUI) that can be opened in a web browser and allows intuitive exploration of results. We have integrated CoverView into our accredited clinical cancer predisposition gene testing laboratory that uses the TruSight Cancer Panel (TSCP). CoverView has been invaluable for optimisation and quality control of our testing pipeline, providing transparent, consistent quality metric information and automatic flagging of regions that fall below quality thresholds. We demonstrate this utility with TSCP data from the Genome in a Bottle reference sample, which CoverView analysed in 13 seconds. CoverView uses data routinely generated by NGS pipelines, reads standard input formats, and rapidly creates easy-to-parse output text (.txt) files that are customised by a simple configuration file. CoverView can therefore be easily integrated into any NGS pipeline. CoverView and detailed documentation for its use are freely available at
github.com/RahmanTeamDevelopment/CoverView/releases and
www.icr.ac.uk/CoverView
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Affiliation(s)
- Márton Münz
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Shazia Mahamdallie
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Shawn Yost
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Andrew Rimmer
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Emma Poyastro-Pearson
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Ann Strydom
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Sheila Seal
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Elise Ruark
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Nazneen Rahman
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK.,Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, SM2 5PT, UK
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Vlachogiannis G, Hedayat S, Vatsiou A, Jamin Y, Fernández-Mateos J, Khan K, Lampis A, Eason K, Huntingford I, Burke R, Rata M, Koh DM, Tunariu N, Collins D, Hulkki-Wilson S, Ragulan C, Spiteri I, Moorcraft SY, Chau I, Rao S, Watkins D, Fotiadis N, Bali M, Darvish-Damavandi M, Lote H, Eltahir Z, Smyth EC, Begum R, Clarke PA, Hahne JC, Dowsett M, de Bono J, Workman P, Sadanandam A, Fassan M, Sansom OJ, Eccles S, Starling N, Braconi C, Sottoriva A, Robinson SP, Cunningham D, Valeri N. Patient-derived organoids model treatment response of metastatic gastrointestinal cancers. Science 2018; 359:920-926. [PMID: 29472484 PMCID: PMC6112415 DOI: 10.1126/science.aao2774] [Citation(s) in RCA: 1142] [Impact Index Per Article: 190.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 10/26/2017] [Accepted: 01/11/2018] [Indexed: 12/20/2022]
Abstract
Patient-derived organoids (PDOs) have recently emerged as robust preclinical models; however, their potential to predict clinical outcomes in patients has remained unclear. We report on a living biobank of PDOs from metastatic, heavily pretreated colorectal and gastroesophageal cancer patients recruited in phase 1/2 clinical trials. Phenotypic and genotypic profiling of PDOs showed a high degree of similarity to the original patient tumors. Molecular profiling of tumor organoids was matched to drug-screening results, suggesting that PDOs could complement existing approaches in defining cancer vulnerabilities and improving treatment responses. We compared responses to anticancer agents ex vivo in organoids and PDO-based orthotopic mouse tumor xenograft models with the responses of the patients in clinical trials. Our data suggest that PDOs can recapitulate patient responses in the clinic and could be implemented in personalized medicine programs.
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Affiliation(s)
| | - Somaieh Hedayat
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Alexandra Vatsiou
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Yann Jamin
- Cancer Research UK Cancer Imaging Centre, Division of Radiotherapy and Imaging, The Institute of Cancer Research and Royal Marsden Hospital, London, UK
| | - Javier Fernández-Mateos
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Khurum Khan
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Department of Medicine, The Royal Marsden NHS Trust, London, UK
| | - Andrea Lampis
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Katherine Eason
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Ian Huntingford
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Rosemary Burke
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Mihaela Rata
- Cancer Research UK Cancer Imaging Centre, Division of Radiotherapy and Imaging, The Institute of Cancer Research and Royal Marsden Hospital, London, UK
| | - Dow-Mu Koh
- Cancer Research UK Cancer Imaging Centre, Division of Radiotherapy and Imaging, The Institute of Cancer Research and Royal Marsden Hospital, London, UK
- Department of Radiology, The Royal Marsden NHS Trust, London, UK
| | - Nina Tunariu
- Cancer Research UK Cancer Imaging Centre, Division of Radiotherapy and Imaging, The Institute of Cancer Research and Royal Marsden Hospital, London, UK
- Department of Radiology, The Royal Marsden NHS Trust, London, UK
| | - David Collins
- Cancer Research UK Cancer Imaging Centre, Division of Radiotherapy and Imaging, The Institute of Cancer Research and Royal Marsden Hospital, London, UK
| | - Sanna Hulkki-Wilson
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Chanthirika Ragulan
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Inmaculada Spiteri
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | | | - Ian Chau
- Department of Medicine, The Royal Marsden NHS Trust, London, UK
| | - Sheela Rao
- Department of Medicine, The Royal Marsden NHS Trust, London, UK
| | - David Watkins
- Department of Medicine, The Royal Marsden NHS Trust, London, UK
