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1. Gene-specific ACMG/AMP classification criteria for germline APC variants: Recommendations from the ClinGen InSiGHT Hereditary Colorectal Cancer/ Polyposis Variant Curation Expert Panel

Author

Spier, I, Yin, X, Richardson, M, Pineda, M, Laner, A, Ritter, D, Boyle, J, Mur, P, Hansen, TVO, Shi, X, Mahmood, K, Plazzer, J-P, 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, Capella, G, Tavtigian, S, Latchford, A, Frayling, IM, Plon, SE, Greenblatt, M, Macrae, FA, Aretz, S, Spier, I, Yin, X, Richardson, M, Pineda, M, Laner, A, Ritter, D, Boyle, J, Mur, P, Hansen, TVO, Shi, X, Mahmood, K, Plazzer, J-P, 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, Capella, G, Tavtigian, S, Latchford, A, Frayling, IM, Plon, SE, Greenblatt, M, Macrae, FA, and Aretz, S

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.

Published
2024

2. Uncovering the Contribution of Moderate-Penetrance Susceptibility Genes to Breast Cancer by Whole-Exome Sequencing and Targeted Enrichment Sequencing of Candidate Genes in Women of European Ancestry.

Author

Dumont, M, Weber-Lassalle, N, Joly-Beauparlant, C, Ernst, C, Droit, A, Feng, B-J, Dubois, S, Collin-Deschesnes, A-C, Soucy, P, Vallée, M, Fournier, F, Lemaçon, A, Adank, MA, Allen, J, Altmüller, J, Arnold, N, Ausems, MGEM, Berutti, R, Bolla, MK, Bull, S, Carvalho, S, Cornelissen, S, Dufault, MR, Dunning, AM, Engel, C, Gehrig, A, Geurts-Giele, WRR, Gieger, C, Green, J, Hackmann, K, Helmy, M, Hentschel, J, Hogervorst, FBL, Hollestelle, A, Hooning, MJ, Horváth, J, Ikram, MA, Kaulfuß, S, Keeman, R, Kuang, D, Luccarini, C, Maier, W, Martens, JWM, Niederacher, D, Nürnberg, P, Ott, C-E, Peters, A, Pharoah, PDP, Ramirez, A, Ramser, J, Riedel-Heller, S, Schmidt, G, Shah, M, Scherer, M, Stäbler, A, Strom, TM, Sutter, C, Thiele, H, van Asperen, CJ, van der Kolk, L, van der Luijt, RB, Volk, AE, Wagner, M, Waisfisz, Q, Wang, Q, Wang-Gohrke, S, Weber, BHF, Genome Of The Netherlands Project, Ghs Study Group, Devilee, P, Tavtigian, S, Bader, GD, Meindl, A, Goldgar, DE, Andrulis, IL, Schmutzler, RK, Easton, DF, Schmidt, MK, Hahnen, E, Simard, J, Dumont, M, Weber-Lassalle, N, Joly-Beauparlant, C, Ernst, C, Droit, A, Feng, B-J, Dubois, S, Collin-Deschesnes, A-C, Soucy, P, Vallée, M, Fournier, F, Lemaçon, A, Adank, MA, Allen, J, Altmüller, J, Arnold, N, Ausems, MGEM, Berutti, R, Bolla, MK, Bull, S, Carvalho, S, Cornelissen, S, Dufault, MR, Dunning, AM, Engel, C, Gehrig, A, Geurts-Giele, WRR, Gieger, C, Green, J, Hackmann, K, Helmy, M, Hentschel, J, Hogervorst, FBL, Hollestelle, A, Hooning, MJ, Horváth, J, Ikram, MA, Kaulfuß, S, Keeman, R, Kuang, D, Luccarini, C, Maier, W, Martens, JWM, Niederacher, D, Nürnberg, P, Ott, C-E, Peters, A, Pharoah, PDP, Ramirez, A, Ramser, J, Riedel-Heller, S, Schmidt, G, Shah, M, Scherer, M, Stäbler, A, Strom, TM, Sutter, C, Thiele, H, van Asperen, CJ, van der Kolk, L, van der Luijt, RB, Volk, AE, Wagner, M, Waisfisz, Q, Wang, Q, Wang-Gohrke, S, Weber, BHF, Genome Of The Netherlands Project, Ghs Study Group, Devilee, P, Tavtigian, S, Bader, GD, Meindl, A, Goldgar, DE, Andrulis, IL, Schmutzler, RK, Easton, DF, Schmidt, MK, Hahnen, E, and Simard, J

Abstract

Rare variants in at least 10 genes, including BRCA1, BRCA2, PALB2, ATM, and CHEK2, are associated with increased risk of breast cancer; however, these variants, in combination with common variants identified through genome-wide association studies, explain only a fraction of the familial aggregation of the disease. To identify further susceptibility genes, we performed a two-stage whole-exome sequencing study. In the discovery stage, samples from 1528 breast cancer cases enriched for breast cancer susceptibility and 3733 geographically matched unaffected controls were sequenced. Using five different filtering and gene prioritization strategies, 198 genes were selected for further validation. These genes, and a panel of 32 known or suspected breast cancer susceptibility genes, were assessed in a validation set of 6211 cases and 6019 controls for their association with risk of breast cancer overall, and by estrogen receptor (ER) disease subtypes, using gene burden tests applied to loss-of-function and rare missense variants. Twenty genes showed nominal evidence of association (p-value < 0.05) with either overall or subtype-specific breast cancer. Our study had the statistical power to detect susceptibility genes with effect sizes similar to ATM, CHEK2, and PALB2, however, it was underpowered to identify genes in which susceptibility variants are rarer or confer smaller effect sizes. Larger sample sizes would be required in order to identify such genes.

Published
2022

4. First international workshop of the ATM and Cancer Risk Group (4–5 December 2019)

Author

Lesueur, F., Easton, D. F., Renault, A. -L., Tavtigian, S. V., Bernstein, J. L., Kote-Jarai, Z., Eeles, R. A., Plaseska-Karanfia, D., Feliubadalo, L., Moles-Fernandez, A., Santamarina-Pena, M., Sanchez, A. T., Lopez-Novo, A., Porras, L. -M., Blanco, A., Capella, G., de la Hoya, M., Molina, I. J., Osorio, A., Pineda, M., Rueda, D., de la Cruz, X., Diez, O., Ruiz-Ponte, C., Gutierrez-Enriquez, S., Vega, A., Lazaro, C., Arun, B., Herold, N., Versmold, B., Schmutzler, R. K., Nguyen-Dumont, T., Southey, M. C., Dorling, L., Dunning, A. M., Ghiorzo, P., Dalmasso, B. S., Cavaciuti, E., Le Gal, D., Roberts, N. J., Dominguez-Valentin, M., Rookus, M., Taylor, A. M. R., Goldstein, A. M., Goldgar, D. E., Couch, F., Kraft, P., Weitzel, J., Nathanson, K., Domchek, S., Laduca, H., Stoppa-Lyonnet, D., and Andrieu, N.

Subjects
0301 basic medicine, Cancer Research, medicine.medical_specialty, Heterozygote, Variants classification, ATM, Cancer risk, Cancer spectrum, Tumor profiles, Population, Context (language use), Breast Neoplasms, Ataxia Telangiectasia Mutated Proteins, 030105 genetics & heredity, Article, 03 medical and health sciences, Ataxia Telangiectasia, 0302 clinical medicine, Neoplasms, Epidemiology, Genetics, medicine, Humans, Genetic Predisposition to Disease, education, Genetics (clinical), education.field_of_study, business.industry, Cancer, medicine.disease, Oncology, 030220 oncology & carcinogenesis, Family medicine, Female, France, business
Abstract

The first International Workshop of the ATM and Cancer Risk group focusing on the role of Ataxia-Telangiectasia Mutated (ATM) gene in cancer was held on December 4 and 5, 2019 at Institut Curie in Paris, France. It was motivated by the fact that germline ATM pathogenic variants have been found to be associated with different cancer types. However, due to the lack of precise age-, sex-, and site-specific risk estimates, no consensus on management guidelines for variant carriers exists, and the clinical utility of ATM variant testing is uncertain. The meeting brought together epidemiologists, geneticists, biologists and clinicians to review current knowledge and on-going challenges related to ATM and cancer risk. This report summarizes the meeting sessions content that covered the latest results in family-based and population-based studies, the importance of accurate variant classification, the effect of radiation exposures for ATM variant carriers, and the characteristics of ATM-deficient tumors. The report concludes that ATM variant carriers outside of the context of Ataxia-Telangiectasia may benefit from effective cancer risk management and therapeutic strategies and that efforts to set up large-scale studies in the international framework to achieve this goal are necessary.

