Copy Number Variants with Shallow Sequencing
While working at MIT, Kristin Knouse (Amon Lab) and I developed a workflow to reliably detect copy number variants (CNVs) from shallow whole-genome sequencing data. Our goal was to investigate previous reports of unexpectedly high levels of large-scale CNVs in somatic neural cells. Through simulations, we defined optimal parameters for CNV detection and found that, using these optimized parameters, the prevalence of large CNVs in somatic cells is lower than previously reported, which aligns better with biological expectations. This work established a standard for calling CNVs from shallow whole-genome sequencing data in single cells.
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