Identification and comprehensive characterization of large genomic rearrangements in the BRCA1 and BRCA2 genes

Valle, Jesús Del; Feliubadaló, Lídia; Nadal, Marga; Teulé, Àlex; Miró, Rosa; Cuesta, Raquel; Tornero, Eva; Menéndez, Mireia; Darder, Esther; Brunet, Joan; Capellà, Gabriel; Blanco, Ignacio; Lázaro, Conxi

doi:10.1007/s10549-009-0613-9

Cited by 36 publications

(36 citation statements)

References 32 publications

(48 reference statements)

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“…19,20 These samples were analyzed in subsequent runs mixed with samples without LGRs. In summary, all LGRs were detected (Figure 3 and Supplementary Figure 6B), duplications showed normalized amplicon values above 1.3 and deletions showed values below 0.7.…”

Section: Large Rearrangements Detectionmentioning

confidence: 99%

Next-generation sequencing meets genetic diagnostics: development of a comprehensive workflow for the analysis of BRCA1 and BRCA2 genes

et al. 2012

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Next-generation sequencing (NGS) is changing genetic diagnosis due to its huge sequencing capacity and cost-effectiveness. The aim of this study was to develop an NGS-based workflow for routine diagnostics for hereditary breast and ovarian cancer syndrome (HBOCS), to improve genetic testing for BRCA1 and BRCA2. A NGS-based workflow was designed using BRCA MASTR kit amplicon libraries followed by GS Junior pyrosequencing. Data analysis combined Variant Identification Pipeline freely available software and ad hoc R scripts, including a cascade of filters to generate coverage and variant calling reports. A BRCA homopolymer assay was performed in parallel. A research scheme was designed in two parts. A Training Set of 28 DNA samples containing 23 unique pathogenic mutations and 213 other variants (33 unique) was used. The workflow was validated in a set of 14 samples from HBOCS families in parallel with the current diagnostic workflow (Validation Set). The NGS-based workflow developed permitted the identification of all pathogenic mutations and genetic variants, including those located in or close to homopolymers. The use of NGS for detecting copy-number alterations was also investigated. The workflow meets the sensitivity and specificity requirements for the genetic diagnosis of HBOCS and improves on the cost-effectiveness of current approaches.

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Section: Large Rearrangements Detectionmentioning

confidence: 99%

Next-generation sequencing meets genetic diagnostics: development of a comprehensive workflow for the analysis of BRCA1 and BRCA2 genes

et al. 2012

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“…The high proportion of LGRs detected in the Hispanic population of the USA can be explained by a single founder deletion of exons 9-12 [41]. In Spain, the frequency of LGRs affecting the BRCA1/2 genes has been estimated at around 2% in BRCA1 and 1.5% in BRCA2 in cases previously testing negative for BRCA1/2 point mutations [42]. In Asian populations, LGRs account for 3% of case in Singapore [43] and 0.8% in Korea [44].…”

Section: Large Genomic Rearrangementsmentioning

confidence: 99%

Spectrum of BRCA1/2 point mutations and genomic rearrangements in high-risk breast/ovarian cancer Chilean families

González‐Hormazábal

Gutiérrez-Enríquez

Gaete

et al. 2010

Breast Cancer Res Treat

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The distribution of BRCA1/2 germline mutations in breast/ovarian cancer (BC/OC) families varies among different populations. In the Chilean population, there are only two reports of mutation analysis of BRCA1/2, and these included a low number of BC and/or OC patients. Moreover, the prevalence of BRCA1/2 genomic rearrangements in Chilean and in other South American populations is unknown. In this article, we present the mutation-detection data corresponding to a set of 326 high-risk families analyzed by conformation-sensitive gel electrophoresis and heteroduplex analysis. To determine the contribution of BRCA1/2 LGRs in Chilean BC patients, we analyzed 56 high-risk subjects with no pathogenic BRCA1/2 point mutations. Germline BRCA1/2 point mutations were found in 23 (7.1%) of the 326 Chilean families. Families which had at least three BC and/or OC cases showed the highest frequency of mutations (15.9%). We identified 14 point pathogenic mutations. Three recurrent mutations in BRCA1 (c.187_188delAG, c.2605_2606delTT, and c.3450_3453delCAAG) and three in BRCA2 (c.4969_4970insTG, c.5374_5377delTATG, and c.6503_6504delTT) contributed to 63.6 and 66.7% of all the deleterious mutations of each gene, which may reflect the presence of region-specific founder effects. Taken together BRCA1/2 recurrent point mutations account for 65.2% (15/23) of the BRCA1/2 (+) families. No large deletions or duplications involving BRCA1/2 were identified in a subgroup of 56 index cases negative for BRCA1/2 point mutations. Our study, which is the largest conducted to date in a South American population, provides a comprehensive analysis on the type and distribution of BRCA1/2 mutations and allelic variants.

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“…In relation to point mutations in BRCA1 and BRCA2 in Chilean breast cancer families, it was found that 40% of mutations detected are from Spanish origin [5], being recurrent mutations in the population. In relation to LGRs in BRCA1 found in the Spanish population, the reports describe mainly deletions [33][34][35][36] and few duplications. Among duplications one study reported an extra copy of exon 20 in BRCA1 [33], but no segregation or other analysis were performed in order to determine the pathologic relevance of this duplication.…”

Section: Discussionmentioning

confidence: 99%

Genomic rearrangements of the BRCA1 gene in Chilean breast cancer families: an MLPA analysis

Sánchez

Faundez

Carvallo

2011

Breast Cancer Res Treat

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Point mutations and small deletions and insertions in BRCA1 and BRCA2 genes are responsible of about 20% of hereditary breast cancer cases in Chilean population. Studies in other populations have identified the amplification and/or deletion of one or more exons in these genes as the cause of the disease. In this study the authors determined the presence of these types of alterations in BRCA1 and BRCA2, in 74 Chilean families with breast/ovarian cancer that were negative for germline mutations in these genes. Since these alterations are not detectable using the conventional PCR-based methods, the authors use MLPA (multiplex ligation-dependent probe amplification) to detect amplifications and/or deletions in BRCA1 and BRCA2 genes. The authors identified two different alterations in BRCA1: exon 10 duplication in one family and amplification of exons 3, 5, and 6 in two families. Duplication of exon 10 contains intronic adjacent sequences suggesting gene duplication. The second rearrangement consist of a 4 times amplification of a fragment containing exons 3, 5, and 6 joined together with no introns, suggesting the presence of a processed pseudogene. No alterations were detected in BRCA2. In order to validate the MLPA results and characterize the genomic alterations the authors performed qPCR, long range PCR, and sequencing.

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Identification and comprehensive characterization of large genomic rearrangements in the BRCA1 and BRCA2 genes

Cited by 36 publications

References 32 publications

Next-generation sequencing meets genetic diagnostics: development of a comprehensive workflow for the analysis of BRCA1 and BRCA2 genes

Next-generation sequencing meets genetic diagnostics: development of a comprehensive workflow for the analysis of BRCA1 and BRCA2 genes

Spectrum of BRCA1/2 point mutations and genomic rearrangements in high-risk breast/ovarian cancer Chilean families

Genomic rearrangements of the BRCA1 gene in Chilean breast cancer families: an MLPA analysis

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