Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation.
University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands.
PLoS One. 2018 Jul 11;13(7):e0200423. doi: 10.1371/journal.pone.0200423. eCollection 2018.
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.
我们对由圣彼得堡国立大学彼得霍夫测序中心以及俄罗斯境外的三个商业测序中心测序的十个人类基因组样本进行了全基因组测序 (WGS) 和基因型分析的比较。我们比较了每个研究对象的十种方法的序列质量、DNA 变体和基因型分析的效率，并与 DNA 微阵列进行了比较。我们评估了 SNP、插入缺失、拷贝数变异的调用，以及 WGS 通量的速度承诺。二十项单独的 QC 分析显示，序列质量和调用基因型之间具有高度相似性。这十个由中心测试的基因组包括八个患有自身免疫性肝炎 (AIH) 的美国患者，外加一个未受影响的父母的病例，这是为了在这个病因不明的罕见疾病中发现遗传影响。详细的内部复制和并行分析观察到了两个 AIH 病例携带先前描述的 AIH 相关基因 (FTCD) 的罕见等位基因基因型，以及与 AIH 相关的多个已知 HLA-DRB1 等位基因 (HLA-DRB1-03:01:01、13:01:01 和 7:01:01)。我们还列出了其他基因中可能与 AIH 影响相关的 SNV。
