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Fortuno C, Michailidou K, Parsons M, Dolinsky JS, Pesaran T, Yussuf A, Mester JL, Hruska KS, Hiraki S, O’Connor R, Chan RC, Kim S, Tavtigian SV, Goldgar D, James PA, Spurdle AB. Challenges and approaches to calibrating patient phenotype as evidence for cancer gene variant classification under ACMG/AMP guidelines. Hum Mol Genet 2024; 33:724-732. [PMID: 38271184 PMCID: PMC11000651 DOI: 10.1093/hmg/ddae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/27/2024] Open
Abstract
Since first publication of the American College of Medical Genetics and Genomics/Association for Medical Pathology (ACMG/AMP) variant classification guidelines, additional recommendations for application of certain criteria have been released (https://clinicalgenome.org/docs/), to improve their application in the diagnostic setting. However, none have addressed use of the PS4 and PP4 criteria, capturing patient presentation as evidence towards pathogenicity. Application of PS4 can be done through traditional case-control studies, or "proband counting" within or across clinical testing cohorts. Review of the existing PS4 and PP4 specifications for Hereditary Cancer Gene Variant Curation Expert Panels revealed substantial differences in the approach to defining specifications. Using BRCA1, BRCA2 and TP53 as exemplar genes, we calibrated different methods proposed for applying the "PS4 proband counting" criterion. For each approach, we considered limitations, non-independence with other ACMG/AMP criteria, broader applicability, and variability in results for different datasets. Our findings highlight inherent overlap of proband-counting methods with ACMG/AMP frequency codes, and the importance of calibration to derive dataset-specific code weights that can account for potential between-dataset differences in ascertainment and other factors. Our work emphasizes the advantages and generalizability of logistic regression analysis over simple proband-counting approaches to empirically determine the relative predictive capacity and weight of various personal clinical features in the context of multigene panel testing, for improved variant interpretation. We also provide a general protocol, including instructions for data formatting and a web-server for analysis of personal history parameters, to facilitate dataset-specific calibration analyses required to use such data for germline variant classification.
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Affiliation(s)
- Cristina Fortuno
- Population Health Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
| | - Kyriaki Michailidou
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Michael Parsons
- Population Health Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
| | | | - Tina Pesaran
- Ambry Genetics, Aliso Viejo, CA 92656, United States
| | - Amal Yussuf
- Ambry Genetics, Aliso Viejo, CA 92656, United States
| | | | | | | | | | - Raymond C Chan
- Color Genomics, Inc., Burlingame, CA 94010, United States
| | - Serra Kim
- Color Genomics, Inc., Burlingame, CA 94010, United States
| | - Sean V Tavtigian
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, United States
| | - David Goldgar
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, United States
| | - Paul A James
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC 3052, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Amanda B Spurdle
- Population Health Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
- Faculty of Medicine, The University of Queensland, Herston, QLD 4006, Australia
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Jain S, Bakolitsa C, Brenner SE, Radivojac P, Moult J, Repo S, Hoskins RA, Andreoletti G, Barsky D, Chellapan A, Chu H, Dabbiru N, Kollipara NK, Ly M, Neumann AJ, Pal LR, Odell E, Pandey G, Peters-Petrulewicz RC, Srinivasan R, Yee SF, Yeleswarapu SJ, Zuhl M, Adebali O, Patra A, Beer MA, Hosur R, Peng J, Bernard BM, Berry M, Dong S, Boyle AP, Adhikari A, Chen J, Hu Z, Wang R, Wang Y, Miller M, Wang Y, Bromberg Y, Turina P, Capriotti E, Han JJ, Ozturk K, Carter H, Babbi G, Bovo S, Di Lena P, Martelli PL, Savojardo C, Casadio R, Cline MS, De Baets G, Bonache S, Díez O, Gutiérrez-Enríquez S, Fernández A, Montalban G, Ootes L, Özkan S, Padilla N, Riera C, De la Cruz X, Diekhans M, Huwe PJ, Wei Q, Xu Q, Dunbrack RL, Gotea V, Elnitski L, Margolin G, Fariselli P, Kulakovskiy IV, Makeev VJ, Penzar DD, Vorontsov IE, Favorov AV, Forman JR, Hasenahuer M, Fornasari MS, Parisi G, Avsec Z, Çelik MH, Nguyen TYD, Gagneur J, Shi FY, Edwards MD, Guo Y, Tian K, Zeng H, Gifford DK, Göke J, Zaucha J, Gough J, Ritchie GRS, Frankish A, Mudge JM, Harrow J, Young EL, Yu Y, Huff CD, Murakami K, Nagai Y, Imanishi T, Mungall CJ, Jacobsen JOB, Kim D, Jeong CS, Jones DT, Li MJ, Guthrie VB, Bhattacharya R, Chen YC, Douville C, Fan J, Kim D, Masica D, Niknafs N, Sengupta S, Tokheim C, Turner TN, Yeo HTG, Karchin R, Shin S, Welch R, Keles S, Li Y, Kellis M, Corbi-Verge C, Strokach AV, Kim PM, Klein TE, Mohan R, Sinnott-Armstrong NA, Wainberg M, Kundaje A, Gonzaludo N, Mak ACY, Chhibber A, Lam HYK, Dahary D, Fishilevich S, Lancet D, Lee I, Bachman B, Katsonis P, Lua RC, Wilson SJ, Lichtarge O, Bhat RR, Sundaram L, Viswanath V, Bellazzi R, Nicora G, Rizzo E, Limongelli I, Mezlini AM, Chang R, Kim S, Lai C, O’Connor R, Topper S, van den Akker J, Zhou AY, Zimmer AD, Mishne G, Bergquist TR, Breese MR, Guerrero RF, Jiang Y, Kiga N, Li B, Mort M, Pagel KA, Pejaver V, Stamboulian MH, Thusberg J, Mooney SD, Teerakulkittipong N, Cao C, Kundu K, Yin Y, Yu CH, Kleyman M, Lin CF, Stackpole M, Mount SM, Eraslan G, Mueller NS, Naito T, Rao AR, Azaria JR, Brodie A, Ofran Y, Garg A, Pal D, Hawkins-Hooker A, Kenlay H, Reid J, Mucaki EJ, Rogan PK, Schwarz JM, Searls DB, Lee GR, Seok C, Krämer A, Shah S, Huang CV, Kirsch JF, Shatsky M, Cao Y, Chen H, Karimi M, Moronfoye O, Sun Y, Shen Y, Shigeta R, Ford CT, Nodzak C, Uppal A, Shi X, Joseph T, Kotte S, Rana S, Rao A, Saipradeep VG, Sivadasan N, Sunderam U, Stanke M, Su A, Adzhubey I, Jordan DM, Sunyaev S, Rousseau F, Schymkowitz J, Van Durme J, Tavtigian SV, Carraro M, Giollo M, Tosatto SCE, Adato O, Carmel L, Cohen NE, Fenesh T, Holtzer T, Juven-Gershon T, Unger R, Niroula A, Olatubosun A, Väliaho J, Yang Y, Vihinen M, Wahl ME, Chang B, Chong KC, Hu I, Sun R, Wu WKK, Xia X, Zee BC, Wang MH, Wang M, Wu C, Lu Y, Chen K, Yang Y, Yates CM, Kreimer A, Yan Z, Yosef N, Zhao H, Wei Z, Yao Z, Zhou F, Folkman L, Zhou Y, Daneshjou R, Altman RB, Inoue F, Ahituv N, Arkin AP, Lovisa F, Bonvini P, Bowdin S, Gianni S, Mantuano E, Minicozzi V, Novak L, Pasquo A, Pastore A, Petrosino M, Puglisi R, Toto A, Veneziano L, Chiaraluce R, Ball MP, Bobe JR, Church GM, Consalvi V, Cooper DN, Buckley BA, Sheridan MB, Cutting GR, Scaini MC, Cygan KJ, Fredericks AM, Glidden DT, Neil C, Rhine CL, Fairbrother WG, Alontaga AY, Fenton AW, Matreyek KA, Starita LM, Fowler DM, Löscher BS, Franke A, Adamson SI, Graveley BR, Gray JW, Malloy MJ, Kane JP, Kousi M, Katsanis N, Schubach M, Kircher M, Mak ACY, Tang PLF, Kwok PY, Lathrop RH, Clark WT, Yu GK, LeBowitz JH, Benedicenti F, Bettella E, Bigoni S, Cesca F, Mammi I, Marino-Buslje C, Milani D, Peron A, Polli R, Sartori S, Stanzial F, Toldo I, Turolla L, Aspromonte MC, Bellini M, Leonardi E, Liu X, Marshall C, McCombie WR, Elefanti L, Menin C, Meyn MS, Murgia A, Nadeau KCY, Neuhausen SL, Nussbaum RL, Pirooznia M, Potash JB, Dimster-Denk DF, Rine JD, Sanford JR, Snyder M, Cote AG, Sun S, Verby MW, Weile J, Roth FP, Tewhey R, Sabeti PC, Campagna J, Refaat MM, Wojciak J, Grubb S, Schmitt N, Shendure J, Spurdle AB, Stavropoulos DJ, Walton NA, Zandi PP, Ziv E, Burke W, Chen F, Carr LR, Martinez S, Paik J, Harris-Wai J, Yarborough M, Fullerton SM, Koenig BA, McInnes G, Shigaki D, Chandonia JM, Furutsuki M, Kasak L, Yu C, Chen R, Friedberg I, Getz GA, Cong Q, Kinch LN, Zhang J, Grishin NV, Voskanian A, Kann MG, Tran E, Ioannidis NM, Hunter JM, Udani R, Cai B, Morgan AA, Sokolov A, Stuart JM, Minervini G, Monzon AM, Batzoglou S, Butte AJ, Greenblatt MS, Hart RK, Hernandez R, Hubbard TJP, Kahn S, O’Donnell-Luria A, Ng PC, Shon J, Veltman J, Zook JM. CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods. Genome Biol 2024; 25:53. [PMID: 38389099 PMCID: PMC10882881 DOI: 10.1186/s13059-023-03113-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 11/17/2023] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND The Critical Assessment of Genome Interpretation (CAGI) aims to advance the state-of-the-art for computational prediction of genetic variant impact, particularly where relevant to disease. The five complete editions of the CAGI community experiment comprised 50 challenges, in which participants made blind predictions of phenotypes from genetic data, and these were evaluated by independent assessors. RESULTS Performance was particularly strong for clinical pathogenic variants, including some difficult-to-diagnose cases, and extends to interpretation of cancer-related variants. Missense variant interpretation methods were able to estimate biochemical effects with increasing accuracy. Assessment of methods for regulatory variants and complex trait disease risk was less definitive and indicates performance potentially suitable for auxiliary use in the clinic. CONCLUSIONS Results show that while current methods are imperfect, they have major utility for research and clinical applications. Emerging methods and increasingly large, robust datasets for training and assessment promise further progress ahead.
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Spier I, Yin X, Richardson M, Pineda M, Laner A, Ritter D, Boyle J, Mur P, Hansen TVO, Shi X, Mahmood K, Plazzer JP, Ognedal E, Nordling M, Farrington SM, Yamamoto G, Baert-Desurmont S, Martins A, Borras E, Tops C, Webb E, Beshay V, Genuardi M, Pesaran T, Capellá G, Tavtigian SV, Latchford A, Frayling IM, Plon SE, Greenblatt M, Macrae FA, Aretz S. Gene-specific ACMG/AMP classification criteria for germline APC variants: Recommendations from the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel. Genet Med 2024; 26:100992. [PMID: 37800450 PMCID: PMC10922469 DOI: 10.1016/j.gim.2023.100992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/07/2023] Open
Abstract
PURPOSE The Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (VCEP) was established by the International Society for Gastrointestinal Hereditary Tumours and the Clinical Genome Resource, who set out to develop recommendations for the interpretation of germline APC variants underlying Familial Adenomatous Polyposis, the most frequent hereditary polyposis syndrome. METHODS Through a rigorous process of database analysis, literature review, and expert elicitation, the APC VCEP derived gene-specific modifications to the ACMG/AMP (American College of Medical Genetics and Genomics and Association for Molecular Pathology) variant classification guidelines and validated such criteria through the pilot classification of 58 variants. RESULTS The APC-specific criteria represented gene- and disease-informed specifications, including a quantitative approach to allele frequency thresholds, a stepwise decision tool for truncating variants, and semiquantitative evaluations of experimental and clinical data. Using the APC-specific criteria, 47% (27/58) of pilot variants were reclassified including 14 previous variants of uncertain significance (VUS). CONCLUSION The APC-specific ACMG/AMP criteria preserved the classification of well-characterized variants on ClinVar while substantially reducing the number of VUS by 56% (14/25). Moving forward, the APC VCEP will continue to interpret prioritized lists of VUS, the results of which will represent the most authoritative variant classification for widespread clinical use.
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Affiliation(s)
- Isabel Spier
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany; National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany; European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS) - Project ID No 739547
| | - Xiaoyu Yin
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany; Department of Colorectal Medicine and Genetics, Royal Melbourne Hospital, Parkville, Australia; Department of Medicine, University of Melbourne, Parkville, Australia.
| | | | - Marta Pineda
- European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS) - Project ID No 739547; Hereditary Cancer Program, Catalan Institute of Oncology - ONCOBELL, IDIBELL, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
| | | | - Deborah Ritter
- Baylor College of Medicine, Houston, TX; Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX
| | - Julie Boyle
- Department of Oncological Sciences, School of Medicine, University of Utah, Salt Lake City, UT
| | - Pilar Mur
- Hereditary Cancer Program, Catalan Institute of Oncology - ONCOBELL, IDIBELL, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
| | - Thomas V O Hansen
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Khalid Mahmood
- Colorectal Oncogenomics Group, Department of Clinical Pathology, University of Melbourne, Parkville, Australia; Melbourne Bioinformatics, University of Melbourne, Parkville, Australia
| | - John-Paul Plazzer
- Department of Colorectal Medicine and Genetics, Royal Melbourne Hospital, Parkville, Australia
| | | | - Margareta Nordling
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden; Department of Clinical Genetics, Linköping University Hospital, Linköping, Sweden
| | - Susan M Farrington
- Cancer Research UK Edinburgh Centre, the University of Edinburgh, Edinburgh, United Kingdom
| | - Gou Yamamoto
- Department of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama, Japan
| | | | | | | | - Carli Tops
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Maurizio Genuardi
- Fondazione Policlinico Universitario A. Gemelli IRCCS, and Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - Gabriel Capellá
- European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS) - Project ID No 739547; Hereditary Cancer Program, Catalan Institute of Oncology - ONCOBELL, IDIBELL, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
| | - Sean V Tavtigian
- Department of Oncological Sciences, School of Medicine, University of Utah, Salt Lake City, UT; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Andrew Latchford
- Polyposis Registry, St. Mark's Hospital, London, United Kingdom; Department of Surgery and Cancer, Imperial College, London, United Kingdom
| | - Ian M Frayling
- Polyposis Registry, St. Mark's Hospital, London, United Kingdom; Inherited Tumour Syndromes Research Group, Institute of Cancer & Genetics, Cardiff University, United Kingdom
| | - Sharon E Plon
- Baylor College of Medicine, Houston, TX; Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX
| | - Marc Greenblatt
- Larner College of Medicine, University of Vermont, Burlington, VT
| | - Finlay A Macrae
- Department of Colorectal Medicine and Genetics, Royal Melbourne Hospital, Parkville, Australia; Department of Medicine, University of Melbourne, Parkville, Australia
| | - Stefan Aretz
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany; National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany; European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS) - Project ID No 739547
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Biesecker LG, Byrne AB, Harrison SM, Pesaran T, Schäffer AA, Shirts BH, Tavtigian SV, Rehm HL. ClinGen guidance for use of the PP1/BS4 co-segregation and PP4 phenotype specificity criteria for sequence variant pathogenicity classification. Am J Hum Genet 2024; 111:24-38. [PMID: 38103548 PMCID: PMC10806742 DOI: 10.1016/j.ajhg.2023.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 11/21/2023] [Accepted: 11/21/2023] [Indexed: 12/19/2023] Open
Abstract
The 2015 American College of Medical Genetics and Genomics and the Association for Molecular Pathology variant classification publication established a standard employed internationally to guide laboratories in variant assessment. Those recommendations included both pathogenic (PP1) and benign (BS4) criteria for evaluating the inheritance patterns of variants, but details of how to apply those criteria at appropriate evidence levels were sparse. Several publications have since attempted to provide additional guidance, but anecdotally, this issue is still challenging. Additionally, it is not clear that those prior efforts fully distinguished disease-gene identification considerations from variant pathogenicity considerations nor did they address autosomal-recessive and X-linked inheritance. Here, we have taken a mixed inductive and deductive approach to this problem using real diseases as examples. We have developed a practical heuristic for genetic co-segregation evidence and have also determined that the specific phenotype criterion (PP4) is inseparably coupled to the co-segregation criterion. We have also determined that negative evidence at one locus constitutes positive evidence for other loci for disorders with locus heterogeneity. Finally, we provide a points-based system for evaluating phenotype and co-segregation as evidence types to support or refute a locus and show how that can be integrated into the Bayesian framework now used for variant classification and consistent with the 2015 guidelines.
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Affiliation(s)
- Leslie G Biesecker
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Alicia B Byrne
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Steven M Harrison
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ambry Genetics, Aliso Viejo, CA, USA
| | | | - Alejandro A Schäffer
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Brian H Shirts
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Sean V Tavtigian
- Department of Oncological Sciences, University of Utah School of Medicine and Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT, USA
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
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Seagle HM, Keller SR, Tavtigian SV, Horton C, Holowatyj AN. Clinical Multigene Panel Testing Identifies Racial and Ethnic Differences in Germline Pathogenic Variants Among Patients With Early-Onset Colorectal Cancer. J Clin Oncol 2023; 41:4279-4289. [PMID: 37319387 PMCID: PMC10852379 DOI: 10.1200/jco.22.02378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/03/2023] [Accepted: 03/06/2023] [Indexed: 06/17/2023] Open
Abstract
PURPOSE The early-onset colorectal cancer (EOCRC) burden differs across racial/ethnic groups, yet the role of germline genetic predisposition in EOCRC disparities remains uncharacterized. We defined the prevalence and spectrum of inherited colorectal cancer (CRC) susceptibility gene variations among patients with EOCRC by race and ethnicity. PATIENTS AND METHODS We included individuals diagnosed with a first primary CRC between age 15 and 49 years who identified as Ashkenazi Jewish, Asian, Black, Hispanic, or White and underwent germline genetic testing of 14 CRC susceptibility genes performed by a clinical testing laboratory. Variant comparisons by racial and ethnic groups were evaluated using chi-square tests and multivariable logistic regression adjusted for sex, age, CRC site, and number of primary colorectal tumors. RESULTS Among 3,980 patients with EOCRC, a total of 530 germline pathogenic or likely pathogenic variants were identified in 485 individuals (12.2%). By race/ethnicity, 12.7% of Ashkenazim patients, 9.5% of Asian patients, 10.3% of Black patients, 14.0% of Hispanic patients, and 12.4% of White patients carried a germline variant. The prevalence of Lynch syndrome (P = .037), as well as APC, CHEK2, MLH1, monoallelic MUTYH, and PTEN variants, varied by race/ethnicity among patients with EOCRC (all P < .026). Ashkenazim and Hispanic patients had significantly higher odds of presenting with a pathogenic APC variant, which included p.I1307K (odds ratio [OR], 2.67; 95% CI, 1.30 to 5.49; P = .007) and MLH1 variant (OR, 8.69; 95% CI, 2.68 to 28.20; P = .0003), respectively, versus White patients in adjusted models. CONCLUSION Germline genetic features differed by race/ethnicity in young patients with CRC, suggesting that current multigene panel tests may not be representative of EOCRC risk in diverse populations. Further study is needed to optimize genes selected for genetic testing in EOCRC via ancestry-specific gene and variant discovery to yield equitable clinical benefits for all patients and to mitigate inequities in disease burden.
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Affiliation(s)
- Hannah M. Seagle
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Vanderbilt University School of Medicine, Nashville, TN
| | - Samantha R. Keller
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Vanderbilt University School of Medicine, Nashville, TN
| | - Sean V. Tavtigian
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT
| | - Carolyn Horton
- Department of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, CA
| | - Andreana N. Holowatyj
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Vanderbilt University School of Medicine, Nashville, TN
- Department of Population Health Sciences, University of Utah, Salt Lake City, UT
- Vanderbilt-Ingram Cancer Center, Nashville, TN
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Spurdle AB, Drackley A, Ing A, Tudini E, Yap KL, Tavtigian SV. Correspondence on "Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen)" by Riggs et al. Genet Med 2023:100868. [PMID: 37261439 DOI: 10.1016/j.gim.2023.100868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 02/27/2023] [Indexed: 06/02/2023] Open
Affiliation(s)
- Amanda B Spurdle
- Population Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Andrew Drackley
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, IL; Center for Genomics, Ann & Robert H. Lurie Children's Hospital of Chicago, IL; Division of Genetics, Birth Defects and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, IL; Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Alexander Ing
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, IL; Center for Genomics, Ann & Robert H. Lurie Children's Hospital of Chicago, IL; Division of Genetics, Birth Defects and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, IL; Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Emma Tudini
- Population Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia; Australian Genomics, Melbourne, VIC, Australia
| | - Kai L Yap
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, IL; Center for Genomics, Ann & Robert H. Lurie Children's Hospital of Chicago, IL; Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Sean V Tavtigian
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT; Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT.
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Holowatyj AN, Seagle HM, Keller S, Tavtigian SV, Goldgar DE, Horton C. Racial/ethnic differences of germline pathogenic variants in cancer susceptibility genes among patients with early-onset colorectal cancer. J Clin Oncol 2023. [DOI: 10.1200/jco.2023.41.4_suppl.19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
19 Background: The burden of early-onset colorectal cancer (CRC diagnosed before age 50 years) differs across racial/ethnic groups. Yet the distinct prevalence and spectrum of germline pathogenic variants associated with early-onset CRC by race/ethnicity is uncharacterized. Methods: We identified 3,980 early-onset CRC patients unselected for family CRC history who underwent clinical multi-gene panel testing of 14 CRC susceptibility genes ( MLH1, MSH2, MSH6, PMS2, SMAD4, APC, BMPR1, CHEK2, EPCAM, MUTYH, PTEN, STK11, CDH1, and TP53) performed by a nationwide clinical testing laboratory from 2012 to 2016 and identified as Ashkenazi Jewish, Asian, Black, Hispanic, or White. Multi-gene panel testing was performed by targeted custom capture and sequencing and chromosome rearrangement analysis. Clinical and individual/family histories were ascertained from clinician-completed test requisition forms. Germline variant prevalence and spectrum in early-onset CRC was determined by race/ethnicity. Pathogenic variant comparisons by race/ethnicity were evaluated using chi-square tests and multivariable logistic regression adjusted for sex, age, CRC site and sequence. Results: Among 3,980 early-onset CRC patients, a total of 503 germline genetic variants were identified in 481 individuals (12.1%). By race/ethnicity, 12.7% of Ashkenazi Jewish, 8.6% of Asian, 10.3% of Black, 14.0% of Hispanic, and 12.3% of White individuals presented with a pathogenic variant in a CRC susceptibility gene. Nearly 7% of early-onset CRC patients (n = 268) presented with a germline pathogenic mutation in a mismatch repair gene—with the prevalence of Lynch Syndrome in early-onset CRC differing across racial/ethnic groups ( P= 0.037). The prevalence of germline APC, CHEK2, MLH1, monoallelic MUTYH, and PTEN variants also varied by race/ethnicity (all P< 0.02). Overall, Asian individuals with early-onset CRC had 49% lower odds of carrying a pathogenic germline variant in a CRC susceptibility gene versus White individuals in adjusted models (Odds Ratio [OR] = 0.51, 95% Confidence Interval [CI]: 0.26-0.99, P= 0.046). Ashkenazim and Hispanic individuals had higher odds of presenting with pathogenic APC and MLH1 variants, respectively, compared with White individuals in adjusted models ( APC: OR = 8.69, 95% CI: 2.68-28.21, P= 0.0003; MLH1: OR = 2.67, 95% CI: 1.30-5.49, P= 0.007). Conclusions: Of 3,980 patients with early-onset CRC unselected for family history, the prevalence and spectrum of pathogenic germline variants differed across racial/ethnic populations. Beyond multigene panel testing for all early-onset CRC patients, further study is needed to optimize genes selected for germline genetic testing in early-onset CRC across diverse groups—which would have clinical implications for disease surveillance and intervention.
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Affiliation(s)
- Andreana N Holowatyj
- Vanderbilt University Medical Center, Vanderbilt-Ingram Cancer Center, Nashville, TN
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8
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Pejaver V, Byrne AB, Feng BJ, Pagel KA, Mooney SD, Karchin R, O'Donnell-Luria A, Harrison SM, Tavtigian SV, Greenblatt MS, Biesecker LG, Radivojac P, Brenner SE. Calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for PP3/BP4 criteria. Am J Hum Genet 2022; 109:2163-2177. [PMID: 36413997 PMCID: PMC9748256 DOI: 10.1016/j.ajhg.2022.10.013] [Citation(s) in RCA: 109] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 10/21/2022] [Indexed: 11/23/2022] Open
Abstract
Recommendations from the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) for interpreting sequence variants specify the use of computational predictors as "supporting" level of evidence for pathogenicity or benignity using criteria PP3 and BP4, respectively. However, score intervals defined by tool developers, and ACMG/AMP recommendations that require the consensus of multiple predictors, lack quantitative support. Previously, we described a probabilistic framework that quantified the strengths of evidence (supporting, moderate, strong, very strong) within ACMG/AMP recommendations. We have extended this framework to computational predictors and introduce a new standard that converts a tool's scores to PP3 and BP4 evidence strengths. Our approach is based on estimating the local positive predictive value and can calibrate any computational tool or other continuous-scale evidence on any variant type. We estimate thresholds (score intervals) corresponding to each strength of evidence for pathogenicity and benignity for thirteen missense variant interpretation tools, using carefully assembled independent data sets. Most tools achieved supporting evidence level for both pathogenic and benign classification using newly established thresholds. Multiple tools reached score thresholds justifying moderate and several reached strong evidence levels. One tool reached very strong evidence level for benign classification on some variants. Based on these findings, we provide recommendations for evidence-based revisions of the PP3 and BP4 ACMG/AMP criteria using individual tools and future assessment of computational methods for clinical interpretation.
