Advertisement

Breast Cancer Research and Treatment

, Volume 147, Issue 1, pp 119–132 | Cite as

Development and validation of a new algorithm for the reclassification of genetic variants identified in the BRCA1 and BRCA2 genes

  • Dmitry Pruss
  • Brian Morris
  • Elisha Hughes
  • Julie M. Eggington
  • Lisa Esterling
  • Brandon S. Robinson
  • Aric van Kan
  • Priscilla H. Fernandes
  • Benjamin B. Roa
  • Alexander Gutin
  • Richard J. Wenstrup
  • Karla R. BowlesEmail author
Epidemiology

Abstract

BRCA1 and BRCA2 sequencing analysis detects variants of uncertain clinical significance in approximately 2 % of patients undergoing clinical diagnostic testing in our laboratory. The reclassification of these variants into either a pathogenic or benign clinical interpretation is critical for improved patient management. We developed a statistical variant reclassification tool based on the premise that probands with disease-causing mutations are expected to have more severe personal and family histories than those having benign variants. The algorithm was validated using simulated variants based on approximately 145,000 probands, as well as 286 BRCA1 and 303 BRCA2 true variants. Positive and negative predictive values of ≥99 % were obtained for each gene. Although the history weighting algorithm was not designed to detect alleles of lower penetrance, analysis of the hypomorphic mutations c.5096G>A (p.Arg1699Gln; BRCA1) and c.7878G>C (p.Trp2626Cys; BRCA2) indicated that the history weighting algorithm is able to identify some lower penetrance alleles. The history weighting algorithm is a powerful tool that accurately assigns actionable clinical classifications to variants of uncertain clinical significance. While being developed for reclassification of BRCA1 and BRCA2 variants, the history weighting algorithm is expected to be applicable to other cancer- and non-cancer-related genes.

Keywords

BRCA1 BRCA2 Breast cancer Ovarian cancer Variant classification 

Notes

Acknowledgments

We would like to thank Kirstin Roundy for assistance with manuscript editing and submission.

Conflict of interest

All authors are employees of Myriad Genetics, Inc. and Myriad Genetic Laboratories, Inc. and receive salaries and stock options as compensation.

Supplementary material

10549_2014_3065_MOESM1_ESM.docx (83 kb)
Supplementary material 1 (DOCX 84 kb)

