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Rare Variant Phasing and Haplotypic Expression from RNA-Sequencing with phASER

Stephane E. Castel, Pejman Mohammadi, Wendy K. Chung, Yufeng Shen, Tuuli Lappalainen
doi: https://doi.org/10.1101/039529
Stephane E. Castel
1New York Genome Center, New York, NY
2Department of Systems Biology, Columbia University, New York, NY
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  • For correspondence: scastel@nygenome.org tlappalainen@nygenome.org
Pejman Mohammadi
1New York Genome Center, New York, NY
2Department of Systems Biology, Columbia University, New York, NY
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Wendy K. Chung
3Departments of Pediatrics and Medicine, Columbia University, New York, NY
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Yufeng Shen
2Department of Systems Biology, Columbia University, New York, NY
4Department of Biomedical Informatics, Columbia University, New York, NY
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Tuuli Lappalainen
1New York Genome Center, New York, NY
2Department of Systems Biology, Columbia University, New York, NY
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  • For correspondence: scastel@nygenome.org tlappalainen@nygenome.org
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Abstract

Haplotype phasing of genetic variants is important for clinical interpretation of the genome, population genetic analysis, and functional genomic analysis of allelic activity. Here we present phASER, a fast and accurate approach for phasing variants that are overlapped by sequencing reads, including those from RNA-sequencing (RNA-seq), which often span multiple exons due to splicing. This provides 1) dramatically more accurate phasing of rare and de novo variants compared to population-based phasing; 2) phasing of variants in the same gene up to hundreds of kilobases away which cannot be obtained from DNA-sequencing reads; 3) high confidence measures of haplotypic expression, greatly improving power for allelic expression studies.

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Posted June 03, 2016.
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Rare Variant Phasing and Haplotypic Expression from RNA-Sequencing with phASER
Stephane E. Castel, Pejman Mohammadi, Wendy K. Chung, Yufeng Shen, Tuuli Lappalainen
bioRxiv 039529; doi: https://doi.org/10.1101/039529
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Rare Variant Phasing and Haplotypic Expression from RNA-Sequencing with phASER
Stephane E. Castel, Pejman Mohammadi, Wendy K. Chung, Yufeng Shen, Tuuli Lappalainen
bioRxiv 039529; doi: https://doi.org/10.1101/039529

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