Abstract
Loss-of-function mutations in PALB2 are associated with an increased risk of breast cancer, with recent data showing that female breast cancer risks for PALB2 mutation carriers are comparable in magnitude to those for BRCA2 mutation carriers. This study applied targeted massively parallel sequencing to characterize the mutation spectrum of PALB2 in probands attending breast cancer genetics clinics in the USA. The coding regions and proximal intron–exon junctions of PALB2 were screened in probands not known to carry a mutation in BRCA1 or BCRA2 from 1,250 families enrolled through familial cancer clinics by the Breast Cancer Family Registry. Mutation screening was performed using Hi-Plex, an amplicon-based targeted massively parallel sequencing platform. Screening of PALB2 was successful in 1,240/1,250 probands and identified nine women with protein-truncating mutations (three nonsense mutations and five frameshift mutations). Four of the 33 missense variants were predicted to be deleterious to protein function by in silico analysis using two different programs. Analysis of tumors from carriers of truncating mutations revealed that the majority were high histological grade, invasive ductal carcinomas. Young onset was apparent in most families, with 19 breast cancers under 50 years of age, including eight under the age of 40 years. Our data demonstrate the utility of Hi-Plex in the context of high-throughput testing for rare genetic mutations and provide additional timely information about the nature and prevalence of PALB2 mutations, to enhance risk assessment and risk management of women at high risk of cancer attending clinical genetic services.
Abbreviations
- BCFR:
-
Breast Cancer Family Registry
- ER:
-
Estrogen receptor
- HER2:
-
Human epithelial growth factor-2
- LCL:
-
Lymphoblastoid cell line
- LOVD:
-
Leiden open variant database
- PR:
-
Progesterone receptor
References
Rahman N, Seal S, Thompson D, Kelly P, Renwick A, Elliott A, Reid S, Spanova K, Barfoot R, Chagtai T, Jayatilake H, McGuffog L, Hanks S, Evans DG, Eccles D, Breast Cancer Susceptibility Collaboration (UK), Easton DF, Stratton MR (2007) PALB2, which encodes a BRCA2-interacting protein, is a breast cancer susceptibility gene. Nat Genet 39(2):165–167
Antoniou AC, Casadei S, Heikkinen T, Barrowdale D, Pylkas K, Roberts J, Lee A, Subramanian D, De Leeneer K, Fostira F, Tomiak E, Neuhausen SL, Teo ZL, Khan S, Aittomaki K, Moilanen JS, Turnbull C, Seal S, Mannermaa A, Kallioniemi A, Lindeman GJ, Buys SS, Andrulis IL, Radice P, Tondini C, Manoukian S, Toland AE, Miron P, Weitzel JN, Domchek SM, Poppe B, Claes KB, Yannoukakos D, Concannon P, Bernstein JL, James PA, Easton DF, Goldgar DE, Hopper JL, Rahman N, Peterlongo P, Nevanlinna H, King MC, Couch FJ, Southey MC, Winqvist R, Foulkes WD, Tischkowitz M (2014) Breast-cancer risk in families with mutations in PALB2. N Engl J Med 371(6):497–506. doi:10.1056/NEJMoa1400382
Southey MC, Teo ZL, Dowty JG, Odefrey FA, Park DJ, Tischkowitz M, Sabbaghian N, Apicella C, Byrnes GB, Winship I, Baglietto L, Giles GG, Goldgar DE, Foulkes WD, Hopper JL, kConFab for the Beast Cancer Family R (2010) A PALB2 mutation associated with high risk of breast cancer. Breast Cancer Res 12(6):R109. doi:10.1186/bcr2796
Erkko H, Dowty JG, Nikkila J, Syrjakoski K, Mannermaa A, Pylkas K, Southey MC, Holli K, Kallioniemi A, Jukkola-Vuorinen A, Kataja V, Kosma VM, Xia B, Livingston DM, Winqvist R, Hopper JL (2008) Penetrance analysis of the PALB2 c.1592delT founder mutation. Clinical Cancer Res 14(14):4667–4671. doi:10.1158/1078-0432.CCR-08-0210
Erkko H, Xia B, Nikkila J, Schleutker J, Syrjakoski K, Mannermaa A, Kallioniemi A, Pylkas K, Karppinen SM, Rapakko K, Miron A, Sheng Q, Li G, Mattila H, Bell DW, Haber DA, Grip M, Reiman M, Jukkola-Vuorinen A, Mustonen A, Kere J, Aaltonen LA, Kosma VM, Kataja V, Soini Y, Drapkin RI, Livingston DM, Winqvist R (2007) A recurrent mutation in PALB2 in Finnish cancer families. Nature 446(7133):316–319. doi:10.1038/nature05609