References

  1. 1.
    Claus EB, Schildkraut JM, Thompson WD, Risch NJ (1996) The genetic attributable risk of breast and ovarian cancer. Cancer 77(11):2318–2324. doi: 10.1002/(SICI)1097-0142(19960601)77:11<2318:AID-CNCR21>3.0.CO;2-Z CrossRefPubMedGoogle Scholar
  2. 2.
    Antoniou AC, Gayther SA, Stratton JF, Ponder BA, Easton DF (2000) Risk models for familial ovarian and breast cancer. Genet Epidemiol 18(2):173–190. doi: 10.1002/(SICI)1098-2272(200002)18:2<173:AID-GEPI6>3.0.CO;2-R CrossRefPubMedGoogle Scholar
  3. 3.
    Anglian Breast Cancer Study Group (2000) Prevalence and penetrance of BRCA1 and BRCA2 mutations in a population-based series of breast cancer cases. Anglian Breast Cancer Study Group. Br J Cancer 83(10):1301–1308. doi: 10.1054/bjoc.2000.1407 CrossRefPubMedCentralGoogle Scholar
  4. 4.
    Kurian AW (2010) BRCA1 and BRCA2 mutations across race and ethnicity: distribution and clinical implications. Curr Opin Obstet Gynecol 22(1):72–78. doi: 10.1097/GCO.0b013e328332dca3 CrossRefPubMedGoogle Scholar
  5. 5.
    Richards CS, Bale S, Bellissimo DB, Das S, Grody WW, Hegde MR, Lyon E, Ward BE, Molecular Subcommittee of the ALQAC (2008) ACMG recommendations for standards for interpretation and reporting of sequence variations: revisions 2007. Genet Med 10(4):294–300. doi: 10.1097/GIM.0b013e31816b5cae CrossRefPubMedGoogle Scholar
  6. 6.
    National Comprehensive Cancer Network (2014) Genetic/familial high-risk assessment: breast and ovarian. NCCN Clin Pract Guidel Oncol (1.2014)Google Scholar
  7. 7.
    Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR (2010) A method and server for predicting damaging missense mutations. Nat Methods 7(4):248–249. doi: 10.1038/nmeth0410-248 CrossRefPubMedCentralPubMedGoogle Scholar
  8. 8.
    Ng PC, Henikoff S (2001) Predicting deleterious amino acid substitutions. Genome Res 11(5):863–874. doi: 10.1101/gr.176601 CrossRefPubMedCentralPubMedGoogle Scholar
  9. 9.
    Sunyaev S, Ramensky V, Koch I, Lathe W 3rd, Kondrashov AS, Bork P (2001) Prediction of deleterious human alleles. Hum Mol Genet 10(6):591–597CrossRefPubMedGoogle Scholar
  10. 10.
    Easton DF, Deffenbaugh AM, Pruss D, Frye C, Wenstrup RJ, Allen-Brady K, Tavtigian SV, Monteiro AN, Iversen ES, Couch FJ, Goldgar DE (2007) A systematic genetic assessment of 1,433 sequence variants of unknown clinical significance in the BRCA1 and BRCA2 breast cancer-predisposition genes. Am J Hum Genet 81(5):873–883. doi: 10.1086/521032 CrossRefPubMedCentralPubMedGoogle Scholar
  11. 11.
    Abkevich V, Zharkikh A, Deffenbaugh AM, Frank D, Chen Y, Shattuck D, Skolnick MH, Gutin A, Tavtigian SV (2004) Analysis of missense variation in human BRCA1 in the context of interspecific sequence variation. J Med Genet 41(7):492–507CrossRefPubMedCentralPubMedGoogle Scholar
  12. 12.
    Ford D, Easton DF, Bishop DT, Narod SA, Goldgar DE (1994) Risks of cancer in BRCA1-mutation carriers. Breast Cancer Linkage Consortium. Lancet 343(8899):692–695CrossRefPubMedGoogle Scholar
  13. 13.