| | - Nicos Fotiadis
- Department of Radiology, The Royal Marsden NHS Trust, London, UK
| | - Maria Bali
- Cancer Research UK Cancer Imaging Centre, Division of Radiotherapy and Imaging, The Institute of Cancer Research and Royal Marsden Hospital, London, UK
- Department of Radiology, The Royal Marsden NHS Trust, London, UK
| | | | - Hazel Lote
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Department of Medicine, The Royal Marsden NHS Trust, London, UK
| | - Zakaria Eltahir
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | | | - Ruwaida Begum
- Department of Medicine, The Royal Marsden NHS Trust, London, UK
| | - Paul A Clarke
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Jens C Hahne
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Mitchell Dowsett
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital NHS Trust, London, UK
| | - Johann de Bono
- Division of Clinical Studies, The Institute of Cancer Research, London, UK
| | - Paul Workman
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Anguraj Sadanandam
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Matteo Fassan
- Department of Medicine, Surgical Pathology and Cytopathology Unit, University of Padua, Padua, Italy
| | | | - Suzanne Eccles
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | | | - Chiara Braconi
- Department of Medicine, The Royal Marsden NHS Trust, London, UK
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Andrea Sottoriva
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Simon P Robinson
- Cancer Research UK Cancer Imaging Centre, Division of Radiotherapy and Imaging, The Institute of Cancer Research and Royal Marsden Hospital, London, UK
| | | | - Nicola Valeri
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
- Department of Medicine, The Royal Marsden NHS Trust, London, UK
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Nguyen-Dumont T, Myszka A, Karpinski P, Sasiadek MM, Akopyan H, Hammet F, Tsimiklis H, Park DJ, Pope BJ, Slezak R, Kitsera N, Siekierzynska A, Southey MC. FANCM and RECQL genetic variants and breast cancer susceptibility: relevance to South Poland and West Ukraine. BMC MEDICAL GENETICS 2018; 19:12. [PMID: 29351780 PMCID: PMC5775547 DOI: 10.1186/s12881-018-0524-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 01/09/2018] [Indexed: 12/17/2022]
Abstract
Background FANCM and RECQL have recently been reported as breast cancer susceptibility genes and it has been suggested that they should be included on gene panel tests for breast cancer predisposition. However, the clinical value of testing for mutations in RECQL and FANCM remains to be determined. In this study, we have characterised the spectrum of FANCM and RECQL mutations in women affected with breast or ovarian cancer from South-West Poland and West Ukraine. Methods We applied Hi-Plex, an amplicon-based enrichment method for targeted massively parallel sequencing, to screen the coding exons and proximal intron-exon junctions of FANCM and RECQL in germline DNA from unrelated women affected with breast cancer (n = 338) and ovarian cancer (n = 89) from Poland (n = 304) and Ukraine (n = 123). These women were at high-risk of carrying a genetic predisposition to breast and/or ovarian cancer due to a family history and/or early-onset disease. Results Among 427 women screened, we identified one carrier of the FANCM:c.1972C > T nonsense mutation (0.23%), and two carriers of the frameshift insertion FANCM:c.1491dup (0.47%). None of the variants we observed in RECQL were predicted to be loss-of-function mutations by standard variant effect prediction tools. Conclusions Our study of the Polish and Ukrainian populations has identified a carrier frequency of truncating mutations in FANCM consistent with previous reports. Although initial reports suggesting that mutations in RECQL could be associated with increased breast cancer risk included women from Poland and identified the RECQL:c.1667_1667 + 3delAGTA mutation in 0.23–0.35% of breast cancer cases, we did not observe any carriers in our study cohort. Continued screening, both in research and diagnostic settings, will enable the accumulation of data that is needed to establish the clinical utility of including RECQL and FANCM on gene panel tests. Electronic supplementary material The online version of this article (10.1186/s12881-018-0524-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tú Nguyen-Dumont
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, Australia
| | - Aleksander Myszka
- Institute of Obstetrics and Emergency Medicine, University of Rzeszow, Rzeszow, Poland
| | - Pawel Karpinski
- Department of Genetics, Wroclaw Medical University, Wroclaw, Poland
| | - Maria M Sasiadek
- Department of Genetics, Wroclaw Medical University, Wroclaw, Poland
| | - Hayane Akopyan
- Institute of Obstetrics and Emergency Medicine, University of Rzeszow, Rzeszow, Poland.,Institute of Hereditary Pathology of National Academy of Medical Sciences, Lviv, Ukraine
| | - Fleur Hammet
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, Australia
| | - Helen Tsimiklis
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, Australia
| | - Daniel J Park
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, Australia.,Melbourne Bioinformatics, The University of Melbourne, Carlton, Victoria, Australia
| | - Bernard J Pope
- Melbourne Bioinformatics, The University of Melbourne, Carlton, Victoria, Australia
| | - Ryszard Slezak
- Department of Genetics, Wroclaw Medical University, Wroclaw, Poland
| | - Nataliya Kitsera
- Institute of Hereditary Pathology of National Academy of Medical Sciences, Lviv, Ukraine
| | | | - Melissa C Southey
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, Australia.
