Large Genomic Rearrangements of BRCA1 and BRCA2 among Patients Referred for Genetic Analysis in Galicia (NW Spain): Delimitation and Mechanism of Three Novel BRCA1 Rearrangements
In the Iberian Peninsula, which includes mainly Spain and Portugal, large genomic rearrangements (LGRs) of BRCA1 and BRCA2 have respectively been found in up to 2.33% and 8.4% of families with hereditary breast and/or ovarian cancer (HBOC) that lack point mutations and small indels. In Galicia (Northwest Spain), the spectrum and frequency of BRCA1/BRCA2 point mutations differs from the rest of the Iberian populations. However, to date there are no Galician frequency reports of BRCA1/BRCA2 LGRs. Here we used multiplex ligation-dependent probe amplification (MLPA) to screen 651 Galician index cases (out of the 830 individuals referred for genetic analysis) without point mutations or small indels. We identified three different BRCA1 LGRs in four families. Two of them have been previously classified as pathogenic LGRs: the complete deletion of BRCA1 (identified in two unrelated families) and the deletion of exons 1 to 13. We also identified the duplication of exons 1 and 2 that is a LGR with unknown pathogenicity. Determination of the breakpoints of the BRCA1 LGRs using CNV/SNP arrays and sequencing identified them as NG_005905.2:g.70536_180359del, NG_005905.2:g.90012_97270dup, and NC_000017.10:g.41230935_41399840delinsAl？uSx1,respectively; previous observations of BRCA1 exon1-24del, exon1-2dup, and exon1-13del LGRs have not characterized them in such detail. All the BRCA1 LGRs arose from unequal homologous recombination events involving Alu elements. We also detected, by sequencing, one BRCA2 LGR, the Portuguese founder mutation c.156_157insAluYa5. The low frequency of BRCA1 LGRs within BRCA1 mutation carriers in Galicia (2.34%, 95% CI: 0.61–7.22) seems to differ from the Spanish population (9.93%, 95% CI: 6.76–14.27, P-value = 0.013) and from the rest of the Iberian population (9.76%, 95% CI: 6.69–13.94, P-value = 0.014).
References
[1]
Miki Y, Swensen J, Shattuck-Eidens D, Futreal PA, Harshman K, et al. (1994) A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1. Science 266: 66–71. doi: 10.1126/science.7545954
[2]
Wooster R, Bignell G, Lancaster J, Swift S, Seal S, et al. (1995) Identification of the breast cancer susceptibility gene BRCA2. Nature 378: 789–792. doi: 10.1038/378789a0
[3]
Anglian Breast Cancer Study Group (2000) Prevalence and penetrance of BRCA1 and BRCA2 mutations in a population-based series of breast cancer cases. Br J Cancer 83: 1301–1308.
[4]
Sluiter M, van Rensburg E (2011) Large genomic rearrangements of the BRCA1 and BRCA2 genes: review of the literature and report of a novel BRCA1 mutation. Breast Cancer Res Treat 125: 325–349. doi: 10.1007/s10549-010-0817-z
[5]
Walsh T, Casadei S, Coats KH, Swisher E, Stray SM, et al. (2006) Spectrum of Mutations in BRCA1, BRCA2, CHEK2, and TP53 in Families at High Risk of Breast Cancer. JAMA 295: 1379–1388. doi: 10.1001/jama.295.12.1379
[6]
Peixoto A, Salgueiro N, Santos C, Varzim G, Rocha P, et al. (2006) BRCA1 and BRCA2 germline mutational spectrum and evidence for genetic anticipation in Portuguese breast/ovarian cancer families. Fam Cancer 5: 379–387. doi: 10.1007/s10689-006-0009-5
[7]
Peixoto A, Santos C, Rocha P, Pinheiro M, Príncipe S, et al. (2009) The c.156_157insAlu BRCA2 rearrangement accounts for more than one-fourth of deleterious BRCA mutations in northern/central Portugal. Breast Cancer Res Treat 114: 31–38. doi: 10.1007/s10549-008-9978-4
[8]
Peixoto A, Santos C, Pinheiro M, Pinto P, Soares M, et al. (2011) International distribution and age estimation of the Portuguese BRCA2 c.156_157insAlu founder mutation. Breast Cancer Res Treat 127: 671–679. doi: 10.1007/s10549-010-1036-3