    Ford D, Easton DF, Stratton M, Narod S, Goldgar D, Devilee P, Bishop DT, Weber B, Lenoir G, Chang-Claude J, Sobol H, Teare MD, Struewing J, Arason A, Scherneck S, Peto J, Rebbeck TR, Tonin P, Neuhausen S, Barkardottir R, Eyfjord J, Lynch H, Ponder BA, Gayther SA, Zelada-Hedman M et al (1998) Genetic heterogeneity and penetrance analysis of the BRCA1 and BRCA2 genes in breast cancer families. The Breast Cancer Linkage Consortium. Am J Hum Genet 62(3):676–689CrossRefPubMedCentralPubMedGoogle Scholar
  14. 14.
    Frank TS, Manley SA, Olopade OI, Cummings S, Garber JE, Bernhardt B, Antman K, Russo D, Wood ME, Mullineau L, Isaacs C, Peshkin B, Buys S, Venne V, Rowley PT, Loader S, Offit K, Robson M, Hampel H, Brener D, Winer EP, Clark S, Weber B, Strong LC, Thomas A et al (1998) Sequence analysis of BRCA1 and BRCA2: correlation of mutations with family history and ovarian cancer risk. J Clin Oncol 16(7):2417–2425PubMedGoogle Scholar
  15. 15.
    Verhoog LC, Brekelmans CT, Seynaeve C, van den Bosch LM, Dahmen G, van Geel AN, Tilanus-Linthorst MM, Bartels CC, Wagner A, van den Ouweland A, Devilee P, Meijers-Heijboer EJ, Klijn JG (1998) Survival and tumour characteristics of breast-cancer patients with germline mutations of BRCA1. Lancet 351(9099):316–321CrossRefPubMedGoogle Scholar
  16. 16.
    Breast Cancer Linkage Consortium (1999) Cancer risks in BRCA2 mutation carriers. J Natl Cancer Inst 91(15):1310–1316CrossRefGoogle Scholar
  17. 17.
    Klein AP, Brune KA, Petersen GM, Goggins M, Tersmette AC, Offerhaus GJ, Griffin C, Cameron JL, Yeo CJ, Kern S, Hruban RH (2004) Prospective risk of pancreatic cancer in familial pancreatic cancer kindreds. Cancer Res 64(7):2634–2638CrossRefPubMedGoogle Scholar
  18. 18.
    van Asperen CJ, Brohet RM, Meijers-Heijboer EJ, Hoogerbrugge N, Verhoef S, Vasen HF, Ausems MG, Menko FH, Gomez Garcia EB, Klijn JG, Hogervorst FB, van Houwelingen JC, van’t Veer LJ, Rookus MA, van Leeuwen FE, Netherlands Collaborative Group on Hereditary Breast C (2005) Cancer risks in BRCA2 families: estimates for sites other than breast and ovary. J Med Genet 42(9):711–719. doi: 10.1136/jmg.2004.028829 CrossRefPubMedCentralPubMedGoogle Scholar
  19. 19.
    Verhoog LC, Brekelmans CT, Seynaeve C, Dahmen G, van Geel AN, Bartels CC, Tilanus-Linthorst MM, Wagner A, Devilee P, Halley DJ, van den Ouweland AM, Meijers-Heijboer EJ, Klijn JG (1999) Survival in hereditary breast cancer associated with germline mutations of BRCA2. J Clin Oncol 17(11):3396–3402PubMedGoogle Scholar
  20. 20.
    Eggington JM, Bowles KR, Moyes K, Manley S, Esterling L, Sizemore S, Rosenthal E, Theisen A, Saam J, Arnell C, Pruss D, Bennett J, Burbidge LA, Roa B, Wenstrup RJ (2013) A comprehensive laboratory-based program for classification of variants of uncertain significance in hereditary cancer genes. Clin Genet. doi: 10.1111/cge.12315
  21. 21.
    Biswas K, Das R, Alter BP, Kuznetsov SG, Stauffer S, North SL, Burkett S, Brody LC, Meyer S, Byrd RA, Sharan SK (2011) A comprehensive functional characterization of BRCA2 variants associated with Fanconi anemia using mouse ES cell-based assay. Blood 118(9):2430–2442. doi: 10.1182/blood-2010-12-324541 CrossRefPubMedCentralPubMedGoogle Scholar
  22. 22.
