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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

Rare variant phasing and haplotypic expression from RNA sequencing with phASER.

Stephane E Castel^1,2, Pejman Mohammadi^1,2, Wendy K Chung³

¹New York Genome Center, New York, NY, 10013, USA.

Nature Communications

|September 9, 2016

Summary

Phasing genetic variants using RNA sequencing (RNA-seq) with the phASER tool accurately identifies rare variants and improves the study of compound heterozygotes. This method enhances analyses of allelic expression and rare variant haplotypes.

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Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Haplotype phasing is crucial for understanding genetic variation's clinical and functional impact.
Existing methods struggle with phasing variants overlapped by sequencing reads, especially in RNA sequencing (RNA-seq).

Purpose of the Study:

To introduce phASER, a novel approach for accurate haplotype phasing using RNA-seq data.
To demonstrate phASER's ability to phase variants, including rare ones, over long distances within genes.

Main Methods:

Development and application of the phASER algorithm for variant phasing.
Utilizing diverse RNA-seq datasets to evaluate phasing accuracy.
Comparison with population-based phasing and DNA sequencing (DNA-seq) read-based phasing.

Main Results:

PhASER achieves accurate phasing of variants overlapped by RNA-seq reads, outperforming population-based methods for rare variants.
Enables phasing of variants up to hundreds of kilobases apart within the same gene.
Improves resolution of compound heterozygotes in medical genetics studies.
Provides accurate measures of haplotypic expression, boosting power in allelic expression studies.

Conclusions:

Phasing with RNA-seq and phASER is highly accurate and reliable.
This approach enhances studies requiring rare variant haplotype information or precise allelic expression analysis.