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Huang Y, Cao Y, Li J, Liu Y, Zhong W, Li X, Chen C, Hao P. A survey on cellular RNA editing activity in response to Candida albicans infections. BMC Genomics 2018; 19:43. [PMID: 29363428 PMCID: PMC5780849 DOI: 10.1186/s12864-017-4374-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background Adenosine-to-Inosine (A-to-I) RNA editing is catalyzed by the adenosine deaminase acting on RNA (ADAR) family of enzymes, which induces alterations in mRNA sequence. It has been shown that A-to-I RNA editing events are of significance in the cell’s innate immunity and cellular response to viral infections. However, whether RNA editing plays a role in cellular response to microorganism/fungi infection has not been determined. Candida albicans, one of the most prevalent human pathogenic fungi, usually act as a commensal on skin and superficial mucosal, but has been found to cause candidiasis in immunosuppression patients. Previously, we have revealed the up-regulation of A-to-I RNA editing activity in response to different types of influenza virus infections. The current work is designed to study the effect of microorganism/fungi infection on the activity of A-to-I RNA editing in infected hosts. Results We first detected and characterized the A-to-I RNA editing events in oral epithelial cells (OKF6) and primary human umbilical vein endothelial cells (HUVEC), under normal growth condition or with C. albicans infection. Eighty nine thousand six hundred forty eight and 60,872 A-to-I editing sites were detected in normal OKF6 and HUVEC cells, respectively. They were validated against the RNA editing databases, DARNED, RADAR, and REDIportal with 50, 80, and 80% success rates, respectively. While over 95% editing sites were detected in Alu regions, among the rest of the editing sites in non repetitive regions, the majority was located in introns and UTRs. The distributions of A-to-I editing activity and editing depth were analyzed during the course of C. albicans infection. While the normalized editing levels of common editing sites exhibited a significant increase, especially in Alu regions, no significant change in the expression of ADAR1 or ADAR2 was observed. Second, we performed further analysis on data from in vivo mouse study with C. albicans infection. One thousand one hundred thirty three and 955 A-to-I editing sites were identified in mouse tongue and kidney tissues, respectively. The number of A-to-I editing events was much smaller than in human epithelial or endothelial cells, due to the lack of Alu elements in mouse genome. Furthermore, during the course of C. albicans infection we observed stable level of A-to-I editing activity in 131 and 190 common editing sites in the mouse tongue and kidney tissues, and found no significant change in ADAR1 or ADAR2 expression (with the exception of ADAR2 displaying a significant increase at 12 h after infection in mouse kidney tissue before returning to normal). Conclusions This work represents the first comprehensive analysis of A-to-I RNA editome in human epithelial and endothelial cells. C. albicans infection of human epithelial and endothelial cells led to the up-regulation of A-to-I editing activities, through a mechanism different from that of viral infections in human hosts. However, the in vivo mouse model with C. albicans infection did not show significant changes in A-to-I editing activities in tongue and kidney tissues. The different results in the mouse model were likely due to the presence of more complex in vivo environments, e.g. circulation and mixed cell types. Electronic supplementary material The online version of this article (10.1186/s12864-017-4374-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yaowei Huang
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 20031, China
| | - Yingying Cao
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 20031, China
| | - Jiarui Li
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100102, China.,Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100102, China
| | - Yuanhua Liu
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 20031, China
| | - Wu Zhong
- National Engineering Research Center For the Emergence Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Xuan Li
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 20032, China.
| | - Chen Chen
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100102, China. .,Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100102, China.
| | - Pei Hao
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 20031, China.