    Chang S, Wang RH, Akagi K, Kim KA, Martin BK, Cavallone L, Kathleen Cuningham Foundation Consortium for Research into Familial Breast C, Haines DC, Basik M, Mai P, Poggi E, Isaacs C, Looi LM, Mun KS, Greene MH, Byers SW, Teo SH, Deng CX, Sharan SK (2011) Tumor suppressor BRCA1 epigenetically controls oncogenic microRNA-155. Nat Med 17(10):1275–1282. doi: 10.1038/nm.2459 CrossRefPubMedCentralPubMedGoogle Scholar
  23. 23.
    Lovelock PK, Spurdle AB, Mok MT, Farrugia DJ, Lakhani SR, Healey S, Arnold S, Buchanan D, kConFab I, Couch FJ, Henderson BR, Goldgar DE, Tavtigian SV, Chenevix-Trench G, Brown MA (2007) Identification of BRCA1 missense substitutions that confer partial functional activity: potential moderate risk variants? Breast Cancer Res 9(6):R82. doi: 10.1186/bcr1826 CrossRefPubMedCentralPubMedGoogle Scholar
  24. 24.
    Williams RS, Lee MS, Hau DD, Glover JN (2004) Structural basis of phosphopeptide recognition by the BRCT domain of BRCA1. Nat Struct Mol Biol 11(6):519–525. doi: 10.1038/nsmb776 CrossRefPubMedGoogle Scholar
  25. 25.
    Mazoyer S, Dunning AM, Serova O, Dearden J, Puget N, Healey CS, Gayther SA, Mangion J, Stratton MR, Lynch HT, Goldgar DE, Ponder BA, Lenoir GM (1996) A polymorphic stop codon in BRCA2. Nat Genet 14(3):253–254. doi: 10.1038/ng1196-253 CrossRefPubMedGoogle Scholar
  26. 26.
    Friedman LS, Ostermeyer EA, Szabo CI, Dowd P, Lynch ED, Rowell SE, King MC (1994) Confirmation of BRCA1 by analysis of germline mutations linked to breast and ovarian cancer in ten families. Nat Genet 8(4):399–404. doi: 10.1038/ng1294-399 CrossRefPubMedGoogle Scholar
  27. 27.
    Miki Y, Swensen J, Shattuck-Eidens D, Futreal PA, Harshman K, Tavtigian S, Liu Q, Cochran C, Bennett LM, Ding W et al (1994) A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1. Science 266(5182):66–71CrossRefPubMedGoogle Scholar
  28. 28.
    Lee MS, Green R, Marsillac SM, Coquelle N, Williams RS, Yeung T, Foo D, Hau DD, Hui B, Monteiro AN, Glover JN (2010) Comprehensive analysis of missense variations in the BRCT domain of BRCA1 by structural and functional assays. Cancer Res 70(12):4880–4890. doi: 10.1158/0008-5472.CAN-09-4563 CrossRefPubMedCentralPubMedGoogle Scholar
  29. 29.
    Goldgar DE, Easton DF, Deffenbaugh AM, Monteiro AN, Tavtigian SV, Couch FJ, Breast Cancer Information Core Steering C (2004) Integrated evaluation of DNA sequence variants of unknown clinical significance: application to BRCA1 and BRCA2. Am J Hum Genet 75(4):535–544. doi: 10.1086/424388 CrossRefPubMedCentralPubMedGoogle Scholar
  30. 30.
    Farrugia DJ, Agarwal MK, Pankratz VS, Deffenbaugh AM, Pruss D, Frye C, Wadum L, Johnson K, Mentlick J, Tavtigian SV, Goldgar DE, Couch FJ (2008) Functional assays for classification of BRCA2 variants of uncertain significance. Cancer Res 68(9):3523–3531. doi: 10.1158/0008-5472.CAN-07-1587 CrossRefPubMedCentralPubMedGoogle Scholar
  31. 31.
    Karchin R, Agarwal M, Sali A, Couch F, Beattie MS (2008) Classifying variants of undetermined significance in BRCA2 with protein likelihood ratios. Cancer Inform 6:203–216PubMedCentralPubMedGoogle Scholar
  32. 32.
    Mohammadi L, Vreeswijk MP, Oldenburg R, van den Ouweland A, Oosterwijk JC, van der Hout AH, Hoogerbrugge N, Ligtenberg M, Ausems MG, van der Luijt RB, Dommering CJ, Gille JJ, Verhoef S, Hogervorst FB, van Os TA, Gomez Garcia E, Blok MJ, Wijnen JT, Helmer Q, Devilee P, van Asperen CJ, van Houwelingen HC (2009) A simple method for co-segregation analysis to evaluate the pathogenicity of unclassified variants; BRCA1 and BRCA2 as an example. BMC Cancer 9:211. doi: 10.1186/1471-2407-9-211 CrossRefPubMedCentralPubMedGoogle Scholar
