Aug 16, 2018

Discovery of tandem and interspersed segmental duplications using high throughput sequencing

BioRxiv : the Preprint Server for Biology
Arda SoylevFereydoun Hormozdiari

Abstract

Several algorithms have been developed that use high throughput sequencing technology to characterize structural variations. Most of the existing approaches focus on detecting relatively simple types of SVs such as insertions, deletions, and short inversions. In fact, complex SVs are of crucial importance and several have been associated with genomic disorders. To better understand the contribution of complex SVs to human disease, we need new algorithms to accurately discover and genotype such variants. Additionally, due to similar sequencing signatures, inverted duplications or gene conversion events that include inverted segmental duplications are often characterized as simple inversions; and duplications and gene conversions in direct orientation may be called as simple deletions. Therefore, there is still a need for accurate algorithms to fully characterize complex SVs and thus improve calling accuracy of more simple variants. We developed novel algorithms to accurately characterize tandem, direct and inverted interspersed segmental duplications using short read whole genome sequencing data sets. We integrated these methods to our TARDIS tool, which is now capable of detecting various types of SVs using multiple sequence si...Continue Reading

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Mentioned in this Paper

Genome
Genes
Segmental Duplications, Genomic
Synaptic Vesicles
Gene Deletion
LECT1 gene
Haploid Cell
Genomics
Sequencing
Tandem

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