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Genome-wide reconstruction of complex structural variants using read clouds
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Genome-wide reconstruction of complex structural variants using read clouds
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Journal Article
Genome-wide reconstruction of complex structural variants using read clouds
2017
Overview
GROC-SVs enables the accurate detection and reconstruction of large and complex structural variants from read clouds generated by the 10x Genomics platform and subsequent Illumina sequencing.
In read cloud approaches, microfluidic partitioning of long genomic DNA fragments and barcoding of shorter fragments derived from these fragments retains long-range information in short sequencing reads. This combination of short reads with long-range information represents a powerful alternative to single-molecule long-read sequencing. We develop Genome-wide Reconstruction of Complex Structural Variants (GROC-SVs) for SV detection and assembly from read cloud data and apply this method to Illumina-sequenced 10x Genomics sarcoma and breast cancer data sets. Compared with short-fragment sequencing, GROC-SVs substantially improves the specificity of breakpoint detection at comparable sensitivity. This approach also performs sequence assembly across multiple breakpoints simultaneously, enabling the reconstruction of events exhibiting remarkable complexity. We show that chromothriptic rearrangements occurred before copy number amplifications, and that rates of single-nucleotide variants and SVs are not correlated. Our results support the use of read cloud approaches to advance the characterization of large and complex structural variation.
Publisher
Nature Publishing Group US,Nature Publishing Group
Subject
