Biology Faculty Articles

Document Type

Article

Publication Date

7-11-2018

Publication Title

PLoS One

Keywords

Genome sequencing, Variant genotypes, Genotyping, Genomics, Genomic medicine, DNA libraries, Genomic libraries, Sequence assembly tools

ISSN

1932-6203

Volume

13

Issue/No.

7

First Page

e0200423

Abstract

A comparative analysis of whole genome sequencing (WGS) and genotype calling was initiated for ten human genome samples sequenced by St. Petersburg State University Peterhof Sequencing Center and by three commercial sequencing centers outside of Russia. The sequence quality, efficiency of DNA variant and genotype calling were compared with each other and with DNA microarrays for each of ten study subjects. We assessed calling of SNPs, indels, copy number variation, and the speed of WGS throughput promised. Twenty separate QC analyses showed high similarities among the sequence quality and called genotypes. The ten genomes tested by the centers included eight American patients afflicted with autoimmune hepatitis (AIH), plus one case’s unaffected parents, in a prelude to discovering genetic influences in this rare disease of unknown etiology. The detailed internal replication and parallel analyses allowed the observation of two of eight AIH cases carrying a rare allele genotype for a previously described AIH-associated gene (FTCD), plus multiple occurrences of known HLA-DRB1 alleles associated with AIH (HLA-DRB1-03:01:01, 13:01:01 and 7:01:01). We also list putative SNVs in other genes as suggestive in AIH influence.

Comments

©2018 Zhernakova et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Additional Comments

St. Petersburg State University Genome Russia Grant #: 1.52.1647.2016

ORCID ID

0000-0001-7353-8301

ResearcherID

N-1726-2015

DOI

10.1371/journal.pone.0200423

Peer Reviewed

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