TY - JOUR

T1 - Analytical "bake-off" of whole genome sequencing quality for the Genome Russia project using a small cohort for autoimmune hepatitis

AU - Zhernakova, Daria

AU - Kliver, Sergei

AU - Cherkasov, Nikolay

AU - Tamazian, Gaik

AU - Rotkevich, Mikhail

AU - Krasheninnikova, Ksenia

AU - Evsyukov, Igor

AU - Sidorov, Sviatoslav

AU - Dobrynin, Pavel

AU - Yurchenko, Andrey A

AU - Shimansky, Valentin

AU - Shcherbakova, Irina V

AU - Glotov, Andrey S

AU - Valle, David L

AU - Tang, Minzhong

AU - Shin, Emilia

AU - Schwarz, Kathleen B

AU - O'Brien, Stephen J

PY - 2018/7/11

Y1 - 2018/7/11

N2 - 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.

AB - 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.

KW - ALIGNMENT

KW - GENE POLYMORPHISMS

KW - REGION

KW - SUSCEPTIBILITY

KW - TYPE-1

KW - VARIANTS

KW - WIDE ASSOCIATION

UR - http://www.scopus.com/inward/record.url?scp=85049688029&partnerID=8YFLogxK

UR - http://www.mendeley.com/research/analytical-bakeoff-whole-genome-sequencing-quality-genome-russia-project-using-small-cohort-autoimmu

U2 - 10.1371/journal.pone.0200423

DO - 10.1371/journal.pone.0200423

M3 - Article

C2 - 29995946

VL - 13

SP - e0200423

JO - PLoS ONE

JF - PLoS ONE

SN - 1932-6203

IS - 7

M1 - e0200423

ER -