Analytical "bake-off" of whole genome sequencing quality for the Genome Russia project using a small cohort for autoimmune hepatitis.
Analytical "bake-off" of whole genome sequencing quality for the Genome Russia project using a small cohort for autoimmune hepatitis.
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DOI：
10.1371/journal.pone.0200423
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发表时间：
2018
期刊：
影响因子：
3.7
通讯作者：
O'Brien SJ
中科院分区：
文献类型：
--
作者：
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;O'Brien SJ
对由圣彼得堡州立大学彼得霍夫测序中心和俄罗斯以外的三个商业测序中心进行的10个人类基因组样本进行了全基因组测序(WGS)和基因叫号的比较分析。比较10个受试者的DNA序列质量、DNA变异体效率和基因呼唤效率，并与DNA芯片进行比较。我们评估了SNP的调用、INDELs、拷贝数变化以及WGS承诺的吞吐量速度。20个独立的QC分析显示，序列质量和称为基因型之间有很高的相似性。这些中心测试的10个基因组包括8名患有自身免疫性肝炎(AIH)的美国患者，以及1名患者的未受影响的父母，这是发现这种未知病因的罕见疾病的遗传影响的前奏。通过详细的内部复制和平行分析，可以观察到8例AIH病例中有2例携带先前描述的AIH相关基因(FTCD)的罕见等位基因，以及与AIH相关的已知HLA-DRB1等位基因的多次出现(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的SNV在AIH影响中的作用。
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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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
30.8
作者：
Alkan, Can;Kidd, Jeffrey M.;Marques-Bonet, Tomas;Aksay, Gozde;Antonacci, Francesca;Hormozdiari, Fereydoun;Kitzman, Jacob O.;Baker, Carl;Malig, Maika;Mutlu, Onur;Sahinalp, S. Cenk;Gibbs, Richard A.;Eichler, Evan E.
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Eichler, Evan E.
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14.8
作者：
Kumar, Prateek;Henikoff, Steven;Ng, Pauline C.
通讯作者：
Ng, Pauline C.
影响因子：
13.5
作者：
Agarwal, K;Czaja, AJ;Donaldson, PT
通讯作者：
Donaldson, PT