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Sandmann S, de Graaf AO, Dugas M. BBCAnalyzer: a visual approach to facilitate variant calling. BMC Bioinformatics 2017; 18:133. [PMID: 28241736 PMCID: PMC5330023 DOI: 10.1186/s12859-017-1549-4] [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: 10/22/2016] [Accepted: 02/16/2017] [Indexed: 11/10/2022] Open
Abstract
Background Deriving valid variant calling results from raw next-generation sequencing data is a particularly challenging task, especially with respect to clinical diagnostics and personalized medicine. However, when using classic variant calling software, the user usually obtains nothing more than a list of variants that pass the corresponding caller’s internal filters. Any expected mutations (e.g. hotspot mutations), that have not been called by the software, need to be investigated manually. Results BBCAnalyzer (Bases By CIGAR Analyzer) provides a novel visual approach to facilitate this step of time-consuming, manual inspection of common mutation sites. BBCAnalyzer is able to visualize base counts at predefined positions or regions in any sequence alignment data that are available as BAM files. Thereby, the tool provides a straightforward solution for evaluating any list of expected mutations like hotspot mutations, or even whole regions of interest. In addition to an ordinary textual report, BBCAnalyzer reports highly customizable plots. Information on the counted number of bases, the reference bases, known mutations or polymorphisms, called mutations and base qualities is summarized in a single plot. By uniting this information in a graphical way, the user may easily decide on a variant being present or not – completely independent of any internal filters or frequency thresholds. Conclusions BBCAnalyzer provides a unique, novel approach to facilitate variant calling where classical tools frequently fail to call. The R package is freely available at http://bioconductor.org. The local web application is available at Additional file 2. A documentation of the R package (Additional file 1) as well as the web application (Additional file 2) with detailed descriptions, examples of all input- and output elements, exemplary code as well as exemplary data are included. A video demonstrates the exemplary usage of the local web application (Additional file 3). Additional file 3: Supplement_3. Video demonstrating the exemplary usage of the web application “BBCAnalyzer”. (MP4 11571 kb)
Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1549-4) contains supplementary material, which is available to authorized users.
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Sekse C, Holst-Jensen A, Dobrindt U, Johannessen GS, Li W, Spilsberg B, Shi J. High Throughput Sequencing for Detection of Foodborne Pathogens. Front Microbiol 2017; 8:2029. [PMID: 29104564 PMCID: PMC5655695 DOI: 10.3389/fmicb.2017.02029] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 10/04/2017] [Indexed: 12/23/2022] Open
Abstract
High-throughput sequencing (HTS) is becoming the state-of-the-art technology for typing of microbial isolates, especially in clinical samples. Yet, its application is still in its infancy for monitoring and outbreak investigations of foods. Here we review the published literature, covering not only bacterial but also viral and Eukaryote food pathogens, to assess the status and potential of HTS implementation to inform stakeholders, improve food safety and reduce outbreak impacts. The developments in sequencing technology and bioinformatics have outpaced the capacity to analyze and interpret the sequence data. The influence of sample processing, nucleic acid extraction and purification, harmonized protocols for generation and interpretation of data, and properly annotated and curated reference databases including non-pathogenic "natural" strains are other major obstacles to the realization of the full potential of HTS in analytical food surveillance, epidemiological and outbreak investigations, and in complementing preventive approaches for the control and management of foodborne pathogens. Despite significant obstacles, the achieved progress in capacity and broadening of the application range over the last decade is impressive and unprecedented, as illustrated with the chosen examples from the literature. Large consortia, often with broad international participation, are making coordinated efforts to cope with many of the mentioned obstacles. Further rapid progress can therefore be prospected for the next decade.
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Affiliation(s)
- Camilla Sekse
- Department of Animal Health and Food Safety, Norwegian Veterinary Institute, Oslo, Norway
| | - Arne Holst-Jensen
- Department of Animal Health and Food Safety, Norwegian Veterinary Institute, Oslo, Norway
| | - Ulrich Dobrindt
- Institute of Hygiene, University of Münster, Münster, Germany
| | - Gro S. Johannessen
- Department of Animal Health and Food Safety, Norwegian Veterinary Institute, Oslo, Norway
| | - Weihua Li
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Bjørn Spilsberg
- Department of Analysis and Diagnostics, Norwegian Veterinary Institute, Oslo, Norway
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Yost S, de Wolf B, Hanks S, Zachariou A, Marcozzi C, Clarke M, de Voer R, Etemad B, Uijttewaal E, Ramsay E, Wylie H, Elliott A, Picton S, Smith A, Smithson S, Seal S, Ruark E, Houge G, Pines J, Kops GJ, Rahman N. Biallelic TRIP13 mutations predispose to Wilms tumor and chromosome missegregation. Nat Genet 2017; 49:1148-1151. [PMID: 28553959 PMCID: PMC5493194 DOI: 10.1038/ng.3883] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 05/01/2017] [Indexed: 12/18/2022]
Abstract
Through exome sequencing, we identified six individuals with biallelic loss-of-function mutations in TRIP13. All six developed Wilms tumor. Constitutional mosaic aneuploidies, microcephaly, developmental delay and seizures, which are features of mosaic variegated aneuploidy (MVA) syndrome, were more variably present. Through functional studies, we show that TRIP13-mutant patient cells have no detectable TRIP13 and have substantial impairment of the spindle assembly checkpoint (SAC), leading to a high rate of chromosome missegregation. Accurate segregation, as well as SAC proficiency, is rescued by restoring TRIP13 function. Individuals with biallelic TRIP13 or BUB1B mutations have a high risk of embryonal tumors, and here we show that their cells display severe SAC impairment. MVA due to biallelic CEP57 mutations, or of unknown cause, is not associated with embryonal tumors and cells from these individuals show minimal SAC deficiency. These data provide insights into the complex relationships between aneuploidy and carcinogenesis.
