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Updated: May 30, 2026

Detection of Copy Number Alterations Using Single Cell Sequencing
Published on: February 17, 2017
Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV
Jarupon Fah Sathirapongsasuti1, Hane Lee, Basil A J Horst
1Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA. fsathira@fas.harvard.edu
Motivation:
The ability to detect copy-number variation (CNV) and loss of heterozygosity (LOH) from exome sequencing data extends the utility of this powerful approach that has mainly been used for point or small insertion/deletion detection.
Results:
We present ExomeCNV, a statistical method to detect CNV and LOH using depth-of-coverage and B-allele frequencies, from mapped short sequence reads, and we assess both the method's power and the effects of confounding variables. We apply our method to a cancer exome resequencing dataset. As expected, accuracy and resolution are dependent on depth-of-coverage and capture probe design.
Availability:
CRAN package 'ExomeCNV'.
Contact:
fsathira@fas.harvard.edu; snelson@ucla.edu
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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