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Affiliation(s)
- Vikas Pejaver
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA 98195, USA
| | - Alicia B Byrne
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Bing-Jian Feng
- Department of Dermatology, University of Utah, Salt Lake City, UT 84132, USA; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Kymberleigh A Pagel
- The Institute for Computational Medicine, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Sean D Mooney
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA 98195, USA
| | - Rachel Karchin
- The Institute for Computational Medicine, The Johns Hopkins University, Baltimore, MD 21218, USA; Departments of Biomedical Engineering, Oncology, and Computer Science, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Steven M Harrison
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Sean V Tavtigian
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Marc S Greenblatt
- Department of Medicine and University of Vermont Cancer Center, University of Vermont, Larner College of Medicine, Burlington, VT 05405, USA
| | - Leslie G Biesecker
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Predrag Radivojac
- Khoury College of Computer Sciences, Northeastern University, Boston, MA 02115, USA.
| | - Steven E Brenner
- Department of Plant and Microbial Biology and Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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9
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Rath A, Radecki AA, Rahman K, Gilmore RB, Hudson JR, Cenci M, Tavtigian SV, Grady JP, Heinen CD. A calibrated cell-based functional assay to aid classification of MLH1 DNA mismatch repair gene variants. Hum Mutat 2022; 43:2295-2307. [PMID: 36054288 PMCID: PMC9772141 DOI: 10.1002/humu.24462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 06/21/2022] [Accepted: 08/30/2022] [Indexed: 01/25/2023]
Abstract
Functional assays provide important evidence for classifying the disease significance of germline variants in DNA mismatch repair genes. Numerous laboratories, including our own, have developed functional assays to study mismatch repair gene variants. However, previous assays are limited due to the model system employed, the manner of gene expression, or the environment in which function is assessed. Here, we developed a human cell-based approach for testing the function of variants of uncertain significance (VUS) in the MLH1 gene. Using clustered regularly interspaced short palindromic repeats gene editing, we knocked in MLH1 VUS into the endogenous MLH1 loci in human embryonic stem cells. We examined their impact on RNA and protein, including their ability to prevent microsatellite instability and instigate a DNA damage response. A statistical clustering analysis determined the range of functions associated with known pathogenic or benign variants, and linear regression was performed using existing odds in favor of pathogenicity scores for these control variants to calibrate our functional assay results. By converting the functional outputs into a single odds in favor of pathogenicity score, variant classification expert panels can use these results to readily reassess these VUS. Ultimately, this information will guide proper diagnosis and disease management for suspected Lynch syndrome patients.
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Affiliation(s)
- Abhijit Rath
- Center for Molecular Oncology, UConn Health, Farmington, CT
| | | | - Kaussar Rahman
- Center for Molecular Oncology, UConn Health, Farmington, CT
| | - Rachel B. Gilmore
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT
| | - Jonathan R. Hudson
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT
| | - Matthew Cenci
- Center for Molecular Oncology, UConn Health, Farmington, CT
| | - Sean V. Tavtigian
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT
| | - James P. Grady
- Connecticut Institute for Clinical and Translational Science, UConn Health, Farmington, CT
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10
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Holowatyj AN, Washington MK, Tavtigian SV, Eng C, Horton C. Inherited Cancer Susceptibility Gene Sequence Variations Among Patients With Appendix Cancer. JAMA Oncol 2022; 9:2798729. [PMID: 36368039 PMCID: PMC9652767 DOI: 10.1001/jamaoncol.2022.5425] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022]
Abstract
Importance Germline sequence variations in APC, BMPR1A, CDH1, CHEK2, EPCAM, MLH1, MSH2, MSH6, MUTYH, PMS2, PTEN, SMAD4, STK11, and TP53 genes are associated with susceptibility to gastrointestinal cancers. As a rare cancer, the evaluation of appendiceal cancer (AC) predisposition has been limited. Objective To assess the prevalence and spectrum of inherited cancer susceptibility gene sequence variations in patients with AC and the utility of germline genetic testing for this population. Design, Setting, and Participants This cohort study included patients with AC who underwent germline genetic testing of 14 cancer susceptibility genes performed by a clinical testing laboratory between March 1, 2012, and December 31, 2016. Data were analyzed from March to August 2022. Clinical, individual, and family histories were obtained from clinician-completed test requisition forms. Multigene panel testing was performed by targeted custom capture and sequencing and chromosome rearrangement analysis. Main Outcomes and Measures The main outcomes were germline sequence variation prevalence and spectrum in patients with AC. Results Among the 131 patients with AC in the cohort (90 female [68.7%]), a total of 16 deleterious sequence variations were identified in 15 patients (11.5%). Similarly, when limited to the 74 patients with AC as the first and only primary tumor, a total of 8 patients (10.8%) had at least 1 deleterious sequence variation in a cancer susceptibility gene. Overall, 6 patients (4.6%) had a deleterious sequence variation observed in MUTYH (5 with monoallelic MUTYH and 1 with biallelic MUTYH). All 4 patients with Lynch syndrome (3.1%) had a sequence variation in the MLH1 gene, of whom 3 were aged 50 years or older at AC diagnosis. Five patients (3.8%) had deleterious sequence variations in other cancer predisposition genes (1 with APC [c.3920T>A, p.I1307K], 2 with CHEK2 [c.470T>C, p.I157T], 1 with SMAD4 [c.263 287dup, p.L98IFS*14], and 1 with TP53 [c.524G>A, p.R175H]). Conclusions and Relevance In this cohort study, 1 in every 10 patients with AC who underwent testing for hereditary cancer predisposition carried an inherited gene sequence variation associated with cancer susceptibility. Given the high frequency and broad spectrum of germline gene sequence variations, these data suggest that genetic evaluation might be warranted for all patients diagnosed with this rare malignant tumor. A systemic sequencing effort for all patients with AC may also identify cancer vulnerabilities to exploit for therapeutic development in a cancer type for which clinical trials are limited.
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Affiliation(s)
- Andreana N. Holowatyj
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
- Department of Population Health Sciences, University of Utah, Salt Lake City
| | - Mary K. Washington
- Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Sean V. Tavtigian
- Department of Oncological Sciences, University of Utah, Salt Lake City
| | - Cathy Eng
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
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11
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Clark KA, Paquette A, Tao K, Bell R, Boyle JL, Rosenthal J, Snow AK, Stark AW, Thompson BA, Unger J, Gertz J, Varley KE, Boucher KM, Goldgar DE, Foulkes WD, Thomas A, Tavtigian SV. Comprehensive evaluation and efficient classification of BRCA1 RING domain missense substitutions. Am J Hum Genet 2022; 109:1153-1174. [PMID: 35659930 PMCID: PMC9247830 DOI: 10.1016/j.ajhg.2022.05.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 05/09/2022] [Indexed: 11/21/2022] Open
Abstract
BRCA1 is a high-risk susceptibility gene for breast and ovarian cancer. Pathogenic protein-truncating variants are scattered across the open reading frame, but all known missense substitutions that are pathogenic because of missense dysfunction are located in either the amino-terminal RING domain or the carboxy-terminal BRCT domain. Heterodimerization of the BRCA1 and BARD1 RING domains is a molecularly defined obligate activity. Hence, we tested every BRCA1 RING domain missense substitution that can be created by a single nucleotide change for heterodimerization with BARD1 in a mammalian two-hybrid assay. Downstream of the laboratory assay, we addressed three additional challenges: assay calibration, validation thereof, and integration of the calibrated results with other available data, such as computational evidence and patient/population observational data to achieve clinically applicable classification. Overall, we found that 15%-20% of BRCA1 RING domain missense substitutions are pathogenic. Using a Bayesian point system for data integration and variant classification, we achieved clinical classification of 89% of observed missense substitutions. Moreover, among missense substitutions not present in the human observational data used here, we find an additional 45 with concordant computational and functional assay evidence in favor of pathogenicity plus 223 with concordant evidence in favor of benignity; these are particularly likely to be classified as likely pathogenic and likely benign, respectively, once human observational data become available.
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Affiliation(s)
- Kathleen A Clark
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA
| | - Andrew Paquette
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Kayoko Tao
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA
| | - Russell Bell
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA
| | - Julie L Boyle
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA
| | - Judith Rosenthal
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA
| | - Angela K Snow
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA
| | - Alex W Stark
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Bryony A Thompson
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA
| | - Joshua Unger
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA
| | - Jason Gertz
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA; Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Katherine E Varley
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA; Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Kenneth M Boucher
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA; Division of Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT 84108, USA
| | - David E Goldgar
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA; Department of Dermatology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - William D Foulkes
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC H3T 1E2, Canada; Research Institute McGill University Health Center, Montreal, QC H3T 1E2, Canada; Departments of Medicine, Human Genetics, and Oncology, McGill University, Montreal, QC H3T 1E2, Canada
| | - Alun Thomas
- Division of Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT 84108, USA
| | - Sean V Tavtigian
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA; Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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12
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Fortuno C, Pesaran T, Dolinsky J, Yussuf A, McGoldrick K, Tavtigian SV, Goldgar D, Spurdle AB, James PA. An updated quantitative model to classify missense variants in the TP53 gene: A novel multifactorial strategy. Hum Mutat 2021; 42:1351-1361. [PMID: 34273903 DOI: 10.1002/humu.24264] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 06/25/2021] [Accepted: 07/15/2021] [Indexed: 11/07/2022]
Abstract
Multigene panel testing has led to an increase in the number of variants of uncertain significance identified in the TP53 gene, associated with Li-Fraumeni syndrome. We previously developed a quantitative model for predicting the pathogenicity of P53 missense variants based on the combination of calibrated bioinformatic information and somatic to germline ratio. Here, we extended this quantitative model for the classification of P53 predicted missense variants by adding new pieces of evidence (personal and family history parameters, loss-of-function results, population allele frequency, healthy individual status by age 60, and breast tumor pathology). We also annotated which missense variants might have an effect on splicing based on bioinformatic predictions. This updated model plus annotation led to the classification of 805 variants into a clinically relevant class, which correlated well with existing ClinVar classifications, and resolved a large number of conflicting and uncertain classifications. We propose this model as a reliable approach to TP53 germline variant classification and emphasize its use in contributing to optimize TP53-specific ACMG/AMP guidelines.
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Affiliation(s)
- Cristina Fortuno
- Genetics and Computational Division, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | | | - Amal Yussuf
- Ambry Genetics, Aliso Viejo, California, USA
| | | | - Sean V Tavtigian
- Huntsman Cancer Institute and Department of Dermatology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - David Goldgar
- Huntsman Cancer Institute and Department of Dermatology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Amanda B Spurdle
- Genetics and Computational Division, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Paul A James
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Australia
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13
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Steely CJ, Russell KL, Feusier JE, Qiao Y, Tavtigian SV, Marth G, Jorde LB. Mobile element insertions and associated structural variants in longitudinal breast cancer samples. Sci Rep 2021; 11:13020. [PMID: 34158539 PMCID: PMC8219704 DOI: 10.1038/s41598-021-92444-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/07/2021] [Indexed: 02/05/2023] Open
Abstract
While mobile elements are largely inactive in healthy somatic tissues, increased activity has been found in cancer tissues, with significant variation among different cancer types. In addition to insertion events, mobile elements have also been found to mediate many structural variation events in the genome. Here, to better understand the timing and impact of mobile element insertions and associated structural variants in cancer, we examined their activity in longitudinal samples of four metastatic breast cancer patients. We identified 11 mobile element insertions or associated structural variants and found that the majority of these occurred early in tumor progression. Most of the variants impact intergenic regions; however, we identified a translocation interrupting MAP2K4 involving Alu elements and a deletion in YTHDF2 involving mobile elements that likely inactivate reported tumor suppressor genes. The high variant allele fraction of the translocation, the loss of the other copy of MAP2K4, the recurrent loss-of-function mutations found in this gene in other cancers, and the important function of MAP2K4 indicate that this translocation is potentially a driver mutation. Overall, using a unique longitudinal dataset, we find that most variants are likely passenger mutations in the four patients we examined, but some variants impact tumor progression.
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Affiliation(s)
- Cody J Steely
- Department of Human Genetics, University of Utah School of Medicine, 15 N. 2030 E. Rm 5100, Salt Lake City, UT, 84112, USA.
| | - Kristi L Russell
- Department of Human Genetics, University of Utah School of Medicine, 15 N. 2030 E. Rm 5100, Salt Lake City, UT, 84112, USA
| | - Julie E Feusier
- Department of Human Genetics, University of Utah School of Medicine, 15 N. 2030 E. Rm 5100, Salt Lake City, UT, 84112, USA
| | - Yi Qiao
- Department of Human Genetics, University of Utah School of Medicine, 15 N. 2030 E. Rm 5100, Salt Lake City, UT, 84112, USA
- Utah Center for Genetic Discovery, Salt Lake City, UT, 84112, USA
| | - Sean V Tavtigian
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Gabor Marth
- Department of Human Genetics, University of Utah School of Medicine, 15 N. 2030 E. Rm 5100, Salt Lake City, UT, 84112, USA
- Utah Center for Genetic Discovery, Salt Lake City, UT, 84112, USA
| | - Lynn B Jorde
- Department of Human Genetics, University of Utah School of Medicine, 15 N. 2030 E. Rm 5100, Salt Lake City, UT, 84112, USA
- Utah Center for Genetic Discovery, Salt Lake City, UT, 84112, USA
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14
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Thompson BA, Snow AK, Koptiuch C, Kohlmann WK, Mooney R, Johnson S, Huff CD, Yu Y, Teerlink CC, Feng BJ, Neklason DW, Cannon-Albright LA, Tavtigian SV. A novel ribosomal protein S20 variant in a family with unexplained colorectal cancer and polyposis. Clin Genet 2021; 97:943-944. [PMID: 32424863 DOI: 10.1111/cge.13757] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/21/2020] [Accepted: 02/23/2020] [Indexed: 01/23/2023]
Affiliation(s)
- Bryony A Thompson
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA.,Department of Pathology, Royal Melbourne Hospital, Melbourne, Australia.,Department of Clinical Pathology, University of Melbourne, Melbourne, Australia
| | - Angela K Snow
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Cathryn Koptiuch
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Wendy K Kohlmann
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Ryan Mooney
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Sara Johnson
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Chad D Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yao Yu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Craig C Teerlink
- Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Bing-Jian Feng
- Department of Dermatology, University of Utah, Salt Lake City, Utah, USA
| | - Deborah W Neklason
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA.,Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, Utah, USA.,Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Lisa A Cannon-Albright
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA.,Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, Utah, USA.,Research and Development Service, George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, Utah, USA
| | - Sean V Tavtigian
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA.,Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, Utah, USA
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15
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Kim J, Light N, Subasri V, Young EL, Wegman-Ostrosky T, Barkauskas DA, Hall D, Lupo PJ, Patidar R, Maese LD, Jones K, Wang M, Tavtigian SV, Wu D, Shlien A, Telfer F, Goldenberg A, Skapek SX, Wei JS, Wen X, Catchpoole D, Hawkins DS, Schiffman JD, Khan J, Malkin D, Stewart DR. Pathogenic Germline Variants in Cancer Susceptibility Genes in Children and Young Adults With Rhabdomyosarcoma. JCO Precis Oncol 2021; 5:PO.20.00218. [PMID: 34095712 PMCID: PMC8169077 DOI: 10.1200/po.20.00218] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/10/2020] [Accepted: 11/06/2020] [Indexed: 12/30/2022] Open
Abstract
Rhabdomyosarcoma (RMS) is the most common pediatric soft-tissue sarcoma and accounts for 3% of all pediatric cancer. In this study, we investigated germline sequence and structural variation in a broad set of genes in two large, independent RMS cohorts. MATERIALS AND METHODS Genome sequencing of the discovery cohort (n = 273) and exome sequencing of the secondary cohort (n = 121) were conducted on germline DNA. Analyses were performed on 130 cancer susceptibility genes (CSG). Pathogenic or likely pathogenic (P/LP) variants were predicted using the American College of Medical Genetics and Genomics (ACMG) criteria. Structural variation and survival analyses were performed on the discovery cohort. RESULTS We found that 6.6%-7.7% of patients with RMS harbored P/LP variants in dominant-acting CSG. An additional approximately 1% have structural variants (ATM, CDKN1C) in CSGs. CSG variants did not influence survival, although there was a significant correlation with an earlier age of tumor onset. There was a nonsignificant excess of P/LP variants in dominant inheritance genes in the patients with FOXO1 fusion-negative RMS patients versus the patients with FOXO1 fusion-positive RMS. We identified pathogenic germline variants in CSGs previously (TP53, NF1, DICER1, mismatch repair genes), rarely (BRCA2, CBL, CHEK2, SMARCA4), or never (FGFR4) reported in RMS. Numerous genes (TP53, BRCA2, mismatch repair) were on the ACMG Secondary Findings 2.0 list. CONCLUSION In two cohorts of patients with RMS, we identified pathogenic germline variants for which gene-specific therapies and surveillance guidelines may be beneficial. In families with a proband with an RMS-risk P/LP variant, genetic counseling and cascade testing should be considered, especially for ACMG Secondary Findings genes and/or with gene-specific surveillance guidelines.
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Affiliation(s)
- Jung Kim
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
| | - Nicholas Light
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Vallijah Subasri
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, ON, Canada
- Vector Institute of Artificial Intelligence, Toronto, ON, Canada
| | - Erin L. Young
- Department of Pediatrics, University of Utah, Salt Lake City, UT
| | - Talia Wegman-Ostrosky
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
- Basic Research Subdirection, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Donald A. Barkauskas
- QuadW-COG Childhood Sarcoma Biostatistics and Annotation Office, Children's Oncology Group, Monrovia, CA
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA
| | - David Hall
- QuadW-COG Childhood Sarcoma Biostatistics and Annotation Office, Children's Oncology Group, Monrovia, CA
| | - Philip J. Lupo
- Department of Pediatrics, Hematology-Oncology Section, Baylor College of Medicine, Houston, TX
| | - Rajesh Patidar
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Luke D. Maese
- Department of Pediatrics, University of Utah, Salt Lake City, UT
| | - Kristine Jones
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Mingyi Wang
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Sean V. Tavtigian
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Dongjing Wu
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Adam Shlien
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathology, University of Toronto, Toronto, ON, Canada
| | - Frank Telfer
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, ON, Canada
| | - Anna Goldenberg
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Vector Institute of Artificial Intelligence, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | | | - Jun S. Wei
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Xinyu Wen
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Daniel Catchpoole
- The Tumour Bank, Children's Cancer Research Unit, Kids Research Institute, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Douglas S. Hawkins
- Division of Hematology/Oncology, Seattle Children's Hospital, University of Washington, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Joshua D. Schiffman
- Department of Pediatrics, University of Utah, Salt Lake City, UT
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Javed Khan
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - David Malkin
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, ON, Canada
- Division of Hematology-Oncology, The Hospital for Sick Children, Department of Pediatrics, University of Toronto, Toronto, ON, Canada
| | - Douglas R. Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
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16
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Cannon-Albright LA, Teerlink CC, Stevens J, Snow AK, Thompson BA, Bell R, Nguyen KN, Sargent NR, Kohlmann WK, Neklason DW, Tavtigian SV. FANCM c5791C>T stopgain mutation (rs144567652) is a familial colorectal cancer risk factor. Mol Genet Genomic Med 2020; 8:e1532. [PMID: 33118316 PMCID: PMC7767553 DOI: 10.1002/mgg3.1532] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/09/2020] [Accepted: 09/25/2020] [Indexed: 12/19/2022] Open
Abstract
Purpose While familial aggregation of colorectal cancer (CRC) is recognized, the majority of the germline predisposition factors remain unidentified, and many high‐risk CRC pedigrees remain unexplained by known risk variants. Fanconi Anemia genes have been recognized to be associated with cancer risk. Notably, FANCM (OMIM 609644) variants have been reported to confer risk for CRC and breast cancer. Methods Exome sequencing of CRC‐affected cousins in a set of 47 independent extended high‐risk CRC pedigrees identified a candidate set of rare, shared variants. Variants were tested for association with risk in 744 Utah CRC cases and 1525 controls, and for segregation with CRC in affected relatives. Results A FANCM stopgain variant was observed in two CRC‐affected cousin pairs, each from an independent Utah high‐risk pedigree, and yielded a nonsignificant, but elevated OR = 2.05 in a set of Utah cases and controls. Segregation of the variant to other related CRC‐affected cases was observed in the two extended pedigrees. Conclusion A rare stopgain variant in FANCM (rs144567652) that is recognized as a breast cancer predisposition variant, and that has previously been proposed, but not confirmed, as a CRC predisposition variant, is validated here as a risk factor for familial CRC.
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Affiliation(s)
- Lisa A Cannon-Albright
- Division of Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Craig C Teerlink
- Division of Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Jeffrey Stevens
- Division of Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Angela K Snow
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Bryony A Thompson
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.,Department of Pathology, Royal Melbourne Hospital, Melbourne, Australia
| | - Russell Bell
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Kim N Nguyen
- Division of Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Nykole R Sargent
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Wendy K Kohlmann
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Deborah W Neklason
- Division of Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Sean V Tavtigian
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.,Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT, USA
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17
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Tavtigian SV, Harrison SM, Boucher KM, Biesecker LG. Fitting a naturally scaled point system to the ACMG/AMP variant classification guidelines. Hum Mutat 2020; 41:1734-1737. [PMID: 32720330 PMCID: PMC8011844 DOI: 10.1002/humu.24088] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/18/2020] [Accepted: 07/23/2020] [Indexed: 12/29/2022]
Abstract
Recently, we demonstrated that the qualitative American College of Medical Genetics and Genomics/Association for Medical Pathology (ACMG/AMP) guidelines for evaluation of Mendelian disease gene variants are fundamentally compatible with a quantitative Bayesian formulation. Here, we show that the underlying ACMG/AMP "strength of evidence categories" can be abstracted into a point system. These points are proportional to Log(odds), are additive, and produce a system that recapitulates the Bayesian formulation of the ACMG/AMP guidelines. The strengths of this system are its simplicity and that the connection between point values and odds of pathogenicity allows empirical calibration of the strength of evidence for individual data types. Weaknesses include that a narrow range of prior probabilities is locked in and that the Bayesian nature of the system is inapparent. We conclude that a points-based system has the practical attribute of user-friendliness and can be useful so long as the underlying Bayesian principles are acknowledged.
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Affiliation(s)
- Sean V. Tavtigian
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT, USA.,Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT, USA
| | | | - Kenneth M. Boucher
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT, USA.,Department of Internal Medicine, Division of Epidemiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Leslie G. Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD, USA
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18
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Thompson BA, Walters R, Parsons MT, Dumenil T, Drost M, Tiersma Y, Lindor NM, Tavtigian SV, de Wind N, Spurdle AB. Contribution of mRNA Splicing to Mismatch Repair Gene Sequence Variant Interpretation. Front Genet 2020; 11:798. [PMID: 32849802 PMCID: PMC7398121 DOI: 10.3389/fgene.2020.00798] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 07/03/2020] [Indexed: 12/25/2022] Open
Abstract
Functional assays that assess mRNA splicing can be used in interpretation of the clinical significance of sequence variants, including the Lynch syndrome-associated mismatch repair (MMR) genes. The purpose of this study was to investigate the contribution of splicing assay data to the classification of MMR gene sequence variants. We assayed mRNA splicing for 24 sequence variants in MLH1, MSH2, and MSH6, including 12 missense variants that were also assessed using a cell-free in vitro MMR activity (CIMRA) assay. Multifactorial likelihood analysis was conducted for each variant, combining CIMRA outputs and clinical data where available. We collated these results with existing public data to provide a dataset of splicing assay results for a total of 671 MMR gene sequence variants (328 missense/in-frame indel), and published and unpublished repair activity measurements for 154 of these variants. There were 241 variants for which a splicing aberration was detected: 92 complete impact, 33 incomplete impact, and 116 where it was not possible to determine complete versus incomplete splicing impact. Splicing results mostly aided in the interpretation of intronic (72%) and silent (92%) variants and were the least useful for missense substitutions/in-frame indels (10%). MMR protein functional activity assays were more useful in the analysis of these exonic variants but by design they were not able to detect clinically important splicing aberrations identified by parallel mRNA assays. The development of high throughput assays that can quantitatively assess impact on mRNA transcript expression and protein function in parallel will streamline classification of MMR gene sequence variants.
