Abstract
Recent advances in single cell technology have enabled dissection of cellular heterogeneity in great detail. However, analysis of single cell DNA sequencing data remains challenging due to bias and artifacts that arise during DNA extraction and whole-genome amplification, including allelic imbalance and dropout. Here, we present a framework for statistical estimation of allele-specific amplification imbalance at any given position in single cell whole-genome sequencing data by utilizing the allele frequencies of heterozygous single nucleotide polymorphisms in the neighborhood. The resulting allelic imbalance profile is critical for determining whether the variant allele fraction of an observed mutation is consistent with the expected fraction for a true variant. This method, implemented in SCAN-SNV (Single Cell ANalysis of SNVs), substantially improves the identification of somatic variants in single cells. Our allele balance framework is broadly applicable to genotype analysis of any variant type in any data that might exhibit allelic imbalance.
Highlights
Recent advances in single cell technology have enabled dissection of cellular heterogeneity in great detail
We demonstrate how allelic imbalance can lead to false positive (FP) variant calls in practice and how estimating amplification balance (AB) can help to avoid such erroneous calls
We show how to approximate the prevalence of single-cell artifacts and bound the somatic mutation rate prior to genotyping, which can help to control the false discovery rate (FDR)
Summary
Recent advances in single cell technology have enabled dissection of cellular heterogeneity in great detail. The resulting allelic imbalance profile is critical for determining whether the variant allele fraction of an observed mutation is consistent with the expected fraction for a true variant This method, implemented in SCAN-SNV (Single Cell ANalysis of SNVs), substantially improves the identification of somatic variants in single cells. For example, the maternal copy of a gene can be amplified to a different level than the paternal copy, leading to a large disparity in the number of sequencing reads generated from each allele. This allelic imbalance is common in MDA-amplified DNA libraries and substantially complicates the identification of somatic mutations—which appear as heterozygous variants—in scDNA-
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