Published
2021

6. Personalized Risk Assessment for Prevention and Early Detection of Breast Cancer: Integration and Implementation (PERSPECTIVE I&I)

Author

Brooks, JD, Nabi, HH, Andrulis, IL, Antoniou, AC, Chiquette, J, Despres, P, Devilee, P, Dorval, M, Droit, A, Easton, DF, Eisen, A, Eloy, L, Fienberg, S, Goldgar, D, Hahnen, E, Joly, Y, Knoppers, BM, Lofters, A, Masson, J-Y, Mittmann, N, Paquette, J-S, Pashayan, N, Schmutzler, R, Stockley, T, Tavtigian, S, Walker, MJ, Wolfson, M, Chiarelli, AM, Simard, J, Brooks, JD, Nabi, HH, Andrulis, IL, Antoniou, AC, Chiquette, J, Despres, P, Devilee, P, Dorval, M, Droit, A, Easton, DF, Eisen, A, Eloy, L, Fienberg, S, Goldgar, D, Hahnen, E, Joly, Y, Knoppers, BM, Lofters, A, Masson, J-Y, Mittmann, N, Paquette, J-S, Pashayan, N, Schmutzler, R, Stockley, T, Tavtigian, S, Walker, MJ, Wolfson, M, Chiarelli, AM, and Simard, J

Abstract

Early detection of breast cancer through screening reduces breast cancer mortality. The benefits of screening must also be considered within the context of potential harms (e.g., false positives, overdiagnosis). Furthermore, while breast cancer risk is highly variable within the population, most screening programs use age to determine eligibility. A risk-based approach is expected to improve the benefit-harm ratio of breast cancer screening programs. The PERSPECTIVE I&I (Personalized Risk Assessment for Prevention and Early Detection of Breast Cancer: Integration and Implementation) project seeks to improve personalized risk assessment to allow for a cost-effective, population-based approach to risk-based screening and determine best practices for implementation in Canada. This commentary describes the four inter-related activities that comprise the PERSPECTIVE I&I project. 1: Identification and validation of novel moderate to high-risk susceptibility genes. 2: Improvement, validation, and adaptation of a risk prediction web-tool for the Canadian context. 3: Development and piloting of a socio-ethical framework to support implementation of risk-based breast cancer screening. 4: Economic analysis to optimize the implementation of risk-based screening. Risk-based screening and prevention is expected to benefit all women, empowering them to work with their healthcare provider to make informed decisions about screening and prevention.

Published
2021

13. FANCM c5791C>T stopgain mutation (rs144567652) is a familial colorectal cancer risk factor

Author

Cannon-Albright, LA, Teerlink, CC, Stevens, J, Snow, AK, Thompson, BA, Bell, R, Nguyen, KN, Sargent, NR, Kohlmann, WK, Neklason, DW, Tavtigian, S, Cannon-Albright, LA, Teerlink, CC, Stevens, J, Snow, AK, Thompson, BA, Bell, R, Nguyen, KN, Sargent, NR, Kohlmann, WK, Neklason, DW, and Tavtigian, S

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.

Published
2020

14. Classification of BRCA1 missense variants of unknown clinical significance

Author

Phelan, C M, Đapić, V, Tice, B, Favis, R, Kwan, E, Barany, F, Manoukian, S, Radice, P, van der Luijt, R B, van Nesselrooij, B P M, Chenevix-Trench, G, kConFab, Caldes, T, de La Hoya, M, Lindquist, S, Tavtigian, S V, Goldgar, D, Borg, Å, Narod, S A, and Monteiro, A N A

Published
2005

16. BRCA Challenge: BRCA Exchange as a global resource for variants in BRCA1 and BRCA2

Author

Cline, M.S., Liao, R.G., Parsons, M.T., Paten, B., Alquaddoomi, F., Antoniou, A., Baxter, S., Brody, L., Cook-Deegan, R., Coffin, A., Couch, F.J., Craft, B., Currie, R., Dlott, C.C., Dolman, L., Dunnen, J.T. den, Dyke, S.O.M., Domchek, S.M., Easton, D., Fischmann, Z., Foulkes, W.D., Garber, J., Goldgar, D., Goldman, M.J., Goodhand, P., Harrison, S., Haussler, D., Kato, K., Knoppers, B., Markello, C., Nussbaum, R., Offit, K., Plon, S.E., Rashbass, J., Rehm, H.L., Robson, M., Rubinstein, W.S., Stoppa-Lyonnet, D., Tavtigian, S., Thorogood, A., Zhang, C., Zimmermann, M., Burn, J., Chanock, S., Ratsch, G., Spurdle, A.B., Andreoletti, G., Baker, D., Brenner, S., Brush, M., Caputo, S., Castera, L., Cunningham, F., Hoya, M. de la, Diekhans, M., Dolinsky, J., Dwight, S., Eccles, D., Feng, B., Fiume, M., Flicek, P., Gaudet, P., Garcia, E.G., Haendel, M., Haeussler, M., Hahnen, E., Houdayer, C., Hunt, S., James, P., Lebo, M., Lee, J., Lerner-Ellis, J., Lin, M., Lincoln, S., Malheiro, A., Mesenkamp, A., Monteiro, A., Natzijl-Visser, E., Ngeow, J., North, K., Parkinson, H., Paschall, J., Patrinos, G., Phimister, B., Radice, P., Rainville, I., Rasmussen, M., Riley, G., Rouleau, E., Schmutzler, R., Shefchek, K., Sofia, H., Southey, M., Stuart, J., Thomas, J., Toland, A., Truty, R., Turn-Bull, C., Vaur, D., Vreeswijk, M.P.G., Walker, L., Walsh, M., Wappenschmidt, B., Weitzel, J., Wright, M., Zalunin, V., Zaranek, A., Zerbino, D., Zhou, A., Zhou, J., Zook, J., BRCA Challenge Authors, Eng, Charis, Liao, Rachel G [0000-0002-7830-1976], Parsons, Michael T [0000-0003-3242-8477], Alquaddoomi, Faisal [0000-0003-4297-8747], Baxter, Samantha [0000-0003-4616-9234], Coffin, Amy [0000-0003-2723-8222], Currie, Robert [0000-0003-1828-1827], Dlott, Chloe C [0000-0002-7268-7230], Dolman, Lena [0000-0002-3938-588X], Fischmann, Zachary [0000-0002-7687-0972], Foulkes, William D [0000-0001-7427-4651], Goldman, Mary J [0000-0002-9808-6388], Goodhand, Peter [0000-0002-2624-2820], Harrison, Steven [0000-0002-9614-9111], Haussler, David [0000-0003-1533-4575], Markello, Charles [0000-0002-3653-7155], Plon, Sharon E [0000-0002-9626-0936], Rehm, Heidi L [0000-0002-6025-0015], Rubinstein, Wendy S [0000-0002-8790-9959], Tavtigian, Sean [0000-0002-7543-8221], Thorogood, Adrian [0000-0001-5078-8164], Chanock, Stephen [0000-0002-2324-3393], Rätsch, Gunnar [0000-0001-5486-8532], Spurdle, Amanda B [0000-0003-1337-7897], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, Male, Cancer Research, Research Facilities, endocrine system diseases, Epidemiology, Genes, BRCA2, Genes, BRCA1, Social Sciences, Penetrance, QH426-470, Patient advocacy, Database and Informatics Methods, 0302 clinical medicine, Resource (project management), Sociology, Gene Frequency, Consortia, Risk Factors, Databases, Genetic, Medicine and Health Sciences, Aetiology, skin and connective tissue diseases, Genetics (clinical), Cancer, Ovarian Neoplasms, education.field_of_study, Cancer Risk Factors, Genomics, Genomic Databases, 3. Good health, Viewpoints, Phenotype, Oncology, 030220 oncology & carcinogenesis, Female, Research Laboratories, Population, Genetic Causes of Cancer, MEDLINE, Information Dissemination, Breast Neoplasms, Patient Advocacy, Biology, Research and Analysis Methods, Human Genomics, 03 medical and health sciences, Databases, Genetic, Breast Cancer, Genetics, Humans, Genetic Predisposition to Disease, education, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Alleles, Human Genome, Biology and Life Sciences, Computational Biology, Genetic Variation, Genome Analysis, Genomic Libraries, BRCA1, Data science, BRCA2, Data sharing, Health Care, 030104 developmental biology, Biological Databases, Good Health and Well Being, Genes, Genetic Loci, Medical Risk Factors, BRCA Challenge Authors, Mutation, Leiden Open Variation Database, 2.6 Resources and infrastructure (aetiology), Government Laboratories, Developmental Biology
Abstract

The BRCA Challenge is a long-term data-sharing project initiated within the Global Alliance for Genomics and Health (GA4GH) to aggregate BRCA1 and BRCA2 data to support highly collaborative research activities. Its goal is to generate an informed and current understanding of the impact of genetic variation on cancer risk across the iconic cancer predisposition genes, BRCA1 and BRCA2. Initially, reported variants in BRCA1 and BRCA2 available from public databases were integrated into a single, newly created site, www.brcaexchange.org. The purpose of the BRCA Exchange is to provide the community with a reliable and easily accessible record of variants interpreted for a high-penetrance phenotype. More than 20,000 variants have been aggregated, three times the number found in the next-largest public database at the project’s outset, of which approximately 7,250 have expert classifications. The data set is based on shared information from existing clinical databases—Breast Cancer Information Core (BIC), ClinVar, and the Leiden Open Variation Database (LOVD)—as well as population databases, all linked to a single point of access. The BRCA Challenge has brought together the existing international Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) consortium expert panel, along with expert clinicians, diagnosticians, researchers, and database providers, all with a common goal of advancing our understanding of BRCA1 and BRCA2 variation. Ongoing work includes direct contact with national centers with access to BRCA1 and BRCA2 diagnostic data to encourage data sharing, development of methods suitable for extraction of genetic variation at the level of individual laboratory reports, and engagement with participant communities to enable a more comprehensive understanding of the clinical significance of genetic variation in BRCA1 and BRCA2., Author summary The goal of this study and paper has been to develop an international resource to generate an informed and current understanding of the impact of genetic variation on cancer risk across the cancer predisposition genes, BRCA1 and BRCA2. Reported variants in BRCA1 and BRCA2 available from public databases were integrated into a single, newly created site, www.brcaexchange.org, to provide a reliable and easily accessible record of variants interpreted for a high-penetrance phenotype.

