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- Study Description
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Important Links and Information
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Request access via Authorized Access
- Instructions for requestors
- Data Use Certification (DUC) Agreement
- Talking Glossary of Genetic Terms
The project developed a suite of new methods (FAVR) designed to assist the shortlisting of genetic variants under a rare variant-phenotype/disease model. The methods were designed to work with commonly used massively parallel sequencing analysis pipelines, such as the GATK or ANNOVAR, and have been made publically available as a suite of software tools (https://github.com/bjpop/favr). The FAVR methods use signatures in comparator sequence alignment files to facilitate the filtering of mapping artifacts and common genetic variants, and annotation of genetic variants based on evidence of co-occurrence in individuals. As relevant, FAVR methods can also be used to filter out artifacts derived from imbalanced paired-end sequencing.
Pope et al., BMC Bioinformatics, accepted Dec 2012.
- Study Design:
- Family/Twin/Trios
- Study Type:
- Family
- dbGaP estimated ancestry using GRAF-pop
- Total number of consented subjects: 20
- Subject Sample Telemetry Report (SSTR)
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- Authorized Access
- Publicly Available Data
- Link to other NCBI resources related to this study
- Study Inclusion/Exclusion Criteria
Multiple-case breast cancer families.
- Molecular Data
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Type Source Platform Number of Oligos/SNPs SNP Batch Id Comment Whole Exome Sequencing Roche NimbleGen SeqCap EZ Human Exome Library v2.0 N/A N/A - Study History
See above.
- Selected Publications
- Diseases/Traits Related to Study (MeSH terms)
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- Primary Phenotype: Breast Neoplasms
- Authorized Data Access Requests
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See articles in PMC citing this study accession
- Study Attribution
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Principal Investigator
- Melissa Southey, PhD. The University of Melbourne, Melbourne, Australia.
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Co-investigator
- Daniel Park, PhD. The University of Melbourne, Melbourne, Australia.
- Bernard Pope, PhD. The University of Melbourne, Melbourne, Australia.
- Tu Nguyen-Dumont, PhD. The University of Melbourne, Melbourne, Australia.
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Funding Source
- R01CA155767. National Institutes of Health, Bethesda, MD, USA.
- APP1025145. National Health and Medical Research Council, Australia.
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Principal Investigator