Reliability of genomic variants across different next-generation sequencing platforms and bioinformatic processing pipelines.
Reliability of genomic variants across different next-generation sequencing platforms and bioinformatic processing pipelines.
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DOI：
10.1186/s12864-020-07362-8
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发表时间：
2021-01-19
期刊：
影响因子：
4.4
通讯作者：
Gerber S
中科院分区：
文献类型：
--
作者：
Weißbach S;Sys S;Hewel C;Todorov H;Schweiger S;Winter J;Pfenninger M;Torkamani A;Evans D;Burger J;Everschor-Sitte K;May-Simera HL;Gerber S
下一代测序（NGS）是各种研究的基础，为生物学和医学问题提供见解。然而，整合来自不同实验背景的数据可能会引入强烈的偏见。为了系统地研究单核苷酸变异调用中的系统误差的大小，我们对99名受试者的基因组队列进行了横断面观察性研究，每个受试者通过（i）Illumina HiSeq X，（ii）Illumina HiSeq和（iii）Complete Genomics测序，并用各自的生物信息学管道处理。我们还用GATK重复了Illumina群组的变体调用，这使我们能够研究生物信息学分析策略的效果与测序平台的影响分开。每个个体检测到的变体/变体类别的数量高度依赖于实验设置。我们观察到由单一设置唯一调用的变体在统计学上显著过高，表明潜在的系统性偏倚。与单核苷酸多态性（SNP）相比，插入/缺失多态性（indels）与一致性降低相关。插入缺失绝对数的差异在内含子、Alu元件、简单重复序列和中等GC含量的区域尤为突出。值得注意的是，按照GATK的最佳实践建议重新处理测序数据大大提高了相应设置之间的一致性。我们提供了替代实验和数据分析设置之间的变异调用的系统异质性的经验证据。此外，我们的结果证明了在整合来自不同研究的数据时，使用协调的管道重新处理基因组数据的好处。在线版本包含补充材料，可通过10.1186/s12864-020-07362-8获得。
Next Generation Sequencing (NGS) is the fundament of various studies, providing insights into questions from biology and medicine. Nevertheless, integrating data from different experimental backgrounds can introduce strong biases. In order to methodically investigate the magnitude of systematic errors in single nucleotide variant calls, we performed a cross-sectional observational study on a genomic cohort of 99 subjects each sequenced via (i) Illumina HiSeq X, (ii) Illumina HiSeq, and (iii) Complete Genomics and processed with the respective bioinformatic pipeline. We also repeated variant calling for the Illumina cohorts with GATK, which allowed us to investigate the effect of the bioinformatics analysis strategy separately from the sequencing platform’s impact. The number of detected variants/variant classes per individual was highly dependent on the experimental setup. We observed a statistically significant overrepresentation of variants uniquely called by a single setup, indicating potential systematic biases. Insertion/deletion polymorphisms (indels) were associated with decreased concordance compared to single nucleotide polymorphisms (SNPs). The discrepancies in indel absolute numbers were particularly prominent in introns, Alu elements, simple repeats, and regions with medium GC content. Notably, reprocessing sequencing data following the best practice recommendations of GATK considerably improved concordance between the respective setups. We provide empirical evidence of systematic heterogeneity in variant calls between alternative experimental and data analysis setups. Furthermore, our results demonstrate the benefit of reprocessing genomic data with harmonized pipelines when integrating data from different studies. The online version contains supplementary material available at 10.1186/s12864-020-07362-8.
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影响因子：
14.8
作者：
Clarke, Geraldine M.;Anderson, Carl A.;Pettersson, Fredrik H.;Cardon, Lon R.;Morris, Andrew P.;Zondervan, Krina T.
通讯作者：
Zondervan, Krina T.
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影响因子：
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作者：
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