  33. 33.
    Ricevuto E, Sobol H, Stoppa-Lyonnet D, Gulino A, Marchetti P, Ficorella C, Martinotti S, Meo T, Tosi M (2001) Diagnostic strategy for analytical scanning of BRCA1 gene by fluorescence-assisted mismatch analysis using large, bifluorescently labeled amplicons. Clin Cancer Res 7(6):1638–1646PubMedGoogle Scholar
  34. 34.
    Spurdle AB, Whiley PJ, Thompson B, Feng B, Healey S, Brown MA, Pettigrew C, Van Asperen CJ, Ausems MG, Kattentidt-Mouravieva AA, van den Ouweland AM, Lindblom A, Pigg MH, Schmutzler RK, Engel C, Meindl A, Caputo S, Sinilnikova OM, Lidereau R, Couch FJ, Guidugli L, Hansen T, Thomassen M, Eccles DM, Tucker K, Benitez J, Domchek SM, Toland AE, Van Rensburg EJ, Wappenschmidt B, Borg A, Vreeswijk MP, Goldgar DE (2012) BRCA1 R1699Q variant displaying ambiguous functional abrogation confers intermediate breast and ovarian cancer risk. J Med Genet 49(8):525–532. doi: 10.1136/jmedgenet-2012-101037 CrossRefPubMedGoogle Scholar
  35. 35.
    Vallee MP, Francy TC, Judkins MK, Babikyan D, Lesueur F, Gammon A, Goldgar DE, Couch FJ, Tavtigian SV (2012) Classification of missense substitutions in the BRCA genes: a database dedicated to Ex-UVs. Hum Mutat 33(1):22–28. doi: 10.1002/humu.21629 CrossRefPubMedCentralPubMedGoogle Scholar
  36. 36.
    Guidugli L, Pankratz VS, Singh N, Thompson J, Erding CA, Engel C, Schmutzler R, Domchek S, Nathanson K, Radice P, Singer C, Tonin PN, Lindor NM, Goldgar DE, Couch FJ (2013) A classification model for BRCA2 DNA binding domain missense variants based on homology-directed repair activity. Cancer Res 73(1):265–275. doi: 10.1158/0008-5472.can-12-2081 CrossRefPubMedCentralPubMedGoogle Scholar
  37. 37.
    Meza JE, Brzovic PS, King MC, Klevit RE (1999) Mapping the functional domains of BRCA1. Interaction of the ring finger domains of BRCA1 and BARD1. J Biol Chem 274(9):5659–5665CrossRefPubMedGoogle Scholar
  38. 38.
    Castilla LH, Couch FJ, Erdos MR, Hoskins KF, Calzone K, Garber JE, Boyd J, Lubin MB, Deshano ML, Brody LC et al (1994) Mutations in the BRCA1 gene in families with early-onset breast and ovarian cancer. Nat Genet 8(4):387–391. doi: 10.1038/ng1294-387 CrossRefPubMedGoogle Scholar
  39. 39.
    Wu LC, Wang ZW, Tsan JT, Spillman MA, Phung A, Xu XL, Yang MC, Hwang LY, Bowcock AM, Baer R (1996) Identification of a RING protein that can interact in vivo with the BRCA1 gene product. Nat Genet 14(4):430–440. doi: 10.1038/ng1296-430 CrossRefPubMedGoogle Scholar
  40. 40.
    Friedman LS, Szabo CI, Ostermeyer EA, Dowd P, Butler L, Park T, Lee MK, Goode EL, Rowell SE, King MC (1995) Novel inherited mutations and variable expressivity of BRCA1 alleles, including the founder mutation 185delAG in Ashkenazi Jewish families. Am J Hum Genet 57(6):1284–1297PubMedCentralPubMedGoogle Scholar
  41. 41.
    Panguluri RC, Brody LC, Modali R, Utley K, Adams-Campbell L, Day AA, Whitfield-Broome C, Dunston GM (1999) BRCA1 mutations in African Americans. Hum Genet 105(1–2):28–31CrossRefPubMedGoogle Scholar
