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

Daria 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 L Valle, Minzhong Tang, Emilia Shin, Kathleen B Schwarz, Stephen J O'Brien

Research output

2 Citations (Scopus)

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
Pages (from-to)e0200423
JournalPLoS ONE
Volume13
Issue number7
DOIs
Publication statusPublished - 11 Jul 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

Cite this

Zhernakova, Daria ; 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 L ; Tang, Minzhong ; Shin, Emilia ; Schwarz, Kathleen B ; 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. pp. e0200423.
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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.",
author = "Daria Zhernakova and Sergei Kliver and Nikolay Cherkasov and Gaik Tamazian and Mikhail Rotkevich and Ksenia Krasheninnikova and Igor Evsyukov and Sviatoslav Sidorov and Pavel Dobrynin and Yurchenko, {Andrey A} and Valentin Shimansky and Shcherbakova, {Irina V} and Glotov, {Andrey S} and Valle, {David L} and Minzhong Tang and Emilia Shin and Schwarz, {Kathleen B} and O'Brien, {Stephen J}",
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Zhernakova, D, 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, DL, Tang, M, Shin, E, Schwarz, KB & 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, pp. 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; 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 L; Tang, Minzhong; Shin, Emilia; Schwarz, Kathleen B; O'Brien, Stephen J.

In: PLoS ONE, Vol. 13, No. 7, 11.07.2018, p. e0200423.

Research output

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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.

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DO - 10.1371/journal.pone.0200423

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VL - 13

SP - e0200423

JO - PLoS ONE

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