Analytical “bake-off” of whole genome sequencing quality for the genome Russia project using a small cohort for autoimmune hepatitis

Daria V. Zhernakova, Sergei Kliver, Nikolay Cherkasov, Gaik Tamazian, Mikhail Rotkevich, Ksenia Krasheninnikova, Igor Evsyukov, Sviatoslav Sidorov, Pavel Dobrynin, Andrey A. Yurchenko, Valentin Shimansky, Irina V. Shcherbakova, Andrey S. Glotov, David Valle, Minzhong Tang, Emilia Shin, Kathleen Schwarz, Stephen J. O’Brien

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Article numbere0200423
JournalPLoS One
Volume13
Issue number7
DOIs
StatePublished - Jul 1 2018

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autoimmune hepatitis
Autoimmune Hepatitis
Russia
Genes
Genome
Genotype
genome
genotype
Alleles
alleles
HLA-DRB1 Chains
Human Genome
Rare Diseases
Oligonucleotide Array Sequence Analysis
DNA
Single Nucleotide Polymorphism
etiology
Microarrays
genes
Parents

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Zhernakova, D. V., Kliver, S., Cherkasov, N., Tamazian, G., Rotkevich, M., Krasheninnikova, K., ... O’Brien, S. J. (2018). Analytical “bake-off” of whole genome sequencing quality for the genome Russia project using a small cohort for autoimmune hepatitis. PLoS One, 13(7), [e0200423]. https://doi.org/10.1371/journal.pone.0200423

Analytical “bake-off” of whole genome sequencing quality for the genome Russia project using a small cohort for autoimmune hepatitis. / Zhernakova, Daria V.; Kliver, Sergei; Cherkasov, Nikolay; Tamazian, Gaik; Rotkevich, Mikhail; Krasheninnikova, Ksenia; Evsyukov, Igor; Sidorov, Sviatoslav; Dobrynin, Pavel; Yurchenko, Andrey A.; Shimansky, Valentin; Shcherbakova, Irina V.; Glotov, Andrey S.; Valle, David; Tang, Minzhong; Shin, Emilia; Schwarz, Kathleen; O’Brien, Stephen J.

In: PLoS One, Vol. 13, No. 7, e0200423, 01.07.2018.

Research output: Contribution to journalArticle

Zhernakova, DV, Kliver, S, Cherkasov, N, Tamazian, G, Rotkevich, M, Krasheninnikova, K, Evsyukov, I, Sidorov, S, Dobrynin, P, Yurchenko, AA, Shimansky, V, Shcherbakova, IV, Glotov, AS, Valle, D, Tang, M, Shin, E, Schwarz, K & O’Brien, SJ 2018, 'Analytical “bake-off” of whole genome sequencing quality for the genome Russia project using a small cohort for autoimmune hepatitis', PLoS One, vol. 13, no. 7, e0200423. https://doi.org/10.1371/journal.pone.0200423
Zhernakova, Daria V. ; Kliver, Sergei ; Cherkasov, Nikolay ; Tamazian, Gaik ; Rotkevich, Mikhail ; Krasheninnikova, Ksenia ; Evsyukov, Igor ; Sidorov, Sviatoslav ; Dobrynin, Pavel ; Yurchenko, Andrey A. ; Shimansky, Valentin ; Shcherbakova, Irina V. ; Glotov, Andrey S. ; Valle, David ; Tang, Minzhong ; Shin, Emilia ; Schwarz, Kathleen ; O’Brien, Stephen J. / Analytical “bake-off” of whole genome sequencing quality for the genome Russia project using a small cohort for autoimmune hepatitis. In: PLoS One. 2018 ; Vol. 13, No. 7.
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