法医学遗传学中 NUMTs 的解读：见林而非树。

Interpreting NUMTs in forensic genetics: Seeing the forest for the trees.

机构信息

Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, DE 19902, USA; SNA International, Contractor Supporting the AFMES-AFDIL, Alexandria, VA 22314, USA; Forensic Science Program, The Pennsylvania State University, University Park, PA 16802, USA.

Forensic Science Program, The Pennsylvania State University, University Park, PA 16802, USA; Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria.

出版信息

Forensic Sci Int Genet. 2021 Jul;53:102497. doi: 10.1016/j.fsigen.2021.102497. Epub 2021 Mar 15.

DOI:10.1016/j.fsigen.2021.102497

PMID:33740708

Abstract

Nuclear mitochondrial DNA (mtDNA) segments (NUMTs) were discovered shortly after sequencing the first human mitochondrial genome. They have earlier been considered to represent archaic elements of ancient insertion events, but modern sequencing technologies and growing databases of mtDNA and NUMT sequences confirm that they are abundant and some of them phylogenetically young. Here, we build upon mtDNA/NUMT review articles published in the mid 2010 s and focus on the distinction of NUMTs and other artefacts that can be observed in aligned sequence reads, such as mixtures (contamination), point heteroplasmy, sequencing error and cytosine deamination. We show practical examples of the effect of the mtDNA enrichment method on the representation of NUMTs in the mapped sequence data and discuss methods to bioinformatically filter NUMTs from mtDNA reads.

摘要

核线粒体 DNA（mtDNA）片段（NUMTs）在首次测序人类线粒体基因组后不久就被发现了。它们早些时候被认为代表了古代插入事件的古老元素，但现代测序技术和不断增长的 mtDNA 和 NUMT 序列数据库证实，它们非常丰富，其中一些在系统发育上是年轻的。在这里，我们参考了 2010 年代中期发表的 mtDNA/NUMT 综述文章，并重点介绍了 NUMTs 与其他在对齐序列读段中观察到的伪迹之间的区别，例如混合物（污染）、点异质性、测序错误和胞嘧啶脱氨酶。我们展示了 mtDNA 富集方法对映射序列数据中 NUMTs 表示的影响的实际示例，并讨论了从 mtDNA 读段中生物信息学过滤 NUMTs 的方法。