Tischkowitz MD, Sabbaghian N, Hamel N, Borgida A, Rosner C, Taherian N, Srivastava A, Holter S, Rothenmund H, Ghadirian P, Foulkes WD, Gallinger S (2009) Analysis of the gene coding for the BRCA2-interacting protein PALB2 in familial and sporadic pancreatic cancer. Gastroenterology 137(3):1183–1186. doi:10.1053/j.gastro.2009.06.055
Peterlongo P, Catucci I, Pasquini G, Verderio P, Peissel B, Barile M, Varesco L, Riboni M, Fortuzzi S, Manoukian S, Radice P (2011) PALB2 germline mutations in familial breast cancer cases with personal and family history of pancreatic cancer. Breast Cancer Res Treat 126(3):825–828. doi:10.1007/s10549-010-1305-1
Dansonka-Mieszkowska A, Kluska A, Moes J, Dabrowska M, Nowakowska D, Niwinska A, Derlatka P, Cendrowski K, Kupryjanczyk J (2010) A novel germline PALB2 deletion in Polish breast and ovarian cancer patients. BMC Med Genet 11:20. doi:10.1186/1471-2350-11-20
Southey MC, Teo ZL, Winship I (2013) PALB2 and breast cancer: ready for clinical translation! The Appl Clinical Genet 6:43–52. doi:10.2147/TACG.S34116
Nguyen-Dumont T, Teo ZL, Pope BJ, Hammet F, Mahmoodi M, Tsimiklis H, Sabbaghian N, Tischkowitz M, Foulkes WD, Giles GG, Hopper JL, Southey MC, Park DJ (2013) Hi-Plex for high-throughput mutation screening: application to the breast cancer susceptibility gene PALB2. BMC Med Genomics 6(1):48. doi:10.1186/1755-8794-6-48
Strahm B, Malkin D (2006) Hereditary cancer predisposition in children: genetic basis and clinical implications. Int J Cancer 119(9):2001–2006. doi:10.1002/ijc.21962
Wu HC, Delgado-Cruzata L, Machella N, Wang Q, Santella RM, Terry MB (2013) DNA double-strand break repair genotype and phenotype and breast cancer risk within sisters from the New York site of the Breast Cancer Family Registry (BCFR). Cancer Causes Control 24(12):2157–2168. doi:10.1007/s10552-013-0292-z
Taylor MD, Liu L, Raffel C, Hui CC, Mainprize TG, Zhang X, Agatep R, Chiappa S, Gao L, Lowrance A, Hao A, Goldstein AM, Stavrou T, Scherer SW, Dura WT, Wainwright B, Squire JA, Rutka JT, Hogg D (2002) Mutations in SUFU predispose to medulloblastoma. Nat Genet 31(3):306–310. doi:10.1038/ng916
Delgado-Cruzata L, Wu HC, Perrin M, Liao Y, Kappil MA, Ferris JS, Flom JD, Yazici H, Santella RM, Terry MB (2012) Global DNA methylation levels in white blood cell DNA from sisters discordant for breast cancer from the New York site of the Breast Cancer Family Registry. Epigenetics 7(8):868–874. doi:10.4161/epi.20830
Wu HC, Delgado-Cruzata L, Flom JD, Perrin M, Liao Y, Ferris JS, Santella RM, Terry MB (2012) Repetitive element DNA methylation levels in white blood cell DNA from sisters discordant for breast cancer from the New York site of the Breast Cancer Family Registry. Carcinogenesis 33(10):1946–1952. doi:10.1093/carcin/bgs201
John EM, Hopper JL, Beck JC, Knight JA, Neuhausen SL, Senie RT, Ziogas A, Andrulis IL, Anton-Culver H, Boyd N, Buys SS, Daly MB, O’Malley FP, Santella RM, Southey MC, Venne VL, Venter DJ, West DW, Whittemore AS, Seminara D, Breast Cancer Family R (2004) The Breast Cancer Family Registry: an infrastructure for cooperative multinational, interdisciplinary and translational studies of the genetic epidemiology of breast cancer. Breast cancer Res 6(4):R375–R389. doi:10.1186/bcr801
Neuhausen SL, Ozcelik H, Southey MC, John EM, Godwin AK, Chung W, Iriondo-Perez J, Miron A, Santella RM, Whittemore A, Andrulis IL, Buys SS, Daly MB, Hopper JL, Seminara D, Senie RT, Terry MB, Breast Cancer Family R (2009) BRCA1 and BRCA2 mutation carriers in the Breast Cancer Family Registry: an open resource for collaborative research. Breast Cancer Res Treat 116(2):379–386. doi:10.1007/s10549-008-0153-8
Nguyen-Dumont T, Pope BJ, Hammet F, Southey MC, Park DJ (2013) A high-plex PCR approach for massively parallel sequencing. Biotechniques 55(2):69–74. doi:10.2144/000114052
Pope BJ, Nguyen-Dumont T, Hammet F, Park DJ (2014) ROVER variant caller: read-pair overlap considerate variant-calling software applied to PCR-based massively parallel sequencing datasets. Source Code Biol Med 9(1):3. doi:10.1186/1751-0473-9-3
Wang K, Li M, Hakonarson H (2010) ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 38(16):e164. doi:10.1093/nar/gkq603