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Affiliation(s)
- Bryony A Thompson
- Department of Pathology, The Royal Melbourne Hospital, Melbourne, VIC, Australia.,Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia
| | - Rhiannon Walters
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Michael T Parsons
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Troy Dumenil
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Mark Drost
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Yvonne Tiersma
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Noralane M Lindor
- Department of Health Sciences Research, Mayo Clinic, Scottsdale, AZ, United States
| | - Sean V Tavtigian
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Niels de Wind
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Amanda B Spurdle
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
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19
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Brnich SE, Abou Tayoun AN, Couch FJ, Cutting GR, Greenblatt MS, Heinen CD, Kanavy DM, Luo X, McNulty SM, Starita LM, Tavtigian SV, Wright MW, Harrison SM, Biesecker LG, Berg JS. Recommendations for application of the functional evidence PS3/BS3 criterion using the ACMG/AMP sequence variant interpretation framework. Genome Med 2019; 12:3. [PMID: 31892348 PMCID: PMC6938631 DOI: 10.1186/s13073-019-0690-2] [Citation(s) in RCA: 266] [Impact Index Per Article: 53.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 11/13/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) clinical variant interpretation guidelines established criteria for different types of evidence. This includes the strong evidence codes PS3 and BS3 for "well-established" functional assays demonstrating a variant has abnormal or normal gene/protein function, respectively. However, they did not provide detailed guidance on how functional evidence should be evaluated, and differences in the application of the PS3/BS3 codes are a contributor to variant interpretation discordance between laboratories. This recommendation seeks to provide a more structured approach to the assessment of functional assays for variant interpretation and guidance on the use of various levels of strength based on assay validation. METHODS The Clinical Genome Resource (ClinGen) Sequence Variant Interpretation (SVI) Working Group used curated functional evidence from ClinGen Variant Curation Expert Panel-developed rule specifications and expert opinions to refine the PS3/BS3 criteria over multiple in-person and virtual meetings. We estimated the odds of pathogenicity for assays using various numbers of variant controls to determine the minimum controls required to reach moderate level evidence. Feedback from the ClinGen Steering Committee and outside experts were incorporated into the recommendations at multiple stages of development. RESULTS The SVI Working Group developed recommendations for evaluators regarding the assessment of the clinical validity of functional data and a four-step provisional framework to determine the appropriate strength of evidence that can be applied in clinical variant interpretation. These steps are as follows: (1) define the disease mechanism, (2) evaluate the applicability of general classes of assays used in the field, (3) evaluate the validity of specific instances of assays, and (4) apply evidence to individual variant interpretation. We found that a minimum of 11 total pathogenic and benign variant controls are required to reach moderate-level evidence in the absence of rigorous statistical analysis. CONCLUSIONS The recommendations and approach to functional evidence evaluation described here should help clarify the clinical variant interpretation process for functional assays. Further, we hope that these recommendations will help develop productive partnerships with basic scientists who have developed functional assays that are useful for interrogating the function of a variety of genes.
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Affiliation(s)
- Sarah E Brnich
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, 120 Mason Farm Rd., Chapel Hill, NC, 27599-7264, USA
| | - Ahmad N Abou Tayoun
- Genomics Department, Al Jalila Children's Specialty Hospital, Dubai, United Arab Emirates
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Garry R Cutting
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Marc S Greenblatt
- Department of Medicine and University of Vermont Cancer Center, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | | | - Dona M Kanavy
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, 120 Mason Farm Rd., Chapel Hill, NC, 27599-7264, USA
| | - Xi Luo
- Department of Pediatrics/Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Shannon M McNulty
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, 120 Mason Farm Rd., Chapel Hill, NC, 27599-7264, USA
| | - Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Sean V Tavtigian
- Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Matt W Wright
- Stanford University School of Medicine, Stanford, CA, USA
| | | | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Jonathan S Berg
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, 120 Mason Farm Rd., Chapel Hill, NC, 27599-7264, USA.
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20
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Samadder NJ, Kuwada SK, Boucher KM, Byrne K, Kanth P, Samowitz W, Jones D, Tavtigian SV, Westover M, Berry T, Jasperson K, Pappas L, Smith L, Sample D, Burt RW, Neklason DW. Association of Sulindac and Erlotinib vs Placebo With Colorectal Neoplasia in Familial Adenomatous Polyposis: Secondary Analysis of a Randomized Clinical Trial. JAMA Oncol 2019; 4:671-677. [PMID: 29423501 DOI: 10.1001/jamaoncol.2017.5431] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Importance Patients with familial adenomatous polyposis (FAP) are at markedly increased risk for colorectal polyps and cancer. A combination of sulindac and erlotinib led to a 71% reduction in duodenal polyp burden in a phase 2 trial. Objective To evaluate effect of sulindac and erlotinib on colorectal adenoma regression in patients with FAP. Design, Setting, and Participants Prespecified secondary analysis for colorectal adenoma regression was carried out using data from a double-blind, randomized, placebo-controlled trial, enrolling 92 patients with FAP, conducted from July 2010 to June 2014 in Salt Lake City, Utah. Interventions Patients were randomized to sulindac, 150 mg twice daily, and erlotinib, 75 mg daily (n = 46), vs placebo (n = 46) for 6 months. Main Outcomes and Measurements The total number of polyps in the intact colorectum, ileal pouch anal anastomosis, or ileo-rectum were recorded at baseline and 6 months. The primary outcomes were change in total colorectal polyp count and percentage change in colorectal polyps, following 6 months of treatment. Results Eighty-two randomized patients (mean [SD] age, 40 [13] years; 49 [60%] women) had colorectal polyp count data available for this secondary analysis: 22 with intact colon, 44 with ileal pouch anal anastomosis and 16 with ileo-rectal anastomosis; 41 patients received sulindac/erlotinib and 41 placebo. The total colorectal polyp count was significantly different between the placebo and sulindac-erlotinib group at 6 months in patients with net percentage change of 69.4% in those with an intact colorectum compared with placebo (95% CI, 28.8%-109.2%; P = .009). Conclusion and Relevance In this double-blind, placebo-controlled, randomized trial we showed that combination treatment with sulindac and erlotinib compared with placebo resulted in significantly lower colorectal polyp burden after 6 months of treatment. There was a reduction in polyp burden in both those with an entire colorectum and those with only a rectal pouch or rectum. Trial Registration clinicaltrials.gov Identifier: NCT01187901.
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Affiliation(s)
- N Jewel Samadder
- Huntsman Cancer Institute, The University of Utah, Salt Lake City.,Department of Medicine (Gastroenterology), The University of Utah, Salt Lake City.,Division of Gastroenterology and Hepatology, Mayo Clinic, Scottsdale, Arizona
| | | | - Kenneth M Boucher
- Huntsman Cancer Institute, The University of Utah, Salt Lake City.,Department of Medicine (Epidemiology), The University of Utah, Salt Lake City
| | - Kathryn Byrne
- Department of Medicine (Gastroenterology), The University of Utah, Salt Lake City
| | - Priyanka Kanth
- Department of Medicine (Gastroenterology), The University of Utah, Salt Lake City
| | - Wade Samowitz
- Huntsman Cancer Institute, The University of Utah, Salt Lake City.,Department of Pathology, The University of Utah, Salt Lake City
| | - David Jones
- Huntsman Cancer Institute, The University of Utah, Salt Lake City.,Department of Oncological Sciences, The University of Utah, Salt Lake City
| | - Sean V Tavtigian
- Huntsman Cancer Institute, The University of Utah, Salt Lake City.,Department of Oncological Sciences, The University of Utah, Salt Lake City
| | | | - Therese Berry
- Huntsman Cancer Institute, The University of Utah, Salt Lake City
| | - Kory Jasperson
- Huntsman Cancer Institute, The University of Utah, Salt Lake City
| | - Lisa Pappas
- Huntsman Cancer Institute, The University of Utah, Salt Lake City
| | - Laurel Smith
- Huntsman Cancer Institute, The University of Utah, Salt Lake City
| | - Danielle Sample
- Huntsman Cancer Institute, The University of Utah, Salt Lake City
| | - Randall W Burt
- Huntsman Cancer Institute, The University of Utah, Salt Lake City.,Department of Medicine (Gastroenterology), The University of Utah, Salt Lake City.,Department of Oncological Sciences, The University of Utah, Salt Lake City
| | - Deborah W Neklason
- Huntsman Cancer Institute, The University of Utah, Salt Lake City.,Department of Oncological Sciences, The University of Utah, Salt Lake City.,Department of Medicine (Genetic Epidemiology), The University of Utah, Salt Lake City
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21
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Voskanian A, Katsonis P, Lichtarge O, Pejaver V, Radivojac P, Mooney SD, Capriotti E, Bromberg Y, Wang Y, Miller M, Martelli PL, Savojardo C, Babbi G, Casadio R, Cao Y, Sun Y, Shen Y, Garg A, Pal D, Yu Y, Huff CD, Tavtigian SV, Young E, Neuhausen SL, Ziv E, Pal LR, Andreoletti G, Brenner S, Kann MG. Assessing the performance of in silico methods for predicting the pathogenicity of variants in the gene CHEK2, among Hispanic females with breast cancer. Hum Mutat 2019; 40:1612-1622. [PMID: 31241222 PMCID: PMC6744287 DOI: 10.1002/humu.23849] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/23/2019] [Accepted: 06/21/2019] [Indexed: 01/22/2023]
Abstract
The availability of disease-specific genomic data is critical for developing new computational methods that predict the pathogenicity of human variants and advance the field of precision medicine. However, the lack of gold standards to properly train and benchmark such methods is one of the greatest challenges in the field. In response to this challenge, the scientific community is invited to participate in the Critical Assessment for Genome Interpretation (CAGI), where unpublished disease variants are available for classification by in silico methods. As part of the CAGI-5 challenge, we evaluated the performance of 18 submissions and three additional methods in predicting the pathogenicity of single nucleotide variants (SNVs) in checkpoint kinase 2 (CHEK2) for cases of breast cancer in Hispanic females. As part of the assessment, the efficacy of the analysis method and the setup of the challenge were also considered. The results indicated that though the challenge could benefit from additional participant data, the combined generalized linear model analysis and odds of pathogenicity analysis provided a framework to evaluate the methods submitted for SNV pathogenicity identification and for comparison to other available methods. The outcome of this challenge and the approaches used can help guide further advancements in identifying SNV-disease relationships.
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Affiliation(s)
- Alin Voskanian
- Department of Biological Sciences, University of Maryland, Baltimore County, MD, U.S.A
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, U.S.A
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, U.S.A
- Department of Pharmacology, Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Vikas Pejaver
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington, U.S.A
- The eScience Institute, University of Washington, Seattle, Washington, U.S.A
| | - Predrag Radivojac
- Khoury College of Computer and Information Sciences, Northeastern University, Boston, Massachusetts, U.S.A
| | - Sean D. Mooney
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington, U.S.A
| | - Emidio Capriotti
- BioFolD Unit, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Yana Bromberg
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, U.S.A
- Department of Genetics, Rutgers University, New Brunswick, New Jersey, U.S.A
- Technical University of Munich Institute for Advanced Study, (TUM-IAS), Lichtenbergstr. 2a, 85748 Garching/Munich, Germany
| | - Yanran Wang
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, U.S.A
| | - Max Miller
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, U.S.A
| | - Pier Luigi Martelli
- Biocomputing Group, BiGeA/Giorgio Prodi Interdepartmental Center for Cancer Research, University of Bologna, Via F. Selmi 3, Bologna, 40126, Italy
| | - Castrense Savojardo
- Biocomputing Group, BiGeA/Giorgio Prodi Interdepartmental Center for Cancer Research, University of Bologna, Via F. Selmi 3, Bologna, 40126, Italy
| | - Giulia Babbi
- Biocomputing Group, BiGeA/Giorgio Prodi Interdepartmental Center for Cancer Research, University of Bologna, Via F. Selmi 3, Bologna, 40126, Italy
| | - Rita Casadio
- Biocomputing Group, BiGeA/Giorgio Prodi Interdepartmental Center for Cancer Research, University of Bologna, Via F. Selmi 3, Bologna, 40126, Italy
| | - Yue Cao
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843-3128, U.S.A
| | - Yuanfei Sun
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843-3128, U.S.A
| | - Yang Shen
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843-3128, U.S.A
| | - Aditi Garg
- Department of Computational and Data Sciences Indian Institute of Science, Bengaluru 560 012, India
| | - Debnath Pal
- Department of Computational and Data Sciences Indian Institute of Science, Bengaluru 560 012, India
| | - Yao Yu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, U.S.A
| | - Chad D. Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, U.S.A
| | - Sean V. Tavtigian
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84132, U.S.A
| | - Erin Young
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84132, U.S.A
| | - Susan L. Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010 U.S.A
| | - Elad Ziv
- Division of General Internal Medicine, Department of Medicine, Institute of Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA,U.S.A
| | - Lipika R. Pal
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Gaia Andreoletti
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Steven Brenner
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Maricel G. Kann
- Department of Biological Sciences, University of Maryland, Baltimore County, MD, U.S.A
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Parsons MT, Tudini E, Li H, Hahnen E, Wappenschmidt B, Feliubadaló L, Aalfs CM, Agata S, Aittomäki K, Alducci E, Alonso‐Cerezo MC, Arnold N, Auber B, Austin R, Azzollini J, Balmaña J, Barbieri E, Bartram CR, Blanco A, Blümcke B, Bonache S, Bonanni B, Borg Å, Bortesi B, Brunet J, Bruzzone C, Bucksch K, Cagnoli G, Caldés T, Caliebe A, Caligo MA, Calvello M, Capone GL, Caputo SM, Carnevali I, Carrasco E, Caux‐Moncoutier V, Cavalli P, Cini G, Clarke EM, Concolino P, Cops EJ, Cortesi L, Couch FJ, Darder E, de la Hoya M, Dean M, Debatin I, Del Valle J, Delnatte C, Derive N, Diez O, Ditsch N, Domchek SM, Dutrannoy V, Eccles DM, Ehrencrona H, Enders U, Evans DG, Farra C, Faust U, Felbor U, Feroce I, Fine M, Foulkes WD, Galvao HC, Gambino G, Gehrig A, Gensini F, Gerdes A, Germani A, Giesecke J, Gismondi V, Gómez C, Gómez Garcia EB, González S, Grau E, Grill S, Gross E, Guerrieri‐Gonzaga A, Guillaud‐Bataille M, Gutiérrez‐Enríquez S, Haaf T, Hackmann K, Hansen TV, Harris M, Hauke J, Heinrich T, Hellebrand H, Herold KN, Honisch E, Horvath J, Houdayer C, Hübbel V, Iglesias S, Izquierdo A, James PA, Janssen LA, Jeschke U, Kaulfuß S, Keupp K, Kiechle M, Kölbl A, Krieger S, Kruse TA, Kvist A, Lalloo F, Larsen M, Lattimore VL, Lautrup C, Ledig S, Leinert E, Lewis AL, Lim J, Loeffler M, López‐Fernández A, Lucci‐Cordisco E, Maass N, Manoukian S, Marabelli M, Matricardi L, Meindl A, Michelli RD, Moghadasi S, Moles‐Fernández A, Montagna M, Montalban G, Monteiro AN, Montes E, Mori L, Moserle L, Müller CR, Mundhenke C, Naldi N, Nathanson KL, Navarro M, Nevanlinna H, Nichols CB, Niederacher D, Nielsen HR, Ong K, Pachter N, Palmero EI, Papi L, Pedersen IS, Peissel B, Perez‐Segura P, Pfeifer K, Pineda M, Pohl‐Rescigno E, Poplawski NK, Porfirio B, Quante AS, Ramser J, Reis RM, Revillion F, Rhiem K, Riboli B, Ritter J, Rivera D, Rofes P, Rump A, Salinas M, Sánchez de Abajo AM, Schmidt G, Schoenwiese U, Seggewiß J, Solanes A, Steinemann D, Stiller M, Stoppa‐Lyonnet D, Sullivan KJ, Susman R, Sutter C, Tavtigian SV, Teo SH, Teulé A, Thomassen M, Tibiletti MG, Tischkowitz M, Tognazzo S, Toland AE, Tornero E, Törngren T, Torres‐Esquius S, Toss A, Trainer AH, Tucker KM, van Asperen CJ, van Mackelenbergh MT, Varesco L, Vargas‐Parra G, Varon R, Vega A, Velasco Á, Vesper A, Viel A, Vreeswijk MPG, Wagner SA, Waha A, Walker LC, Walters RJ, Wang‐Gohrke S, Weber BHF, Weichert W, Wieland K, Wiesmüller L, Witzel I, Wöckel A, Woodward ER, Zachariae S, Zampiga V, Zeder‐Göß C, Investigators KC, Lázaro C, De Nicolo A, Radice P, Engel C, Schmutzler RK, Goldgar DE, Spurdle AB. Large scale multifactorial likelihood quantitative analysis of BRCA1 and BRCA2 variants: An ENIGMA resource to support clinical variant classification. Hum Mutat 2019; 40:1557-1578. [PMID: 31131967 PMCID: PMC6772163 DOI: 10.1002/humu.23818] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/08/2019] [Accepted: 05/12/2019] [Indexed: 12/24/2022]
Abstract
The multifactorial likelihood analysis method has demonstrated utility for quantitative assessment of variant pathogenicity for multiple cancer syndrome genes. Independent data types currently incorporated in the model for assessing BRCA1 and BRCA2 variants include clinically calibrated prior probability of pathogenicity based on variant location and bioinformatic prediction of variant effect, co-segregation, family cancer history profile, co-occurrence with a pathogenic variant in the same gene, breast tumor pathology, and case-control information. Research and clinical data for multifactorial likelihood analysis were collated for 1,395 BRCA1/2 predominantly intronic and missense variants, enabling classification based on posterior probability of pathogenicity for 734 variants: 447 variants were classified as (likely) benign, and 94 as (likely) pathogenic; and 248 classifications were new or considerably altered relative to ClinVar submissions. Classifications were compared with information not yet included in the likelihood model, and evidence strengths aligned to those recommended for ACMG/AMP classification codes. Altered mRNA splicing or function relative to known nonpathogenic variant controls were moderately to strongly predictive of variant pathogenicity. Variant absence in population datasets provided supporting evidence for variant pathogenicity. These findings have direct relevance for BRCA1 and BRCA2 variant evaluation, and justify the need for gene-specific calibration of evidence types used for variant classification.
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Affiliation(s)
- Michael T. Parsons
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | - Emma Tudini
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | - Hongyan Li
- Cancer Control and Population Science, Huntsman Cancer InstituteUniversity of UtahSalt Lake CityUtah
| | - Eric Hahnen
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - Barbara Wappenschmidt
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - Lidia Feliubadaló
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Cora M. Aalfs
- Department of Clinical GeneticsAmsterdam UMCAmsterdamThe Netherlands
| | - Simona Agata
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOVIRCCSPaduaItaly
| | - Kristiina Aittomäki
- Department of Clinical Genetics, Helsinki University HospitalUniversity of HelsinkiHelsinkiFinland
| | - Elisa Alducci
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOVIRCCSPaduaItaly
| | | | - Norbert Arnold
- Department of Gynaecology and Obstetrics, University Hospital of Schleswig‐Holstein, Campus KielChristian‐Albrechts University KielKielGermany
- Institute of Clinical Molecular Biology, University Hospital of Schleswig‐Holstein, Campus KielChristian‐Albrechts University KielKielGermany
| | - Bernd Auber
- Institute of Human GeneticsHannover Medical SchoolHannoverGermany
| | - Rachel Austin
- Genetic Health QueenslandRoyal Brisbane and Women's HospitalBrisbaneAustralia
| | - Jacopo Azzollini
- Unit of Medical Genetics, Department of Medical Oncology and HematologyFondazione IRCCS Istituto Nazionale dei Tumori di MilanoMilanItaly
| | - Judith Balmaña
- High Risk and Cancer Prevention GroupVall d'Hebron Institute of OncologyBarcelonaSpain
- Department of Medical OncologyUniversity Hospital of Vall d'HebronBarcelonaSpain
| | - Elena Barbieri
- Department of Oncology and HaematologyUniversity of Modena and Reggio EmiliaModenaItaly
| | - Claus R. Bartram
- Institute of Human GeneticsUniversity Hospital HeidelbergHeidelbergGermany
| | - Ana Blanco
- Fundación Pública galega Medicina Xenómica‐SERGASGrupo de Medicina Xenómica‐USC, CIBERER, IDISSantiago de CompostelaSpain
| | - Britta Blümcke
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - Sandra Bonache
- Oncogenetics GroupVall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics, IEOEuropean Institute of Oncology IRCCSMilanItaly
| | - Åke Borg
- Division of Oncology and Pathology, Department of Clinical Sciences LundLund UniversityLundSweden
| | | | - Joan Brunet
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Carla Bruzzone
- Unit of Hereditary CancerIRCCS Ospedale Policlinico San MartinoGenoaItaly
| | - Karolin Bucksch
- Institute for Medical Informatics, Statistics and EpidemiologyUniversity of LeipzigLeipzigGermany
| | - Giulia Cagnoli
- Unit of Medical Genetics, Department of Medical Oncology and HematologyFondazione IRCCS Istituto Nazionale dei Tumori di MilanoMilanItaly
| | - Trinidad Caldés
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San CarlosIdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Almuth Caliebe
- Institute of Human Genetics, University Hospital of Schleswig‐Holstein, Campus KielChristian‐Albrechts University KielKielGermany
| | | | - Mariarosaria Calvello
- Division of Cancer Prevention and Genetics, IEOEuropean Institute of Oncology IRCCSMilanItaly
| | - Gabriele L. Capone
- Department of Experimental and Clinical Biomedical Sciences 'Mario Serio', Medical Genetics UnitUniversity of FlorenceFlorenceItaly
| | - Sandrine M. Caputo
- Service de GénétiqueInstitut CurieParisFrance
- Paris Sciences Lettres Research UniversityParisFrance
| | - Ileana Carnevali
- UO Anatomia PatologicaOspedale di Circolo ASST SettelaghiVareseItaly
| | - Estela Carrasco
- High Risk and Cancer Prevention GroupVall d'Hebron Institute of OncologyBarcelonaSpain
| | | | | | - Giulia Cini
- Division of Functional Onco‐genomics and Genetics, Centro di Riferimento Oncologico di Aviano (CRO)IRCCSAvianoItaly
| | - Edward M. Clarke
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | - Paola Concolino
- Fondazione Policlinico Universitario A.GemelliIRCCSRomeItaly
| | - Elisa J. Cops
- Parkville Familial Cancer CentrePeter MacCallum Cancer CenterMelbourneVictoriaAustralia
| | - Laura Cortesi
- Department of Oncology and HaematologyUniversity of Modena and Reggio EmiliaModenaItaly
| | - Fergus J. Couch
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesota
| | - Esther Darder
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San CarlosIdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Michael Dean
- Laboratory of Translational Genomics, DCEGNational Cancer InstituteGaithersburgMaryland
| | - Irmgard Debatin
- Institute of Human GeneticsUniversity Hospital UlmUlmGermany
| | - Jesús Del Valle
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | | | - Nicolas Derive
- Service de GénétiqueInstitut CurieParisFrance
- Paris Sciences Lettres Research UniversityParisFrance
| | - Orland Diez
- Oncogenetics GroupVall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
- Clinical and Molecular Genetics AreaUniversity Hospital Vall d'HebronBarcelonaSpain
| | - Nina Ditsch
- Department of Gynecology and ObstetricsUniversity of MunichMunichGermany
| | - Susan M. Domchek
- Basser Center for BRCA, Abramson Cancer CenterUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Véronique Dutrannoy
- Institute of Medical and Human GeneticsCharité –Universitätsmedizin BerlinBerlinGermany
| | | | - Hans Ehrencrona
- Department of Clinical Genetics and Pathology, Laboratory MedicineOffice for Medical Services ‐ Region SkåneLundSweden
- Division of Clinical Genetics, Department of Laboratory MedicineLund UniversityLundSweden
| | - Ute Enders
- Institute for Medical Informatics, Statistics and EpidemiologyUniversity of LeipzigLeipzigGermany
| | - D. Gareth Evans
- Genomic Medicine, Division of Evolution and Genomic Sciences, The University of Manchester, Manchester Academic Health Science Centre, Manchester Universities Foundation TrustSt. Mary's HospitalManchesterUK
- Genomic Medicine, North West Genomics hub, Manchester Academic Health Science Centre, Manchester Universities Foundation TrustSt. Mary's HospitalManchesterUK
| | - Chantal Farra
- Medical GeneticsAmerican University of Beirut Medical CenterBeirutLebanon
| | - Ulrike Faust
- Institute of Medical Genetics and Applied GenomicsUniversity of TübingenTübingenGermany
| | - Ute Felbor
- Institute of Human GeneticsUniversity Medicine GreifswaldGreifswaldGermany
| | - Irene Feroce
- Division of Cancer Prevention and Genetics, IEOEuropean Institute of Oncology IRCCSMilanItaly
| | - Miriam Fine
- Adult Genetics UnitRoyal Adelaide HospitalAdelaideAustralia
| | - William D. Foulkes
- Program in Cancer Genetics, Departments of Human Genetics and OncologyMcGill UniversityMontréalQCCanada
| | | | | | - Andrea Gehrig
- Department of Human GeneticsUniversity of WürzburgWürzburgGermany
| | - Francesca Gensini
- Department of Experimental and Clinical Biomedical Sciences 'Mario Serio', Medical Genetics UnitUniversity of FlorenceFlorenceItaly
| | - Anne‐Marie Gerdes
- Department of Clinical Genetics, RigshospitaletCopenhagen University HospitalCopenhagenDenmark
| | - Aldo Germani
- Department of Clinical and Molecular Medicine, Sant'Andrea University HospitalSapienza UniversityRomeItaly
| | - Jutta Giesecke
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - Viviana Gismondi
- Unit of Hereditary CancerIRCCS Ospedale Policlinico San MartinoGenoaItaly
| | - Carolina Gómez
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Encarna B. Gómez Garcia
- Department of Clinical GeneticsMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Sara González
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Elia Grau
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Sabine Grill
- Division of Gynaecology and Obstetrics, Klinikum rechts der Isar der TechnischenUniversität MünchenMunichGermany
| | - Eva Gross
- Department of Gynecology and ObstetricsUniversity of MunichMunichGermany
| | | | | | | | - Thomas Haaf
- Department of Human GeneticsUniversity of WürzburgWürzburgGermany
| | - Karl Hackmann
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav CarusTU DresdenDresdenGermany
| | - Thomas V.O. Hansen
- Department of Clinical Genetics, RigshospitaletCopenhagen University HospitalCopenhagenDenmark
| | | | - Jan Hauke
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - Tilman Heinrich
- Institute of Medical Genetics and Applied GenomicsUniversity of TübingenTübingenGermany
| | - Heide Hellebrand
- Division of Gynaecology and Obstetrics, Klinikum rechts der Isar der TechnischenUniversität MünchenMunichGermany
| | | | - Ellen Honisch
- Department of Gynecology and Obstetrics, University Hospital DüsseldorfHeinrich‐Heine University DüsseldorfDüsseldorfGermany
