Kim Kijeong, Kim Dong-Han, Kim Kyung-Yong
Institute of Gene and Genome Research, College of Medicine, Chung-Ang University, Seoul 06974, Republic of Korea.
Faculty of Science, University of Sydney, Sydney NSW 2016, Australia.
Biomed Res Int. 2022 Mar 18;2022:5344418. doi: 10.1155/2022/5344418. eCollection 2022.
Mitochondrial DNA haplogroup classification is used to study maternal lineage of ancient human populations. The haplogrouping of ancient DNA is not easy because the DNA is usually found in small pieces in limited quantities. We have developed Haplotracker, a straightforward and efficient high-resolution haplogroup classification tool optimized specifically for ancient DNA samples. Haplotracker offers a user-friendly input interface for multiple mitochondrial DNA sequence fragments in a sample. It provides accurate haplogroup classification with full-length mitochondrial genome sequences and provides high-resolution haplogroup predictions for some fragmented control region sequences using a novel algorithm built on Phylotree mtDNA Build 17 (Phylotree) and our haplotype database ( = 118,869). Its performance for accuracy was demonstrated to be high through haplogroup classification using 8,216 Phylotree full-length and control region mitochondrial DNA sequences compared with HaploGrep 2, one of the most accurate current haplogroup classifiers. Haplotracker provides a novel haplogroup tracking solution for fragmented sequences to track subhaplogroups or verify the haplogroups efficiently. Using Haplotracker, we classified mitochondrial haplogroups to the final subhaplogroup level in nine ancient DNA samples extracted from human skeletal remains found in 2,000-year-old elite Xiongnu cemetery in Northeast Mongolia. Haplotracker can be freely accessed at https://haplotracker.cau.ac.kr.
线粒体DNA单倍群分类用于研究古代人类群体的母系谱系。对古代DNA进行单倍群分类并不容易，因为通常发现的DNA片段小且数量有限。我们开发了Haplotracker，这是一种简单高效的高分辨率单倍群分类工具，专门针对古代DNA样本进行了优化。Haplotracker为样本中的多个线粒体DNA序列片段提供了用户友好的输入界面。它能根据完整的线粒体基因组序列进行准确的单倍群分类，并使用基于Phylotree线粒体DNA构建17版（Phylotree）和我们的单倍型数据库（=118,869）构建的新算法，为一些片段化的控制区序列提供高分辨率的单倍群预测。与当前最准确的单倍群分类器之一HaploGrep 2相比，通过对8216条Phylotree全长和控制区线粒体DNA序列进行单倍群分类，证明了其准确性表现很高。Haplotracker为片段化序列提供了一种新颖的单倍群追踪解决方案，以有效地追踪亚单倍群或验证单倍群。使用Haplotracker，我们对从蒙古东北部有2000年历史的匈奴精英墓地出土的人类骨骼遗骸中提取的9个古代DNA样本的线粒体单倍群分类到了最终的亚单倍群水平。可通过https://haplotracker.cau.ac.kr免费访问Haplotracker。