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Affiliation(s)
- Shawn Yost
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG, UK
| | - Bas de Wolf
- Hubrecht Institute – KNAW (Royal Netherlands Academy of Arts and Sciences), Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Sandra Hanks
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG, UK
| | - Anna Zachariou
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG, UK
| | - Chiara Marcozzi
- The Gurdon Institute and Department of Zoology, University of Cambridge, Cambridge CB2 1QN, UK
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Matthew Clarke
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG, UK
| | - Richarda de Voer
- Hubrecht Institute – KNAW (Royal Netherlands Academy of Arts and Sciences), Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Banafsheh Etemad
- Hubrecht Institute – KNAW (Royal Netherlands Academy of Arts and Sciences), Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Esther Uijttewaal
- Hubrecht Institute – KNAW (Royal Netherlands Academy of Arts and Sciences), Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Emma Ramsay
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG, UK
| | - Harriet Wylie
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG, UK
| | - Anna Elliott
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG, UK
| | - Susan Picton
- Children's and Adolescent Oncology and Haematology Unit, Leeds General Infirmary, Leeds, LS1 3EX, UK
| | - Audrey Smith
- Yorkshire Regional Clinical Genetics Service, Chapel Allerton Hospital, Chapeltown Road, Leeds, LS7 4SA, UK
| | - Sarah Smithson
- Clinical Genetics Service, St Michael's Hospital, Southwell Street, Bristol, BS2 8EG, UK
| | - Sheila Seal
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG, UK
| | - Elise Ruark
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG, UK
| | - Gunnar Houge
- Center for Medical Genetics, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Jonathan Pines
- The Gurdon Institute and Department of Zoology, University of Cambridge, Cambridge CB2 1QN, UK
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Geert J.P.L. Kops
- Hubrecht Institute – KNAW (Royal Netherlands Academy of Arts and Sciences), Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Cancer Genomics Netherlands, Utrecht, The Netherlands
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG, Utrecht, The Netherlands
| | - Nazneen Rahman
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG, UK
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, UK SM2 5PT, UK
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42
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Tatton-Brown K, Loveday C, Yost S, Clarke M, Ramsay E, Zachariou A, Elliott A, Wylie H, Ardissone A, Rittinger O, Stewart F, Temple IK, Cole T, Mahamdallie S, Seal S, Ruark E, Rahman N. Mutations in Epigenetic Regulation Genes Are a Major Cause of Overgrowth with Intellectual Disability. Am J Hum Genet 2017; 100:725-736. [PMID: 28475857 PMCID: PMC5420355 DOI: 10.1016/j.ajhg.2017.03.010] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 03/24/2017] [Indexed: 12/04/2022] Open
Abstract
To explore the genetic architecture of human overgrowth syndromes and human growth control, we performed experimental and bioinformatic analyses of 710 individuals with overgrowth (height and/or head circumference ≥+2 SD) and intellectual disability (OGID). We identified a causal mutation in 1 of 14 genes in 50% (353/710). This includes HIST1H1E, encoding histone H1.4, which has not been associated with a developmental disorder previously. The pathogenic HIST1H1E mutations are predicted to result in a product that is less effective in neutralizing negatively charged linker DNA because it has a reduced net charge, and in DNA binding and protein-protein interactions because key residues are truncated. Functional network analyses demonstrated that epigenetic regulation is a prominent biological process dysregulated in individuals with OGID. Mutations in six epigenetic regulation genes—NSD1, EZH2, DNMT3A, CHD8, HIST1H1E, and EED—accounted for 44% of individuals (311/710). There was significant overlap between the 14 genes involved in OGID and 611 genes in regions identified in GWASs to be associated with height (p = 6.84 × 10−8), suggesting that a common variation impacting function of genes involved in OGID influences height at a population level. Increased cellular growth is a hallmark of cancer and there was striking overlap between the genes involved in OGID and 260 somatically mutated cancer driver genes (p = 1.75 × 10−14). However, the mutation spectra of genes involved in OGID and cancer differ, suggesting complex genotype-phenotype relationships. These data reveal insights into the genetic control of human growth and demonstrate that exome sequencing in OGID has a high diagnostic yield.