| | - Judit Horvath
- Institute of Human GeneticsUniversity of MünsterMünsterGermany
| | - Claude Houdayer
- Department of Genetics, F76000 and Normandy University, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized MedicineRouen University HospitalRouenFrance
| | - Verena Hübbel
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - Silvia Iglesias
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Angel Izquierdo
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Paul A. James
- Parkville Familial Cancer CentrePeter MacCallum Cancer CenterMelbourneVictoriaAustralia
- Sir Peter MacCallum Department of OncologyThe University of MelbourneMelbourneVictoriaAustralia
| | - Linda A.M. Janssen
- Department of Clinical GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Udo Jeschke
- Department of Gynecology and ObstetricsUniversity of MunichMunichGermany
| | - Silke Kaulfuß
- Institute of Human GeneticsUniversity Medical Center GöttingenGöttingenGermany
| | - Katharina Keupp
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - Marion Kiechle
- Division of Gynaecology and Obstetrics, Klinikum rechts der Isar der TechnischenUniversität MünchenMunichGermany
| | - Alexandra Kölbl
- Department of Gynecology and ObstetricsUniversity of MunichMunichGermany
| | - Sophie Krieger
- Laboratoire de Biologie Clinique et OncologiqueCentre Francois BaclesseCaenFrance
- Genomics and Personalized Medecine in Cancer and Neurological DisordersNormandy Centre for Genomic and Personalized MedicineRouenFrance
- Normandie UniversitéUNICAENCaenFrance
| | - Torben A. Kruse
- Department of Clinical GeneticsOdense University HospitalOdense CDenmark
| | - Anders Kvist
- Division of Oncology and Pathology, Department of Clinical Sciences LundLund UniversityLundSweden
| | - Fiona Lalloo
- Genomic Medicine, North West Genomics hub, Manchester Academic Health Science Centre, Manchester Universities Foundation TrustSt. Mary's HospitalManchesterUK
| | - Mirjam Larsen
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - Vanessa L. Lattimore
- Department of Pathology and Biomedical ScienceUniversity of OtagoChristchurchNew Zealand
| | - Charlotte Lautrup
- Department of Clinical GeneticsAalborg University HospitalAalborgDenmark
- Clinical Cancer Research CenterAalborg University HospitalAalborgDenmark
| | - Susanne Ledig
- Institute of Human GeneticsUniversity of MünsterMünsterGermany
| | - Elena Leinert
- Department of Gynaecology and ObstetricsUniversity Hospital UlmUlmGermany
| | | | - Joanna Lim
- Breast Cancer Research ProgrammeCancer Research MalaysiaSubang JayaSelangorMalaysia
| | - Markus Loeffler
- Institute for Medical Informatics, Statistics and EpidemiologyUniversity of LeipzigLeipzigGermany
| | - Adrià López‐Fernández
- High Risk and Cancer Prevention GroupVall d'Hebron Institute of OncologyBarcelonaSpain
| | - Emanuela Lucci‐Cordisco
- UOC Genetica Medica, Fondazione Policlinico Universitario A.Gemelli IRCCS and Istituto di Medicina GenomicaUniversità Cattolica del Sacro CuoreRomeItaly
| | - Nicolai Maass
- Department of Gynaecology and Obstetrics, University Hospital of Schleswig‐Holstein, Campus KielChristian‐Albrechts University KielKielGermany
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Medical Oncology and HematologyFondazione IRCCS Istituto Nazionale dei Tumori di MilanoMilanItaly
| | - Monica Marabelli
- Division of Cancer Prevention and Genetics, IEOEuropean Institute of Oncology IRCCSMilanItaly
| | - Laura Matricardi
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOVIRCCSPaduaItaly
| | - Alfons Meindl
- Department of Gynecology and ObstetricsUniversity of MunichMunichGermany
| | | | - Setareh Moghadasi
- Department of Clinical GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | | | - Marco Montagna
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOVIRCCSPaduaItaly
| | - Gemma Montalban
- Oncogenetics GroupVall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | | | - Eva Montes
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Luigi Mori
- Department of Clinical and Experimental Science, University of Brescia c/o 2nd Internal MedicineHospital of BresciaBresciaItaly
| | - Lidia Moserle
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOVIRCCSPaduaItaly
| | | | - Christoph Mundhenke
- Department of Gynaecology and Obstetrics, University Hospital of Schleswig‐Holstein, Campus KielChristian‐Albrechts University KielKielGermany
| | - Nadia Naldi
- Division of OncologyUniversity Hospital of ParmaParmaItaly
| | - Katherine L. Nathanson
- Basser Center for BRCA, Abramson Cancer CenterUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Matilde Navarro
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University HospitalUniversity of HelsinkiHelsinkiFinland
| | - Cassandra B. Nichols
- Genetic Services of Western AustraliaKing Edward Memorial HospitalPerthAustralia
| | - Dieter Niederacher
- Department of Gynecology and Obstetrics, University Hospital DüsseldorfHeinrich‐Heine University DüsseldorfDüsseldorfGermany
| | | | - Kai‐ren Ong
- West Midlands Regional Genetics ServiceBirmingham Women's Hospital Healthcare NHS TrustBirminghamUK
| | - Nicholas Pachter
- Genetic Services of Western AustraliaKing Edward Memorial HospitalPerthAustralia
- Faculty of Health and Medical SciencesUniversity of Western AustraliaPerthAustralia
| | - Edenir I. Palmero
- Molecular Oncology Research CenterBarretos Cancer HospitalSão PauloBrazil
- Barretos School of Health SciencesDr. Paulo Prata ‐ FACISBSão PauloBrazil
| | - Laura Papi
- Department of Experimental and Clinical Biomedical Sciences 'Mario Serio', Medical Genetics UnitUniversity of FlorenceFlorenceItaly
| | - Inge Sokilde Pedersen
- Clinical Cancer Research CenterAalborg University HospitalAalborgDenmark
- Molecular DiagnosticsAalborg University HospitalAalborgDenmark
- Department of Clinical MedicineAalborg UniversityAalborgDenmark
| | - Bernard Peissel
- Unit of Medical Genetics, Department of Medical Oncology and HematologyFondazione IRCCS Istituto Nazionale dei Tumori di MilanoMilanItaly
| | - Pedro Perez‐Segura
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San CarlosIdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Katharina Pfeifer
- Division of Gynaecology and Obstetrics, Klinikum rechts der Isar der TechnischenUniversität MünchenMunichGermany
| | - Marta Pineda
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Esther Pohl‐Rescigno
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - Nicola K. Poplawski
- Adult Genetics UnitRoyal Adelaide HospitalAdelaideAustralia
- School of Paediatrics and Reproductive HealthUniversity of AdelaideAdelaideAustralia
| | - Berardino Porfirio
- Department of Experimental and Clinical Biomedical Sciences 'Mario Serio', Medical Genetics UnitUniversity of FlorenceFlorenceItaly
| | - Anne S. Quante
- Division of Gynaecology and Obstetrics, Klinikum rechts der Isar der TechnischenUniversität MünchenMunichGermany
| | - Juliane Ramser
- Division of Gynaecology and Obstetrics, Klinikum rechts der Isar der TechnischenUniversität MünchenMunichGermany
| | - Rui M. Reis
- Molecular Oncology Research CenterBarretos Cancer HospitalSão PauloBrazil
- Health Sciences SchoolUniversity of MinhoBragaPortugal
- ICVS/3B's‐PT Government Associate LaboratoryBragaPortugal
| | - Françoise Revillion
- Laboratoire d'Oncogenetique Moleculaire HumaineCentre Oscar LambretLilleFrance
| | - Kerstin Rhiem
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | | | - Julia Ritter
- Institute of Medical and Human GeneticsCharité –Universitätsmedizin BerlinBerlinGermany
| | - Daniela Rivera
- Unit of Hereditary CancerIRCCS Ospedale Policlinico San MartinoGenoaItaly
| | - Paula Rofes
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Andreas Rump
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav CarusTU DresdenDresdenGermany
| | - Monica Salinas
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Ana María Sánchez de Abajo
- Servicio de Análisis Clínicos y Bioquímica Clínica, Complejo HospitalarioUniversitario Insular Materno‐Infantil de Gran CanariaLas Palmas de Gran CanaríaSpain
| | - Gunnar Schmidt
- Institute of Human GeneticsHannover Medical SchoolHannoverGermany
| | - Ulrike Schoenwiese
- Institute for Medical Informatics, Statistics and EpidemiologyUniversity of LeipzigLeipzigGermany
| | - Jochen Seggewiß
- Institute of Human GeneticsUniversity of MünsterMünsterGermany
| | - Ares Solanes
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Doris Steinemann
- Institute of Human GeneticsHannover Medical SchoolHannoverGermany
| | - Mathias Stiller
- Institute of Human GeneticsUniversity Hospital LeipzigLeipzigGermany
| | - Dominique Stoppa‐Lyonnet
- Service de GénétiqueInstitut CurieParisFrance
- Department of Tumour BiologyINSERM U830ParisFrance
- Université Paris DescartesParisFrance
| | - Kelly J. Sullivan
- Genetic Health Service NZ‐ Northern HubAuckland District Health BoardAucklandNew Zealand
| | - Rachel Susman
- Genetic Health QueenslandRoyal Brisbane and Women's HospitalBrisbaneAustralia
| | - Christian Sutter
- Institute of Human GeneticsUniversity Hospital HeidelbergHeidelbergGermany
| | - Sean V. Tavtigian
- Department of Oncological ServicesUniversity of Utah School of MedicineSalt Lake CityUtah
- Huntsman Cancer InstituteUniversity of UtahSalt Lake CityUtah
| | - Soo H. Teo
- Breast Cancer Research ProgrammeCancer Research MalaysiaSubang JayaSelangorMalaysia
- Department of Surgery, Faculty of MedicineUniversity MalayaKuala LumpurMalaysia
| | - Alex Teulé
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Mads Thomassen
- Department of Clinical GeneticsOdense University HospitalOdense CDenmark
| | | | - Marc Tischkowitz
- Department of Medical GeneticsUniversity of CambridgeCambridgeUK
| | - Silvia Tognazzo
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOVIRCCSPaduaItaly
| | - Amanda E. Toland
- Department of Cancer Biology and GeneticsThe Ohio State UniversityColumbusOhio
| | - Eva Tornero
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Therese Törngren
- Division of Oncology and Pathology, Department of Clinical Sciences LundLund UniversityLundSweden
| | - Sara Torres‐Esquius
- High Risk and Cancer Prevention GroupVall d'Hebron Institute of OncologyBarcelonaSpain
| | - Angela Toss
- Department of Oncology and HaematologyUniversity of Modena and Reggio EmiliaModenaItaly
| | - Alison H. Trainer
- Parkville Familial Cancer CentrePeter MacCallum Cancer CenterMelbourneVictoriaAustralia
- Department of medicineUniversity of MelbourneMelbourneVictoriaAustralia
| | - Katherine M. Tucker
- Prince of Wales Clinical SchoolUniversity of NSWSydneyNew South WalesAustralia
- Hereditary Cancer Clinic, Department of Medical OncologyPrince of Wales HospitalRandwickNew South WalesAustralia
| | | | - Marion T. van Mackelenbergh
- Department of Gynaecology and Obstetrics, University Hospital of Schleswig‐Holstein, Campus KielChristian‐Albrechts University KielKielGermany
| | - Liliana Varesco
- Unit of Hereditary CancerIRCCS Ospedale Policlinico San MartinoGenoaItaly
| | - Gardenia Vargas‐Parra
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Raymonda Varon
- Institute of Medical and Human GeneticsCharité –Universitätsmedizin BerlinBerlinGermany
| | - Ana Vega
- Fundación Pública galega Medicina Xenómica‐SERGASGrupo de Medicina Xenómica‐USC, CIBERER, IDISSantiago de CompostelaSpain
| | - Ángela Velasco
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | - Anne‐Sophie Vesper
- Department of Gynecology and Obstetrics, University Hospital DüsseldorfHeinrich‐Heine University DüsseldorfDüsseldorfGermany
| | - Alessandra Viel
- Division of Functional Onco‐genomics and Genetics, Centro di Riferimento Oncologico di Aviano (CRO)IRCCSAvianoItaly
| | | | - Sebastian A. Wagner
- Department of MedicineHematology/Oncology, Goethe‐University FrankfurtFrankfurtGermany
| | - Anke Waha
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - Logan C. Walker
- Department of Pathology and Biomedical ScienceUniversity of OtagoChristchurchNew Zealand
| | - Rhiannon J. Walters
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | - Shan Wang‐Gohrke
- Department of Gynaecology and ObstetricsUniversity Hospital UlmUlmGermany
| | | | - Wilko Weichert
- Institute of PathologyTechnische Universität MünchenMunichGermany
| | - Kerstin Wieland
- Institute for Medical Informatics, Statistics and EpidemiologyUniversity of LeipzigLeipzigGermany
| | - Lisa Wiesmüller
- Department of Gynaecology and ObstetricsUniversity Hospital UlmUlmGermany
| | - Isabell Witzel
- Department of GynecologyUniversity Medical Center HamburgHamburgGermany
| | - Achim Wöckel
- Department of Gynecology and ObstetricsUniversity Hospital WürzburgWürzburgGermany
| | - Emma R. Woodward
- Genomic Medicine, Division of Evolution and Genomic Sciences, The University of Manchester, Manchester Academic Health Science Centre, Manchester Universities Foundation TrustSt. Mary's HospitalManchesterUK
- Genomic Medicine, North West Genomics hub, Manchester Academic Health Science Centre, Manchester Universities Foundation TrustSt. Mary's HospitalManchesterUK
| | - Silke Zachariae
- Institute for Medical Informatics, Statistics and EpidemiologyUniversity of LeipzigLeipzigGermany
| | - Valentina Zampiga
- Biosciences LaboratoryIstituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCSMeldolaItaly
| | | | - KConFab Investigators
- Sir Peter MacCallum Department of OncologyThe University of MelbourneMelbourneVictoriaAustralia
- Research DepartmentPeter MacCallum Cancer CenterMelbourneVictoriaAustralia
| | - Conxi Lázaro
- Hereditary Cancer Program, ONCOBELL‐IDIBELL‐IDIBGI‐IGTP, Catalan Institute of OncologyCIBERONCBarcelonaSpain
| | | | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of ResearchFondazione IRCCS Istituto Nazionale dei Tumori (INT)MilanItaly
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and EpidemiologyUniversity of LeipzigLeipzigGermany
| | - Rita K. Schmutzler
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - David E. Goldgar
- Department of Dermatology, Huntsman Cancer InstituteUniversity of Utah School of MedicineSalt Lake CityUtah
| | - Amanda B. Spurdle
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
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23
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Fortuno C, Cipponi A, Ballinger ML, Tavtigian SV, Olivier M, Ruparel V, Haupt Y, Haupt S, Study ISK, Tucker K, Spurdle AB, Thomas DM, James PA. A quantitative model to predict pathogenicity of missense variants in the TP53 gene. Hum Mutat 2019; 40:788-800. [PMID: 30840781 DOI: 10.1002/humu.23739] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 02/27/2019] [Accepted: 03/04/2019] [Indexed: 12/20/2022]
Abstract
Germline pathogenic variants in the TP53 gene cause Li-Fraumeni syndrome, a condition that predisposes individuals to a wide range of cancer types. Identification of individuals carrying a TP53 pathogenic variant is linked to clinical management decisions, such as the avoidance of radiotherapy and use of high-intensity screening programs. The aim of this study was to develop an evidence-based quantitative model that integrates independent in silico data (Align-GVGD and BayesDel) and somatic to germline ratio (SGR), to assign pathogenicity to every possible missense variant in the TP53 gene. To do this, a likelihood ratio for pathogenicity (LR) was derived from each component calibrated using reference sets of assumed pathogenic and benign missense variants. A posterior probability of pathogenicity was generated by combining LRs, and algorithm outputs were validated using different approaches. A total of 730 TP53 missense variants could be assigned to a clinically interpretable class. The outputs of the model correlated well with existing clinical information, functional data, and ClinVar classifications. In conclusion, these quantitative outputs provide the basis for individualized assessment of cancer risk useful for clinical interpretation. In addition, we propose the value of the novel SGR approach for use within the ACMG/AMP guidelines for variant classification.
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Affiliation(s)
- Cristina Fortuno
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Arcadi Cipponi
- Cancer Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Mandy L Ballinger
- Cancer Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Sean V Tavtigian
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | - Magali Olivier
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon, France
| | - Vatsal Ruparel
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Ygal Haupt
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Sue Haupt
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - International Sarcoma Kindred Study
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Kathy Tucker
- Hereditary Cancer Clinic, Prince of Wales Hospital, Randwick, New South Wales, Australia
- Prince of Wales Medical School, University of New South Wales, Randwick, New South Wales, Australia
| | - Amanda B Spurdle
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - David M Thomas
- Cancer Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Paul A James
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
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Valle L, Vilar E, Tavtigian SV, Stoffel EM. Genetic predisposition to colorectal cancer: syndromes, genes, classification of genetic variants and implications for precision medicine. J Pathol 2019; 247:574-588. [PMID: 30584801 PMCID: PMC6747691 DOI: 10.1002/path.5229] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/21/2018] [Accepted: 12/23/2018] [Indexed: 12/15/2022]
Abstract
This article reviews genes and syndromes associated with predisposition to colorectal cancer (CRC), with an overview of gene variant classification. We include updates on the application of preventive and therapeutic measures, focusing on the use of non-steroidal anti-inflammatory drugs (NSAIDs) and immunotherapy. Germline pathogenic variants in genes conferring high or moderate risk to cancer are detected in 6-10% of all CRCs and 20% of those diagnosed before age 50. CRC syndromes can be subdivided into nonpolyposis and polyposis entities, the most common of which are Lynch syndrome and familial adenomatous polyposis, respectively. In addition to known and novel genes associated with highly penetrant CRC risk, identification of pathogenic germline variants in genes associated with moderate-penetrance cancer risk and/or hereditary cancer syndromes not traditionally linked to CRC may have an impact on genetic testing, counseling, and surveillance. The use of multigene panels in genetic testing has exposed challenges in the classification of variants of uncertain significance. We provide an overview of the main classification systems and strategies for improving these. Finally, we highlight approaches for integrating chemoprevention in the care of individuals with genetic predisposition to CRC and use of targeted agents and immunotherapy for treatment of mismatch repair-deficient and hypermutant tumors. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Barcelona, Spain
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Eduardo Vilar
- Departments of Clinical Cancer Prevention, GI Medical Oncology and Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Sean V. Tavtigian
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT, United States
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, United States
| | - Elena M. Stoffel
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
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25
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Fortuno C, James PA, Young EL, Feng B, Olivier M, Pesaran T, Tavtigian SV, Spurdle AB. Improved, ACMG-compliant, in silico prediction of pathogenicity for missense substitutions encoded by TP53 variants. Hum Mutat 2018; 39:1061-1069. [PMID: 29775997 PMCID: PMC6043381 DOI: 10.1002/humu.23553] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 05/11/2018] [Accepted: 05/15/2018] [Indexed: 02/02/2023]
Abstract
Clinical interpretation of germline missense variants represents a major challenge, including those in the TP53 Li-Fraumeni syndrome gene. Bioinformatic prediction is a key part of variant classification strategies. We aimed to optimize the performance of the Align-GVGD tool used for p53 missense variant prediction, and compare its performance to other bioinformatic tools (SIFT, PolyPhen-2) and ensemble methods (REVEL, BayesDel). Reference sets of assumed pathogenic and assumed benign variants were defined using functional and/or clinical data. Area under the curve and Matthews correlation coefficient (MCC) values were used as objective functions to select an optimized protein multisequence alignment with best performance for Align-GVGD. MCC comparison of tools using binary categories showed optimized Align-GVGD (C15 cut-off) combined with BayesDel (0.16 cut-off), or with REVEL (0.5 cut-off), to have the best overall performance. Further, a semi-quantitative approach using multiple tiers of bioinformatic prediction, validated using an independent set of nonfunctional and functional variants, supported use of Align-GVGD and BayesDel prediction for different strength of evidence levels in ACMG/AMP rules. We provide rationale for bioinformatic tool selection for TP53 variant classification, and have also computed relevant bioinformatic predictions for every possible p53 missense variant to facilitate their use by the scientific and medical community.
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Affiliation(s)
- Cristina Fortuno
- QIMR Berghofer Medical Research Institute, Genetics and Computational Division, 300 Herston Rd, Herston QLD 4006, Australia
| | - Paul A James
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital
| | - Erin L. Young
- Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - Bing Feng
- Department of Dermatology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - Magali Olivier
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, 69008 Lyon, France
| | | | - Sean V. Tavtigian
- Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - Amanda B. Spurdle
- QIMR Berghofer Medical Research Institute, Genetics and Computational Division, 300 Herston Rd, Herston QLD 4006, Australia
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Young EL, Thompson BA, Neklason DW, Firpo MA, Werner T, Bell R, Berger J, Fraser A, Gammon A, Koptiuch C, Kohlmann WK, Neumayer L, Goldgar DE, Mulvihill SJ, Cannon-Albright LA, Tavtigian SV. Pancreatic cancer as a sentinel for hereditary cancer predisposition. BMC Cancer 2018; 18:697. [PMID: 29945567 PMCID: PMC6020441 DOI: 10.1186/s12885-018-4573-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 06/01/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Genes associated with hereditary breast and ovarian cancer (HBOC) and colorectal cancer (CRC) predisposition have been shown to play a role in pancreatic cancer susceptibility. Growing evidence suggests that pancreatic cancer may be useful as a sentinel cancer to identify families that could benefit from HBOC or CRC surveillance, but to date pancreatic cancer is only considered an indication for genetic testing in the context of additional family history. METHODS Preliminary data generated at the Huntsman Cancer Hospital (HCH) included variants identified on a custom 34-gene panel or 59-gene panel including both known HBOC and CRC genes for respective sets of 66 and 147 pancreatic cancer cases, unselected for family history. Given the strength of preliminary data and corresponding literature, 61 sequential pancreatic cancer cases underwent a custom 14-gene clinical panel. Sequencing data from HCH pancreatic cancer cases, pancreatic cancer cases of the Cancer Genome Atlas (TCGA), and an unselected pancreatic cancer screen from the Mayo Clinic were combined in a meta-analysis to estimate the proportion of carriers with pathogenic and high probability of pathogenic variants of uncertain significance (HiP-VUS). RESULTS Approximately 8.6% of unselected pancreatic cancer cases at the HCH carried a variant with potential HBOC or CRC screening recommendations. A meta-analysis of unselected pancreatic cancer cases revealed that approximately 11.5% carry a pathogenic variant or HiP-VUS. CONCLUSION With the inclusion of both HBOC and CRC susceptibility genes in a panel test, unselected pancreatic cancer cases act as a useful sentinel cancer to identify asymptomatic at-risk relatives who could benefit from relevant HBOC and CRC surveillance measures.
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Affiliation(s)
- Erin L. Young
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, United States
| | - Bryony A. Thompson
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - Deborah W. Neklason
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
- Division of Genetic Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, United States
| | - Matthew A. Firpo
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
- Department of Surgery, University of Utah School of Medicine, Salt Lake City, United States
| | - Theresa Werner
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
- Division of Oncology, Department of Medicine, University of Utah, Salt Lake City, United States
| | - Russell Bell
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, United States
| | - Justin Berger
- Population Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, United States
| | - Alison Fraser
- Population Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, United States
| | - Amanda Gammon
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
| | - Cathryn Koptiuch
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
| | - Wendy K. Kohlmann
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
| | - Leigh Neumayer
- Department of Surgery and Arizona Cancer Center, University of Arizona, Tucson, United States
| | - David E. Goldgar
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
- Department of Dermatology, University of Utah School of Medicine, Salt Lake City, United States
| | - Sean J. Mulvihill
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
- Department of Surgery, University of Utah School of Medicine, Salt Lake City, United States
| | - Lisa A. Cannon-Albright
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
- Division of Genetic Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, United States
- George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, United States
| | - Sean V. Tavtigian
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, United States
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
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27
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Li J, Li H, Makunin I, Thompson BA, Tao K, Young EL, Lopez J, Camp NJ, Tavtigian SV, John EM, Andrulis IL, Khanna KK, Goldgar D, Chenevix-Trench G. Panel sequencing of 264 candidate susceptibility genes and segregation analysis in a cohort of non-BRCA1, non-BRCA2 breast cancer families. Breast Cancer Res Treat 2017; 166:937-949. [PMID: 28840378 DOI: 10.1007/s10549-017-4469-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 08/16/2017] [Indexed: 12/18/2022]
Abstract
PURPOSE The main aim of this study was to screen epigenetic modifier genes and known breast cancer driver genes for germline mutations in non-BRCA1/2 (BRCAx) breast cancer families in order to identify novel susceptibility genes of moderate-high penetrance. METHODS We screened 264 candidate susceptibility genes in 656 index cases from non-BRCA1/2 families. Potentially pathogenic candidate mutations were then genotyped in all available family members for the assessment of co-segregation of the variant with disease in the family in order to estimate the breast cancer risks associated with these mutations. For 11 of the candidate susceptibility genes, we screened an additional 800 non-BRCA1/2 breast cancer cases and 787 controls. RESULTS Only two genes, CHD8 and USH2A showed any evidence of an increased risk of breast cancer (RR = 2.40 (95% CI 1.0-7.32) and 2.48 (95% CI 1.11-6.67), respectively). CONCLUSIONS We found no convincing evidence that epigenetic modifier and known breast cancer driver genes carry germline mutations that increase breast cancer risk. USH2A is no longer regarded as a breast cancer driver gene and seems an implausible candidate given its association with Usher syndrome. However, somatic mutations in CHD8 have been recently reported, making it an even more promising candidate, but further analysis of CHD8 in very large cohorts of families or case-control studies would be required to determine if it is a moderate-risk breast cancer susceptibility gene.