Tavtigian SV, Byrnes GB, Goldgar DE, Thomas A (2008) Classification of rare missense substitutions, using risk surfaces, with genetic- and molecular-epidemiology applications. Hum Mutat 29(11):1342–1354. doi:10.1002/humu.20896
Tischkowitz M, Capanu M, Sabbaghian N, Li L, Liang X, Vallee MP, Tavtigian SV, Concannon P, Foulkes WD, Bernstein L, Group WSC, Bernstein JL, Begg CB (2012) Rare germline mutations in PALB2 and breast cancer risk: a population-based study. Hum Mutat 33(4):674–680. doi:10.1002/humu.22022
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
Adzhubei I, Jordan DM, Sunyaev SR (2013) Predicting functional effect of human missense mutations using PolyPhen-2. Current protocols in human genetics Chapter 7:Unit7.20. doi:10.1002/0471142905.hg0720s76
Exome Variant Server. http://evs.gs.washington.edu/EVS/. Accessed 2 Oct 2014
Hellebrand H, Sutter C, Honisch E, Gross E, Wappenschmidt B, Schem C, Deissler H, Ditsch N, Gress V, Kiechle M, Bartram CR, Schmutzler RK, Niederacher D, Arnold N, Meindl A (2011) Germline mutations in the PALB2 gene are population specific and occur with low frequencies in familial breast cancer. Hum Mutat 32(6):E2176–E2188. doi:10.1002/humu.21478
Teo ZL, Park DJ, Provenzano E, Chatfield CA, Odefrey FA, Nguyen-Dumont T, kConFab, Dowty JG, Hopper JL, Winship I, Goldgar DE, Southey MC (2013) Prevalence of PALB2 mutations in Australasian multiple-case breast cancer families. Breast cancer Res 15(1):R17. doi:10.1186/bcr3392
Park JY, Singh TR, Nassar N, Zhang F, Freund M, Hanenberg H, Meetei AR, Andreassen PR (2014) Breast cancer-associated missense mutants of the PALB2 WD40 domain, which directly binds RAD51C, RAD51 and BRCA2, disrupt DNA repair. Oncogene 33(40):4803–4812. doi:10.1038/onc.2013.421
LOVD P PALB2 LOVD. https://grenada.lumc.nl/LOVD2/shared1/home.php?select_db=PALB2. Accessed 6 Oct 2014
Teo ZL, Provenzano E, Dite GS, Park DJ, Apicella C, Sawyer SD, James PA, Mitchell G, Trainer AH, Lindeman GJ, Shackleton K, Cicciarelli L, kConFab, Buys SS, Andrulis IL, Mulligan AM, Glendon G, John EM, Terry MB, Daly M, Odefrey FA, Nguyen-Dumont T, Giles GG, Dowty JG, Winship I, Goldgar DE, Hopper JL, Southey MC (2013) Tumour morphology predicts PALB2 germline mutation status. Br J Cancer 109(1):154–163. doi:10.1038/bjc.2013.295
Heikkinen T, Karkkainen H, Aaltonen K, Milne RL, Heikkila P, Aittomaki K, Blomqvist C, Nevanlinna H (2009) The breast cancer susceptibility mutation PALB2 1592delT is associated with an aggressive tumor phenotype. Clinical Cancer Res 15(9):3214–3222. doi:10.1158/1078-0432.CCR-08-3128
Acknowledgments
TN-D is a Susan G. Komen for the Cure Postdoctoral Fellow. ZLT was supported by Postgraduate Scholarships provided by the Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne and the National Health and Medical Research Council (NHMRC, Australia). RL is supported by UROP, a program of Biomedical Research Victoria, by the Victorian Life Sciences Computation Initiative (VLSCI) and by the Department of Pathology, The University of Melbourne. MCS is an NHMRC Senior Research Fellow. The Utah, New York, and Philadelphia sites of the Breast Cancer Family Registry were supported by Grant UM1 CA164920 from the National Cancer Institute (USA). The content of this manuscript does not necessarily reflect the views or policies of the National Cancer Institute or any of the collaborating centers in the Breast Cancer Family Registry (BCFR), or does mention of trade names, commercial products, or organizations imply endorsement by the USA Government or the BCFR. This work was supported by the Australian National Health and Medical Research Council (NHMRC) (APP1025879 and APP1029974), the Victorian Breast Cancer Research Consortium and by a VLSCI Grant (number VR0182) on its Peak Computing Facility, an initiative of the Victorian Government.
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Nguyen-Dumont, T., Hammet, F., Mahmoodi, M. et al. Mutation screening of PALB2 in clinically ascertained families from the Breast Cancer Family Registry. Breast Cancer Res Treat 149, 547–554 (2015). https://doi.org/10.1007/s10549-014-3260-8
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DOI: https://doi.org/10.1007/s10549-014-3260-8