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Affiliation(s)
- Katrina Tatton-Brown
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK; South West Thames Regional Genetics Service, St George's University Hospitals NHS Foundation Trust, London SW17 0QT, UK
| | - Chey Loveday
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK
| | - Shawn Yost
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK
| | - Matthew Clarke
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK
| | - Emma Ramsay
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK
| | - Anna Zachariou
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK
| | - Anna Elliott
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK
| | - Harriet Wylie
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK
| | - Anna Ardissone
- Child Neurology Unit, Foundation IRCCS C Besta Neurological Institute, Milan 20133, Italy
| | - Olaf Rittinger
- Landeskrankenanstalten Salzburg, Kinderklinik Department of Pediatrics, Klinische Genetik, Salzburg 5020, Austria
| | - Fiona Stewart
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast BT9 7AB, Northern Ireland
| | - I Karen Temple
- Human Development and Health Academic Unit, Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK; Wessex Clinical Genetics Service, University Hospital Southampton NHS Trust, Southampton SO16 6YD, UK
| | - Trevor Cole
- West Midlands Regional Genetics Service, Birmingham Women's Hospital NHS Foundation Trust and University of Birmingham, Birmingham Health Partners, Birmingham B15 2TG, UK
| | - Shazia Mahamdallie
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK
| | - Sheila Seal
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK
| | - Elise Ruark
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK
| | - Nazneen Rahman
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, UK; Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK.
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Ahdesmäki MJ, Chapman BA, Cingolani P, Hofmann O, Sidoruk A, Lai Z, Zakharov G, Rodichenko M, Alperovich M, Jenkins D, Carr TH, Stetson D, Dougherty B, Barrett JC, Johnson JH. Prioritisation of structural variant calls in cancer genomes. PeerJ 2017; 5:e3166. [PMID: 28392986 PMCID: PMC5382922 DOI: 10.7717/peerj.3166] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/09/2017] [Indexed: 12/24/2022] Open
Abstract
Sensitivity of short read DNA-sequencing for gene fusion detection is improving, but is hampered by the significant amount of noise composed of uninteresting or false positive hits in the data. In this paper we describe a tiered prioritisation approach to extract high impact gene fusion events from existing structural variant calls. Using cell line and patient DNA sequence data we improve the annotation and interpretation of structural variant calls to best highlight likely cancer driving fusions. We also considerably improve on the automated visualisation of the high impact structural variants to highlight the effects of the variants on the resulting transcripts. The resulting framework greatly improves on readily detecting clinically actionable structural variants.
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Affiliation(s)
- Miika J Ahdesmäki
- Innovative Medicines and Early Development, Oncology, AstraZeneca , Cambridge , United Kingdom
| | - Brad A Chapman
- Harvard T.H. Chan School of Public Health, Harvard University , Boston , MA , United States
| | | | - Oliver Hofmann
- Centre for Cancer Research, University of Melbourne , Melbourne , Australia
| | - Aleksandr Sidoruk
- EPAM Systems Inc., Newtown, PA, United States; Department of software engineering, St. Petersburg State University, St. Petersburg, Russia
| | - Zhongwu Lai
- Innovative Medicines and Early Development, Oncology, AstraZeneca , Waltham , MA , United States
| | - Gennadii Zakharov
- EPAM Systems Inc., Newtown, PA, United States; Pavlov Institute of Physiology, Russian Academy of Sciences, St. Petersburg, Russia
| | | | | | | | - T Hedley Carr
- Innovative Medicines and Early Development, Oncology, AstraZeneca , Cambridge , United Kingdom
| | - Daniel Stetson
- Innovative Medicines and Early Development, Oncology, AstraZeneca , Waltham , MA , United States
| | - Brian Dougherty
- Innovative Medicines and Early Development, Oncology, AstraZeneca , Waltham , MA , United States
| | - J Carl Barrett
- Innovative Medicines and Early Development, Oncology, AstraZeneca , Waltham , MA , United States
| | - Justin H Johnson
- Innovative Medicines and Early Development, Oncology, AstraZeneca , Waltham , MA , United States
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OpEx - a validated, automated pipeline optimised for clinical exome sequence analysis. Sci Rep 2016; 6:31029. [PMID: 27485037 PMCID: PMC4971567 DOI: 10.1038/srep31029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 07/12/2016] [Indexed: 11/09/2022] Open
Abstract
We present an easy-to-use, open-source Optimised Exome analysis tool, OpEx (http://icr.ac.uk/opex) that accurately detects small-scale variation, including indels, to clinical standards. We evaluated OpEx performance with an experimentally validated dataset (the ICR142 NGS validation series), a large 1000 exome dataset (the ICR1000 UK exome series), and a clinical proband-parent trio dataset. The performance of OpEx for high-quality base substitutions and short indels in both small and large datasets is excellent, with overall sensitivity of 95%, specificity of 97% and low false detection rate (FDR) of 3%. Depending on the individual performance requirements the OpEx output allows one to optimise the inevitable trade-offs between sensitivity and specificity. For example, in the clinical setting one could permit a higher FDR and lower specificity to maximise sensitivity. In contexts where experimental validation is not possible, minimising the FDR and improving specificity may be a preferable trade-off for slightly lower sensitivity. OpEx is simple to install and use; the whole pipeline is run from a single command. OpEx is therefore well suited to the increasing research and clinical laboratories undertaking exome sequencing, particularly those without in-house dedicated bioinformatics expertise.