Published
2018

17. A quantitative model to predict pathogenicity of missense variants in the TP53 gene

Author

Fortuno, C, Cipponi, A, Ballinger, ML, Tavtigian, S, Olivier, M, Ruparel, V, Haupt, Y, Haupt, S, Tucker, K, Spurdle, AB, Thomas, DM, James, PA, Fortuno, C, Cipponi, A, Ballinger, ML, Tavtigian, S, Olivier, M, Ruparel, V, Haupt, Y, Haupt, S, Tucker, K, Spurdle, AB, Thomas, DM, and James, PA

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.

Published
2019

18. Large scale multifactorial likelihood quantitative analysis of BRCA1 and BRCA2 variants: An ENIGMA resource to support clinical variant classification

Author

Parsons, MT, Tudini, E, Li, H, Hahnen, E, Wappenschmidt, B, Feliubadalo, L, Aalfs, CM, Agata, S, Aittomaki, K, Alducci, E, Concepcion Alonso-Cerezo, M, Arnold, N, Auber, B, Austin, R, Azzollini, J, Balmana, J, Barbieri, E, Bartram, CR, Blanco, A, Bluemcke, B, Bonache, S, Bonanni, B, Borg, A, Bortesi, B, Brunet, J, Bruzzone, C, Bucksch, K, Cagnoli, G, Caldes, 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-M, Germani, A, Giesecke, J, Gismondi, V, Gomez, C, Garcia, EBG, Gonzalez, S, Grau, E, Grill, S, Gross, E, Guerrieri-Gonzaga, A, Guillaud-Bataille, M, Gutierrez-Enriquez, S, Haaf, T, Hackmann, K, Hansen, TV, Harris, M, Hauke, J, Heinrich, T, Hellebrand, H, Herold, KN, Honisch, E, Horvath, J, Houdayer, C, Huebbel, V, Iglesias, S, Izquierdo, A, James, PA, Janssen, LA, Jeschke, U, Kaulfuss, S, Keupp, K, Kiechle, M, Koelbl, 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, Lopez-Fernandez, A, Lucci-Cordisco, E, Maass, N, Manoukian, S, Marabelli, M, Matricardi, L, Meindl, A, Michelli, RD, Moghadasi, S, Moles-Fernandez, A, Montagna, M, Montalban, G, Monteiro, AN, Montes, E, Mori, L, Moserle, L, Mueller, CR, Mundhenke, C, Naldi, N, Nathanson, KL, Navarro, M, Nevanlinna, H, Nichols, CB, Niederacher, D, Nielsen, HR, Ong, K-R, Pachter, N, Palmero, E, 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, Sanchez 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, S, Teo, SH, Teule, A, Thomassen, M, Tibiletti, MG, Tischkowitz, M, Tognazzo, S, Toland, AE, Tornero, E, Torngren, 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, A, Vesper, A-S, Viel, A, Vreeswijk, MPG, Wagner, SA, Waha, A, Walker, LC, Walters, RJ, Wang-Gohrke, S, Weber, BHF, Weichert, W, Wieland, K, Wiesmueller, L, Witzel, I, Woeckel, A, Woodward, ER, Zachariae, S, Zampiga, V, Zeder-Goss, C, Lazaro, C, De Nicolo, A, Radice, P, Engel, C, Schmutzler, RK, Goldgar, DE, Spurdle, AB, Parsons, MT, Tudini, E, Li, H, Hahnen, E, Wappenschmidt, B, Feliubadalo, L, Aalfs, CM, Agata, S, Aittomaki, K, Alducci, E, Concepcion Alonso-Cerezo, M, Arnold, N, Auber, B, Austin, R, Azzollini, J, Balmana, J, Barbieri, E, Bartram, CR, Blanco, A, Bluemcke, B, Bonache, S, Bonanni, B, Borg, A, Bortesi, B, Brunet, J, Bruzzone, C, Bucksch, K, Cagnoli, G, Caldes, 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-M, Germani, A, Giesecke, J, Gismondi, V, Gomez, C, Garcia, EBG, Gonzalez, S, Grau, E, Grill, S, Gross, E, Guerrieri-Gonzaga, A, Guillaud-Bataille, M, Gutierrez-Enriquez, S, Haaf, T, Hackmann, K, Hansen, TV, Harris, M, Hauke, J, Heinrich, T, Hellebrand, H, Herold, KN, Honisch, E, Horvath, J, Houdayer, C, Huebbel, V, Iglesias, S, Izquierdo, A, James, PA, Janssen, LA, Jeschke, U, Kaulfuss, S, Keupp, K, Kiechle, M, Koelbl, 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, Lopez-Fernandez, A, Lucci-Cordisco, E, Maass, N, Manoukian, S, Marabelli, M, Matricardi, L, Meindl, A, Michelli, RD, Moghadasi, S, Moles-Fernandez, A, Montagna, M, Montalban, G, Monteiro, AN, Montes, E, Mori, L, Moserle, L, Mueller, CR, Mundhenke, C, Naldi, N, Nathanson, KL, Navarro, M, Nevanlinna, H, Nichols, CB, Niederacher, D, Nielsen, HR, Ong, K-R, Pachter, N, Palmero, E, 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, Sanchez 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, S, Teo, SH, Teule, A, Thomassen, M, Tibiletti, MG, Tischkowitz, M, Tognazzo, S, Toland, AE, Tornero, E, Torngren, 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, A, Vesper, A-S, Viel, A, Vreeswijk, MPG, Wagner, SA, Waha, A, Walker, LC, Walters, RJ, Wang-Gohrke, S, Weber, BHF, Weichert, W, Wieland, K, Wiesmueller, L, Witzel, I, Woeckel, A, Woodward, ER, Zachariae, S, Zampiga, V, Zeder-Goss, C, Lazaro, C, De Nicolo, A, Radice, P, Engel, C, Schmutzler, RK, Goldgar, DE, and Spurdle, AB

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.

Published
2019

19. Large scale multifactorial likelihood quantitative analysis of BRCA1 and BRCA2 variants: An ENIGMA resource to support clinical variant classification

