Deep sequencing of target linkage assay-identified regions in familial breast cancer: methods, analysis pipeline and troubleshooting

Rosa-Rosa, J. M., Gracia-Aznarez, F. J., Hodges, E., Pita, G., Rooks, M., Xuan, Z., Bhattacharjee, A., Brizuela, L., Silva, J. M., Hannon, G. J., Benitez, J. (2010) Deep sequencing of target linkage assay-identified regions in familial breast cancer: methods, analysis pipeline and troubleshooting. PLoS One, 5 (4). e9976. ISSN 1932-6203

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URL: http://www.ncbi.nlm.nih.gov/pubmed/20368986
DOI: 10.1371/journal.pone.0009976

Abstract

BACKGROUND: The classical candidate-gene approach has failed to identify novel breast cancer susceptibility genes. Nowadays, massive parallel sequencing technology allows the development of studies unaffordable a few years ago. However, analysis protocols are not yet sufficiently developed to extract all information from the huge amount of data obtained. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we performed high throughput sequencing in two regions located on chromosomes 3 and 6, recently identified by linkage studies by our group as candidate regions for harbouring breast cancer susceptibility genes. In order to enrich for the coding regions of all described genes located in both candidate regions, a hybrid-selection method on tiling microarrays was performed. CONCLUSIONS/SIGNIFICANCE: We developed an analysis pipeline based on SOAP aligner to identify candidate variants with a high real positive confirmation rate (0.89), with which we identified eight variants considered candidates for functional studies. The results suggest that the present strategy might be a valid second step for identifying high penetrance genes.

Item Type: Paper
Uncontrolled Keywords: Breast Neoplasms/epidemiology/*genetics Chromosomes, Human, Pair 3 Chromosomes, Human, Pair 6 Family Health Female *Genetic Linkage Genetic Predisposition to Disease Genetic Variation Humans Penetrance Polymorphism, Single Nucleotide Sequence Analysis, DNA/*methods
Subjects: diseases & disorders > cancer > cancer types > breast cancer
Investigative techniques and equipment > assays > whole genome sequencing
CSHL Authors:
Communities: CSHL labs > Hannon lab
CSHL Cancer Center Shared Resources > Bioinformatics Service
Depositing User: Matt Covey
Date: 2010
Date Deposited: 30 Dec 2014 15:30
Last Modified: 30 Dec 2014 15:30
PMCID: PMC2848842
Related URLs:
URI: http://repository.cshl.edu/id/eprint/30996

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