A method for positive forensic identification of samples from extremely low-coverage sequence data.
A method for positive forensic identification of samples from extremely low-coverage sequence data.
复制标题
DOI：
10.1186/s12864-015-2241-6
复制
发表时间：
2015-12-07
期刊：
影响因子：
4.4
通讯作者：
Green RE
中科院分区：
文献类型：
--
作者：
Vohr SH;Buen Abad Najar CF;Shapiro B;Green RE
当可回收的 DNA 数量有限时，确定两个 DNA 样本是否来自同一个体是很困难的。对于古代、历史和法医样本来说，情况往往如此。最广泛使用的方法依赖于一组确定的多等位标记的扩增以及与其他样本的类似数据的比较。当可回收的 DNA 量较低时，这些方法就会失败。我们描述了一种新方法，用于评估两个样本的霰弹枪 DNA 序列数据是否与源自相同或不同个体一致。我们的方法利用大量的单核苷酸多态性 (SNP) 标记来最大限度地提高观察潜在区别等位基因的机会。我们通过利用单倍型参考组建模的连锁不平衡模式来间接比较连锁 SNP 对的观察结果，进一步减少了所需的数据量。使用聚结模拟和来自现代和古代来源的真实测序数据，我们表明这种方法相对于参考组来说是稳健的，并且能够从每个样本中随机和非重叠基因组覆盖率低于 1% 的 DNA 文库中检测出阳性同一性。我们提出了一种强大的新方法，即使只能从每个样本中回收微量的 DNA，也可以确定两个样本中的 DNA 是否源自同一个体。本文的在线版本 (doi:10.1186/s12864-015-2241-6) 包含补充材料，可供授权用户使用。
Determining whether two DNA samples originate from the same individual is difficult when the amount of retrievable DNA is limited. This is often the case for ancient, historic, and forensic samples. The most widely used approaches rely on amplification of a defined panel of multi-allelic markers and comparison to similar data from other samples. When the amount retrievable DNA is low these approaches fail. We describe a new method for assessing whether shotgun DNA sequence data from two samples are consistent with originating from the same or different individuals. Our approach makes use of the large catalogs of single nucleotide polymorphism (SNP) markers to maximize the chances of observing potentially discriminating alleles. We further reduce the amount of data required by taking advantage of patterns of linkage disequilibrium modeled by a reference panel of haplotypes to indirectly compare observations at pairs of linked SNPs. Using both coalescent simulations and real sequencing data from modern and ancient sources, we show that this approach is robust with respect to the reference panel and has power to detect positive identity from DNA libraries with less than 1 % random and non-overlapping genome coverage in each sample. We present a powerful new approach that can determine whether DNA from two samples originated from the same individual even when only minute quantities of DNA are recoverable from each. The online version of this article (doi:10.1186/s12864-015-2241-6) contains supplementary material, which is available to authorized users.