Author

Parsons, M. T., Tudini, E., Li, H., Hahnen, E., Wappenschmidt, B., Feliubadalo, L., Aalfs, C. M., Agata, S., Aittomaki, K., Alducci, E., Alonso-Cerezo, M. C., Arnold, N., Auber, B., Austin, R., Azzollini, J., Balmana, J., Barbieri, E., Bartram, C. R., Blanco, A., Blumcke, B., Bonache, S., Bonanni, B., Borg, A., Bortesi, B., Brunet, J., Bruzzone, C., Bucksch, K., Cagnoli, G., Caldes, T., Caliebe, A., Caligo, M. A., Calvello, M., Capone, G. L., Caputo, S. M., Carnevali, I., Carrasco, E., Caux-Moncoutier, V., Cavalli, P., Cini, G., Clarke, E. M., Concolino, Paola, Cops, E. J., Cortesi, L., Couch, F. J., Darder, E., de la Hoya, M., Dean, M., Debatin, I., Del Valle, J., Delnatte, C., Derive, N., Diez, O., Ditsch, N., Domchek, S. M., Dutrannoy, V., Eccles, D. M., Ehrencrona, H., Enders, U., Evans, D. G., Farra, C., Faust, U., Felbor, U., Feroce, I., Fine, M., Foulkes, W. D., Galvao, H. C. R., Gambino, G., Gehrig, A., Gensini, F., Gerdes, A. -M., Germani, A., Giesecke, J., Gismondi, V., Gomez, C., Gomez Garcia, E. B., Gonzalez, S., Grau, E., Grill, S., Gross, E., Guerrieri-Gonzaga, A., Guillaud-Bataille, M., Gutierrez-Enriquez, S., Haaf, T., Hackmann, K., Hansen, T. V. O., Harris, M., Hauke, J., Heinrich, T., Hellebrand, H., Herold, K. N., Honisch, E., Horvath, J., Houdayer, C., Hubbel, V., Iglesias, S., Izquierdo, A., James, P. A., Janssen, L. A. M., Jeschke, U., Kaulfuss, S., Keupp, K., Kiechle, M., Kolbl, A., Krieger, S., Kruse, T. A., Kvist, A., Lalloo, F., Larsen, M., Lattimore, V. L., Lautrup, C., Ledig, S., Leinert, E., Lewis, A. L., Lim, J., Loeffler, M., Lopez-Fernandez, A., Lucci Cordisco, Emanuela, Maass, N., Manoukian, S., Marabelli, M., Matricardi, L., Meindl, A., Michelli, R. D., Moghadasi, S., Moles-Fernandez, A., Montagna, M., Montalban, G., Monteiro, A. N., Montes, E., Mori, L., Moserle, L., Muller, C. R., Mundhenke, C., Naldi, N., Nathanson, K. L., Navarro, M., Nevanlinna, H., Nichols, C. B., Niederacher, D., Nielsen, H. R., Ong, K. -R., Pachter, N., Palmero, E. I., Papi, L., Pedersen, I. S., Peissel, B., Perez-Segura, P., Pfeifer, K., Pineda, M., Pohl-Rescigno, E., Poplawski, N. K., Porfirio, B., Quante, A. S., Ramser, J., Reis, R. M., Revillion, F., Rhiem, K., Riboli, B., Ritter, J., Rivera, D., Rofes, P., Rump, A., Salinas, M., Sanchez de Abajo, A. M., Schmidt, G., Schoenwiese, U., Seggewiss, J., Solanes, A., Steinemann, D., Stiller, M., Stoppa-Lyonnet, D., Sullivan, K. J., Susman, R., Sutter, C., Tavtigian, S. V., Teo, S. H., Teule, A., Thomassen, M., Tibiletti, M. G., Tischkowitz, M., Tognazzo, S., Toland, A. E., Tornero, E., Torngren, T., Torres-Esquius, S., Toss, A., Trainer, A. H., Tucker, K. M., van Asperen, C. J., van Mackelenbergh, M. T., Varesco, L., Vargas-Parra, G., Varon, R., Vega, A., Velasco, A., Vesper, A. -S., Viel, A., Vreeswijk, M. P. G., Wagner, S. A., Waha, A., Walker, L. C., Walters, R. J., Wang-Gohrke, S., Weber, B. H. F., Weichert, W., Wieland, K., Wiesmuller, L., Witzel, I., Wockel, A., Woodward, E. R., Zachariae, S., Zampiga, V., Zeder-Goss, C., Investigators, K., Lazaro, C., De Nicolo, A., Radice, P., Engel, C., Schmutzler, R. K., Goldgar, D. E., Spurdle, A. B., Concolino P., Lucci Cordisco E. (ORCID:0000-0002-6279-7604), Parsons, M. T., Tudini, E., Li, H., Hahnen, E., Wappenschmidt, B., Feliubadalo, L., Aalfs, C. M., Agata, S., Aittomaki, K., Alducci, E., Alonso-Cerezo, M. C., Arnold, N., Auber, B., Austin, R., Azzollini, J., Balmana, J., Barbieri, E., Bartram, C. R., Blanco, A., Blumcke, B., Bonache, S., Bonanni, B., Borg, A., Bortesi, B., Brunet, J., Bruzzone, C., Bucksch, K., Cagnoli, G., Caldes, T., Caliebe, A., Caligo, M. A., Calvello, M., Capone, G. L., Caputo, S. M., Carnevali, I., Carrasco, E., Caux-Moncoutier, V., Cavalli, P., Cini, G., Clarke, E. M., Concolino, Paola, Cops, E. J., Cortesi, L., Couch, F. J., Darder, E., de la Hoya, M., Dean, M., Debatin, I., Del Valle, J., Delnatte, C., Derive, N., Diez, O., Ditsch, N., Domchek, S. M., Dutrannoy, V., Eccles, D. M., Ehrencrona, H., Enders, U., Evans, D. G., Farra, C., Faust, U., Felbor, U., Feroce, I., Fine, M., Foulkes, W. D., Galvao, H. C. R., Gambino, G., Gehrig, A., Gensini, F., Gerdes, A. -M., Germani, A., Giesecke, J., Gismondi, V., Gomez, C., Gomez Garcia, E. B., Gonzalez, S., Grau, E., Grill, S., Gross, E., Guerrieri-Gonzaga, A., Guillaud-Bataille, M., Gutierrez-Enriquez, S., Haaf, T., Hackmann, K., Hansen, T. V. O., Harris, M., Hauke, J., Heinrich, T., Hellebrand, H., Herold, K. N., Honisch, E., Horvath, J., Houdayer, C., Hubbel, V., Iglesias, S., Izquierdo, A., James, P. A., Janssen, L. A. M., Jeschke, U., Kaulfuss, S., Keupp, K., Kiechle, M., Kolbl, A., Krieger, S., Kruse, T. A., Kvist, A., Lalloo, F., Larsen, M., Lattimore, V. L., Lautrup, C., Ledig, S., Leinert, E., Lewis, A. L., Lim, J., Loeffler, M., Lopez-Fernandez, A., Lucci Cordisco, Emanuela, Maass, N., Manoukian, S., Marabelli, M., Matricardi, L., Meindl, A., Michelli, R. D., Moghadasi, S., Moles-Fernandez, A., Montagna, M., Montalban, G., Monteiro, A. N., Montes, E., Mori, L., Moserle, L., Muller, C. R., Mundhenke, C., Naldi, N., Nathanson, K. L., Navarro, M., Nevanlinna, H., Nichols, C. B., Niederacher, D., Nielsen, H. R., Ong, K. -R., Pachter, N., Palmero, E. I., Papi, L., Pedersen, I. S., Peissel, B., Perez-Segura, P., Pfeifer, K., Pineda, M., Pohl-Rescigno, E., Poplawski, N. K., Porfirio, B., Quante, A. S., Ramser, J., Reis, R. M., Revillion, F., Rhiem, K., Riboli, B., Ritter, J., Rivera, D., Rofes, P., Rump, A., Salinas, M., Sanchez de Abajo, A. M., Schmidt, G., Schoenwiese, U., Seggewiss, J., Solanes, A., Steinemann, D., Stiller, M., Stoppa-Lyonnet, D., Sullivan, K. J., Susman, R., Sutter, C., Tavtigian, S. V., Teo, S. H., Teule, A., Thomassen, M., Tibiletti, M. G., Tischkowitz, M., Tognazzo, S., Toland, A. E., Tornero, E., Torngren, T., Torres-Esquius, S., Toss, A., Trainer, A. H., Tucker, K. M., van Asperen, C. J., van Mackelenbergh, M. T., Varesco, L., Vargas-Parra, G., Varon, R., Vega, A., Velasco, A., Vesper, A. -S., Viel, A., Vreeswijk, M. P. G., Wagner, S. A., Waha, A., Walker, L. C., Walters, R. J., Wang-Gohrke, S., Weber, B. H. F., Weichert, W., Wieland, K., Wiesmuller, L., Witzel, I., Wockel, A., Woodward, E. R., Zachariae, S., Zampiga, V., Zeder-Goss, C., Investigators, K., Lazaro, C., De Nicolo, A., Radice, P., Engel, C., Schmutzler, R. K., Goldgar, D. E., Spurdle, A. B., Concolino P., and Lucci Cordisco E. (ORCID:0000-0002-6279-7604)

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.

Published
2019

20. Deciphering the Colon Cancer Genes-Report of the InSiGHT-Human Variome Project Workshop, UNESCO, Paris 2010

Author

Kohonen-Corish, M.R.J., Macrae, F., Genuardi, M., Aretz, S., Bapat, B., Bernstein, I.T., Burn, J., Cotton, R.G.H., Dunnen, J.T. den, Frebourg, T., Greenblatt, M.S., Hofstra, R., Holinski-Feder, E., Lappalainen, I., Lindblom, A., Maglott, D., Moller, P., Morreau, H., Moslein, G., Sijmons, R., Spurdle, A.B., Tavtigian, S., Tops, C.M.J., Weber, T.K., Wind, N. de, Woods, M.O., Contributors InSiGHT-HVP Workshop, Faculteit Medische Wetenschappen/UMCG, and Guided Treatment in Optimal Selected Cancer Patients (GUTS)

Subjects
MISMATCH-REPAIR GENES, COLORECTAL-CANCER, SEQUENCE VARIANTS, CLASSIFICATION, MUTATIONS, DATABASE, MLH1, Colorectal cancer, Human Variome Project, Library science, HNPCC, Biology, Settore MED/03 - GENETICA MEDICA, Data submission, Bioinformatics, Genetics, medicine, Pilot program, cancer, Pathogenicity, Genetics (clinical), colon, Cancer, medicine.disease, Tumor Pathology, variant, HVP, InSiGHT
Abstract

The Human Variome Project (HVP) has established a pilot program with the International Society for Gastrointestinal Hereditary Tumours (InSiGHT) to compile all inherited variation affecting colon cancer susceptibility genes. An HVP-InSiGHT Workshop was held on May 10, 2010, prior to the HVP Integration and Implementation Meeting at UNESCO in Paris, to review the progress of this pilot program. A wide range of topics were covered, including issues relating to genotype-phenotype data submission to the InSiGHT Colon Cancer Gene Variant Databases (chromium.liacs.nl/LOVD2/colon_cancer/home.php). The meeting also canvassed the recent exciting developments in models to evaluate the pathogenicity of unclassified variants using in silico data, tumor pathology information, and functional assays, and made further plans for the future progress and sustainability of the pilot program. Hum Mutat 32: 491-494, 2011. (C) 2011 Wiley-Liss, Inc.