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Affiliation(s)
- Jun Li
- QIMR Berghofer, Brisbane, QLD, 4006, Australia
| | - Hongyan Li
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, 84132, USA
| | - Igor Makunin
- QIMR Berghofer, Brisbane, QLD, 4006, Australia.,Research Computing Centre, The University of Queensland, St Lucia, QLD, 4072, Australia
| | | | - Bryony A Thompson
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, 84132, USA.,Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Kayoko Tao
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, 84132, USA
| | - Erin L Young
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, 84132, USA
| | - Jacqueline Lopez
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, 84132, USA
| | - Nicola J Camp
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, 84132, USA
| | - Sean V Tavtigian
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, 84132, USA
| | - Esther M John
- Department of Epidemiology, Cancer Prevention Institute of California, Fremont, CA, 94538, USA.,Department of Health Research and Policy (Epidemiology) and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Irene L Andrulis
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5G 1X5, Canada
| | | | - David Goldgar
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, 84132, USA.,Department of Dermatology, University of Utah School of Medicine, Salt Lake City, UT, 84132, USA
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Southey MC, Goldgar DE, Winqvist R, Pylkäs K, Couch F, Tischkowitz M, Foulkes WD, Dennis J, Michailidou K, van Rensburg EJ, Heikkinen T, Nevanlinna H, Hopper JL, Dörk T, Claes KB, Reis-Filho J, Teo ZL, Radice P, Catucci I, Peterlongo P, Tsimiklis H, Odefrey FA, Dowty JG, Schmidt MK, Broeks A, Hogervorst FB, Verhoef S, Carpenter J, Clarke C, Scott RJ, Fasching PA, Haeberle L, Ekici AB, Beckmann MW, Peto J, Dos-Santos-Silva I, Fletcher O, Johnson N, Bolla MK, Sawyer EJ, Tomlinson I, Kerin MJ, Miller N, Marme F, Burwinkel B, Yang R, Guénel P, Truong T, Menegaux F, Sanchez M, Bojesen S, Nielsen SF, Flyger H, Benitez J, Zamora MP, Perez JIA, Menéndez P, Anton-Culver H, Neuhausen S, Ziogas A, Clarke CA, Brenner H, Arndt V, Stegmaier C, Brauch H, Brüning T, Ko YD, Muranen TA, Aittomäki K, Blomqvist C, Bogdanova NV, Antonenkova NN, Lindblom A, Margolin S, Mannermaa A, Kataja V, Kosma VM, Hartikainen JM, Spurdle AB, Investigators KC, Wauters E, Smeets D, Beuselinck B, Floris G, Chang-Claude J, Rudolph A, Seibold P, Flesch-Janys D, Olson JE, Vachon C, Pankratz VS, McLean C, Haiman CA, Henderson BE, Schumacher F, Le Marchand L, Kristensen V, Alnæs GG, Zheng W, Hunter DJ, Lindstrom S, Hankinson SE, Kraft P, Andrulis I, Knight JA, Glendon G, Mulligan AM, Jukkola-Vuorinen A, Grip M, Kauppila S, Devilee P, Tollenaar RAEM, Seynaeve C, Hollestelle A, Garcia-Closas M, Figueroa J, Chanock SJ, Lissowska J, Czene K, Darabi H, Eriksson M, Eccles DM, Rafiq S, Tapper WJ, Gerty SM, Hooning MJ, Martens JWM, Collée JM, Tilanus-Linthorst M, Hall P, Li J, Brand JS, Humphreys K, Cox A, Reed MWR, Luccarini C, Baynes C, Dunning AM, Hamann U, Torres D, Ulmer HU, Rüdiger T, Jakubowska A, Lubinski J, Jaworska K, Durda K, Slager S, Toland AE, Ambrosone CB, Yannoukakos D, Swerdlow A, Ashworth A, Orr N, Jones M, González-Neira A, Pita G, Alonso MR, Álvarez N, Herrero D, Tessier DC, Vincent D, Bacot F, Simard J, Dumont M, Soucy P, Eeles R, Muir K, Wiklund F, Gronberg H, Schleutker J, Nordestgaard BG, Weischer M, Travis RC, Neal D, Donovan JL, Hamdy FC, Khaw KT, Stanford JL, Blot WJ, Thibodeau S, Schaid DJ, Kelley JL, Maier C, Kibel AS, Cybulski C, Cannon-Albright L, Butterbach K, Park J, Kaneva R, Batra J, Teixeira MR, Kote-Jarai Z, Olama AAA, Benlloch S, Renner SP, Hartmann A, Hein A, Ruebner M, Lambrechts D, Van Nieuwenhuysen E, Vergote I, Lambretchs S, Doherty JA, Rossing MA, Nickels S, Eilber U, Wang-Gohrke S, Odunsi K, Sucheston-Campbell LE, Friel G, Lurie G, Killeen JL, Wilkens LR, Goodman MT, Runnebaum I, Hillemanns PA, Pelttari LM, Butzow R, Modugno F, Edwards RP, Ness RB, Moysich KB, du Bois A, Heitz F, Harter P, Kommoss S, Karlan BY, Walsh C, Lester J, Jensen A, Kjaer SK, Høgdall E, Peissel B, Bonanni B, Bernard L, Goode EL, Fridley BL, Vierkant RA, Cunningham JM, Larson MC, Fogarty ZC, Kalli KR, Liang D, Lu KH, Hildebrandt MAT, Wu X, Levine DA, Dao F, Bisogna M, Berchuck A, Iversen ES, Marks JR, Akushevich L, Cramer DW, Schildkraut J, Terry KL, Poole EM, Stampfer M, Tworoger SS, Bandera EV, Orlow I, Olson SH, Bjorge L, Salvesen HB, van Altena AM, Aben KKH, Kiemeney LA, Massuger LFAG, Pejovic T, Bean Y, Brooks-Wilson A, Kelemen LE, Cook LS, Le ND, Górski B, Gronwald J, Menkiszak J, Høgdall CK, Lundvall L, Nedergaard L, Engelholm SA, Dicks E, Tyrer J, Campbell I, McNeish I, Paul J, Siddiqui N, Glasspool R, Whittemore AS, Rothstein JH, McGuire V, Sieh W, Cai H, Shu XO, Teten RT, Sutphen R, McLaughlin JR, Narod SA, Phelan CM, Monteiro AN, Fenstermacher D, Lin HY, Permuth JB, Sellers TA, Chen YA, Tsai YY, Chen Z, Gentry-Maharaj A, Gayther SA, Ramus SJ, Menon U, Wu AH, Pearce CL, Van Den Berg D, Pike MC, Dansonka-Mieszkowska A, Plisiecka-Halasa J, Moes-Sosnowska J, Kupryjanczyk J, Pharoah PD, Song H, Winship I, Chenevix-Trench G, Giles GG, Tavtigian SV, Easton DF, Milne RL. PALB2, CHEK2 and ATM rare variants and cancer risk: data from COGS. J Med Genet 2016; 53:800-811. [PMID: 27595995 PMCID: PMC5200636 DOI: 10.1136/jmedgenet-2016-103839] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 06/01/2016] [Accepted: 06/21/2016] [Indexed: 12/21/2022]
Abstract
BACKGROUND The rarity of mutations in PALB2, CHEK2 and ATM make it difficult to estimate precisely associated cancer risks. Population-based family studies have provided evidence that at least some of these mutations are associated with breast cancer risk as high as those associated with rare BRCA2 mutations. We aimed to estimate the relative risks associated with specific rare variants in PALB2, CHEK2 and ATM via a multicentre case-control study. METHODS We genotyped 10 rare mutations using the custom iCOGS array: PALB2 c.1592delT, c.2816T>G and c.3113G>A, CHEK2 c.349A>G, c.538C>T, c.715G>A, c.1036C>T, c.1312G>T, and c.1343T>G and ATM c.7271T>G. We assessed associations with breast cancer risk (42 671 cases and 42 164 controls), as well as prostate (22 301 cases and 22 320 controls) and ovarian (14 542 cases and 23 491 controls) cancer risk, for each variant. RESULTS For European women, strong evidence of association with breast cancer risk was observed for PALB2 c.1592delT OR 3.44 (95% CI 1.39 to 8.52, p=7.1×10-5), PALB2 c.3113G>A OR 4.21 (95% CI 1.84 to 9.60, p=6.9×10-8) and ATM c.7271T>G OR 11.0 (95% CI 1.42 to 85.7, p=0.0012). We also found evidence of association with breast cancer risk for three variants in CHEK2, c.349A>G OR 2.26 (95% CI 1.29 to 3.95), c.1036C>T OR 5.06 (95% CI 1.09 to 23.5) and c.538C>T OR 1.33 (95% CI 1.05 to 1.67) (p≤0.017). Evidence for prostate cancer risk was observed for CHEK2 c.1343T>G OR 3.03 (95% CI 1.53 to 6.03, p=0.0006) for African men and CHEK2 c.1312G>T OR 2.21 (95% CI 1.06 to 4.63, p=0.030) for European men. No evidence of association with ovarian cancer was found for any of these variants. CONCLUSIONS This report adds to accumulating evidence that at least some variants in these genes are associated with an increased risk of breast cancer that is clinically important.
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Affiliation(s)
- Melissa C Southey
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, Australia
| | | | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter Oulu, University of Oulu, Nordlab Oulu, Oulu, Finland
| | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter Oulu, University of Oulu, Nordlab Oulu, Oulu, Finland
| | - Fergus Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Marc Tischkowitz
- Department of Medical Genetics and National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, and the Department of Clinical Genetics, East Anglian Regional Genetics Service, Addenbrooke's Hospital
| | - William D Foulkes
- Program in Cancer Genetics, Department of Human Genetics and Oncology, Lady Davis Institute, and Research Institute, McGill University Health Centre, McGill University, Montreal, Canada
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Laboratory, Worts Causeway, Cambridge, UK
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Laboratory, Worts Causeway, Cambridge, UK
| | | | - Tuomas Heikkinen
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Kathleen Bm Claes
- Center for Medical Genetics, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium
| | - Jorge Reis-Filho
- Department of Pathology and Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Zhi Ling Teo
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, Australia
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Irene Catucci
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | | | - Helen Tsimiklis
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, Australia
| | - Fabrice A Odefrey
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, Australia
| | - James G Dowty
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Marjanka K Schmidt
- Netherlands Cancer Institute, Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Annegien Broeks
- Netherlands Cancer Institute, Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Frans B Hogervorst
- Netherlands Cancer Institute, Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Senno Verhoef
- Netherlands Cancer Institute, Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Jane Carpenter
- Australian Breast Cancer Tissue Bank, University of Sydney at the Westmead Institute for Medical Research, NSW, Australia
| | - Christine Clarke
- Centre for Cancer Research, University of Sydney at the Westmead Institute for Medical Research, NSW, Australia
| | - Rodney J Scott
- Division of Molecular Medicine, Pathology North, Newcastle and University of Newcastle, NSW, Australia
| | - Peter A Fasching
- University Breast Center Franconia, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
- David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology, University of California at Los Angeles, CA, USA
| | - Lothar Haeberle
- University Breast Center Franconia, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
- Unit of Biostatistics, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Arif B Ekici
- Institute of Human Genetics, University Hospital Erlangen, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Matthias W Beckmann
- University Breast Center Franconia, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Julian Peto
- Non-communicable Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Isabel Dos-Santos-Silva
- Non-communicable Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Olivia Fletcher
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - Nichola Johnson
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Laboratory, Worts Causeway, Cambridge, UK
| | - Elinor J Sawyer
- Division of Cancer Studies, NIHR Comprehensive Biomedical Research Centre, Guy's & St. Thomas' NHS Foundation Trust in partnership with King's College London, London, UK
| | - Ian Tomlinson
- Wellcome Trust Centre for Human Genetics and Oxford Biomedical Research Centre, University of Oxford, UK and Oxford NIHR Biomedical Research Centre, Headington, OX3 7LE
| | - Michael J Kerin
- Surgery, Lambe Institute for Translational Science, NUIGalway, University Hospital Galway, Galway, Ireland
| | - Nicola Miller
- Surgery, Lambe Institute for Translational Science, NUIGalway, University Hospital Galway, Galway, Ireland
| | - Federik Marme
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases, University of Heidelberg, Heidelberg, Germany
| | - Barbara Burwinkel
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
- Molecular Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rongxi Yang
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
- Molecular Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Pascal Guénel
- Inserm (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), U1018, Environmental Epidemiology of Cancer, Villejuif, France
- University Paris-Sud, UMRS 1018, Villejuif, France
| | - Thérèse Truong
- Inserm (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), U1018, Environmental Epidemiology of Cancer, Villejuif, France
- University Paris-Sud, UMRS 1018, Villejuif, France
| | - Florence Menegaux
- Inserm (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), U1018, Environmental Epidemiology of Cancer, Villejuif, France
- University Paris-Sud, UMRS 1018, Villejuif, France
| | - Marie Sanchez
- Inserm (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), U1018, Environmental Epidemiology of Cancer, Villejuif, France
- University Paris-Sud, UMRS 1018, Villejuif, France
| | - Stig Bojesen
- Copenhagen General Population Study, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Sune F Nielsen
- Copenhagen General Population Study, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Flyger
- Department of Breast Surgery, Herlev Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Javier Benitez
- Human Genetics Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Valencia, Spain
| | - M Pilar Zamora
- Servicio de Oncología Médica, Hospital Universitario La Paz, Madrid, Spain
| | | | | | - Hoda Anton-Culver
- Department of Epidemiology, University of California Irvine, Irvine, California, USA
| | - Susan Neuhausen
- Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Argyrios Ziogas
- Department of Epidemiology, University of California Irvine, Irvine, California, USA
| | | | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Hiltrud Brauch
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart
- University of Tübingen, Tübingen, Germany
| | - Thomas Brüning
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr University, Bochum (IPA), Germany
| | - Yon-Dschun Ko
- Department of Internal Medicine, Evangelische Kliniken Bonn gGmbH, Johanniter Krankenhaus, Bonn, Germany
| | - Taru A Muranen
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Kristiina Aittomäki
- Department of Clinical Genetics, Helsinki University Central Hospital, Helsinki, Finland
| | - Carl Blomqvist
- Department of Oncology, Helsinki University Central Hospital, Helsinki, Finland
| | - Natalia V Bogdanova
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
| | - Natalia N Antonenkova
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Sara Margolin
- Department of Oncology - Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Arto Mannermaa
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, and Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Vesa Kataja
- School of Medicine, Institute of Clinical Medicine, Oncology, University of Eastern Finland, Kuopio, Finland
- Biocenter Kuopio, Cancer Center of Eastern Finland, Kuopio University Hospital, Kuopio, Finland
| | - Veli-Matti Kosma
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, and Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Jaana M Hartikainen
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, and Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | | | - kConFab Investigators
- Research Department, Peter MacCallum Cancer Centre and The Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
| | - Els Wauters
- Vesalius Research Center (VRC), VIB, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Leuven, Belgium
| | - Dominiek Smeets
- Vesalius Research Center (VRC), VIB, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Leuven, Belgium
| | | | | | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anja Rudolph
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Petra Seibold
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dieter Flesch-Janys
- Department of Cancer Epidemiology/Clinical Cancer Registry and Institute for Medical Biometrics and Epidemiology, University Clinic Hamburg-Eppendorf, Hamburg, Germany
| | - Janet E Olson
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Celine Vachon
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Vernon S Pankratz
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Catriona McLean
- Anatomical Pathology, The Alfred Hospital, Melbourne, Australia
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Brian E Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Fredrick Schumacher
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Loic Le Marchand
- Epidemiology Program, Cancer Research Center, University of Hawaii, Honolulu, HI, USA
| | - Vessela Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, Oslo, Norway
- Faculty of Medicine (Faculty Division Ahus), University of Oslo (UiO), Norway
| | - Grethe Grenaker Alnæs
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, Oslo, Norway
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - David J Hunter
- Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - Sara Lindstrom
- Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - Susan E Hankinson
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
- Channing Laboratory, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Peter Kraft
- Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - Irene Andrulis
- Ontario Cancer Genetics Network, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Julia A Knight
- Prosserman Centre for Health Research, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Gord Glendon
- Ontario Cancer Genetics Network, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Anna Marie Mulligan
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Laboratory Medicine Program, University Health Network, Toronto, Ontario; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | | | - Mervi Grip
- Department of Surgery, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Saila Kauppila
- Department of Pathology, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Peter Devilee
- Department of Surgical Oncology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Robert A E M Tollenaar
- Department of Surgical Oncology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Caroline Seynaeve
- Family Cancer Clinic, Department of Medical Oncology, Erasmus MC-Daniel den Hoed Cancer Centre, Rotterdam, The Netherlands
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Antoinette Hollestelle
- Family Cancer Clinic, Department of Medical Oncology, Erasmus MC-Daniel den Hoed Cancer Centre, Rotterdam, The Netherlands
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Montserrat Garcia-Closas
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Jonine Figueroa
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, M. Sklodowska-Curie Memorial Cancer Center & Institute of Oncology, Warsaw, Poland
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Hatef Darabi
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Mikael Eriksson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Diana M Eccles
- Faculty of Medicine, University of Southampton (UoS), Southampton UK
| | - Sajjad Rafiq
- Faculty of Medicine, University of Southampton (UoS), Southampton UK
| | - William J Tapper
- Faculty of Medicine, University of Southampton (UoS), Southampton UK
| | - Sue M Gerty
- Faculty of Medicine, University of Southampton (UoS), Southampton UK
| | - Maartje J Hooning
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - J Margriet Collée
- Department of Clinical Genetics, Family Cancer Clinic, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Madeleine Tilanus-Linthorst
- Department of Surgical Oncology, Family Cancer Clinic, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Jingmei Li
- Human Genetics Division, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Judith S Brand
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Keith Humphreys
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Angela Cox
- Sheffield Cancer Research, Department of Oncology, University of Sheffield, Sheffield, UK
| | - Malcolm W R Reed
- Sheffield Cancer Research, Department of Oncology, University of Sheffield, Sheffield, UK
| | - Craig Luccarini
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Caroline Baynes
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Diana Torres
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Human Genetics, Pontificia Universidad Javeriana, Bogota, Colombia
| | | | - Thomas Rüdiger
- Institute of Pathology, Städtisches Klinikum Karlsruhe, Karlsruhe, Germany
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Katarzyna Jaworska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
- Postgraduate School of Molecular Medicine, Warsaw Medical University, Warsaw, Poland
| | - Katarzyna Durda
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Susan Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Amanda E Toland
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | | | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, IRRP, National Centre for Scientific Research "Demokritos", Aghia Paraskevi Attikis, Athens, Greece
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
- Division of Breast Cancer Research, Institute of Cancer Research, London, UK
| | - Alan Ashworth
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Nick Orr
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Michael Jones
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Anna González-Neira
- Human Genetics Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Guillermo Pita
- Human Genetics Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - M Rosario Alonso
- Human Genetics Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Nuria Álvarez
- Human Genetics Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Daniel Herrero
- Human Genetics Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Daniel C Tessier
- Centre d'innovation Genome Quebec et University McGill Montreal Quebec, Canada
| | | | | | - Jacques Simard
- Cancer Genomics Laboratory, Centre Hospitalier Universitaire de Quebec Research Center. Laval University, Quebec, Canada
| | - Martine Dumont
- Cancer Genomics Laboratory, Centre Hospitalier Universitaire de Quebec Research Center. Laval University, Quebec, Canada
| | - Penny Soucy
- Cancer Genomics Laboratory, Centre Hospitalier Universitaire de Quebec Research Center. Laval University, Quebec, Canada
| | - Rosalind Eeles
- The Institute of Cancer Research, London, SM2 5NG, UK
- Royal Marsden NHS Foundation Trust, Fulham, London, SW3 6JJ, UK
| | | | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Henrik Gronberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Johanna Schleutker
- Department of Medical Biochemistry and Genetics, University of Turku, and Tyks Microbiology and Genetics, Department of Medical Genetics, Turku University Hospital, Turku, Finland
- Institute of Biomedical Technology/BioMediTech, University of Tampere, Tampere, Finland
| | - Børge G Nordestgaard
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, Herlev Ringvej 75, DK-2730 Herlev, Denmark
| | - Maren Weischer
- Department of Human Genetics University of Utah, Salt Lake City, UT, USA and Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Ruth C Travis
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - David Neal
- Surgical Oncology (Uro-Oncology: S4), University of Cambridge, Box 279, Addenbrooke's Hospital, Hills Road, Cambridge, UK and Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK
| | - Jenny L Donovan
- Professor of Social Medicine, University of Bristol, Canynge Hall, 39 Whatley Road, Bristol BS8 2PS
| | - Freddie C Hamdy
- Nuffield Department of Surgical Sciences, Old Road Campus Research Building (off Roosevelt Drive), University of Oxford, Headington, Oxford, OX3 7DQ
| | - Kay-Tee Khaw
- Cambridge Institute of Public Health, University of Cambridge, Forvie Site, Robinson Way, Cambridge CB2 0SR
| | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington, USA
| | - William J Blot
- International Epidemiology Institute, 1455 Research Blvd., Suite 550, Rockville, MD 20850
| | - Stephen Thibodeau
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Daniel J Schaid
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Joseph L Kelley
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Christiane Maier
- Department of Urology, University Hospital Ulm, Germany
- Institute of Human Genetics University Hospital Ulm, Germany
| | - Adam S Kibel
- Brigham and Women's Hospital/Dana-Farber Cancer Institute, 45 Francis Street- ASB II-3, Boston, MA 02115
- Washington University, St Louis, Missouri
| | - Cezary Cybulski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Lisa Cannon-Albright
- Division of Genetic Epidemiology, Department of Medicine, University of Utah School of Medicine
| | - Katja Butterbach
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jong Park
- Division of Cancer Prevention and Control, H. Lee Moffitt Cancer Center, 12902 Magnolia Dr., Tampa, Florida, USA
| | - Radka Kaneva
- Molecular Medicine Center and Department of Medical Chemistry and Biochemistry, Medical University - Sofia, 2 Zdrave St, 1431, Sofia, Bulgaria
| | - Jyotsna Batra
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation and Schools of Life Science and Public Health, Queensland University of Technology, Brisbane, Australia
| | - Manuel R Teixeira
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal and Biomedical Sciences Institute (ICBAS), Porto University, Porto, Portugal
| | | | - Ali Amin Al Olama
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Laboratory, Worts Causeway, Cambridge, UK
| | - Sara Benlloch
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Laboratory, Worts Causeway, Cambridge, UK
| | - Stefan P Renner
- University Hospital Erlangen, Department of Gynecology and Obstetrics, Friedrich-Alexander-University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Universitaetsstrasse 21-23, 91054 Erlangen, Germany
| | - Arndt Hartmann
- University Hospital Erlangen, Institute of Pathology, Friedrich-Alexander-University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Universitaetsstrasse 21-23, 91054 Erlangen, German
| | - Alexander Hein
- University Hospital Erlangen, Department of Gynecology and Obstetrics, Friedrich-Alexander-University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Universitaetsstrasse 21-23, 91054 Erlangen, Germany
| | - Matthias Ruebner
- University Hospital Erlangen, Department of Gynecology and Obstetrics, Friedrich-Alexander-University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Universitaetsstrasse 21-23, 91054 Erlangen, Germany
| | - Diether Lambrechts
- Vesalius Research Center, VIB, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Belgium
| | - Els Van Nieuwenhuysen
- Department of Epidemiology, The Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Ignace Vergote
- Department of Epidemiology, The Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Sandrina Lambretchs
- Department of Epidemiology, The Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Jennifer A Doherty
- Department of Epidemiology, The Geisel School of Medicine at Dartmouth, Hannover, NH, USA
| | - Mary Anne Rossing
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Stefan Nickels
- German Cancer Research Center, Division of Cancer Epidemiology, Heidelberg, Germany
| | - Ursula Eilber
- German Cancer Research Center, Division of Cancer Epidemiology, Heidelberg, Germany
| | - Shan Wang-Gohrke
- Department of Obstetrics and Gynecology, University of Ulm, Ulm, Germany
| | - Kunle Odunsi
- Department of Gynecological Oncology, Roswell Park Cancer Institute, Buffalo, NY
| | | | - Grace Friel
- Department of Gynecological Oncology, Roswell Park Cancer Institute, Buffalo, NY
| | - Galina Lurie
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Hawaii, USA
| | - Jeffrey L Killeen
- Department of Pathology, Kapiolani Medical Center for Women and Children, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii 96826, USA
| | - Lynne R Wilkens
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Hawaii, USA
| | - Marc T Goodman
- Cancer Prevention and Control, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Community and Population Health Research Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Ingo Runnebaum
- Department of Gynecology and Obstetrics, Friedrich Schiller University, Jena University Hospital, Jena, Germany
| | - Peter A Hillemanns
- Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Liisa M Pelttari
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Ralf Butzow
- Department of Pathology, Helsinki University Central Hospital, Helsinki, 00029 HUS, Finland
| | - Francesmary Modugno
- University of Pittsburgh Department of Obstetrics, Gynecology and Reproductive Sciences and Ovarian Cancer Center of Excellence Pittsburgh PA USA
- University of Pittsburgh Department of Epidemiology, University of Pittsburgh Graduate School of Public Health and Womens Cancer Research Program, Magee-Womens Research Institute and University of Pittsburgh Cancer Institute Pittsburgh PA USA
| | - Robert P Edwards
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Roberta B Ness
- The University of Texas School of Public Health, Houston, TX, USA
| | - Kirsten B Moysich
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY
| | - Andreas du Bois
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte/ Evang. Huyssens-Stiftung/ Knappschaft GmbH, Essen, Germany
- Department of Gynecology and Gynecologic Oncology, Dr. Horst Schmidt Kliniken Wiesbaden, Wiesbaden, Germany
| | - Florian Heitz
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte/ Evang. Huyssens-Stiftung/ Knappschaft GmbH, Essen, Germany
- Department of Gynecology and Gynecologic Oncology, Dr. Horst Schmidt Kliniken Wiesbaden, Wiesbaden, Germany
| | - Philipp Harter
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte/ Evang. Huyssens-Stiftung/ Knappschaft GmbH, Essen, Germany
- Department of Gynecology and Gynecologic Oncology, Dr. Horst Schmidt Kliniken Wiesbaden, Wiesbaden, Germany
| | - Stefan Kommoss
- Department of Gynecology and Gynecologic Oncology, Dr. Horst Schmidt Kliniken Wiesbaden, Wiesbaden, Germany
- Tuebingen University Hospital, Department of Women's Health, Tuebingen, Germany
| | - Beth Y Karlan
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Christine Walsh
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jenny Lester
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Allan Jensen
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Susanne Krüger Kjaer
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Obstetrics and Gynecology, Rigshospitalet, Copenhagen, Denmark
| | - Estrid Høgdall
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
- Molecular Unit, Department of Pathology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Bernard Peissel
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia (IEO), Milan, Italy
| | - Loris Bernard
- Department of Experimental Oncology, Istituto Europeo di Oncologia (IEO), Milan, Italy and Cogentech Cancer Genetic Test Laboratory, Milan, Italy
| | - Ellen L Goode
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | | | - Robert A Vierkant
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Julie M Cunningham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Melissa C Larson
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Zachary C Fogarty
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Kimberly R Kalli
- Department of Medical Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Dong Liang
- College of Pharmacy and Health Sciences, Texas Southern University, Houston, Texas, USA
| | - Karen H Lu
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Michelle A T Hildebrandt
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Douglas A Levine
- Gynecology Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Fanny Dao
- Gynecology Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Maria Bisogna
- Gynecology Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Andrew Berchuck
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA
| | - Edwin S Iversen
- Department of Statistical Science, Duke University, Durham, North Carolina, USA
| | - Jeffrey R Marks
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Lucy Akushevich
- Cancer Prevention, Detection & Control Research Program, Duke Cancer Institute, Durham, North Carolina, USA
| | - Daniel W Cramer
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Joellen Schildkraut
- Cancer Prevention, Detection & Control Research Program, Duke Cancer Institute, Durham, North Carolina, USA
| | - Kathryn L Terry
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Elizabeth M Poole
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, Massachusetts, USA
| | - Meir Stampfer
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School
| | - Shelley S Tworoger
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, Massachusetts, USA
| | - Elisa V Bandera
- Cancer Prevention and Control Program, Rutgers Cancer Institute of New Jersey, The State University of New Jersey, New Brunswick, NJ, USA
| | - Irene Orlow
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sara H Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Line Bjorge
- Department of Gynecology and Obstetrics, Haukeland University Horpital, Bergen, Norway
- Centre for Cancer Biomarkers, Department of Clinical Sciences, University of Bergen, Bergen, Norway
