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Detection of Copy Number Alterations Using Single Cell Sequencing

Detection of Copy Number Alterations Using Single Cell Sequencing

Published on: February 17, 2017

XCAVATOR: accurate detection and genotyping of copy number variants from second and third generation whole-genome

Alberto Magi¹, Tommaso Pippucci², Carlo Sidore³

¹Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, Florence, 50134, Italy. albertomagi@gmail.com.

|September 23, 2017

Abstract

Background:

We developed a novel software package, XCAVATOR, for the identification of genomic regions involved in copy number variants/alterations (CNVs/CNAs) from short and long reads whole-genome sequencing experiments.

Results:

By using simulated and real datasets we showed that our tool, based on read count approach, is capable to predict the boundaries and the absolute number of DNA copies CNVs/CNAs with high resolutions. To demonstrate the power of our software we applied it to the analysis Illumina and Pacific Bioscencies data and we compared its performance to other ten state of the art tools.

Conclusion:

All the analyses we performed demonstrate that XCAVATOR is capable to detect germline and somatic CNVs/CNAs outperforming all the other tools we compared. XCAVATOR is freely available at http://sourceforge.net/projects/xcavator/ .

Keywords:

CNVs HMM Whole-Genome Sequencing

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Comparing Copy Number Variations and SNPs

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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...

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