Published
2011

21. PALB2, CHEK2 and ATM rare variants and cancer risk:data from COGS

Author

Southey, M. C. (Melissa C.), Goldgar, D. E. (David E.), Winqvist, R. (Robert), Pylkäs, K. (Katri), Couch, F. (Fergus), Tischkowitz, M. (Marc), Foulkes, W. D. (William D.), Dennis, J. (Joe), Michailidou, K. (Kyriaki), van Rensburg, E. J. (Elizabeth J.), Heikkinen, T. (Tuomas), Nevanlinna, H. (Heli), Hopper, J. L. (John L.), Doerk, T. (Thilo), Claes, K. B. (Kathleen B. M.), Reis-Filho, J. (Jorge), Teo, Z. L. (Zhi Ling), Radice, P. (Paolo), Catucci, I. (Irene), Peterlongo, P. (Paolo), Tsimiklis, H. (Helen), Odefrey, F. A. (Fabrice A.), Dowty, J. G. (James G.), Schmidt, M. K. (Marjanka K.), Broeks, A. (Annegien), Hogervorst, F. B. (Frans B.), Verhoef, S. (Senno), Carpenter, J. (Jane), Clarke, C. (Christine), Scott, R. J. (Rodney J.), Fasching, P. A. (Peter A.), Haeberle, L. (Lothar), Ekici, A. B. (Arif B.), Beckmann, M. W. (Matthias W.), Peto, J. (Julian), dos-Santos-Silva, I. (Isabel), Fletcher, O. (Olivia), Johnson, N. (Nichola), Bolla, M. K. (Manjeet K.), Sawyer, E. J. (Elinor J.), Tomlinson, I. (Ian), Kerin, M. J. (Michael J.), Miller, N. (Nicola), Marme, F. (Federik), Burwinkel, B. (Barbara), Yang, R. (Rongxi), Guenel, P. (Pascal), Menegaux, F. (Florence), Sanchez, M. (Marie), Bojesen, S. (Stig), Nielsen, S. F. (Sune F.), Flyger, H. (Henrik), Benitez, J. (Javier), Pilar Zamora, M. (M.), Arias Perez, J. I. (Jose Ignacio), Menendez, P. (Primitiva), Anton-Culver, H. (Hoda), Neuhausen, S. (Susan), Ziogas, A. (Argyrios), Clarke, C. A. (Christina A.), Brenner, H. (Hermann), Arndt, V. (Volker), Stegmaier, C. (Christa), Brauch, H. (Hiltrud), Bruening, T. (Thomas), Ko, Y.-D. (Yon-Dschun), Muranen, T. A. (Taru A.), Aittomaki, K. (Kristiina), Blomqvist, C. (Carl), Bogdanova, N. V. (Natalia V.), Antonenkova, N. N. (Natalia N.), Lindblom, A. (Annika), Margolin, S. (Sara), Mannermaa, A. (Arto), Kataja, V. (Vesa), Kosma, V.-M. (Veli-Matti), Hartikainen, J. M. (Jaana M.), Spurdle, A. B. (Amanda B.), Wauters, E. (Els), Smeets, D. (Dominiek), Beuselinck, B. (Benoit), Floris, G. (Giuseppe), Chang-Claude, J. (Jenny), Rudolph, A. (Anja), Seibold, P. (Petra), Flesch-Janys, D. (Dieter), Olson, J. E. (Janet E.), Vachon, C. (Celine), Pankratz, V. S. (Vernon S.), McLean, C. (Catriona), Haiman, C. A. (Christopher A.), Henderson, B. E. (Brian E.), Schumacher, F. (Fredrick), Le Marchand, L. (Loic), Kristensen, V. (Vessela), Alnaes, G. G. (Grethe Grenaker), Zheng, W. (Wei), Hunter, D. J. (David J.), Lindstrom, S. (Sara), Hankinson, S. E. (Susan E.), Kraft, P. (Peter), Andrulis, I. (Irene), Knight, J. A. (Julia A.), Glendon, G. (Gord), Mulligan, A. M. (Anna Marie), Jukkola-Vuorinen, A. (Arja), Grip, M. (Mervi), Kauppila, S. (Saila), Devilee, P. (Peter), Tollenaar, R. A. (Robert A. E. M.), Seynaeve, C. (Caroline), Hollestelle, A. (Antoinette), Garcia-Closas, M. (Montserrat), Figueroa, J. (Jonine), Chanock, S. J. (Stephen J.), Lissowska, J. (Jolanta), Czene, K. (Kamila), Darabi, H. (Hatef), Eriksson, M. (Mikael), Eccles, D. M. (Diana M.), Rafiq, S. (Sajjad), Tapper, W. J. (William J.), Gerty, S. M. (Sue M.), Hooning, M. J. (Maartje J.), Martens, J. W. (John W. M.), Collee, J. M. (J. Margriet), Tilanus-Linthorst, M. (Madeleine), Hall, P. (Per), Li, J. (Jingmei), Brand, J. S. (Judith S.), Humphreys, K. (Keith), Cox, A. (Angela), Reed, M. W. (Malcolm W. R.), Luccarini, C. (Craig), Baynes, C. (Caroline), Dunning, A. M. (Alison M.), Hamann, U. (Ute), Torres, D. (Diana), Ulmer, H. U. (Hans Ulrich), Ruediger, T. (Thomas), Jakubowska, A. (Anna), Lubinski, J. (Jan), Jaworska, K. (Katarzyna), Durda, K. (Katarzyna), Slager, S. (Susan), Toland, A. E. (Amanda E.), Ambrosone, C. B. (Christine B.), Yannoukakos, D. (Drakoulis), Swerdlow, A. (Anthony), Ashworth, A. (Alan), Orr, N. (Nick), Jones, M. (Michael), Gonzalez-Neira, A. (Anna), Pita, G. (Guillermo), Rosario Alonso, M. (M.), Alvarez, N. (Nuria), Herrero, D. (Daniel), Tessier, D. C. (Daniel C.), Vincent, D. (Daniel), Bacot, F. (Francois), Simard, J. (Jacques), Dumont, M. (Martine), Soucy, P. (Penny), Eeles, R. (Rosalind), Muir, K. (Kenneth), Wiklund, F. (Fredrik), Gronberg, H. (Henrik), Schleutker, J. (Johanna), Nordestgaard, B. G. (Borge G.), Weischer, M. (Maren), Travis, R. C. (Ruth C.), Neal, D. (David), Donovan, J. L. (Jenny L.), Hamdy, F. C. (Freddie C.), Khaw, K.-T. (Kay-Tee), Stanford, J. L. (Janet L.), Blot, W. J. (William J.), Thibodeau, S. (Stephen), Schaid, D. J. (Daniel J.), Kelley, J. L. (Joseph L.), Maier, C. (Christiane), Kibel, A. S. (Adam S.), Cybulski, C. (Cezary), Cannon-Albright, L. (Lisa), Butterbach, K. (Katja), Park, J. (Jong), Kaneva, R. (Radka), Batra, J. (Jyotsna), Teixeira, M. R. (Manuel R.), Kote-Jarai, Z. (Zsofia), Al Olama, A. A. (Ali Amin), Benlloch, S. (Sara), Renner, S. P. (Stefan P.), Hartmann, A. (Arndt), Hein, A. (Alexander), Ruebner, M. (Matthias), Lambrechts, D. (Diether), Van Nieuwenhuysen, E. (Els), Vergote, I. (Ignace), Lambretchs, S. (Sandrina), Doherty, J. A. (Jennifer A.), Rossing, M. A. (Mary Anne), Nickels, S. (Stefan), Eilber, U. (Ursula), Wang-Gohrke, S. (Shan), Odunsi, K. (Kunle), Sucheston-Campbell, L. E. (Lara E.), Friel, G. (Grace), Lurie, G. (Galina), Killeen, J. L. (Jeffrey L.), Wilkens, L. R. (Lynne R.), Goodman, M. T. (Marc T.), Runnebaum, I. (Ingo), Hillemanns, P. A. (Peter A.), Pelttari, L. M. (Liisa M.), Butzow, R. (Ralf), Modugno, F. (Francesmary), Edwards, R. P. (Robert P.), Ness, R. B. (Roberta B.), Moysich, K. B. (Kirsten B.), du Bois, A. (Andreas), Heitz, F. (Florian), Harter, P. (Philipp), Kommoss, S. (Stefan), Karlan, B. Y. (Beth Y.), Walsh, C. (Christine), Lester, J. (Jenny), Jensen, A. (Allan), Kjaer, S. K. (Susanne Kruger), Hogdall, E. (Estrid), Peissel, B. (Bernard), Bonanni, B. (Bernardo), Bernard, L. (Loris), Goode, E. L. (Ellen L.), Fridley, B. L. (Brooke L.), Vierkant, R. A. (Robert A.), Cunningham, J. M. (Julie M.), Larson, M. C. (Melissa C.), Fogarty, Z. C. (Zachary C.), Kalli, K. R. (Kimberly R.), Liang, D. (Dong), Lu, K. H. (Karen H.), Hildebrandt, M. A. (Michelle A. T.), Wu, X. (Xifeng), Levine, D. A. (Douglas A.), Dao, F. (Fanny), Bisogna, M. (Maria), Berchuck, A. (Andrew), Iversen, E. S. (Edwin S.), Marks, J. R. (Jeffrey R.), Akushevich, L. (Lucy), Cramer, D. W. (Daniel W.), Schildkraut, J. (Joellen), Terry, K. L. (Kathryn L.), Poole, E. M. (Elizabeth M.), Stampfer, M. (Meir), Tworoger, S. S. (Shelley S.), Bandera, E. V. (Elisa V.), Orlow, I. (Irene), Olson, S. H. (Sara H.), Bjorge, L. (Line), Salvesen, H. B. (Helga B.), van Altena, A. M. (Anne M.), Aben, K. K. (Katja K. H.), Kiemeney, L. A. (Lambertus A.), Massuger, L. F. (Leon F. A. G.), Pejovic, T. (Tanja), Bean, Y. (Yukie), Brooks-Wilson, A. (Angela), Kelemen, L. E. (Linda E.), Cook, L. S. (Linda S.), Le, N. D. (Nhu D.), Grski, B. (Bohdan), Gronwald, J. (Jacek), Menkiszak, J. (Janusz), Hogdall, C. K. (Claus K.), Lundvall, L. (Lene), Nedergaard, L. (Lotte), Engelholm, S. A. (Svend Aage), Dicks, E. (Ed), Tyrer, J. (Jonathan), Campbell, I. (Ian), McNeish, I. (Iain), Paul, J. (James), Siddiqui, N. (Nadeem), Glasspool, R. (Rosalind), Whittemore, A. S. (Alice S.), Rothstein, J. H. (Joseph H.), McGuire, V. (Valerie), Sieh, W. (Weiva), Cai, H. (Hui), Shu, X.-O. (Xiao-Ou), Teten, R. T. (Rachel T.), Sutphen, R. (Rebecca), McLaughlin, J. R. (John R.), Narod, S. A. (Steven A.), Phelan, C. M. (Catherine M.), Monteiro, A. N. (Alvaro N.), Fenstermacher, D. (David), Lin, H.-Y. (Hui-Yi), Permuth, J. B. (Jennifer B.), Sellers, T. A. (Thomas A.), Chen, Y. A. (Y. Ann), Tsai, Y.-Y. (Ya-Yu), Chen, Z. (Zhihua), Gentry-Maharaj, A. (Aleksandra), Gayther, S. A. (Simon A.), Ramus, S. J. (Susan J.), Menon, U. (Usha), Wu, A. H. (Anna H.), Pearce, C. L. (Celeste L.), Van den Berg, D. (David), Pike, M. C. (Malcolm C.), Dansonka-Mieszkowska, A. (Agnieszka), Plisiecka-Halasa, J. (Joanna), Moes-Sosnowska, J. (Joanna), Kupryjanczyk, J. (Jolanta), Pharoah, P. D. (Paul D. P.), Song, H. (Honglin), Winship, I. (Ingrid), Chenevix-Trench, G. (Georgia), Giles, G. G. (Graham G.), Tavtigian, S. V. (Sean V.), Easton, D. F. (Doug F.), and Milne, R. L. (Roger L.)