| | - Helga B Salvesen
- Department of Gynecology and Obstetrics, Haukeland University Horpital, Bergen, Norway
- Centre for Cancer Biomarkers, Department of Clinical Sciences, University of Bergen, Bergen, Norway
| | - Anne M van Altena
- Radboud university medical center, Department of Gynaecology, Nijmegen, Netherlands
| | - Katja K H Aben
- Radboud university medical centre, Radboud Institute for Health Sciences, Nijmegen, Netherlands
- Netherlands Comprehensive Cancer Organisation, Utrecht, Netherlands
- Department of Obstetrcs & Gynecology, Oregon Health & Science University
| | - Lambertus A Kiemeney
- Radboud university medical centre, Radboud Institute for Health Sciences, Nijmegen, Netherlands
| | - Leon F A G Massuger
- Radboud university medical center, Department of Gynaecology, Nijmegen, Netherlands
| | - Tanja Pejovic
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Yukie Bean
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Angela Brooks-Wilson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC Canada
| | - Linda E Kelemen
- Department of Public Health Sciences, College of Medicine, Medical University of South Carolina, SC, USA
- Hollings Cancer Center, Medical University of South Carolina, SC, USA
| | - Linda S Cook
- Division of Epidemiology and Biostatistics, Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico, USA
| | - Nhu D Le
- Cancer Control Research, BC Cancer Agency, Vancouver, BC, Canada
| | - Bohdan Górski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Jacek Gronwald
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Janusz Menkiszak
- Department of Gynecological Surgery and Gynecological Oncology of Adults and Adolescents, Pomeranian Medical University, Szczecin, Poland
| | - Claus K Høgdall
- Department of Obstetrics and Gynecology, Rigshospitalet, Copenhagen, Denmark
| | - Lene Lundvall
- Gyn Clinic, Rigshospitalet, University of Copenhagen, Denmark
| | - Lotte Nedergaard
- Department of Pathology, Rigshospitalet, University of Copenhagen, Denmark
| | | | - Ed Dicks
- Department of Oncology, University of Cambridge, Strangeways Research laboratory, Cambridge, UK
| | - Jonathan Tyrer
- Department of Oncology, University of Cambridge, Strangeways Research laboratory, Cambridge, UK
| | - Ian Campbell
- Cancer Genetics Laboratory, Research Division, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne
| | - Iain McNeish
- Institute of Cancer Sciences, University of Glasgow, Wolfson Wohl Cancer Research Centre, Beatson Institute for Cancer Research, Glasgow, UK
| | - James Paul
- The Cancer Research UK Clinical Trials Unit, Beatson West of Scotland Cancer Centre, 1053 Great Western Road, Glasgow, G12 0YN
| | - Nadeem Siddiqui
- Department of Gynaecological Oncology, Glasgow Royal Infirmary
| | | | - Alice S Whittemore
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford CA, USA
| | - Joseph H Rothstein
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford CA, USA
| | - Valerie McGuire
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford CA, USA
| | - Weiva Sieh
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford CA, USA
| | - Hui Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Rachel T Teten
- Epidemiology Center, College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Rebecca Sutphen
- Epidemiology Center, College of Medicine, University of South Florida, Tampa, Florida, USA
| | | | - Steven A Narod
- Women's College Research Institute, University of Toronto, Toronto, Ontario, Canada
| | - Catherine M Phelan
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Alvaro N Monteiro
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - David Fenstermacher
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Hui-Yi Lin
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Jennifer B Permuth
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Thomas A Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Y Ann Chen
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Ya-Yu Tsai
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Zhihua Chen
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | | | - Simon A Gayther
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California, USA
| | - Susan J Ramus
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California, USA
| | - Usha Menon
- Women's Cancer, Institute for Women's Health, UCL, London, United Kingdom
| | - Anna H Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California, USA
| | - Celeste L Pearce
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California, USA
| | - David Van Den Berg
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California, USA
| | - Malcolm C Pike
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Agnieszka Dansonka-Mieszkowska
- Department of Pathology and Laboratory Diagnostics, The Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Joanna Plisiecka-Halasa
- Department of Pathology and Laboratory Diagnostics, The Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Joanna Moes-Sosnowska
- Department of Pathology and Laboratory Diagnostics, The Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Jolanta Kupryjanczyk
- Department of Pathology and Laboratory Diagnostics, The Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Paul Dp Pharoah
- Department of Oncology, University of Cambridge, Strangeways Research laboratory, Cambridge, UK
| | - Honglin Song
- Department of Oncology, University of Cambridge, Strangeways Research laboratory, Cambridge, UK
| | - Ingrid Winship
- Department of Medicine, The University of Melbourne Health, Australia
- The Royal Melbourne Hospital, Victoria 3050, Australia
| | | | - Graham G Giles
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Melbourne, Australia
- Cancer Epidemiology Centre, Cancer Council Victoria, Victoria, Australia
| | | | - Doug F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Laboratory, Worts Causeway, Cambridge, UK
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Melbourne, Australia
- Cancer Epidemiology Centre, Cancer Council Victoria, Victoria, Australia
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Renault AL, Lesueur F, Coulombe Y, Gobeil S, Soucy P, Hamdi Y, Desjardins S, Le Calvez-Kelm F, Vallée M, Voegele C, Hopper JL, Andrulis IL, Southey MC, John EM, Masson JY, Tavtigian SV, Simard J. ABRAXAS (FAM175A) and Breast Cancer Susceptibility: No Evidence of Association in the Breast Cancer Family Registry. PLoS One 2016; 11:e0156820. [PMID: 27270457 PMCID: PMC4896418 DOI: 10.1371/journal.pone.0156820] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 05/19/2016] [Indexed: 11/17/2022] Open
Abstract
Approximately half of the familial aggregation of breast cancer remains unexplained. This proportion is less for early-onset disease where familial aggregation is greater, suggesting that other susceptibility genes remain to be discovered. The majority of known breast cancer susceptibility genes are involved in the DNA double-strand break repair pathway. ABRAXAS is involved in this pathway and mutations in this gene impair BRCA1 recruitment to DNA damage foci and increase cell sensitivity to ionizing radiation. Moreover, a recurrent germline mutation was reported in Finnish high-risk breast cancer families. To determine if ABRAXAS could be a breast cancer susceptibility gene in other populations, we conducted a population-based case-control mutation screening study of the coding exons and exon/intron boundaries of ABRAXAS in the Breast Cancer Family Registry. In addition to the common variant p.Asp373Asn, sixteen distinct rare variants were identified. Although no significant difference in allele frequencies between cases and controls was observed for the identified variants, two variants, p.Gly39Val and p.Thr141Ile, were shown to diminish phosphorylation of gamma-H2AX in MCF7 human breast adenocarcinoma cells, an important biomarker of DNA double-strand breaks. Overall, likely damaging or neutral variants were evenly represented among cases and controls suggesting that rare variants in ABRAXAS may explain only a small proportion of hereditary breast cancer.
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Affiliation(s)
- Anne-Laure Renault
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center and Laval University, Quebec, Canada
| | | | - Yan Coulombe
- Genome Stability Laboratory, Centre Hospitalier Universitaire de Québec Research Center, HDQ Pavillon, Oncology Axis, Quebec, Canada
| | - Stéphane Gobeil
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center and Laval University, Quebec, Canada
| | - Penny Soucy
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center and Laval University, Quebec, Canada
| | - Yosr Hamdi
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center and Laval University, Quebec, Canada
| | - Sylvie Desjardins
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center and Laval University, Quebec, Canada
| | - Florence Le Calvez-Kelm
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, Lyon, France
| | - Maxime Vallée
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center and Laval University, Quebec, Canada
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, Lyon, France
| | - Catherine Voegele
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, Lyon, France
| | - The Breast Cancer Family Registry
- Center for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Victoria, Australia
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Genetic Epidemiology Laboratory, The University of Melbourne, Victoria, Australia
- Cancer Prevention Institute of California, Fremont, United States of America
- Stanford University School of Medicine and Stanford Cancer Institute, Stanford, United States of America
| | - John L. Hopper
- Center for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Victoria, Australia
| | - Irene L. Andrulis
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Melissa C. Southey
- Genetic Epidemiology Laboratory, The University of Melbourne, Victoria, Australia
| | - Esther M. John
- Cancer Prevention Institute of California, Fremont, United States of America
- Stanford University School of Medicine and Stanford Cancer Institute, Stanford, United States of America
| | - Jean-Yves Masson
- Genome Stability Laboratory, Centre Hospitalier Universitaire de Québec Research Center, HDQ Pavillon, Oncology Axis, Quebec, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Quebec, Canada
| | - Sean V. Tavtigian
- Department of Oncological Sciences, University of Utah, Salt Lake City, United States of America
- Huntsman Cancer Institute, University of Utah, Salt Lake City, United States of America
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center and Laval University, Quebec, Canada
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Young EL, Feng BJ, Stark AW, Damiola F, Durand G, Forey N, Francy TC, Gammon A, Kohlmann WK, Kaphingst KA, McKay-Chopin S, Nguyen-Dumont T, Oliver J, Paquette AM, Pertesi M, Robinot N, Rosenthal JS, Vallee M, Voegele C, Hopper JL, Southey MC, Andrulis IL, John EM, Hashibe M, Gertz J, Le Calvez-Kelm F, Lesueur F, Goldgar DE, Tavtigian SV. Multigene testing of moderate-risk genes: be mindful of the missense. J Med Genet 2016; 53:366-76. [PMID: 26787654 PMCID: PMC4893078 DOI: 10.1136/jmedgenet-2015-103398] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 12/18/2015] [Indexed: 12/13/2022]
Abstract
BACKGROUND Moderate-risk genes have not been extensively studied, and missense substitutions in them are generally returned to patients as variants of uncertain significance lacking clearly defined risk estimates. The fraction of early-onset breast cancer cases carrying moderate-risk genotypes and quantitative methods for flagging variants for further analysis have not been established. METHODS We evaluated rare missense substitutions identified from a mutation screen of ATM, CHEK2, MRE11A, RAD50, NBN, RAD51, RINT1, XRCC2 and BARD1 in 1297 cases of early-onset breast cancer and 1121 controls via scores from Align-Grantham Variation Grantham Deviation (GVGD), combined annotation dependent depletion (CADD), multivariate analysis of protein polymorphism (MAPP) and PolyPhen-2. We also evaluated subjects by polygenotype from 18 breast cancer risk SNPs. From these analyses, we estimated the fraction of cases and controls that reach a breast cancer OR≥2.5 threshold. RESULTS Analysis of mutation screening data from the nine genes revealed that 7.5% of cases and 2.4% of controls were carriers of at least one rare variant with an average OR≥2.5. 2.1% of cases and 1.2% of controls had a polygenotype with an average OR≥2.5. CONCLUSIONS Among early-onset breast cancer cases, 9.6% had a genotype associated with an increased risk sufficient to affect clinical management recommendations. Over two-thirds of variants conferring this level of risk were rare missense substitutions in moderate-risk genes. Placement in the estimated OR≥2.5 group by at least two of these missense analysis programs should be used to prioritise variants for further study. Panel testing often creates more heat than light; quantitative approaches to variant prioritisation and classification may facilitate more efficient clinical classification of variants.
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Affiliation(s)
- E L Young
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - B J Feng
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - A W Stark
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - F Damiola
- Breast Cancer Genetics Group, Cancer Research Centre of Lyon, Centre Léon Bérard, Lyon, France
| | - G Durand
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, Lyon, France
| | - N Forey
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, Lyon, France
| | - T C Francy
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - A Gammon
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - W K Kohlmann
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - K A Kaphingst
- Department of Communication and Huntsman Cancer Institute, University of Utah
| | - S McKay-Chopin
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, Lyon, France
| | - T Nguyen-Dumont
- Genetic Epidemiology Laboratory, The University of Melbourne, Melbourne, Victoria, Australia
| | - J Oliver
- Instituto de Ciencias Básicas y Medicina Experimental del Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - A M Paquette
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - M Pertesi
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, Lyon, France
| | - N Robinot
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, Lyon, France
| | - J S Rosenthal
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - M Vallee
- Cancer Genomics Laboratory, CHUQ Research Center, Quebec City, Canada
| | - C Voegele
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, Lyon, France
| | - J L Hopper
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia Department of Epidemiology (Genome Epidemiology Lab), Seoul National University School of Public Health, Seoul, Korea
| | - M C Southey
- Department of Communication and Huntsman Cancer Institute, University of Utah
| | - I L Andrulis
- Department of Molecular Genetics, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - E M John
- Cancer Prevention Institute of California, Fremont, California, USA Department of Health Research and Policy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California, USA
| | - M Hashibe
- Department of Family and Preventive Medicine, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - J Gertz
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - F Le Calvez-Kelm
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, Lyon, France
| | - F Lesueur
- Genetic Epidemiology of Cancer Team, Inserm, U900, Institut Curie, Paris, France
| | - D E Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - S V Tavtigian
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
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31
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Easton DF, Lesueur F, Decker B, Michailidou K, Li J, Allen J, Luccarini C, Pooley KA, Shah M, Bolla MK, Wang Q, Dennis J, Ahmad J, Thompson ER, Damiola F, Pertesi M, Voegele C, Mebirouk N, Robinot N, Durand G, Forey N, Luben RN, Ahmed S, Aittomäki K, Anton-Culver H, Arndt V, Baynes C, Beckman MW, Benitez J, Van Den Berg D, Blot WJ, Bogdanova NV, Bojesen SE, Brenner H, Chang-Claude J, Chia KS, Choi JY, Conroy DM, Cox A, Cross SS, Czene K, Darabi H, Devilee P, Eriksson M, Fasching PA, Figueroa J, Flyger H, Fostira F, García-Closas M, Giles GG, Glendon G, González-Neira A, Guénel P, Haiman CA, Hall P, Hart SN, Hartman M, Hooning MJ, Hsiung CN, Ito H, Jakubowska A, James PA, John EM, Johnson N, Jones M, Kabisch M, Kang D, Kosma VM, Kristensen V, Lambrechts D, Li N, Lindblom A, Long J, Lophatananon A, Lubinski J, Mannermaa A, Manoukian S, Margolin S, Matsuo K, Meindl A, Mitchell G, Muir K, Nevelsteen I, van den Ouweland A, Peterlongo P, Phuah SY, Pylkäs K, Rowley SM, Sangrajrang S, Schmutzler RK, Shen CY, Shu XO, Southey MC, Surowy H, Swerdlow A, Teo SH, Tollenaar RAEM, Tomlinson I, Torres D, Truong T, Vachon C, Verhoef S, Wong-Brown M, Zheng W, Zheng Y, Nevanlinna H, Scott RJ, Andrulis IL, Wu AH, Hopper JL, Couch FJ, Winqvist R, Burwinkel B, Sawyer EJ, Schmidt MK, Rudolph A, Dörk T, Brauch H, Hamann U, Neuhausen SL, Milne RL, Fletcher O, Pharoah PDP, Campbell IG, Dunning AM, Le Calvez-Kelm F, Goldgar DE, Tavtigian SV, Chenevix-Trench G. No evidence that protein truncating variants in BRIP1 are associated with breast cancer risk: implications for gene panel testing. J Med Genet 2016; 53:298-309. [PMID: 26921362 PMCID: PMC4938802 DOI: 10.1136/jmedgenet-2015-103529] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 12/16/2015] [Indexed: 12/13/2022]
Abstract
BACKGROUND BRCA1 interacting protein C-terminal helicase 1 (BRIP1) is one of the Fanconi Anaemia Complementation (FANC) group family of DNA repair proteins. Biallelic mutations in BRIP1 are responsible for FANC group J, and previous studies have also suggested that rare protein truncating variants in BRIP1 are associated with an increased risk of breast cancer. These studies have led to inclusion of BRIP1 on targeted sequencing panels for breast cancer risk prediction. METHODS We evaluated a truncating variant, p.Arg798Ter (rs137852986), and 10 missense variants of BRIP1, in 48 144 cases and 43 607 controls of European origin, drawn from 41 studies participating in the Breast Cancer Association Consortium (BCAC). Additionally, we sequenced the coding regions of BRIP1 in 13 213 cases and 5242 controls from the UK, 1313 cases and 1123 controls from three population-based studies as part of the Breast Cancer Family Registry, and 1853 familial cases and 2001 controls from Australia. RESULTS The rare truncating allele of rs137852986 was observed in 23 cases and 18 controls in Europeans in BCAC (OR 1.09, 95% CI 0.58 to 2.03, p=0.79). Truncating variants were found in the sequencing studies in 34 cases (0.21%) and 19 controls (0.23%) (combined OR 0.90, 95% CI 0.48 to 1.70, p=0.75). CONCLUSIONS These results suggest that truncating variants in BRIP1, and in particular p.Arg798Ter, are not associated with a substantial increase in breast cancer risk. Such observations have important implications for the reporting of results from breast cancer screening panels.
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Affiliation(s)
- Douglas F Easton
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Fabienne Lesueur
- Genetic Epidemiology of Cancer team, Inserm, U900, Institut Curie, Mines ParisTech, Paris, France
| | - Brennan Decker
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK Cancer Genetics and Comparative Genomics Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kyriaki Michailidou
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Jun Li
- Department of Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Jamie Allen
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Craig Luccarini
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Karen A Pooley
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Mitul Shah
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Manjeet K Bolla
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Qin Wang
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Joe Dennis
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Jamil Ahmad
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon, France
| | - Ella R Thompson
- Research Division, Peter MacCallum Cancer Centre, East Melbourne, Australia Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - Francesca Damiola
- Genetic of Breast Cancer Team, Cancer Research Center of Lyon, Centre Léon Bérard, Lyon, France
| | - Maroulio Pertesi
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon, France
| | - Catherine Voegele
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon, France
| | - Noura Mebirouk
- Genetic Epidemiology of Cancer team, Inserm, U900, Institut Curie, Mines ParisTech, Paris, France
| | - Nivonirina Robinot
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon, France
| | - Geoffroy Durand
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon, France
| | - Nathalie Forey
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon, France
| | - Robert N Luben
- Clinical Gerontology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Shahana Ahmed
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Kristiina Aittomäki
- Department of Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Hoda Anton-Culver
- Department of Epidemiology, University of California Irvine, Irvine, California, USA
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Caroline Baynes
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Matthias W Beckman
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Javier Benitez
- Human Cancer Genetics Program, Spanish National Cancer Research Centre, Madrid, Spain Centro de Investigación en Red de Enfermedades Raras (CIBERER), Valencia, Spain
| | - David Van Den Berg
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - William J Blot
- International Epidemiology Institute, Rockville, Maryland, USA Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Natalia V Bogdanova
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
| | - Stig E Bojesen
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kee Seng Chia
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Ji-Yeob Choi
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Don M Conroy
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Angela Cox
- Sheffield Cancer Research, Department of Oncology, University of Sheffield, Sheffield, UK
| | - Simon S Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, Sheffield, UK
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Hatef Darabi
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Mikael Eriksson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Peter A Fasching
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology, University of California, Los Angeles, California, USA
| | - Jonine Figueroa
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh Medical School, Edinburgh, UK
| | - Henrik Flyger
- Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research "Demokritos", Athens, Greece
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Graham G Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria, Australia Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Gord Glendon
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Anna González-Neira
- Human Cancer Genetics Program, Spanish National Cancer Research Centre, Madrid, Spain
| | - Pascal Guénel
- University Paris-Sud, UMRS 1018, Villejuif, France Inserm, CESP Center for research in Epidemiology and Population Health, U1018, Cancer & Environment Group, Villejuif, France
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Steven N Hart
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Mikael Hartman
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore Department of Surgery, National University Health System, Singapore, Singapore
| | - Maartje J Hooning
- Department of Medical Oncology, Family Cancer Clinic, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Chia-Ni Hsiung
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Hidemi Ito
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Aichi, Japan
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Paul A James
- Department of Pathology, The University of Melbourne, Melbourne, Victoria, Australia Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Esther M John
- Department of Epidemiology, Cancer Prevention Institute of California, Fremont, California, USA Department of Health Research and Policy-Epidemiology, Stanford University School of Medicine, Stanford, California, USA Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Nichola Johnson
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Michael Jones
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Maria Kabisch
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daehee Kang
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea Department of Preventive Medicine, Seoul National University College of Medicine, Seoul National University, Seoul, Korea
| | - Veli-Matti Kosma
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland
| | - Vessela Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, Oslo, Norway Faculty of Medicine, K.G. Jebsen Center for Breast Cancer Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway Department of Clinical Molecular Biology (EpiGen), University of Oslo (UiO), Oslo, Norway
| | - Diether Lambrechts
- Vesalius Research Center, VIB, Leuven, Belgium Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Leuven, Belgium
| | - Na Li
- Research Division, Peter MacCallum Cancer Centre, East Melbourne, Australia Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Artitaya Lophatananon
- Division of Health Sciences, Warwick Medical school, Warwick University, Coventry, UK
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Arto Mannermaa
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale Tumori (INT), Milan, Italy
| | - Sara Margolin
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Keitaro Matsuo
- Division of Molecular Medicine, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Alfons Meindl
- Division of Gynaecology and Obstetrics, Technische Universität München, Munich, Germany
| | - Gillian Mitchell
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Kenneth Muir
- Division of Health Sciences, Warwick Medical school, Warwick University, Coventry, UK Institute of Population Health, University of Manchester, Manchester, UK
| | | | - Ans van den Ouweland
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Paolo Peterlongo
- IFOM, The FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology, Milan, Italy
| | - Sze Yee Phuah
- Breast Cancer Research Unit, University Malaya Cancer Research Institute, University Malaya Medical Centre (UMMC), Kuala Lumpur, Malaysia Cancer Research Initiatives Foundation, Sime Darby Medical Centre, Subang Jaya, Malaysia
| | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre NordLab, Oulu, Finland Laboratory of Cancer Genetics and Tumor Biology, Cancer Research and Translational Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Simone M Rowley
- Research Division, Peter MacCallum Cancer Centre, East Melbourne, Australia
| | | | - Rita K Schmutzler
- Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Germany Medical Faculty, Center for Hereditary Breast and Ovarian Cancer, University Hospital Cologne, Germany Center for Molecular Medicine Cologne (CMMC), University of Cologne, Germany
| | - Chen-Yang Shen
- School of Public Health, China Medical University, Taichung, Taiwan Taiwan Biobank, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Melissa C Southey
- Department of Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Harald Surowy
- Molecular Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
| | - Anthony Swerdlow
- Division of Breast Cancer Research, The Institute of Cancer Research, London, UK Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Soo H Teo
- Breast Cancer Research Unit, University Malaya Cancer Research Institute, University Malaya Medical Centre (UMMC), Kuala Lumpur, Malaysia Cancer Research Initiatives Foundation, Sime Darby Medical Centre, Subang Jaya, Malaysia
| | - Rob A E M Tollenaar
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands
| | - Ian Tomlinson
- Wellcome Trust Centre for Human Genetics and Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Diana Torres
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany Institute of Human Genetics, Pontificia Universidad Javeriana, Bogota, Colombia
| | - Thérèse Truong
- University Paris-Sud, UMRS 1018, Villejuif, France Inserm, CESP Center for research in Epidemiology and Population Health, U1018, Cancer & Environment Group, Villejuif, France
| | - Celine Vachon
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Senno Verhoef
- Netherlands Cancer Institute, Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Michelle Wong-Brown
- Division of Genetics, Hunter Area Pathology Service, John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Ying Zheng
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Rodney J Scott
- Division of Genetics, Hunter Area Pathology Service, John Hunter Hospital, Newcastle, New South Wales, Australia Division of Molecular Medicine, Pathology North, John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Irene L Andrulis
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Anna H Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, University of Melbourne, Melbourne, Victoria, Australia
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre NordLab, Oulu, Finland Laboratory of Cancer Genetics and Tumor Biology, Cancer Research and Translational Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Barbara Burwinkel
- Molecular Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
| | - Elinor J Sawyer
- Research Oncology, Division of Cancer Studies, King's College London, Guy's Hospital, London, UK
| | - Marjanka K Schmidt
- Netherlands Cancer Institute, Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Anja Rudolph
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Hiltrud Brauch
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany University of Tübingen, Tübingen, Germany
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Roger L Milne
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria, Australia Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Olivia Fletcher
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Paul D P Pharoah
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Ian G Campbell
- Research Division, Peter MacCallum Cancer Centre, East Melbourne, Australia Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia Department of Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Alison M Dunning
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Florence Le Calvez-Kelm
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon, France
| | - David E Goldgar
- Department of Dermatology, University of Utah School of Medicine, Salt Lake City, Utah, USA Cancer Control and Population Sciences, Huntsman Cancer Institute, Salt Lake City, Utah, USA
| | - Sean V Tavtigian
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, USA
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Vallée MP, Di Sera TL, Nix DA, Paquette AM, Parsons MT, Bell R, Hoffman A, Hogervorst FBL, Goldgar DE, Spurdle AB, Tavtigian SV. Adding In Silico Assessment of Potential Splice Aberration to the Integrated Evaluation of BRCA Gene Unclassified Variants. Hum Mutat 2016; 37:627-39. [PMID: 26913838 PMCID: PMC4907813 DOI: 10.1002/humu.22973] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 01/29/2016] [Indexed: 01/05/2023]
Abstract
Clinical mutation screening of the cancer susceptibility genes BRCA1 and BRCA2 generates many unclassified variants (UVs). Most of these UVs are either rare missense substitutions or nucleotide substitutions near the splice junctions of the protein coding exons. Previously, we developed a quantitative method for evaluation of BRCA gene UVs—the “integrated evaluation”—that combines a sequence analysis‐based prior probability of pathogenicity with patient and/or tumor observational data to arrive at a posterior probability of pathogenicity. One limitation of the sequence analysis‐based prior has been that it evaluates UVs from the perspective of missense substitution severity but not probability to disrupt normal mRNA splicing. Here, we calibrated output from the splice‐site fitness program MaxEntScan to generate spliceogenicity‐based prior probabilities of pathogenicity for BRCA gene variants; these range from 0.97 for variants with high probability to damage a donor or acceptor to 0.02 for exonic variants that do not impact a splice junction and are unlikely to create a de novo donor. We created a database http://priors.hci.utah.edu/PRIORS/ that provides the combined missense substitution severity and spliceogenicity‐based probability of pathogenicity for BRCA gene single‐nucleotide substitutions. We also updated the BRCA gene Ex‐UV LOVD, available at http://hci‐exlovd.hci.utah.edu, with 77 re‐evaluable variants.
