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Complex Characterization of Germline Large Genomic Rearrangements of the BRCA1 and BRCA2 Genes in High-Risk Breast Cancer Patients-Novel Variants from a Large National Center. Int J Mol Sci 2020; 21:ijms21134650. [PMID: 32629901 PMCID: PMC7370166 DOI: 10.3390/ijms21134650] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/19/2020] [Accepted: 06/27/2020] [Indexed: 12/23/2022] Open
Abstract
Large genomic rearrangements (LGRs) affecting one or more exons of BRCA1 and BRCA2 constitute a significant part of the mutation spectrum of these genes. Since 2004, the National Institute of Oncology, Hungary, has been involved in screening for LGRs of breast or ovarian cancer families enrolled for genetic testing. LGRs were detected by multiplex ligation probe amplification method, or next-generation sequencing. Where it was possible, transcript-level characterization of LGRs was performed. Phenotype data were collected and analyzed too. Altogether 28 different types of LGRs in 51 probands were detected. Sixteen LGRs were novel. Forty-nine cases were deletions or duplications in BRCA1 and two affected BRCA2. Rearrangements accounted for 10% of the BRCA1 mutations. Three exon copy gains, two complex rearrangements, and 23 exon losses were characterized by exact breakpoint determinations. The inferred mechanisms for LGR formation were mainly end-joining repairs utilizing short direct homologies. Comparing phenotype features of the LGR-carriers to that of the non-LGR BRCA1 mutation carriers, revealed no significant differences. Our study is the largest comprehensive report of LGRs of BRCA1/2 in familial breast and ovarian cancer patients in the Middle and Eastern European region. Our data add novel insights to genetic interpretation associated to the LGRs.
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Ewald IP, Cossio SL, Palmero EI, Pinheiro M, Nascimento ILDO, Machado TMB, Sandes KA, Toralles B, Garicochea B, Izetti P, Pereira MLS, Bock H, Vargas FR, Moreira MÂM, Peixoto A, Teixeira MR, Ashton-Prolla P. BRCA1 and BRCA2 rearrangements in Brazilian individuals with Hereditary Breast and Ovarian Cancer Syndrome. Genet Mol Biol 2016; 39:223-31. [PMID: 27303907 PMCID: PMC4910561 DOI: 10.1590/1678-4685-gmb-2014-0350] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Accepted: 03/16/2015] [Indexed: 01/09/2023] Open
Abstract
Approximately 5-10% of breast cancers are caused by germline mutations in high
penetrance predisposition genes. Among these, BRCA1 and
BRCA2, which are associated with the Hereditary Breast and
Ovarian Cancer (HBOC) syndrome, are the most frequently affected genes. Recent
studies confirm that gene rearrangements, especially in BRCA1, are
responsible for a significant proportion of mutations in certain populations. In this
study we determined the prevalence of BRCA rearrangements in 145
unrelated Brazilian individuals at risk for HBOC syndrome who had not been previously
tested for BRCA mutations. Using Multiplex Ligation-dependent Probe
Amplification (MLPA) and a specific PCR-based protocol to identify a Portuguese
founder BRCA2 mutation, we identified two (1,4%) individuals with
germline BRCA1 rearrangements (c.547+240_5193+178del and
c.4675+467_5075-990del) and three probands with the c.156_157insAlu founder
BRCA2 rearrangement. Furthermore, two families with false
positive MLPA results were shown to carry a deleterious point mutation at the probe
binding site. This study comprises the largest Brazilian series of HBOC families
tested for BRCA1 and BRCA2 rearrangements to date
and includes patients from three regions of the country. The overall observed
rearrangement frequency of 3.44% indicates that rearrangements are relatively
uncommon in the admixed population of Brazil.
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Affiliation(s)
- Ingrid Petroni Ewald
- Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Medicina: Ciências Médicas, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Silvia Liliana Cossio
- Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, RS, Brazil
| | - Edenir Inez Palmero
- Centro de Pesquisa em Oncologia Molecular - Hospital do Câncer de Barretos, Barretos, SP, Brazil
| | - Manuela Pinheiro
- Departamento de Genética, Instituto Português de Oncologia do Porto, Porto, Portugal
| | - Ivana Lucia de Oliveira Nascimento
- Laboratório de Imunologia e Biologia Molecular, Instituto de Ciências da Saúde (ICS), Universidade Federal da Bahia (UFBA), Salvador, BA, Brazil
| | - Taisa Manuela Bonfim Machado
- Laboratório de Imunologia e Biologia Molecular, Instituto de Ciências da Saúde (ICS), Universidade Federal da Bahia (UFBA), Salvador, BA, Brazil
| | - Kiyoko Abe Sandes
- Laboratório de Imunologia e Biologia Molecular, Instituto de Ciências da Saúde (ICS), Universidade Federal da Bahia (UFBA), Salvador, BA, Brazil
| | - Betânia Toralles
- Departamento de Pediatria, Universidade Federal da Bahia (UFBA), Salvador, BA, Brazil
| | | | - Patricia Izetti
- Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, RS, Brazil.,Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Maria Luiza Saraiva Pereira
- Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Laboratório de Identificação Genética, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, RS, Brazil
| | - Hugo Bock
- Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, RS, Brazil
| | - Fernando Regla Vargas
- Departamento de Bioquímica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Divisão de Genética, Instituto Nacional de Câncer (INCA), Rio de Janeiro, RJ, Brazil
| | - Miguel Ângelo Martins Moreira
- Departamento de Bioquímica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Instituto Nacional de Genética Médica Populacional (INAGEMP), Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, RS, Brazil.,Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz (IOC-FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Ana Peixoto