Subjects
skin and connective tissue diseases
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.

Published
2016

22. ENIGMA - Evidence-based Network for the Interpretation of Germline Mutant Alleles: An international initiative to evaluate risk and clinical significance associated with sequence variation in BRCA1 and BRCA2 genes

Author

Spurdle, Ab, Healey, S, Devereau, A, Hogervorst, Fb, Monteiro, An, Nathanson, Kl, Radice, P, Stoppa Lyonnet, D, Tavtigian, S, Wappenschmidt, B, Couch, Fj, Goldgar, De, ENIGMA: Goldgar, D, Couch, F, Fackenthal, Jd, Thomassen, M, Teo, Sh, Hansen, Tv, Borg, Å, Eeles, R, Toland, A, Rogan, P, Guidugli, L, Brody, Lc, Brown, M, Kwong, A, Lei po CW, Nevanlinna, H, Garber, J, Foretova, L, Singer, Cf, Blok, Mj, Osorio, A, Kote Jarai, Z, Baralle, D, Vega, A, Blanco, A, Santamariña, M, Fachal, L, Nederlof, P, Peock, S, Pasini, Barbara, Tommasi, S, Lafferty, A, Ansari, A, Konstantopoulou, I, Pal, T, Simard, J, Bonetti, A, Varesco, L, Peissel, B, Evans, Dg, Foulkes, W, Szabo, C, van Asperen, C, Jonkers, J, Walker, L, Mitchell, G, Gutiérrez Enríquez, S, Diez, O, Millot, G, Fostira, F, Selkirk, C, Antoniou, A, Monteiro, A, Carvalho, M, Rubinstein, Ws, de la Hoya, M, Domchek, S, Caputo, S, Houdayer, C, Blanco, I, Lázaro, C, Whiley, P, Becker, A, Aretini, P, Eccles, D, Caldes, T, Viel, A, Izatt, L, Hogervorst, F, Nathanson, K, Pedersen, Is, Vreeswijk, M, Neuhausen, S, Yannoukakos, K, Tucker, K, Southey, M, Leary, J, Caligo, Ma, Gomez Garcia, E, Brandao, R, Lidereau, R, Montagna, M, Pertesi, M, Cornell, M, Rouleau, E, Sharan, S, Rahman, N, Lalloo, F, Weitzel, J, Campbell, J, Cummings, Machakova, E, Olopade, F, Godwin, A, Ozcelik, H, Seminara, D., Klinische Genetica, RS: GROW - R4 - Reproductive and Perinatal Medicine, MUMC+: DA KG Polikliniek (9), Genetica & Celbiologie, and RS: GROW - School for Oncology and Reproduction

Subjects
Evidence-based practice, unclassified variant, RNA Splicing, Genes, BRCA2, Genes, BRCA1, consortium, Breast Neoplasms, Biology, Article, Germline mutation, breast cancer, Risk Factors, Genetic variation, Genetics, medicine, Humans, Clinical significance, Genetic Predisposition to Disease, BRCA1/BRCA2, Genetic Testing, Allele, unclassified variants, Gene, Genetics (clinical), Alleles, Germ-Line Mutation, Genetic testing, Ovarian Neoplasms, medicine.diagnostic_test, Mechanism (biology), Genetic Variation, BRCA1, BRCA2, ovarian cancer, Germ Cells, Organization and Administration, Data Interpretation, Statistical, international collaboration, Practice Guidelines as Topic, Female, Algorithms
Abstract

As genetic testing for predisposition to human diseases has become an increasingly common practice in medicine, the need for clear interpretation of the test results is apparent. However, for many disease genes, including the breast cancer susceptibility genes BRCA1 and BRCA2, a significant fraction of tests results in the detection of a genetic variant for which disease association is not known. The finding of an "unclassified" variant (UV)/variant of uncertain significance (VUS) complicates genetic test reporting and counseling. As these variants are individually rare, a large collaboration of researchers and clinicians will facilitate studies to assess their association with cancer predisposition. It was with this in mind that the ENIGMA consortium (www.enigmaconsortium.org) was initiated in 2009. The membership is both international and interdisciplinary, and currently includes more than 100 research scientists and clinicians from 19 countries. Within ENIGMA, there are presently six working groups focused on the following topics: analysis, clinical, database, functional, tumor histopathology, and mRNA splicing. ENIGMA provides a mechanism to pool resources, exchange methods and data, and coordinately develop and apply algorithms for classification of variants in BRCA1 and BRCA2. It is envisaged that the research and clinical application of models developed by ENIGMA will be relevant to the interpretation of sequence variants in other disease genes. Hum Mutat 00:1-6, 2011. © 2011 Wiley Periodicals, Inc.

Published
2011
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23. How to catch all those mutations--the report of the third Human Variome Project Meeting, UNESCO Paris, May 2010

Author

Kohonen-Corish, M.R.J., Al-Aama, J.Y., Auerbach, A.D., Axton, M., Barash, C.I., Bernstein, I., Beroud, C., Burn, J., Cunningham, F., Cutting, G.R., Dunnen, J.T. den, Greenblatt, M.S., Kaput, J., Katz, M., Lindblom, A., Macrae, F., Maglott, D., Moslein, G., Povey, S., Ramesar, R., Richards, S., Seminara, D., Sobrido, M.J., Tavtigian, S., Taylor, G., Vihinen, M., Winship, I., Cotton, R.G.H., Contributors Human Variome Project, HNPCC-register, Hvidovre Hospital, University of Copenhagen = Københavns Universitet (KU), Laboratoire de génétique des maladies rares. Pathologie moleculaire, etudes fonctionnelles et banque de données génétiques (LGMR), Université Montpellier 1 (UM1)-IFR3, Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University (JHU), Metabolic Unit, Dept Clinical Chemistry, University of Vermont College of Medicine, University of Vermont [Burlington], University of Massachusetts [Amherst] (UMass Amherst), University of Massachusetts System (UMASS), Department of Clinical Genetics, Karolinska University Hospital [Stockholm], Department of Colorectal Medicine and Genetics, The Royal Melbourne Hospital, National Center for Biotechnology Information (NCBI), Dept of Genetics, Evolution and Environment [London] (UCL-GEE), University College of London [London] (UCL), National Cancer Institute [Bethesda] (NCI-NIH), National Institutes of Health [Bethesda] (NIH), Fundacion Publica Galega de Medicina Xenomica, Fundación Pública Galega de Medicina Xenómica, Department of Oncological Sciences, University of Utah-Huntsman Cancer Institute, Imperial College London, Department of Experimental Medical Science, Lund University [Lund], University of Copenhagen = Københavns Universitet (UCPH), IFR3, and Université Montpellier 1 (UM1)-Université Montpellier 1 (UM1)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
education, Human Variome Project, Library science, Human genetic variation, Biology, computer.software_genre, Article, 03 medical and health sciences, 0302 clinical medicine, Health care, Genetics, Genetics (clinical), 030304 developmental biology, 0303 health sciences, Data collection, business.industry, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, 3. Good health, Variome, Incentive, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, 030220 oncology & carcinogenesis, Sustainability, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, computer, Data integration
Abstract

International audience; The third Human Variome Project (HVP) Meeting "Integration and Implementation" was held under UNESCO Patronage in Paris, France, at the UNESCO Headquarters May 10-14, 2010. The major aims of the HVP are the collection, curation, and distribution of all human genetic variation affecting health. The HVP has drawn together disparate groups, by country, gene of interest, and expertise, who are working for the common good with the shared goal of pushing the boundaries of the human variome and collaborating to avoid unnecessary duplication. The meeting addressed the 12 key areas that form the current framework of HVP activities: Ethics; Nomenclature and Standards; Publication, Credit and Incentives; Data Collection from Clinics; Overall Data Integration and Access-Peripheral Systems/Software; Data Collection from Laboratories; Assessment of Pathogenicity; Country Specific Collection; Translation to Healthcare and Personalized Medicine; Data Transfer, Databasing, and Curation; Overall Data Integration and Access-Central Systems; and Funding Mechanisms and Sustainability. In addition, three societies that support the goals and the mission of HVP also held their own Workshops with the view to advance disease-specific variation data collection and utilization: the International Society for Gastrointestinal Hereditary Tumours, the Micronutrient Genomics Project, and the Neurogenetics Consortium.