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45
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Maxwell K, Hart S, Vijai J, Schrader K, Slavin T, Thomas T, Wubbenhorst B, Ravichandran V, Moore R, Hu C, Guidugli L, Wenz B, Domchek S, Robson M, Szabo C, Neuhausen S, Weitzel J, Offit K, Couch F, Nathanson K. Evaluation of ACMG-Guideline-Based Variant Classification of Cancer Susceptibility and Non-Cancer-Associated Genes in Families Affected by Breast Cancer. Am J Hum Genet 2016; 98:801-817. [PMID: 27153395 DOI: 10.1016/j.ajhg.2016.02.024] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 02/26/2016] [Indexed: 01/24/2023] Open
Abstract
Sequencing tests assaying panels of genes or whole exomes are widely available for cancer risk evaluation. However, methods for classification of variants resulting from this testing are not well studied. We evaluated the ability of a variant-classification methodology based on American College of Medical Genetics and Genomics (ACMG) guidelines to define the rate of mutations and variants of uncertain significance (VUS) in 180 medically relevant genes, including all ACMG-designated reportable cancer and non-cancer-associated genes, in individuals who met guidelines for hereditary cancer risk evaluation. We performed whole-exome sequencing in 404 individuals in 253 families and classified 1,640 variants. Potentially clinically actionable (likely pathogenic [LP] or pathogenic [P]) versus nonactionable (VUS, likely benign, or benign) calls were 95% concordant with locus-specific databases and Clinvar. LP or P mutations were identified in 12 of 25 breast cancer susceptibility genes in 26 families without identified BRCA1/2 mutations (11%). Evaluation of 84 additional genes associated with autosomal-dominant cancer susceptibility identified LP or P mutations in only two additional families (0.8%). However, individuals from 10 of 253 families (3.9%) had incidental LP or P mutations in 32 non-cancer-associated genes, and 9% of individuals were monoallelic carriers of a rare LP or P mutation in 39 genes associated with autosomal-recessive cancer susceptibility. Furthermore, 95% of individuals had at least one VUS. In summary, these data support the clinical utility of ACMG variant-classification guidelines. Additionally, evaluation of extended panels of cancer-associated genes in breast/ovarian cancer families leads to only an incremental clinical benefit but substantially increases the complexity of the results.
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46
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Ruark E, Renwick A, Clarke M, Snape K, Ramsay E, Elliott A, Hanks S, Strydom A, Seal S, Rahman N. The ICR142 NGS validation series: a resource for orthogonal assessment of NGS analysis. F1000Res 2016; 5:386. [PMID: 27158454 PMCID: PMC4857748 DOI: 10.12688/f1000research.8219.2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/03/2018] [Indexed: 12/17/2022] Open
Abstract
To provide a useful community resource for orthogonal assessment of NGS analysis software, we present the ICR142 NGS validation series. The dataset includes high-quality exome sequence data from 142 samples together with Sanger sequence data at 704 sites; 416 sites with variants and 288 sites at which variants were called by an NGS analysis tool, but no variant is present in the corresponding Sanger sequence. The dataset includes 293 indel variants and 247 negative indel sites, and thus the ICR142 validation dataset is of particular utility in evaluating indel calling performance. The FASTQ files and Sanger sequence results can be accessed in the European Genome-phenome Archive under the accession number
EGAS00001001332.
