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 V.
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.
N1 - Publisher Copyright:
© 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.
PY - 2018/7
Y1 - 2018/7
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.
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U2 - 10.1371/journal.pone.0200423
DO - 10.1371/journal.pone.0200423
M3 - Article
C2 - 29995946
AN - SCOPUS:85049688029
SN - 1932-6203
VL - 13
JO - PloS one
JF - PloS one
IS - 7
M1 - e0200423
ER -