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Series GSE20406 Query DataSets for GSE20406
Status Public on Feb 18, 2011
Title Mutational screening of linkage assay-identified candidate regions in familial breast cancer
Organism Homo sapiens
Experiment type Genome variation profiling by high throughput sequencing
Summary 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 is a valid second step for identifying high penetrance genes.
 
Overall design 20 Samples / 4 Pooled Controls
 
Contributor(s) Rosa-Rosa JM, Gracia-Aznárez FJ, Hodges E, Pita G, Rooks M, Xuan Z, Bhattacharjee A, Brizuela L, Silva JM, Hannon G, Benitez J
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Submission date Feb 18, 2010
Last update date Dec 03, 2018
Contact name Javier Benitez
E-mail(s) jbenitez@cnio.es
Phone 00 34 917328057
Fax 00 34 912246911
URL http://www.cnio.es
Organization name National Cancer Research Centre CNIO
Department Human Cancer Genetics Program
Street address Melchor Fernandez Almagro 3
City Madrid
ZIP/Postal code 28029
Country Spain
 
Platforms (1)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
Samples (21)
GSM511164 Blood-extracted DNA_affected_Seq_07S722
GSM511165 Blood-extracted DNA_affected_Seq_07S723
GSM511166 Blood-extracted DNA_affected_Seq_07S724
Relations
BioProject PRJNA125541

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE20406_RAW.tar 6.1 Gb (http)(custom) TAR (of TXT)
GSE20406_Readme.txt 2.9 Kb (ftp)(http) TXT
Processed data provided as supplementary file

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