- Departamento de Genética, Instituto Português de Oncologia do Porto, Porto, Portugal
| | - Manuel R Teixeira
- Departamento de Genética, Instituto Português de Oncologia do Porto, Porto, Portugal.,Departamento de Genética e Biologia Molecular, Centro de Ciências Biológicas e da Saúde, Universidade Federal do Estado do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Patricia Ashton-Prolla
- Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Medicina: Ciências Médicas, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Porto, Portugal.,Divisão de Genética, Instituto Nacional de Câncer (INCA), Rio de Janeiro, RJ, Brazil
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Mancini-DiNardo D, Judkins T, Woolstenhulme N, Burton C, Schoenberger J, Ryder M, Murray A, Gutin N, Theisen A, Holladay J, Craft J, Arnell C, Moyes K, Roa B. Design and validation of an oligonucleotide microarray for the detection of genomic rearrangements associated with common hereditary cancer syndromes. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2014; 33:74. [PMID: 25204323 PMCID: PMC4174268 DOI: 10.1186/s13046-014-0074-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 08/29/2014] [Indexed: 12/14/2022]
Abstract
Background Conventional Sanger sequencing reliably detects the majority of genetic mutations associated with hereditary cancers, such as single-base changes and small insertions or deletions. However, detection of genomic rearrangements, such as large deletions and duplications, requires special technologies. Microarray analysis has been successfully used to detect large rearrangements (LRs) in genetic disorders. Methods We designed and validated a high-density oligonucleotide microarray for the detection of gene-level genomic rearrangements associated with hereditary breast and ovarian cancer (HBOC), Lynch, and polyposis syndromes. The microarray consisted of probes corresponding to the exons and flanking introns of BRCA1 and BRCA2 (≈1,700) and Lynch syndrome/polyposis genes MLH1, MSH2, MSH6, APC, MUTYH, and EPCAM (≈2,200). We validated the microarray with 990 samples previously tested for LR status in BRCA1, BRCA2, MLH1, MSH2, MSH6, APC, MUTYH, or EPCAM. Microarray results were 100% concordant with previous results in the validation studies. Subsequently, clinical microarray analysis was performed on samples from patients with a high likelihood of HBOC mutations (13,124), Lynch syndrome mutations (18,498), and polyposis syndrome mutations (2,739) to determine the proportion of LRs. Results Our results demonstrate that LRs constitute a substantial proportion of genetic mutations found in patients referred for hereditary cancer genetic testing. Conclusion The use of microarray comparative genomic hybridization (CGH) for the detection of LRs is well-suited as an adjunct technology for both single syndrome (by Sanger sequencing analysis) and extended gene panel testing by next generation sequencing analysis. Genetic testing strategies using microarray analysis will help identify additional patients carrying LRs, who are predisposed to various hereditary cancers.
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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. PLoS One 2014; 9:e93306. [PMID: 24686251 PMCID: PMC3970959 DOI: 10.1371/journal.pone.0093306] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 02/28/2014] [Indexed: 11/19/2022] Open
Abstract
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_41399840delinsAluSx1, 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).
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Ruiz de Garibay G, Gutiérrez-Enríquez S, Garre P, Bonache S, Romero A, Palomo L, Sánchez de Abajo A, Benítez J, Balmaña J, Pérez-Segura P, Díaz-Rubio E, Díez O, Caldés T, de la Hoya M. 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 2012; 133:273-83. [PMID: 22434521 DOI: 10.1007/s10549-011-1909-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 11/30/2011] [Indexed: 11/30/2022]
Abstract
Large genomic rearrangements (LGRs) at the BRCA2 locus explain a non-negligible proportion of hereditary breast and ovarian cancer (HBOC) syndromes. The multiplex ligation and probe amplification (MLPA) assay has permitted in recent years to identify several families carrying LGRs at this locus, but very few such alterations have been fully characterized at the molecular level. Yet, molecular characterization is essential to identify recurrent alterations, to analyze the genetic mechanisms underlying such alterations, or to investigate potential genotype/phenotype relationships. We have used MLPA to identify BRCA2 LGRs in 7 out of 813 Spanish HBOC families previously tested negative for BRCA1 and BRCA2 small genomic alterations (substitutions and indels) and BRCA1 LGRs. We used a combination of long-range PCR, restriction mapping, and cDNA analysis to characterize the alterations at the molecular level. We found that Del Exon1-Exon2, Del Exon12-Exon16 and Del Exon22-Exon24 explain one family each, while Del Exon2 appears to be a Spanish founder mutation explaining four independent families. Finally, we have combined our data with a comprehensive review of the literature to reevaluate the genetic mechanisms underlying LGRs at the BRCA2 locus. Our study substantially increases the spectrum of BRCA2 LGRs fully characterized at the molecular level. Further on, we provide data to suggest that non-allelic homologous recombination has been overestimated as a mechanism underlying these alterations, while the opposite might be true for microhomology-mediated events.
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Affiliation(s)
- Gorka Ruiz de Garibay
- Laboratorio de Oncología Molecular, Instituto de Investigación Sanitaria San Carlos, Hospital Clínico San Carlos, C/Martín Lagos s/n, 28040 Madrid, Spain
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