[9]
de la Hoya M, Gutiérrez-Enríquez S, Velasco E, Osorio A, de Abajo AS, et al. (2006) Genomic rearrangements at the BRCA1 locus in Spanish families with breast/ovarian cancer. Clin Chem 52: 1480–1485. doi: 10.1373/clinchem.2006.070110
[10]
Gutiérrez-Enríquez S, de La Hoya M, Martínez-Bouzas C, de Abajo A, Cajal T, et al. (2007) Screening for large rearrangements of the BRCA2 gene in Spanish families with breast/ovarian cancer. Breast Cancer Res Treat 103: 103–107. doi: 10.1007/s10549-006-9376-8
[11]
Miramar M, Calvo M, Rodríguez A, Antón A, Lorente F, et al. (2008) Genetic analysis of BRCA1 and BRCA2 in breast/ovarian cancer families from Aragon (Spain): two novel truncating mutations and a large genomic deletion in BRCA1. Breast Cancer Res Treat 112: 353–358. doi: 10.1007/s10549-007-9868-1
[12]
del Valle J, Feliubadaló L, Nadal M, Teulé A, Miró R, et al. (2010) Identification and comprehensive characterization of large genomic rearrangements in the BRCA1 and BRCA2 genes. Breast Cancer Res Treat 122: 733–743. doi: 10.1007/s10549-009-0613-9
[13]
Rodríguez M, Torres A, Borràs J, Salvat M, Gumà J (2010) Large genomic rearrangements in mutation-negative BRCA families: a population-based study. Clin Genet 78: 405–407. doi: 10.1111/j.1399-0004.2010.01463.x
[14]
Ruiz de Garibay G, Gutiérrez-Enríquez S, Garre P, Bonache S, Romero A, et al. (2012) Characterization of four novel BRCA2 large genomic rearrangements in Spanish breast/ovarian cancer families: review of the literature, and reevaluation of the genetic mechanisms involved in their origin. Breast Cancer Res Treat 133: 273–283. doi: 10.1007/s10549-011-1909-0
[15]
Juan Jiménez I, García Casado Z, Palanca Suela S, Esteban Carde？osa E, López Guerrero J, et al.. (2013) Novel and recurrent BRCA1/BRCA2 mutations in early onset and familial breast and ovarian cancer detected in the Program of Genetic Counseling in Cancer of Valencian Community (eastern Spain). Relationship of family phenotypes with mutation prevalence. Fam Cancer: 1–11.
[16]
Blay P, Santamaria I, Pitiot A, Luque M, Alvarado M, et al. (2013) Mutational analysis of BRCA1 and BRCA2 in hereditary breast and ovarian cancer families from Asturias (Northern Spain). BMC Cancer 13: 243. doi: 10.1186/1471-2407-13-243
[17]
Palanca Suela S, Esteban Carde？osa E, Barragán González E, Oltra Soler S, de Juan Jiménez I, et al. (2008) Identification of a novel BRCA1 large genomic rearrangement in a Spanish breast/ovarian cancer family. Breast Cancer Res Treat 112: 63–67. doi: 10.1007/s10549-007-9839-6
[18]
Fachal L, Rodríguez-Pazos L, Ginarte M, Toribio J, Salas A, et al. (2012) Multiple local and recent founder effects of TGM1 in Spanish families. PLoS One 7: e33580. doi: 10.1371/journal.pone.0033580
[19]
Vega A, Campos B, Bressac-de-Paillerets B, Bond PM, Janin N, et al. (2001) The R71G BRCA1 is a founder Spanish mutation and leads to aberrant splicing of the transcript. Hum Mutat 17: 520–521. doi: 10.1002/humu.1136
[20]
Loidi L, Quinteiro C, Parajes S, Barreiro J, Lestón DG, et al. (2006) High variability in CYP21A2 mutated alleles in Spanish 21-hydroxylase deficiency patients, six novel mutations and a founder effect. Clin Endocrinol (Oxf) 64: 330–336. doi: 10.1111/j.1365-2265.2006.02465.x
[21]
Vega A, Torres M, Martínez JI, Ruiz-Ponte C, Barros F, et al. (2002) Analysis of BRCA1 and BRCA2 in breast and breast/ovarian cancer families shows population substructure in the Iberian peninsula. Ann Hum Genet 66: 29–36. doi: 10.1017/s0003480001001014
[22]
Galician Society of Medical Oncology (2011) Galician Hereditary Cancer Guide; Oncology GSoM, editor.
