1. Analytical "bake-off" of whole genome sequencing quality for the Genome Russia project using a small cohort for autoimmune hepatitis.
- Author
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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 DL, Tang M, Shin E, Schwarz KB, and O'Brien SJ
- Subjects
- Adolescent, Ammonia-Lyases genetics, Child, Child, Preschool, Cohort Studies, DNA Copy Number Variations, Female, Genetic Predisposition to Disease, Glutamate Formimidoyltransferase genetics, HLA-DRB1 Chains genetics, Humans, INDEL Mutation, Male, Multifunctional Enzymes, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, Quality Control, Russia, Time Factors, Genotyping Techniques, Hepatitis, Autoimmune genetics, Whole Genome Sequencing
- 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., Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2018
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