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Affiliation(s)
- Maxime P Vallée
- Department of Molecular Medicine, CHUQ Research Center, Quebec City, Canada
| | - Tonya L Di Sera
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah
| | - David A Nix
- ARUP Laboratories, University of Utah School of Medicine, Salt Lake City, Utah
| | - Andrew M Paquette
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | | | - Russel Bell
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | - Andrea Hoffman
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | - David E Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | | | - Sean V Tavtigian
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
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Samadder NJ, Neklason DW, Boucher KM, Byrne KR, Kanth P, Samowitz W, Jones D, Tavtigian SV, Done MW, Berry T, Jasperson K, Pappas L, Smith L, Sample D, Davis R, Topham MK, Lynch P, Strait E, McKinnon W, Burt RW, Kuwada SK. Effect of Sulindac and Erlotinib vs Placebo on Duodenal Neoplasia in Familial Adenomatous Polyposis: A Randomized Clinical Trial. JAMA 2016; 315:1266-75. [PMID: 27002448 PMCID: PMC5003411 DOI: 10.1001/jama.2016.2522] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
IMPORTANCE Patients with familial adenomatous polyposis (FAP) are at markedly increased risk for duodenal polyps and cancer. Surgical and endoscopic management of duodenal neoplasia is difficult and chemoprevention has not been successful. OBJECTIVE To evaluate the effect of a combination of sulindac and erlotinib on duodenal adenoma regression in patients with FAP. DESIGN, SETTING, AND PARTICIPANTS Double-blind, randomized, placebo-controlled trial, enrolling 92 participants with FAP, conducted from July 2010 through June 2014 at Huntsman Cancer Institute in Salt Lake City, Utah. INTERVENTIONS Participants with FAP were randomized to sulindac (150 mg) twice daily and erlotinib (75 mg) daily (n = 46) vs placebo (n = 46) for 6 months. MAIN OUTCOMES AND MEASURES The total number and diameter of polyps in the proximal duodenum were mapped at baseline and 6 months. The primary outcome was change in total polyp burden at 6 months. Polyp burden was calculated as the sum of the diameters of polyps. The secondary outcomes were change in total duodenal polyp count, change in duodenal polyp burden or count stratified by genotype and initial polyp burden, and percentage of change from baseline in duodenal polyp burden. RESULTS Ninety-two participants (mean age, 41 years [range, 24-55]; women, 56 [61%]) were randomized when the trial was stopped by the external data and safety monitoring board because the second preplanned interim analysis met the prespecified stopping rule for superiority. Grade 1 and 2 adverse events were more common in the sulindac-erlotinib group, with an acne-like rash observed in 87% of participants receiving treatment and 20% of participants receiving placebo (P < .001). Only 2 participants experienced grade 3 adverse events. [table: see text]. CONCLUSIONS AND RELEVANCE Among participants with FAP, the use of sulindac and erlotinib compared with placebo resulted in a lower duodenal polyp burden after 6 months. Adverse events may limit the use of these medications at the doses used in this study. Further research is necessary to evaluate these preliminary findings in a larger study population with longer follow-up to determine whether the observed effects will result in improved clinical outcomes. TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT 01187901.
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Affiliation(s)
- N Jewel Samadder
- Huntsman Cancer Institute, University of Utah, Salt Lake City2Department of Medicine (Gastroenterology), University of Utah, Salt Lake City
| | - Deborah W Neklason
- Huntsman Cancer Institute, University of Utah, Salt Lake City3Department of Oncological Sciences, University of Utah, Salt Lake City4Department of Medicine (Genetic Epidemiology), University of Utah, Salt Lake City
| | - Kenneth M Boucher
- Huntsman Cancer Institute, University of Utah, Salt Lake City5Department of Medicine (Epidemiology), University of Utah, Salt Lake City
| | - Kathryn R Byrne
- Department of Medicine (Gastroenterology), University of Utah, Salt Lake City
| | - Priyanka Kanth
- Department of Medicine (Gastroenterology), University of Utah, Salt Lake City
| | - Wade Samowitz
- Huntsman Cancer Institute, University of Utah, Salt Lake City6Department of Pathology, University of Utah, Salt Lake City
| | - David Jones
- Huntsman Cancer Institute, University of Utah, Salt Lake City3Department of Oncological Sciences, University of Utah, Salt Lake City
| | - Sean V Tavtigian
- Huntsman Cancer Institute, University of Utah, Salt Lake City3Department of Oncological Sciences, University of Utah, Salt Lake City
| | - Michelle W Done
- Huntsman Cancer Institute, University of Utah, Salt Lake City
| | - Therese Berry
- Huntsman Cancer Institute, University of Utah, Salt Lake City
| | - Kory Jasperson
- Huntsman Cancer Institute, University of Utah, Salt Lake City
| | - Lisa Pappas
- Huntsman Cancer Institute, University of Utah, Salt Lake City
| | - Laurel Smith
- Huntsman Cancer Institute, University of Utah, Salt Lake City
| | - Danielle Sample
- Huntsman Cancer Institute, University of Utah, Salt Lake City
| | - Rian Davis
- Huntsman Cancer Institute, University of Utah, Salt Lake City
| | - Matthew K Topham
- Huntsman Cancer Institute, University of Utah, Salt Lake City3Department of Oncological Sciences, University of Utah, Salt Lake City7Department of Medicine (Pulmonary), University of Utah, Salt Lake City
| | - Patrick Lynch
- Department of Gastroenterology, University of Texas MD Anderson Cancer Center, Houston
| | | | | | - Randall W Burt
- Huntsman Cancer Institute, University of Utah, Salt Lake City2Department of Medicine (Gastroenterology), University of Utah, Salt Lake City3Department of Oncological Sciences, University of Utah, Salt Lake City
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Easton DF, Pharoah PDP, Antoniou AC, Tischkowitz M, Tavtigian SV, Nathanson KL, Devilee P, Meindl A, Couch FJ, Southey M, Goldgar DE, Evans DGR, Chenevix-Trench G, Rahman N, Robson M, Domchek SM, Foulkes WD. Gene-panel sequencing and the prediction of breast-cancer risk. N Engl J Med 2015; 372:2243-57. [PMID: 26014596 PMCID: PMC4610139 DOI: 10.1056/nejmsr1501341] [Citation(s) in RCA: 634] [Impact Index Per Article: 70.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Douglas F Easton
- From the Departments of Public Health and Primary Care (D.F.E., P.D.P.P., A.C.A.), Oncology (D.F.E., P.D.P.P.), and Medical Genetics (M.T.), University of Cambridge, Cambridge, the Centre for Genomic Medicine, Institute of Human Development, Manchester Academic Health Science Centre, University of Manchester and St. Mary's Hospital, Manchester (D.G.R.E.), and the Division of Genetics and Epidemiology, Institute of Cancer Research, London (N.R.) - all in the United Kingdom; the Departments of Oncological Sciences (S.V.T.) and Dermatology (D.E.G.), Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City; the Basser Research Center for BRCA and Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia (K.L.N., S.M.D.); the Department of Human Genetics and Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands (P.D.); the Department of Obstetrics and Gynecology, Division of Tumor Genetics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany (A.M.); the Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN (F.J.C.); the Department of Pathology, School of Biomedical Sciences, Faculty of Medicine, Dentistry, and Health Sciences at the University of Melbourne, Parkville, VIC (M.S.), and the QIMR Berghofer Medical Research Institute, Herston, QLD (G.C.-T.) - both in Australia; the Clinical Genetics Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York (M.R.); and the Program in Cancer Genetics, Departments of Human Genetics and Oncology, the Lady Davis Institute for Medical Research, and the Research Institute of the McGill University Health Center, McGill University, Montreal (W.D.F.)
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Jhuraney A, Velkova A, Johnson RC, Kessing B, Carvalho RS, Whiley P, Spurdle AB, Vreeswijk MPG, Caputo SM, Millot GA, Vega A, Coquelle N, Galli A, Eccles D, Blok MJ, Pal T, van der Luijt RB, Santamariña Pena M, Neuhausen SL, Donenberg T, Machackova E, Thomas S, Vallée M, Couch FJ, Tavtigian SV, Glover JNM, Carvalho MA, Brody LC, Sharan SK, Monteiro AN. BRCA1 Circos: a visualisation resource for functional analysis of missense variants. J Med Genet 2015; 52:224-30. [PMID: 25643705 PMCID: PMC4392196 DOI: 10.1136/jmedgenet-2014-102766] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 11/29/2014] [Accepted: 12/05/2014] [Indexed: 11/17/2022]
Abstract
BACKGROUND Inactivating germline mutations in the tumour suppressor gene BRCA1 are associated with a significantly increased risk of developing breast and ovarian cancer. A large number (>1500) of unique BRCA1 variants have been identified in the population and can be classified as pathogenic, non-pathogenic or as variants of unknown significance (VUS). Many VUS are rare missense variants leading to single amino acid changes. Their impact on protein function cannot be directly inferred from sequence information, precluding assessment of their pathogenicity. Thus, functional assays are critical to assess the impact of these VUS on protein activity. BRCA1 is a multifunctional protein and different assays have been used to assess the impact of variants on different biochemical activities and biological processes. METHODS AND RESULTS To facilitate VUS analysis, we have developed a visualisation resource that compiles and displays functional data on all documented BRCA1 missense variants. BRCA1 Circos is a web-based visualisation tool based on the freely available Circos software package. The BRCA1 Circos web tool (http://research.nhgri.nih.gov/bic/circos/) aggregates data from all published BRCA1 missense variants for functional studies, harmonises their results and presents various functionalities to search and interpret individual-level functional information for each BRCA1 missense variant. CONCLUSIONS This research visualisation tool will serve as a quick one-stop publically available reference for all the BRCA1 missense variants that have been functionally assessed. It will facilitate meta-analysis of functional data and improve assessment of pathogenicity of VUS.
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Affiliation(s)
- Ankita Jhuraney
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
- University of South Florida Cancer Biology PhD Program, Tampa, Florida, USA
| | - Aneliya Velkova
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Randall C Johnson
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Fredrick, Maryland, USA
| | - Bailey Kessing
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Fredrick, Maryland, USA
| | - Renato S Carvalho
- Instituto Federal de Educação, Ciência e Tecnologia, Rio de Janeiro, RJ, Brazil
- Instituto Nacional de Câncer, Divisão de Farmacologia, Rio de Janeiro, Brazil
| | - Phillip Whiley
- Genetics and Population Health Division, QIMR, BNE, Brisbane, Queensland, Australia
| | - Amanda B Spurdle
- Genetics and Population Health Division, QIMR, BNE, Brisbane, Queensland, Australia
| | - Maaike P G Vreeswijk
- Department of Human Genetics, Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Sandrine M Caputo
- Service de Génétique, Institut Curie, Hôpital René Huguenin, Paris, France
| | - Gael A Millot
- Institut Curie, Université Pierre et Marie Curie, Paris, France
| | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica, Santiago, Spain
| | - Nicolas Coquelle
- Department of Biochemistry, University of Alberta, Alberta, Canada
| | - Alvaro Galli
- Instituto di Fisiologia Clinica, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | | | - Marinus J Blok
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Tuya Pal
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Rob B van der Luijt
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of the City of Hope, Duarte, California, USA
| | | | - Eva Machackova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Simon Thomas
- Salisbury District Hospital, Salisbury, Wiltshire, UK
| | - Maxime Vallée
- International Agency for Research on Cancer, Lyon, France
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, and Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Sean V Tavtigian
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - J N Mark Glover
- Department of Biochemistry, University of Alberta, Alberta, Canada
| | - Marcelo A Carvalho
- Instituto Federal de Educação, Ciência e Tecnologia, Rio de Janeiro, RJ, Brazil
- Instituto Nacional de Câncer, Divisão de Farmacologia, Rio de Janeiro, Brazil
| | - Lawrence C Brody
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Shyam K Sharan
- Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Alvaro N Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
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Tavtigian SV. Shotgun Approach to Functional Annotation of Genes. Hum Mutat 2015. [DOI: 10.1002/humu.22746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sean V. Tavtigian
- Huntsman Cancer Institute and University of Utah School of Medicine; USA
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Tavtigian SV, Chenevix-Trench G. Growing recognition of the role for rare missense substitutions in breast cancer susceptibility. Biomark Med 2014; 8:589-603. [PMID: 24796624 DOI: 10.2217/bmm.13.143] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Most cancer susceptibility genes function as tumor suppressors; accordingly, the focus of mutation screening in breast cancer families has been to identify protein-truncating mutations. However, it is now clear that, for some breast cancer susceptibility genes, a significant proportion of the burden of disease comes from rare missense substitutions. Among genes that have been extensively evaluated, BRCA1, BRCA2, PALB2 and BRIP1 stand as examples where the majority of mutations lead to protein truncation;TP53 provides a counter example, where the majority of pathogenic variants are missense substitutions. In ATM and CHEK2, missense substitutions are probably equally or more important in terms of their frequency and attributable risk. Therefore, ongoing efforts to identify new susceptibility genes should not ignore missense variation.
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Affiliation(s)
- Sean V Tavtigian
- Huntsman Cancer Institute and Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
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Hernández-Vargas H, Ouzounova M, Le Calvez-Kelm F, Lambert MP, McKay-Chopin S, Tavtigian SV, Puisieux A, Matar C, Herceg Z. Methylome analysis reveals Jak-STAT pathway deregulation in putative breast cancer stem cells. Epigenetics 2014; 6:428-39. [DOI: 10.4161/epi.6.4.14515] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Park DJ, Tao K, Le Calvez-Kelm F, Nguyen-Dumont T, Robinot N, Hammet F, Odefrey F, Tsimiklis H, Teo ZL, Thingholm LB, Young EL, Voegele C, Lonie A, Pope BJ, Roane TC, Bell R, Hu H, Shankaracharya, Huff CD, Ellis J, Li J, Makunin IV, John EM, Andrulis IL, Terry MB, Daly M, Buys SS, Snyder C, Lynch HT, Devilee P, Giles GG, Hopper JL, Feng BJ, Lesueur F, Tavtigian SV, Southey MC, Goldgar DE. Rare mutations in RINT1 predispose carriers to breast and Lynch syndrome-spectrum cancers. Cancer Discov 2014; 4:804-15. [PMID: 25050558 PMCID: PMC4234633 DOI: 10.1158/2159-8290.cd-14-0212] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
UNLABELLED Approximately half of the familial aggregation of breast cancer remains unexplained. A multiple-case breast cancer family exome-sequencing study identified three likely pathogenic mutations in RINT1 (NM_021930.4) not present in public sequencing databases: RINT1 c.343C>T (p.Q115X), c.1132_1134del (p.M378del), and c.1207G>T (p.D403Y). On the basis of this finding, a population-based case-control mutation-screening study was conducted that identified 29 carriers of rare (minor allele frequency < 0.5%), likely pathogenic variants: 23 in 1,313 early-onset breast cancer cases and six in 1,123 frequency-matched controls [OR, 3.24; 95% confidence interval (CI), 1.29-8.17; P = 0.013]. RINT1 mutation screening of probands from 798 multiple-case breast cancer families identified four additional carriers of rare genetic variants. Analysis of the incidence of first primary cancers in families of women carrying RINT1 mutations estimated that carriers were at increased risk of Lynch syndrome-spectrum cancers [standardized incidence ratio (SIR), 3.35; 95% CI, 1.7-6.0; P = 0.005], particularly for relatives diagnosed with cancer under the age of 60 years (SIR, 10.9; 95% CI, 4.7-21; P = 0.0003). SIGNIFICANCE The work described in this study adds RINT1 to the growing list of genes in which rare sequence variants are associated with intermediate levels of breast cancer risk. Given that RINT1 is also associated with a spectrum of cancers with mismatch repair defects, these findings have clinical applications and raise interesting biological questions.
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Affiliation(s)
- Daniel J Park
- Genetic Epidemiology Laboratory, Department of Pathology
| | | | | | | | - Nivonirina Robinot
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon
| | - Fleur Hammet
- Genetic Epidemiology Laboratory, Department of Pathology
| | | | | | - Zhi L Teo
- Genetic Epidemiology Laboratory, Department of Pathology
| | | | | | - Catherine Voegele
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon
| | | | - Bernard J Pope
- Department of Computing and Information Systems; Victorian Life Sciences Computation Initiative
| | | | | | - Hao Hu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shankaracharya
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chad D Huff
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jonathan Ellis
- The QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia; Departments of
| | - Jun Li
- The QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia; Departments of
| | - Igor V Makunin
- The QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia; Departments of
| | - Esther M John
- Cancer Prevention Institute of California, Fremont; Department of Health Research and Policy, Stanford Cancer Institute, Stanford, California
| | - Irene L Andrulis
- Department of Molecular Genetics, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Mary B Terry
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
| | - Mary Daly
- Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Saundra S Buys
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah
| | - Carrie Snyder
- Department of Preventive Medicine, Creighton University, Omaha, Nebraska
| | - Henry T Lynch
- Department of Preventive Medicine, Creighton University, Omaha, Nebraska
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands; and
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne; Centre for Cancer Epidemiology, The Cancer Council Victoria, Carlton, Victoria
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne; School of Public Health, Seoul National University, Seoul, Korea
| | - Bing-Jian Feng
- Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine; Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah
| | - Fabienne Lesueur
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon; Genetic Epidemiology of Cancer Team, Institut National de la Santé et de la Recherche Medicale (INSERM), U900, Institut Curie, Mines ParisTech, Paris, France
| | | | | | - David E Goldgar
- Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine; Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah;
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Damiola F, Pertesi M, Oliver J, Le Calvez-Kelm F, Voegele C, Young EL, Robinot N, Forey N, Durand G, Vallée MP, Tao K, Roane TC, Williams GJ, Hopper JL, Southey MC, Andrulis IL, John EM, Goldgar DE, Lesueur F, Tavtigian SV. Rare key functional domain missense substitutions in MRE11A, RAD50, and NBN contribute to breast cancer susceptibility: results from a Breast Cancer Family Registry case-control mutation-screening study. Breast Cancer Res 2014; 16:R58. [PMID: 24894818 PMCID: PMC4229874 DOI: 10.1186/bcr3669] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 05/08/2014] [Indexed: 12/17/2022] Open
Abstract
INTRODUCTION The MRE11A-RAD50-Nibrin (MRN) complex plays several critical roles related to repair of DNA double-strand breaks. Inherited mutations in the three components predispose to genetic instability disorders and the MRN genes have been implicated in breast cancer susceptibility, but the underlying data are not entirely convincing. Here, we address two related questions: (1) are some rare MRN variants intermediate-risk breast cancer susceptibility alleles, and if so (2) do the MRN genes follow a BRCA1/BRCA2 pattern wherein most susceptibility alleles are protein-truncating variants, or do they follow an ATM/CHEK2 pattern wherein half or more of the susceptibility alleles are missense substitutions? METHODS Using high-resolution melt curve analysis followed by Sanger sequencing, we mutation screened the coding exons and proximal splice junction regions of the MRN genes in 1,313 early-onset breast cancer cases and 1,123 population controls. Rare variants in the three genes were pooled using bioinformatics methods similar to those previously applied to ATM, BRCA1, BRCA2, and CHEK2, and then assessed by logistic regression. RESULTS Re-analysis of our ATM, BRCA1, and BRCA2 mutation screening data revealed that these genes do not harbor pathogenic alleles (other than modest-risk SNPs) with minor allele frequencies>0.1% in Caucasian Americans, African Americans, or East Asians. Limiting our MRN analyses to variants with allele frequencies of <0.1% and combining protein-truncating variants, likely spliceogenic variants, and key functional domain rare missense substitutions, we found significant evidence that the MRN genes are indeed intermediate-risk breast cancer susceptibility genes (odds ratio (OR)=2.88, P=0.0090). Key domain missense substitutions were more frequent than the truncating variants (24 versus 12 observations) and conferred a slightly higher OR (3.07 versus 2.61) with a lower P value (0.029 versus 0.14). CONCLUSIONS These data establish that MRE11A, RAD50, and NBN are intermediate-risk breast cancer susceptibility genes. Like ATM and CHEK2, their spectrum of pathogenic variants includes a relatively high proportion of missense substitutions. However, the data neither establish whether variants in each of the three genes are best evaluated under the same analysis model nor achieve clinically actionable classification of individual variants observed in this study.