  42. 42.
    Campbell IG, Schroff R, Englefield P, Eccles DM (1997) BRCA1 polymorphisms. Br J Cancer 75(12):1854–1855CrossRefPubMedCentralPubMedGoogle Scholar
  43. 43.
    Machackova E, Foretova L, Lukesova M, Vasickova P, Navratilova M, Coene I, Pavlu H, Kosinova V, Kuklova J, Claes K (2008) Spectrum and characterisation of BRCA1 and BRCA2 deleterious mutations in high-risk Czech patients with breast and/or ovarian cancer. BMC Cancer 8:140. doi: 10.1186/1471-2407-8-140 CrossRefPubMedCentralPubMedGoogle Scholar
  44. 44.
    Chapman MS, Verma IM (1996) Transcriptional activation by BRCA1. Nature 382(6593):678–679. doi: 10.1038/382678a0 CrossRefPubMedGoogle Scholar
  45. 45.
    Lovelock PK, Healey S, Au W, Sum EY, Tesoriero A, Wong EM, Hinson S, Brinkworth R, Bekessy A, Diez O, Izatt L, Solomon E, Jenkins M, Renard H, Hopper J, Waring P, Tavtigian SV, Goldgar D, Lindeman GJ, Visvader JE, Couch FJ, Henderson BR, Southey M, Chenevix-Trench G, Spurdle AB, Brown MA (2006) Genetic, functional, and histopathological evaluation of two C-terminal BRCA1 missense variants. J Med Genet 43(1):74–83. doi: 10.1136/jmg.2005.033258 CrossRefPubMedCentralPubMedGoogle Scholar
  46. 46.
    Laskie Ostrow K, DiCioccio RA, McGuire V, Whittemore AS (2001) A BRCA1 variant, IVS23+1G→A, causes abnormal RNA splicing by deleting exon 23. Cancer Genet Cytogenet 127(2):188–190CrossRefPubMedGoogle Scholar
  47. 47.
    Shih HA, Nathanson KL, Seal S, Collins N, Stratton MR, Rebbeck TR, Weber BL (2000) BRCA1 and BRCA2 mutations in breast cancer families with multiple primary cancers. Clin Cancer Res 6(11):4259–4264PubMedGoogle Scholar
  48. 48.
    Healey CS, Dunning AM, Teare MD, Chase D, Parker L, Burn J, Chang-Claude J, Mannermaa A, Kataja V, Huntsman DG, Pharoah PD, Luben RN, Easton DF, Ponder BA (2000) A common variant in BRCA2 is associated with both breast cancer risk and prenatal viability. Nat Genet 26(3):362–364. doi: 10.1038/81691 CrossRefPubMedGoogle Scholar
  49. 49.
    Chen X, Truong TT, Weaver J, Bove BA, Cattie K, Armstrong BA, Daly MB, Godwin AK (2006) Intronic alterations in BRCA1 and BRCA2: effect on mRNA splicing fidelity and expression. Hum Mutat 27(5):427–435. doi: 10.1002/humu.20319 CrossRefPubMedGoogle Scholar
  50. 50.
    Biswas K, Das R, Eggington JM, Qiao H, North SL, Stauffer S, Burkett SS, Martin BK, Southon E, Sizemore SC, Pruss D, Bowles KR, Roa BB, Hunter N, Tessarollo L, Wenstrup RJ, Byrd RA, Sharan SK (2012) Functional evaluation of BRCA2 variants mapping to the PALB2-binding and C-terminal DNA-binding domains using a mouse ES cell-based assay. Hum Mol Genet 21(18):3993–4006. doi: 10.1093/hmg/dds222 CrossRefPubMedCentralPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Dmitry Pruss
    • 1
  • Brian Morris
    • 1
  • Elisha Hughes
    • 1
  • Julie M. Eggington
    • 2
  • Lisa Esterling
    • 2
  • Brandon S. Robinson
    • 2
  • Aric van Kan
    • 2
  • Priscilla H. Fernandes
    • 2
  • Benjamin B. Roa
    • 2
  • Alexander Gutin
    • 1
  • Richard J. Wenstrup
    • 2
  • Karla R. Bowles
    • 2
    Email author
  1. 1.Myriad Genetics, Inc.Salt Lake CityUSA
  2. 2.Myriad Genetic Laboratories, Inc.Salt Lake CityUSA

Personalised recommendations