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Human Parental Relatedness through Time - Detecting Runs of Homozygosity in Ancient DNA
bioRxiv - Genetics Pub Date : 2020-07-30 , DOI: 10.1101/2020.05.31.126912
Harald Ringbauer , John Novembre , Matthias Steinrücken

We present a novel method to detect runs of homozygosity (ROH) from low-coverage genotype data typical for ancient human DNA. ROH are the genetic signature of matings between closely related parents, and as such, the frequency and length distribution of these blocks can give insight into recent population history and mating patterns. Existing methods identify ROH by scanning for regions that lack heterozygote genotypes, but this strategy frequently fails for ancient individuals: The vast majority of ancient DNA data has low read depth <3x, which makes reliable diploid genotype calling infeasible. To overcome this limitation, we make use of linkage disequilibrium information from a panel of modern reference haplotypes using a Hidden Markov Model. Our method scans for long stretches where the read data are consistent with only a single haplotype. When tested on simulated and down-sampled pseudo-haploid data from a targeted set of 1.24 million single nucleotide polymorphisms ("1240k SNPs") widely used in ancient DNA, our implementation robustly works for coverage down to 0.5x and can tolerate error rates up to 3%, with high power and low false positive rate for blocks longer than 4 centiMorgans. Therefore, the method can screen a substantial fraction of human genome-wide ancient DNA data for parental relatedness, which will yield new evidence for questions regarding past demography and social organization.

中文翻译:

通过时间探测人类父母的亲缘关系-古代DNA的纯合子运转。

我们提出了一种新的方法,从古代人类DNA典型的低覆盖基因型数据中检测纯合性(ROH)的运行。ROH是亲缘关系密切的父母之间交配的遗传特征,因此,这些区块的频率和长度分布可以洞悉最近的种群历史和交配模式。现有方法通过扫描缺乏杂合子基因型的区域来识别ROH,但是这种策略对于古代个体而言常常是失败的:绝大多数古代DNA数据的读取深度均小于3x,这使得可靠的二倍体基因型调用变得不可行。为了克服这个限制,我们利用隐马尔可夫模型利用现代参考单倍型的连锁不平衡信息。我们的方法扫描很长一段距离,其中读取的数据仅与单个单倍型一致。当对来自古代DNA中广泛使用的有针对性的124万个单核苷酸多态性(“ 1240k SNP”)的目标集进行模拟和下采样的伪单倍体数据进行测试时,我们的实现可有效地将覆盖率降低至0.5倍,并且容错率最高到3%,长于4厘摩的块具有高功率和低假阳性率。因此,该方法可以筛查人类基因组范围内的古代DNA数据中很大一部分是否具有亲子关系,这将为有关过去人口统计学和社会组织的问题提供新的证据。5倍,可以容忍高达3%的错误率,对于大于4厘摩的模块,具有高功率和低误报率。因此,该方法可以筛查人类基因组范围内的大部分古代DNA数据中是否存在亲子关系,这将为有关过去人口统计学和社会组织的问题提供新的证据。5倍,并且可以容忍高达3%的错误率,对于大于4厘摩的模块,具有高功率和低误报率。因此,该方法可以筛查人类基因组范围内的大部分古代DNA数据中是否存在亲子关系,这将为有关过去人口统计学和社会组织的问题提供新的证据。
更新日期:2020-07-31
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