The presence and impact of reference bias on population genomic studies of prehistoric human populations
The presence and impact of reference bias on population genomic studies of prehistoric human populations
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DOI：
10.1371/journal.pgen.1008302
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发表时间：
2019-07-01
期刊：
影响因子：
4.5
通讯作者：
Nettelblad, Carl
中科院分区：
文献类型：
--
作者：
Gunther, Torsten;Nettelblad, Carl
高质量的参考基因组是基因组研究项目的重要资源。结果是携带参考等位基因的DNA片段将更有可能成功作图，或获得更高的质量分数。当杂合位点被错误地认为是参考等位基因的纯合时，这种参考偏倚可能对下游群体基因组分析产生影响。在人类群体的古基因组学研究中，对照人类参考基因组的作图用于鉴定内源性人类序列。古DNA研究通常在低测序覆盖率的情况下进行，DNA分子的片段化导致大部分测序片段短于50 bp-减少了可接受的错配量，并增加了基因组中多个匹配位点的概率。这些古代DNA的特定性质可能会加剧参考偏倚对下游分析的影响，特别是因为大多数古代人类群体的研究使用伪单倍体数据，即每个位点仅随机取样一个测序读数。我们发现，参考偏见是普遍的，在已发表的古DNA序列数据的史前人类与个别基因组区域之间的一些差异。我们说明，参考偏倚的强度与片段长度呈负相关。我们研究的大多数基因组区域几乎没有显示出定位偏差，但即使是一小部分有偏差的位点也会影响这些特定位点的分析或轻微偏离全基因组估计。因此，参考偏差有可能导致下游分析结果出现微小但显着的差异，例如群体等位基因共享、杂合性估计和古代祖先估计。这些虚假的结果突出了意识到这些技术工件的重要性，我们需要策略来减轻影响。因此，我们建议一些映射后过滤策略来解决参考偏差，这有助于大大减少其影响。
High quality reference genomes are an important resource in genomic research projects. A consequence is that DNA fragments carrying the reference allele will be more likely to map successfully, or receive higher quality scores. This reference bias can have effects on downstream population genomic analysis when heterozygous sites are falsely considered homozygous for the reference allele. In palaeogenomic studies of human populations, mapping against the human reference genome is used to identify endogenous human sequences. Ancient DNA studies usually operate with low sequencing coverages and fragmentation of DNA molecules causes a large proportion of the sequenced fragments to be shorter than 50 bp-reducing the amount of accepted mismatches, and increasing the probability of multiple matching sites in the genome. These ancient DNA specific properties are potentially exacerbating the impact of reference bias on downstream analyses, especially since most studies of ancient human populations use pseudo-haploid data, i.e. they randomly sample only one sequencing read per site. We show that reference bias is pervasive in published ancient DNA sequence data of prehistoric humans with some differences between individual genomic regions. We illustrate that the strength of reference bias is negatively correlated with fragment length. Most genomic regions we investigated show little to no mapping bias but even a small proportion of sites with bias can impact analyses of those particular loci or slightly skew genome-wide estimates. Therefore, reference bias has the potential to cause minor but significant differences in the results of downstream analyses such as population allele sharing, heterozygosity estimates and estimates of archaic ancestry. These spurious results highlight how important it is to be aware of these technical artifacts and that we need strategies to mitigate the effect. Therefore, we suggest some post-mapping filtering strategies to resolve reference bias which help to reduce its impact substantially.