Published
2010
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24. COMPLEXO: identifying the missing heritability of breast cancer via next generation collaboration

Author

Southey, MC, Park, DJ, Nguyen-Dumont, T, Campbell, I, Thompson, E, Trainer, AH, Chenevix-Trench, G, Simard, J, Dumont, M, Soucy, P, Thomassen, M, Jonson, L, Pedersen, IS, Hansen, TVO, Nevanlinna, H, Khan, S, Sinilnikova, O, Mazoyer, S, Lesueur, F, Damiola, F, Schmutzler, R, Meindl, A, Hahnen, E, Dufault, MR, Chan, TC, Kwong, A, Barkardottir, R, Radice, P, Peterlongo, P, Devilee, P, Hilbers, F, Benitez, J, Kvist, A, Torngren, T, Easton, D, Hunter, D, Lindstrom, S, Kraft, P, Zheng, W, Gao, Y-T, Long, J, Ramus, S, Feng, B-J, Weitzel, RN, Nathanson, K, Offit, K, Joseph, V, Robson, M, Schrader, K, Wang, SM, Kim, YC, Lynch, H, Snyder, C, Tavtigian, S, Neuhausen, S, Couch, FJ, Goldgar, DE, Southey, MC, Park, DJ, Nguyen-Dumont, T, Campbell, I, Thompson, E, Trainer, AH, Chenevix-Trench, G, Simard, J, Dumont, M, Soucy, P, Thomassen, M, Jonson, L, Pedersen, IS, Hansen, TVO, Nevanlinna, H, Khan, S, Sinilnikova, O, Mazoyer, S, Lesueur, F, Damiola, F, Schmutzler, R, Meindl, A, Hahnen, E, Dufault, MR, Chan, TC, Kwong, A, Barkardottir, R, Radice, P, Peterlongo, P, Devilee, P, Hilbers, F, Benitez, J, Kvist, A, Torngren, T, Easton, D, Hunter, D, Lindstrom, S, Kraft, P, Zheng, W, Gao, Y-T, Long, J, Ramus, S, Feng, B-J, Weitzel, RN, Nathanson, K, Offit, K, Joseph, V, Robson, M, Schrader, K, Wang, SM, Kim, YC, Lynch, H, Snyder, C, Tavtigian, S, Neuhausen, S, Couch, FJ, and Goldgar, DE

Abstract

Linkage analysis, positional cloning, candidate gene mutation scanning and genome-wide association study approaches have all contributed significantly to our understanding of the underlying genetic architecture of breast cancer. Taken together, these approaches have identified genetic variation that explains approximately 30% of the overall familial risk of breast cancer, implying that more, and likely rarer, genetic susceptibility alleles remain to be discovered.

Published
2013

25. Deciphering the Colon Cancer Genes-Report of the InSiGHT-Human Variome Project Workshop, UNESCO, Paris 2010

Author

Kohonen Corish, M, Macrae, F, Genuardi, Maurizio, Aretz, S, Bapat, B, Bernstein, I, Burn, J, Cotton, R, Den Dunnen, J, Frebourg, T, Greenblatt, M, Hofstra, R, Holinski Feder, E, Lappalainen, I, Lindblom, A, Maglott, D, Moller, P, Morreau, H, Moslein, G, Sijmons, R, Spurdle, A, Tavtigian, S, Tops, C, Weber, T, De Wind, N, Woods, M., Genuardi, Maurizio (ORCID:0000-0002-7410-8351), Kohonen Corish, M, Macrae, F, Genuardi, Maurizio, Aretz, S, Bapat, B, Bernstein, I, Burn, J, Cotton, R, Den Dunnen, J, Frebourg, T, Greenblatt, M, Hofstra, R, Holinski Feder, E, Lappalainen, I, Lindblom, A, Maglott, D, Moller, P, Morreau, H, Moslein, G, Sijmons, R, Spurdle, A, Tavtigian, S, Tops, C, Weber, T, De Wind, N, Woods, M., and Genuardi, Maurizio (ORCID:0000-0002-7410-8351)

Abstract

The Human Variome Project (HVP) has established a pilot program with the International Society for Gastrointestinal Hereditary Tumours (InSiGHT) to compile all inherited variation affecting colon cancer susceptibility genes. An HVP-InSiGHT Workshop was held on May 10, 2010, prior to the HVP Integration and Implementation Meeting at UNESCO in Paris, to review the progress of this pilot program. A wide range of topics were covered, including issues relating to genotype-phenotype data submission to the InSiGHT Colon Cancer Gene Variant Databases (chromium.liacs.nl/LOVD2/colon_cancer/home.php). The meeting also canvassed the recent exciting developments in models to evaluate the pathogenicity of unclassified variants using in silico data, tumor pathology information, and functional assays, and made further plans for the future progress and sustainability of the pilot program.

Published
2011

26. Planning the Human Variome Project: The Spain Report

Author

Kaput, J, Cotton, R, Hardman, L, Watson, M, Al Aqeel, A, Al-Aama, J, Al-Mulla, F, Alonso, S, Aretz, S, Auerbach, A, Bapat, B, Bernstein, I, Bhak, J, Bleoo, S, Blocker, H, Brenner, S, Burn, J, Bustamante, M, Calone, R, Cambon-Thomsen, A, Cargill, M, Carrera, P, Cavedon, L, Cho, Y, Chung, Y, Claustres, M, Cutting, G, Dalgleish, R, den Dunnen, J, Diaz, C, Dobrowolski, S, dos Santos, M, Ekong, R, Flanagan, S, Flicek, P, Furukawa, Y, Genuardi, Maurizio, Ghang, H, Golubenko, M, Greenblatt, M, Hamosh, A, Hancock, J, Hardison, R, Harrison, T, Hoffmann, R, Horaitis, R, Howard, H, Barash, C, Izagirre, N, Jung, J, Kojima, T, Laradi, S, Lee, Y, Lee, J, Gil-da-Silva-Lopes, V, Macrae, F, Maglott, D, Marafie, M, Marsh, S, Matsubara, Y, Messiaen, L, Moslein, G, Netea, M, Norton, M, Oefner, P, Oetting, W, O'Leary, J, de Ramirez, A, Paalman, M, Parboosingh, J, Patrinos, G, Perozzi, G, Phillips, I, Povey, S, Prasad, S, Qi, M, Quinzani, Dario, Ramesar, R, Richards, C, Savige, J, Scheible, D, Scott, R, Seminara, D, Shephard, E, Sijmons, R, Smith, T, Sobrido, M, Tanaka, T, Tavtigian, S, Taylor, G, Teague, J, Topel, T, Ullman-Cullere, M, Utsunomiya, J, van Kranen, H, Vihinen, M, Webb, E, Weber, Bertram, Yeager, M, Yeom, Y, Yim, S, Yoo, H, Genuardi, M (ORCID:0000-0002-7410-8351), Quin, D, Weber, T, Kaput, J, Cotton, R, Hardman, L, Watson, M, Al Aqeel, A, Al-Aama, J, Al-Mulla, F, Alonso, S, Aretz, S, Auerbach, A, Bapat, B, Bernstein, I, Bhak, J, Bleoo, S, Blocker, H, Brenner, S, Burn, J, Bustamante, M, Calone, R, Cambon-Thomsen, A, Cargill, M, Carrera, P, Cavedon, L, Cho, Y, Chung, Y, Claustres, M, Cutting, G, Dalgleish, R, den Dunnen, J, Diaz, C, Dobrowolski, S, dos Santos, M, Ekong, R, Flanagan, S, Flicek, P, Furukawa, Y, Genuardi, Maurizio, Ghang, H, Golubenko, M, Greenblatt, M, Hamosh, A, Hancock, J, Hardison, R, Harrison, T, Hoffmann, R, Horaitis, R, Howard, H, Barash, C, Izagirre, N, Jung, J, Kojima, T, Laradi, S, Lee, Y, Lee, J, Gil-da-Silva-Lopes, V, Macrae, F, Maglott, D, Marafie, M, Marsh, S, Matsubara, Y, Messiaen, L, Moslein, G, Netea, M, Norton, M, Oefner, P, Oetting, W, O'Leary, J, de Ramirez, A, Paalman, M, Parboosingh, J, Patrinos, G, Perozzi, G, Phillips, I, Povey, S, Prasad, S, Qi, M, Quinzani, Dario, Ramesar, R, Richards, C, Savige, J, Scheible, D, Scott, R, Seminara, D, Shephard, E, Sijmons, R, Smith, T, Sobrido, M, Tanaka, T, Tavtigian, S, Taylor, G, Teague, J, Topel, T, Ullman-Cullere, M, Utsunomiya, J, van Kranen, H, Vihinen, M, Webb, E, Weber, Bertram, Yeager, M, Yeom, Y, Yim, S, Yoo, H, Genuardi, M (ORCID:0000-0002-7410-8351), Quin, D, and Weber, T

Abstract

The remarkable progress in characterizing the human genome sequence, exemplified by the Human Genome Project and the HapMap Consortium, has led to the perception that knowledge and the tools (e.g., microarrays) are sufficient for many if not most biomedical research efforts. A large amount of data from diverse studies proves this perception inaccurate at best, and at worst, an impediment for further efforts to characterize the variation in the human genome. Because variation in genotype and environment are the fundamental basis to understand phenotypic variability and heritability at the population level, identifying the range of human genetic variation is crucial to the development of personalized nutrition and medicine. The Human Variome Project (HVP; http://www.humanvariomeproject.org/) was proposed initially to systematically collect mutations that cause human disease and create a cyber infrastructure to link locus specific databases (LSDB). We report here the discussions and recommendations from the 2008 HVP planning meeting held in San Feliu de Guixols Spain, in May 2008. Hum Mutat 30, 496-510, 2009. (C) 2009 Wiley-Liss, Inc.

