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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
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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.
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Overall design |
20 Samples / 4 Pooled Controls
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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 |
Citation missing |
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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
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Phone |
00 34 917328057
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Fax |
00 34 912246911
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URL |
http://www.cnio.es
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Organization name |
National Cancer Research Centre CNIO
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Department |
Human Cancer Genetics Program
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Street address |
Melchor Fernandez Almagro 3
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City |
Madrid |
ZIP/Postal code |
28029 |
Country |
Spain |
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Platforms (1) |
GPL9115 |
Illumina Genome Analyzer II (Homo sapiens) |
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Samples (21)
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GSM511164 |
Blood-extracted DNA_affected_Seq_07S722 |
GSM511165 |
Blood-extracted DNA_affected_Seq_07S723 |
GSM511166 |
Blood-extracted DNA_affected_Seq_07S724 |
GSM511167 |
Blood-extracted DNA_affected_Seq_07S725 |
GSM511168 |
Blood-extracted DNA_affected_Seq_06-240 |
GSM511169 |
Blood-extracted DNA_affected_Seq_96-652 |
GSM511170 |
Blood-extracted DNA_affected_Seq_I-1408 |
GSM511171 |
Blood-extracted DNA_affected_Seq_I-904 |
GSM511172 |
Blood-extracted DNA_affected_Seq_07S635 |
GSM511173 |
Blood-extracted DNA_affected_Seq_07S636 |
GSM511174 |
Blood-extracted DNA_affected_Seq_04-168 |
GSM511175 |
Blood-extracted DNA_affected_Seq_96-265 |
GSM511176 |
Blood-extracted DNA_affected_Seq_07S576 |
GSM511177 |
Blood-extracted DNA_affected_Seq_07S581 |
GSM511178 |
Blood-extracted DNA_affected_Seq_I-1627 |
GSM511179 |
Blood-extracted DNA_affected_Seq_I-3345 |
GSM511180 |
Blood-extracted DNA_affected_Seq_I-1927 |
GSM511181 |
Blood-extracted DNA_affected_Seq_I-1928 |
GSM511182 |
Blood-extracted DNA_affected_Seq_I-2033 |
GSM511183 |
Blood-extracted DNA_affected_Seq_I-4347 |
GSM511184 |
Blood-extracted DNA_healthy_Seq |
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Relations |
BioProject |
PRJNA125541 |