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Affiliation(s)
- Elise Ruark
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, UK
| | - Anthony Renwick
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, UK
| | - Matthew Clarke
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, UK
| | - Katie Snape
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, UK
| | - Emma Ramsay
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, UK
| | - Anna Elliott
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, UK
| | - Sandra Hanks
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, UK
| | - Ann Strydom
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, UK
| | - Sheila Seal
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, UK
| | - Nazneen Rahman
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, UK.,Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, UK
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47
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Ruark E, Renwick A, Clarke M, Snape K, Ramsay E, Elliott A, Hanks S, Strydom A, Seal S, Rahman N. The ICR142 NGS validation series: a resource for orthogonal assessment of NGS analysis. F1000Res 2016; 5:386. [PMID: 27158454 PMCID: PMC4857748 DOI: 10.12688/f1000research.8219.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/03/2018] [Indexed: 10/05/2023] Open
Abstract
To provide a useful community resource for orthogonal assessment of NGS analysis software, we present the ICR142 NGS validation series. The dataset includes high-quality exome sequence data from 142 samples together with Sanger sequence data at 704 sites; 416 sites with variants and 288 sites at which variants were called by an NGS analysis tool, but no variant is present in the corresponding Sanger sequence. The dataset includes 293 indel variants and 247 negative indel sites, and thus the ICR142 validation dataset is of particular utility in evaluating indel calling performance. The FASTQ files and Sanger sequence results can be accessed in the European Genome-phenome Archive under the accession number EGAS00001001332.
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Affiliation(s)
- Elise Ruark
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, UK
| | - Anthony Renwick
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, UK
| | - Matthew Clarke
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, UK
| | - Katie Snape
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, UK
| | - Emma Ramsay
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, UK
| | - Anna Elliott
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, UK
| | - Sandra Hanks
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, UK
| | - Ann Strydom
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, UK
| | - Sheila Seal
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, UK
| | - Nazneen Rahman
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, UK
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, UK
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48
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Turner T, Hormozdiari F, Duyzend M, McClymont S, Hook P, Iossifov I, Raja A, Baker C, Hoekzema K, Stessman H, Zody M, Nelson B, Huddleston J, Sandstrom R, Smith J, Hanna D, Swanson J, Faustman E, Bamshad M, Stamatoyannopoulos J, Nickerson D, McCallion A, Darnell R, Eichler E. Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA. Am J Hum Genet 2016; 98:58-74. [PMID: 26749308 DOI: 10.1016/j.ajhg.2015.11.023] [Citation(s) in RCA: 201] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 11/25/2015] [Indexed: 12/17/2022] Open
Abstract
We performed whole-genome sequencing (WGS) of 208 genomes from 53 families affected by simplex autism. For the majority of these families, no copy-number variant (CNV) or candidate de novo gene-disruptive single-nucleotide variant (SNV) had been detected by microarray or whole-exome sequencing (WES). We integrated multiple CNV and SNV analyses and extensive experimental validation to identify additional candidate mutations in eight families. We report that compared to control individuals, probands showed a significant (p = 0.03) enrichment of de novo and private disruptive mutations within fetal CNS DNase I hypersensitive sites (i.e., putative regulatory regions). This effect was only observed within 50 kb of genes that have been previously associated with autism risk, including genes where dosage sensitivity has already been established by recurrent disruptive de novo protein-coding mutations (ARID1B, SCN2A, NR3C2, PRKCA, and DSCAM). In addition, we provide evidence of gene-disruptive CNVs (in DISC1, WNT7A, RBFOX1, and MBD5), as well as smaller de novo CNVs and exon-specific SNVs missed by exome sequencing in neurodevelopmental genes (e.g., CANX, SAE1, and PIK3CA). Our results suggest that the detection of smaller, often multiple CNVs affecting putative regulatory elements might help explain additional risk of simplex autism.
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49
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Ruark E, Münz M, Renwick A, Clarke M, Ramsay E, Hanks S, Mahamdallie S, Elliott A, Seal S, Strydom A, Gerton L, Rahman N. The ICR1000 UK exome series: a resource of gene variation in an outbred population. F1000Res 2015; 4:883. [PMID: 26834991 PMCID: PMC4706061 DOI: 10.12688/f1000research.7049.1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/10/2015] [Indexed: 12/30/2022] Open
Abstract
To enhance knowledge of gene variation in outbred populations, and to provide a dataset with utility in research and clinical genomics, we performed exome sequencing of 1,000 UK individuals from the general population and applied a high-quality analysis pipeline that includes high sensitivity and specificity for indel detection. Each UK individual has, on average, 21,978 gene variants including 160 rare (0.1%) variants not present in any other individual in the series. These data provide a baseline expectation for gene variation in an outbred population. Summary data of all 295,391 variants we detected are included here and the individual exome sequences are available from the European Genome-phenome Archive as the ICR1000 UK exome series. Furthermore, samples and other phenotype and experimental data for these individuals are obtainable through application to the 1958 Birth Cohort committee.
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Affiliation(s)
- Elise Ruark
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Márton Münz
- Wellcome Trust Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Anthony Renwick
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Matthew Clarke
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Emma Ramsay
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Sandra Hanks
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Shazia Mahamdallie
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Anna Elliott
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Sheila Seal
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Ann Strydom
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Lunter Gerton
- Wellcome Trust Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Nazneen Rahman
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK; Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, SM2 5PT, UK
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