Published
2009

27. Sequence Variant Classification and Reporting: Recommendations for Improving the Interpretation of Cancer Susceptibility Genetic Test Results

Author

Plon, S, Eccles, D, Easton, D, Foulkes, W, Genuardi, Maurizio, Greenblatt, M, Hogervorst, F, Hoogerbrugge, N, Spurdle, A, Tavtigian, S, Genuardi, M (ORCID:0000-0002-7410-8351), Plon, S, Eccles, D, Easton, D, Foulkes, W, Genuardi, Maurizio, Greenblatt, M, Hogervorst, F, Hoogerbrugge, N, Spurdle, A, Tavtigian, S, and Genuardi, M (ORCID:0000-0002-7410-8351)

Abstract

Genetic testing of cancer susceptibility genes is now widely applied in clinical practice to predict risk of developing cancer. In general, sequence-based testing of germline DNA is used to determine whether all individual carries a change that is clearly likely to disrupt normal gene function. Genetic testing may detect changes that are clearly pathogenic, clearly neutral, or variants of unclear clinical significance. Such variants present a considerable challenge to the diagnostic laboratory and the receiving clinician in terms of interpretation and clear presentation of the implications of the result to the patient. There does not appear to be a consistent approach to interpreting and reporting the clinical significance of variants either among genes or among laboratories. The potential for confusion among clinicians and patients is considerable and misinterpretation may lead to inappropriate clinical consequences. In this article we review the current state of sequence-based genetic testing, describe other standardized reporting systems used in oncology, and propose a standardized classification system for application to sequence-based results for cancer predisposition genes. We suggest a system of five classes of variants based on the degree of likelihood of pathogenicity. Each class is associated with specific recommendations for clinical management of at,risk relatives that will depend on the syndrome. We propose that panels of experts on each cancer predisposition syndrome facilitate the classification scheme and designate appropriate surveillance and cancer management guidelines. The international adoption of a standardized reporting system should improve the clinical utility of sequence-based genetic tests to predict cancer risk. Hum Mutat 29(11), 1282-1291, 2008. (C) 2008 Wiley-Liss, Inc.

Published
2008

29. A cell cycle regulator potentially involved in genesis of many tumor types

Author

Kamb, A., Gruis, N., Weaver-Feldhaus, J., Liu, Q., Harshman, K., Tavtigian, S., Stockert, E., Day, R., Johnson, B., and Skolnick, M.

Abstract

A putative tumor suppressor locus on the short arm of human chromosome 9 has been localized to a region of less than 40 kilobases by means of homozygous deletions in melanoma cell lines. This region contained a gene, Multiple Tumor Suppressor 1 (MTS1), that encodes a previously identified inhibitor (p16) of cyclin-dependent kinase 4. MTS1 was homozygously deleted at high frequency in cell lines derived from tumors of lung, breast, brain, bone, skin, bladder, kidney, ovary, and lymphocyte. Melanoma cell lines that carried at least one copy of MTS1 frequently carried nonsense, missense, or frameshift mutations in the gene. These findings suggest that MTS1 mutations are involved in tumor formation in a wide range of tissues.

Published
1994

38. Association of common missense changes in ELAC2 (HPC2) with prostate cancer in a Japanese case–control series

Author

Fujiwara, H., primary, Emi, M., additional, Nagai, H., additional, Nishimura, T., additional, Konishi, N., additional, Kubota, Y., additional, Ichikawa, T., additional, Takahashi, S., additional, Shuin, T., additional, Habuchi, T., additional, Ogawa, O., additional, Inoue, K., additional, Skolnick, M. H., additional, Swensen, J., additional, Camp, N. J., additional, and Tavtigian, S. V., additional

Published
2002
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41. Response

Author

Kamb, A., primary, Liu, Q., additional, Harshman, K., additional, Tavtigian, S., additional, Cordon-Cardo, C., additional, and Skolnick, M. H., additional

Published
1994
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44. RAD51 interacts with the evolutionarily conserved BRC motifs in the human breast cancer susceptibility gene brca2.

Author

Wong, A K, Pero, R, Ormonde, P A, Tavtigian, S V, and Bartel, P L

Abstract

Recent work has shown that the murine BRCA2 tumor suppressor protein interacts with the murine RAD51 protein. This interaction suggests that BRCA2 participates in DNA repair. Residues 3196-3232 of the murine BRCA2 protein were shown to be involved in this interaction. Here, we report the detailed mapping of additional domains that are involved in interactions between the human homologs of these two proteins. Through yeast two-hybrid and biochemical assays, we demonstrate that the RAD51 protein interacts specifically with the eight evolutionarily conserved BRC motifs encoded in exon 11 of brca2 and with a similar motif found in a Caenorhabditis elegans hypothetical protein. Deletion analysis demonstrates that residues 98-339 of human RAD51 interact with the 59-residue minimal region that is conserved in all BRC motifs. These data suggest that the BRC repeats function to bind RAD51.

Published
1997

45. Physical locus of the DNA polymerase gene and genetic maps of bacteriophage T5 mutants

Author

Fujimura, R K, Tavtigian, S V, Choy, T L, and Roop, B C

Abstract

Segments of DNA that contained the DNA polymerase gene of bacteriophage T5 were isolated. The physical locus of the gene was identified by transforming Escherichia coli with purified DNA fragments generated by restriction enzyme digestions, and the transformed cells were used to rescue amber mutants of T5 with mutations in the gene for DNA polymerase. The method is applicable to any other gene that has mutations with low reversion frequencies. We studied the following mutations of the T5 DNA polymerase gene, reading from left to right by the standard convention (D. J. McCorquodale, Crit. Rev. Microbiol. 4:101-159, 1975): D7, D8, aml, ts5E-ts53, am6, and D9. These loci were found to reside within three pieces of DNA with a total length of 3,600 base pairs. Because the structural gene for T5 DNA polymerase is estimated to be 2,600 base pairs long, the whole structural gene may reside in these segments. These are located 58.3 to 61.3% of the distance from the left end of the DNA. The left-end piece of the DNA (1,100 base pairs) containing the polymerase gene has loci D7 and D8, and the right-end piece (1,600 base pairs) has locus D9, according to the results of the transformation assay. These results are consistent with the genetic map.

Published
1985
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48. Interpreting epidemiological research: Blinded comparison of methods used to estimate the prevalence of inherited mutations in BRCA1

Author

Eng, C., Brody, L. C., Wagner, T. M. U., Devilee, P., Vijg, J., Szabo, C., Tavtigian, S. V., Nathanson, K. L., Ostrander, E., Frank, T. S., Borg, A., Couch, F., Easton, D. F., Goldgar, D. F., Nathanson, K. A., Neuhausen, S., Borresen-Dale, A. -L, Casey, G., Friend, S., Futreal, A., Gayther, S. A., Murphy, P., Owens, K. A., Rabin, M., Schubert, E., Shattuck, D. F., Weber, B. L., and Wiseman, R.

50. Exome Sequencing for Head and Neck Cancer Predisposition Genes.

Author

Yu Y, Feng B, Chang CP, Bell R, Wood A, Sturgis E, Li G, Olshan A, Chen CJ, Lou PJ, Hsu WL, Cessna M, Witt B, Neklason D, Hashibe M, Huff C, and Tavtigian S

Abstract

Introduction: While common variants have been studied for head and neck cancer (HNC) risk and exome sequencing has been conducted for head and neck tumor tissue samples, large-scale studies of exome sequencing on head and neck cancer risk have not been conducted. Our study aimed to identify head and neck cancer predisposition genes with exome sequencing and to assess interactions between the head and neck cancer susceptibility genes and tobacco use., Methods: We conducted a case-control analysis to identify germline susceptibility genes for HNC risk. We used whole-exome sequencing data in Phase 1, targeted gene sequencing data in Phase 2 (2,134 HNC cases and 2,072 controls), and publicly available whole-exome sequencing data from the UK Biobank database. We conducted a gene-based association analysis and estimated the effect size of known and novel HNC susceptibility genes and pathways., Results: Six known cancer predisposition genes reached nominal significance (p < 0.05), including BRCA1 , BRCA2 , RAD51B , BAP1 , APC , and MUTYH . Additionally, we identified 21 novel HNC risk genes with meta p-value < 0.05. LoF variants in BRCA1 (OR=5.0, 95% CI: 1.72-14.57), BRCA2 (OR=2.56, 95% CI: 1.22-5.41), and MUTYH (OR=4.84, 95% CI: 1.01-13.86) exhibited significantly elevated effect sizes. APC, BRCA2 , and the DNA repair gene set exhibited borderline interactions with smoking, with synergy indices and 95% confidence intervals of 1.92 [0.98, 3.75], 1.77 [0.91, 3.46], and 1.57 [0.97, 2.54], respectively., Conclusions: We observed associations with HNC risk for DNA repair pathway genes associated with breast cancer and polyposis colorectal cancer predisposition genes. Potential interactions between these genes and tobacco smoking were also identified. Our study utilized targeted gene sequencing and whole-exome sequencing approaches to identify cancer susceptibility genes, while further studies are needed to confirm the associations observed with HNC risk.

Published
2025
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