[23]
MRC-Holland website. Available: www.mrc-holland.com. Accessed 2014 Mar 6.
[24]
RepeatMasker Open-3.0 website. Available: http://www.repeatmasker.org. Accessed 2014 Mar 6.
[25]
García-Casado Z, Romero I, Fernandez-Serra A, Rubio L, Llopis F, et al. (2011) A de novo complete BRCA1 gene deletion identified in a Spanish woman with early bilateral breast cancer. BMC Med Genet 12: 134. doi: 10.1186/1471-2350-12-134
[26]
Konecny M, Zavodna K, Vranova V, Vizvaryova M, Weismanova E, et al. (2008) Identification of rare complete BRCA1 gene deletion using a combination of SNP haplotype analysis, MLPA and array-CGH techniques. Breast Cancer Res Treat 109: 581–583. doi: 10.1007/s10549-007-9670-0
[27]
Engert S, Wappenschmidt B, Betz B, Kast K, Kutsche M, et al. (2008) MLPA screening in the BRCA1 gene from 1,506 German hereditary breast cancer cases: novel deletions, frequent involvement of exon 17, and occurrence in single early-onset cases. Hum Mutat 29: 948–958. doi: 10.1002/humu.20723
[28]
Pylkas K, Erkko H, Nikkila J, Solyom S, Winqvist R (2008) Analysis of large deletions in BRCA1, BRCA2 and PALB2 genes in Finnish breast and ovarian cancer families. BMC Cancer 8: 146. doi: 10.1186/1471-2407-8-146
[29]
Gu W, Zhang F, Lupski JR (2008) Mechanisms for human genomic rearrangements. PathoGenetics 1: 4. doi: 10.1186/1755-8417-1-4
[30]
Palanca S, de Juan I, Perez-Simó G, Barragán E, Chirivella I, et al. (2013) The deletion of exons 3–5 of BRCA1 is the first founder rearrangement identified in breast and/or ovarian cancer Spanish families. Fam Cancer 12: 119–123. doi: 10.1007/s10689-012-9579-6
[31]
Feliubadalo L, Lopez-Doriga A, Castellsague E, del Valle J, Menendez M, et al.. (2012) Next-generation sequencing meets genetic diagnostics: development of a comprehensive workflow for the analysis of BRCA1 and BRCA2 genes. Eur J Hum Genet.
[32]
De Brakeleer S, De Grève J, Lissens W, Teugels E (2013) Systematic Detection of Pathogenic Alu Element Insertions in NGS-Based Diagnostic Screens: The BRCA1/BRCA2 Example. Hum Mutat 34: 785–791. doi: 10.1002/humu.22297
[33]
Hartmann C, John AL, Klaes R, Hofmann W, Bielen R, et al. (2004) Large BRCA1 gene deletions are found in 3% of German high-risk breast cancer families. Hum Mutat 24: 534–534. doi: 10.1002/humu.9291
[34]
Bunyan DJ, Eccles DM, Sillibourne J, Wilkins E, Thomas NS, et al. (2004) Dosage analysis of cancer predisposition genes by multiplex ligation-dependent probe amplification. Br J Cancer 91: 1155–1159.