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Affiliation(s)
- Francesca Damiola
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, 150 cours Albert Thomas, Lyon 69372, France
- Genetic of Breast Cancer group, Cancer Research Center of Lyon, Centre Léon Bérard, 28 rue Laennec, Lyon 69008, France
| | - Maroulio Pertesi
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, 150 cours Albert Thomas, Lyon 69372, France
| | - Javier Oliver
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, 150 cours Albert Thomas, Lyon 69372, France
| | - Florence Le Calvez-Kelm
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, 150 cours Albert Thomas, Lyon 69372, France
| | - Catherine Voegele
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, 150 cours Albert Thomas, Lyon 69372, France
| | - Erin L Young
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, 2000 Circle of Hope, Salt Lake City, UT 84112, USA
| | - Nivonirina Robinot
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, 150 cours Albert Thomas, Lyon 69372, France
| | - Nathalie Forey
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, 150 cours Albert Thomas, Lyon 69372, France
| | - Geoffroy Durand
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, 150 cours Albert Thomas, Lyon 69372, France
| | - Maxime P Vallée
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, 150 cours Albert Thomas, Lyon 69372, France
| | - Kayoko Tao
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, 2000 Circle of Hope, Salt Lake City, UT 84112, USA
| | | | - Gareth J Williams
- Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, 207 Bouverie Street, Melbourne, VIC 3010, Australia
- Department of Epidemiology (Genome Epidemiology Lab), Seoul National University School of Public Health, 599 Gwanak-ro Granak-gu, Seoul 151-742, Korea
| | - Melissa C Southey
- Genetic Epidemiology Laboratory, The University of Melbourne, 207 Bouverie Street, Melbourne, VIC 3010, Australia
| | - Irene L Andrulis
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Department of Molecular Genetics, University of Toronto, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Esther M John
- Cancer Prevention Institute of California, 2201 Walnut Avenue, Fremont, CA 94538, USA
- Stanford University School of Medicine and Stanford Cancer Institute, 875 Blake Wilbur Drive, Stanford, CA 94305, USA
| | - David E Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, 2000 Circle of Hope, Salt Lake City, UT 84112, USA
| | - Fabienne Lesueur
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, 150 cours Albert Thomas, Lyon 69372, France
- Genetic Epidemiology of Cancer team, Inserm, U900, Institut Curie, Mines ParisTech, 26 rue d’Ulm, Paris 75248, France
| | - Sean V Tavtigian
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, 2000 Circle of Hope, Salt Lake City, UT 84112, USA
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41
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Hu H, Roach JC, Coon H, Guthery SL, Voelkerding KV, Margraf RL, Durtschi JD, Tavtigian SV, Shankaracharya, Wu W, Scheet P, Wang S, Xing J, Glusman G, Hubley R, Li H, Garg V, Moore B, Hood L, Galas DJ, Srivastava D, Reese MG, Jorde LB, Yandell M, Huff CD. A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data. Nat Biotechnol 2014; 32:663-9. [PMID: 24837662 DOI: 10.1038/nbt.2895] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 04/04/2014] [Indexed: 01/02/2023]
Abstract
High-throughput sequencing of related individuals has become an important tool for studying human disease. However, owing to technical complexity and lack of available tools, most pedigree-based sequencing studies rely on an ad hoc combination of suboptimal analyses. Here we present pedigree-VAAST (pVAAST), a disease-gene identification tool designed for high-throughput sequence data in pedigrees. pVAAST uses a sequence-based model to perform variant and gene-based linkage analysis. Linkage information is then combined with functional prediction and rare variant case-control association information in a unified statistical framework. pVAAST outperformed linkage and rare-variant association tests in simulations and identified disease-causing genes from whole-genome sequence data in three human pedigrees with dominant, recessive and de novo inheritance patterns. The approach is robust to incomplete penetrance and locus heterogeneity and is applicable to a wide variety of genetic traits. pVAAST maintains high power across studies of monogenic, high-penetrance phenotypes in a single pedigree to highly polygenic, common phenotypes involving hundreds of pedigrees.
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Affiliation(s)
- Hao Hu
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Jared C Roach
- Institute for Systems Biology, Seattle, Washington, USA
| | - Hilary Coon
- Department of Psychiatry, University of Utah, Salt Lake City, Utah, USA
| | - Stephen L Guthery
- Department of Pediatrics, University of Utah, Salt Lake City, Utah, USA
| | - Karl V Voelkerding
- 1] Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA. [2] ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah, USA
| | - Rebecca L Margraf
- ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah, USA
| | - Jacob D Durtschi
- ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah, USA
| | - Sean V Tavtigian
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Shankaracharya
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Wilfred Wu
- Department of Human Genetics and USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, Utah, USA
| | - Paul Scheet
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Shuoguo Wang
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, New Jersey, USA
| | - Jinchuan Xing
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, New Jersey, USA
| | | | - Robert Hubley
- Institute for Systems Biology, Seattle, Washington, USA
| | - Hong Li
- Institute for Systems Biology, Seattle, Washington, USA
| | - Vidu Garg
- 1] Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA. [2] Center for Cardiovascular and Pulmonary Research, Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Barry Moore
- Department of Human Genetics and USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, Utah, USA
| | - Leroy Hood
- Institute for Systems Biology, Seattle, Washington, USA
| | - David J Galas
- 1] Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg. [2] Pacific Northwest Diabetes Research Institute, Seattle, Washington, USA
| | - Deepak Srivastava
- Gladstone Institute of Cardiovascular Disease and University of California, San Francisco, San Francisco, California, USA
| | | | - Lynn B Jorde
- Department of Human Genetics and USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, Utah, USA
| | - Mark Yandell
- Department of Human Genetics and USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, Utah, USA
| | - Chad D Huff
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
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42
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Thompson BA, Spurdle AB, Plazzer JP, Greenblatt MS, Akagi K, Al-Mulla F, Bapat B, Bernstein I, Capellá G, den Dunnen JT, du Sart D, Fabre A, Farrell MP, Farrington SM, Frayling IM, Frebourg T, Goldgar DE, Heinen CD, Holinski-Feder E, Kohonen-Corish M, Robinson KL, Leung SY, Martins A, Moller P, Morak M, Nystrom M, Peltomaki P, Pineda M, Qi M, Ramesar R, Rasmussen LJ, Royer-Pokora B, Scott RJ, Sijmons R, Tavtigian SV, Tops CM, Weber T, Wijnen J, Woods MO, Macrae F, Genuardi M. Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database. Nat Genet 2013; 46:107-115. [PMID: 24362816 DOI: 10.1038/ng.2854] [Citation(s) in RCA: 342] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 11/26/2013] [Indexed: 12/12/2022]
Abstract
The clinical classification of hereditary sequence variants identified in disease-related genes directly affects clinical management of patients and their relatives. The International Society for Gastrointestinal Hereditary Tumours (InSiGHT) undertook a collaborative effort to develop, test and apply a standardized classification scheme to constitutional variants in the Lynch syndrome-associated genes MLH1, MSH2, MSH6 and PMS2. Unpublished data submission was encouraged to assist in variant classification and was recognized through microattribution. The scheme was refined by multidisciplinary expert committee review of the clinical and functional data available for variants, applied to 2,360 sequence alterations, and disseminated online. Assessment using validated criteria altered classifications for 66% of 12,006 database entries. Clinical recommendations based on transparent evaluation are now possible for 1,370 variants that were not obviously protein truncating from nomenclature. This large-scale endeavor will facilitate the consistent management of families suspected to have Lynch syndrome and demonstrates the value of multidisciplinary collaboration in the curation and classification of variants in public locus-specific databases.
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Affiliation(s)
- Bryony A Thompson
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia.,School of Medicine, University of Queensland, Brisbane, Australia
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - John-Paul Plazzer
- Department of Colorectal Medicine and Genetics, Royal Melbourne Hospital, Australia
| | - Marc S Greenblatt
- Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT, USA
| | - Kiwamu Akagi
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama, Japan
| | - Fahd Al-Mulla
- Department of Pathology, Faculty of Medicine, Health Sciences Center, Kuwait University, Safat, Kuwait
| | - Bharati Bapat
- Department of Lab Medicine and Pathobiology, University of Toronto, Canada
| | - Inge Bernstein
- Danish HNPCC Registry, Copenhagen, Denmark.,Surgical Gastroenterology Department, Aalborg University Hospital, Aalborg, Denmark
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology-IDIBELL, Barcelona, Spain
| | - Johan T den Dunnen
- Center of Human and Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Desiree du Sart
- Molecular Genetics Lab, Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, Melbourne, Australia
| | - Aurelie Fabre
- INSERM UMR S910, Department of Medical Genetics and Functional Genomics, Marseille, France
| | - Michael P Farrell
- Department of Cancer Genetics, Mater Private Hospital, Dublin, Ireland
| | - Susan M Farrington
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh, Scotland
| | - Ian M Frayling
- Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK
| | - Thierry Frebourg
- Inserm U1079, Faculty of Medicine, Institute for Biomedical Research, University of Rouen, France
| | - David E Goldgar
- Department of Dermatology, University of Utah Medical School, Salt Lake City, UT, USA.,Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Christopher D Heinen
- Center for Molecular Medicine, UConn Health Center, Farmington, CT, USA.,Neag Comprehensive Cancer Center, UConn Health Center, Farmington, CT, USA
| | - Elke Holinski-Feder
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.,Klinikum der Universität München, Campus Innenstadt, Medizinische Klinik und Poliklinik IV, Munich, Germany
| | - Maija Kohonen-Corish
- School of Medicine, University of Western Sydney, Sydney, Australia.,The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, Australia.,St Vincent's Clinical School, University of NSW, Sydney, Australia
| | - Kristina Lagerstedt Robinson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Suet Yi Leung
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Alexandra Martins
- Inserm U1079, University of Rouen, Institute for Research and Innovation in Biomedicine, Rouen, France
| | - Pal Moller
- Research Group on Inherited Cancer, Department of Medical Genetics, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Monika Morak
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.,Klinikum der Universität München, Campus Innenstadt, Medizinische Klinik und Poliklinik IV, Munich, Germany
| | - Minna Nystrom
- Division of Genetics, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Paivi Peltomaki
- Department of Medical Genetics, Haartman Institute, University of Helsinki, Finland
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology-IDIBELL, Barcelona, Spain
| | - Ming Qi
- Center for Genetic and Genomic Medicine, The First Affiliated Hospital of Zhejiang University School of Medicine, James Watson Institute of Genomic Sciences, Beijing Genome Institute, China.,University of Rochester Medical Center, NY, USA
| | - Rajkumar Ramesar
- MRC Human Genetics Research Unit, Division of Human Genetics, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | | | | | - Rodney J Scott
- Discipline of Medical Genetics, Faculty of Health, University of Newcastle, The Hunter Medical Research Institute, NSW, Australia.,The Division of Molecular Medicine, Hunter Area Pathology Service, John Hunter Hospital, Newcastle, NSW, Australia
| | - Rolf Sijmons
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Carli M Tops
- Center of Human and Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Thomas Weber
- State University of New York at Downstate, Brooklyn, NY, USA
| | - Juul Wijnen
- Center of Human and Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Michael O Woods
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Finlay Macrae
- Department of Colorectal Medicine and Genetics, Royal Melbourne Hospital, Australia
| | - Maurizio Genuardi
- Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Italy.,Fiorgen Foundation for Pharmacogenomics, Sesto Fiorentino, Italy
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Lindor NM, Goldgar DE, Tavtigian SV, Plon SE, Couch FJ. BRCA1/2 sequence variants of uncertain significance: a primer for providers to assist in discussions and in medical management. Oncologist 2013; 18:518-24. [PMID: 23615697 DOI: 10.1634/theoncologist.2012-0452] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
INTRODUCTION DNA variants of uncertain significance (VUS) are common outcomes of clinical genetic testing for susceptibility to cancer. A statistically rigorous model that provides a pathogenicity score for each variant has been developed to aid in the clinical management of patients undergoing genetic testing. METHODS The information in this article is derived from multiple publications on VUS in BRCA genes, distilled for communicating with clinicians who may encounter VUS in their practice. RESULTS The posterior probability scores for BRCA1 or BRCA2 VUS, calculated from a multifactorial likelihood model, are explained, and links for looking up specific VUS are provided. The International Agency on Cancer Research (IARC) of the World Health Organization has proposed a simple five-tier system for clinical management that is not widely known to clinicians. Classes 1 and 2 in this system are managed as neutral variants, classes 4 and 5 are managed as pathogenic variants, and class 3 variants still have insufficient evidence to move to either end of this scale and, thus, cannot be used in medical management. CONCLUSIONS Development of models that integrate multiple independent lines of evidence has allowed classification of a growing number of VUS in the BRCA1 and BRCA2 genes. The pathogenicity score that is generated by this model maps to the IARC system for clinical management, which will assist clinicians in the medical management of those patients who obtain a VUS result upon testing.
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Affiliation(s)
- Noralane M Lindor
- Department of Health Sciences Research, Mayo Clinic, Scottsdale, Arizona 85259, USA.
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44
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Pope BJ, Nguyen-Dumont T, Odefrey F, Hammet F, Bell R, Tao K, Tavtigian SV, Goldgar DE, Lonie A, Southey MC, Park DJ. FAVR (Filtering and Annotation of Variants that are Rare): methods to facilitate the analysis of rare germline genetic variants from massively parallel sequencing datasets. BMC Bioinformatics 2013; 14:65. [PMID: 23441864 PMCID: PMC3599469 DOI: 10.1186/1471-2105-14-65] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 12/05/2012] [Indexed: 11/12/2022] Open
Abstract
Background Characterising genetic diversity through the analysis of massively parallel sequencing (MPS) data offers enormous potential to significantly improve our understanding of the genetic basis for observed phenotypes, including predisposition to and progression of complex human disease. Great challenges remain in resolving genetic variants that are genuine from the millions of artefactual signals. Results FAVR is a suite of new methods designed to work with commonly used MPS analysis pipelines to assist in the resolution of some of the issues related to the analysis of the vast amount of resulting data, with a focus on relatively rare genetic variants. To the best of our knowledge, no equivalent method has previously been described. The most important and novel aspect of FAVR is the use of signatures in comparator sequence alignment files during variant filtering, and annotation of variants potentially shared between individuals. The FAVR methods use these signatures to facilitate filtering of (i) platform and/or mapping-specific artefacts, (ii) common genetic variants, and, where relevant, (iii) artefacts derived from imbalanced paired-end sequencing, as well as annotation of genetic variants based on evidence of co-occurrence in individuals. We applied conventional variant calling applied to whole-exome sequencing datasets, produced using both SOLiD and TruSeq chemistries, with or without downstream processing by FAVR methods. We demonstrate a 3-fold smaller rare single nucleotide variant shortlist with no detected reduction in sensitivity. This analysis included Sanger sequencing of rare variant signals not evident in dbSNP131, assessment of known variant signal preservation, and comparison of observed and expected rare variant numbers across a range of first cousin pairs. The principles described herein were applied in our recent publication identifying XRCC2 as a new breast cancer risk gene and have been made publically available as a suite of software tools. Conclusions FAVR is a platform-agnostic suite of methods that significantly enhances the analysis of large volumes of sequencing data for the study of rare genetic variants and their influence on phenotypes.
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Affiliation(s)
- Bernard J Pope
- Victorian Life Sciences Computation Initiative, The University of Melbourne, 187 Grattan Street Carlton, Melbourne, Victoria 3010, Australia
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45
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Le Calvez-Kelm F, Oliver J, Damiola F, Forey N, Robinot N, Durand G, Voegele C, Vallée MP, Byrnes G, Registry BCF, Hopper JL, Southey MC, Andrulis IL, John EM, Tavtigian SV, Lesueur F. RAD51 and breast cancer susceptibility: no evidence for rare variant association in the Breast Cancer Family Registry study. PLoS One 2012; 7:e52374. [PMID: 23300655 PMCID: PMC3531476 DOI: 10.1371/journal.pone.0052374] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 11/15/2012] [Indexed: 12/12/2022] Open
Abstract
Background Although inherited breast cancer has been associated with germline mutations in genes that are functionally involved in the DNA homologous recombination repair (HRR) pathway, including BRCA1, BRCA2, TP53, ATM, BRIP1, CHEK2 and PALB2, about 70% of breast cancer heritability remains unexplained. Because of their critical functions in maintaining genome integrity and already well-established associations with breast cancer susceptibility, it is likely that additional genes involved in the HRR pathway harbor sequence variants associated with increased risk of breast cancer. RAD51 plays a central biological function in DNA repair and despite the fact that rare, likely dysfunctional variants in three of its five paralogs, RAD51C, RAD51D, and XRCC2, have been associated with breast and/or ovarian cancer risk, no population-based case-control mutation screening data are available for the RAD51 gene. We thus postulated that RAD51 could harbor rare germline mutations that confer increased risk of breast cancer. Methodology/Principal Findings We screened the coding exons and proximal splice junction regions of the gene for germline sequence variation in 1,330 early-onset breast cancer cases and 1,123 controls from the Breast Cancer Family Registry, using the same population-based sampling and analytical strategy that we developed for assessment of rare sequence variants in ATM and CHEK2. In total, 12 distinct very rare or private variants were characterized in RAD51, with 10 cases (0.75%) and 9 controls (0.80%) carrying such a variant. Variants were either likely neutral missense substitutions (3), silent substitutions (4) or non-coding substitutions (5) that were predicted to have little effect on efficiency of the splicing machinery. Conclusion Altogether, our data suggest that RAD51 tolerates so little dysfunctional sequence variation that rare variants in the gene contribute little, if anything, to breast cancer susceptibility.
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Affiliation(s)
- Florence Le Calvez-Kelm
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon, France
| | - Javier Oliver
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon, France
| | - Francesca Damiola
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon, France
| | - Nathalie Forey
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon, France
| | - Nivonirina Robinot
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon, France
| | - Geoffroy Durand
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon, France
| | - Catherine Voegele
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon, France
| | - Maxime P. Vallée
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon, France
| | - Graham Byrnes
- Biostatistics Group, International Agency for Research on Cancer, Lyon, France
| | - Breast Cancer Family Registry
- Center for Molecular, Environmental, Genetic and Analytical Epidemiology, School of Population Health, EGA The University of Melbourne, Victoria, Australia
- Genetic Epidemiology Laboratory, The University of Melbourne, Victoria, Australia
- Department of Molecular Genetics, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Cancer Prevention Institute of California, Fremont, California, United States of America
- Stanford University School of Medicine and Stanford Cancer Institute, Stanford, California, United States of America
| | - John L. Hopper
- Center for Molecular, Environmental, Genetic and Analytical Epidemiology, School of Population Health, EGA The University of Melbourne, Victoria, Australia
| | - Melissa C. Southey
- Genetic Epidemiology Laboratory, The University of Melbourne, Victoria, Australia
| | - Irene L. Andrulis
- Department of Molecular Genetics, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Esther M. John
- Cancer Prevention Institute of California, Fremont, California, United States of America
- Stanford University School of Medicine and Stanford Cancer Institute, Stanford, California, United States of America
| | - Sean V. Tavtigian
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Fabienne Lesueur
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon, France
- * E-mail:
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46
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Thompson BA, Greenblatt MS, Vallee MP, Herkert JC, Tessereau C, Young EL, Adzhubey IA, Li B, Bell R, Feng B, Mooney SD, Radivojac P, Sunyaev SR, Frebourg T, Hofstra RMW, Sijmons RH, Boucher K, Thomas A, Goldgar DE, Spurdle AB, Tavtigian SV. Calibration of multiple in silico tools for predicting pathogenicity of mismatch repair gene missense substitutions. Hum Mutat 2012; 34:255-65. [PMID: 22949387 DOI: 10.1002/humu.22214] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Accepted: 08/26/2012] [Indexed: 11/11/2022]
Abstract
Classification of rare missense substitutions observed during genetic testing for patient management is a considerable problem in clinical genetics. The Bayesian integrated evaluation of unclassified variants is a solution originally developed for BRCA1/2. Here, we take a step toward an analogous system for the mismatch repair (MMR) genes (MLH1, MSH2, MSH6, and PMS2) that confer colon cancer susceptibility in Lynch syndrome by calibrating in silico tools to estimate prior probabilities of pathogenicity for MMR gene missense substitutions. A qualitative five-class classification system was developed and applied to 143 MMR missense variants. This identified 74 missense substitutions suitable for calibration. These substitutions were scored using six different in silico tools (Align-Grantham Variation Grantham Deviation, multivariate analysis of protein polymorphisms [MAPP], MutPred, PolyPhen-2.1, Sorting Intolerant From Tolerant, and Xvar), using curated MMR multiple sequence alignments where possible. The output from each tool was calibrated by regression against the classifications of the 74 missense substitutions; these calibrated outputs are interpretable as prior probabilities of pathogenicity. MAPP was the most accurate tool and MAPP + PolyPhen-2.1 provided the best-combined model (R(2) = 0.62 and area under receiver operating characteristic = 0.93). The MAPP + PolyPhen-2.1 output is sufficiently predictive to feed as a continuous variable into the quantitative Bayesian integrated evaluation for clinical classification of MMR gene missense substitutions.
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Affiliation(s)
- Bryony A Thompson
- Queensland Institute of Medical Research, Herston, Brisbane, Australia
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47
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Thompson BA, Goldgar DE, Paterson C, Clendenning M, Walters R, Arnold S, Parsons MT, Michael D W, Gallinger S, Haile RW, Hopper JL, Jenkins MA, Lemarchand L, Lindor NM, Newcomb PA, Thibodeau SN, Young JP, Buchanan DD, Tavtigian SV, Spurdle AB. A multifactorial likelihood model for MMR gene variant classification incorporating probabilities based on sequence bioinformatics and tumor characteristics: a report from the Colon Cancer Family Registry. Hum Mutat 2012; 34:200-9. [PMID: 22949379 DOI: 10.1002/humu.22213] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2012] [Accepted: 08/22/2012] [Indexed: 01/04/2023]
Abstract
Mismatch repair (MMR) gene sequence variants of uncertain clinical significance are often identified in suspected Lynch syndrome families, and this constitutes a challenge for both researchers and clinicians. Multifactorial likelihood model approaches provide a quantitative measure of MMR variant pathogenicity, but first require input of likelihood ratios (LRs) for different MMR variation-associated characteristics from appropriate, well-characterized reference datasets. Microsatellite instability (MSI) and somatic BRAF tumor data for unselected colorectal cancer probands of known pathogenic variant status were used to derive LRs for tumor characteristics using the Colon Cancer Family Registry (CFR) resource. These tumor LRs were combined with variant segregation within families, and estimates of prior probability of pathogenicity based on sequence conservation and position, to analyze 44 unclassified variants identified initially in Australasian Colon CFR families. In addition, in vitro splicing analyses were conducted on the subset of variants based on bioinformatic splicing predictions. The LR in favor of pathogenicity was estimated to be ~12-fold for a colorectal tumor with a BRAF mutation-negative MSI-H phenotype. For 31 of the 44 variants, the posterior probabilities of pathogenicity were such that altered clinical management would be indicated. Our findings provide a working multifactorial likelihood model for classification that carefully considers mode of ascertainment for gene testing.
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Affiliation(s)
- Bryony A Thompson
- Department of Genetics and Population Health, Queensland Institute of Medical Research, Herston, Brisbane, Australia; School of Medicine, University of Queensland, Brisbane, Australia
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48
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Jhuraney A, Velkova A, Vallée MP, Carvalho RS, Tavtigian SV, Monteiro AN. Abstract 4444: BRCA1 Circos: A visualization tool for BRCA1 missense variants. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-4444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Germline mutations in BRCA1 have been associated with a significantly increased risk of developing breast and ovarian cancers. A large number of variants have been identified in BRCA1 and are reported as pathogenic, non-pathogenic, or as variants of uncertain significance (VUS). Test results reporting pathogenic or non-pathogenic variants can be used by physicians and genetic counselors to help patients in making important clinical decisions. Around 10-15% of the reported BRCA1 and BRCA2 variants are clearly pathogenic and 5% of these reported variants are VUS. Results reporting a VUS can cause anxiety and make it difficult to advise the patient on further clinical intervention to reduce their risk of developing the disease. Many of these VUSs are non-synonymous single amino acid changes leading to missense changes. A number of previous studies have focused on assessing the functional impact of these changes on the BRCA1 protein. BRCA1 is a gene product with pleiotropic functions and therefore, different functional assays are used in these studies to analyze the variant's impact on function. However, information on the functional impact of VUS is currently not consolidated and collecting available information on missense variants depends on multiple database searches and literature review. Moreover, methods to incorporate functional data into multifactorial models have recently been developed highlighting the need for a common resource to facilitate analysis. Realizing the need for a resource that facilitates the global visualization and analysis of these variants we have developed a visualization tool for multidimensional data using Circos (http://circos.ca) to aggregate the data from all published studies that have assessed these missense variants. Circos plots have been used in the literature to represent genomic data and we have used the same concept to illustrate variants in BRCA1. We have included ∼700 variants for which we have 30 different functional experiments from various studies assessing over 150 missense variants. Results are color coded to uniformly depict various degrees of functional impact on the BRCA1 protein function so that information for any variant can be obtained in a snapshot without having to perform extensive literature searches. Therefore, we believe clinical geneticists and genetic counselors can use this research tool as a quick reference to analyze all the missense variants that have been identified along with associated information to characterize them when faced with the challenge of advising a patient with these types of VUSs.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4444. doi:1538-7445.AM2012-4444
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Affiliation(s)
- Ankita Jhuraney
- 1Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Aneliya Velkova
- 1Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | | | - Renato S. Carvalho
- 3Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Sean V. Tavtigian
- 4Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT
| | - Alvaro N. Monteiro
- 1Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
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Feng BJ, Tavtigian SV, Southey MC, Goldgar DE. Design considerations for massively parallel sequencing studies of common familial cancers. Hered Cancer Clin Pract 2012. [PMCID: PMC3327154 DOI: 10.1186/1897-4287-10-s2-a38] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Ahmad J, Le Calvez-Kelm F, Daud S, Voegele C, Vallée M, Ahmad A, Kakar N, McKay JD, Gaborieau V, Léoné M, Sinilnikova O, Sangrajrang S, Tavtigian SV, Lesueur F. Detection of BRCA1/2 mutations in breast cancer patients from Thailand and Pakistan. Clin Genet 2012; 82:594-8. [PMID: 22486713 DOI: 10.1111/j.1399-0004.2012.01869.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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