Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China.
Department of Immunology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China.
Forensic Sci Int Genet. 2024 Jul;71:103062. doi: 10.1016/j.fsigen.2024.103062. Epub 2024 May 17.
Microhaplotypes (MHs) were first recommended by Prof. Kidd for use in forensics because they can improve human identification, kinship analysis, mixture deconvolution, and ancestry prediction. Since their introduction, extensive research has demonstrated the advantages of MHs in forensic applications and provided useful data for different populations. Currently, two databases, ALFRED (ALlele FREquency Database) and MicroHapDB (MicroHaplotype DataBase), house the published MH information and population data. We previously constructed a single nucleotide polymorphism SNP-SNP MH database (D-SNPsDB) of MHs within 50 bp on the whole human genome for 26 populations integrating basic data such as physical genome positions, mapping of variant identifiers (rsIDs), allele frequencies, and basic variant information. Building upon the previous research, we further selected MHs containing at least two variants (SNPs and/or insertions/deletions [InDels]) within a short DNA fragment (≤ 50 bp) in 26 populations based on the 1000 Genomes Project dataset (Phase 3) to construct a more comprehensive database. Subsequently, we established a user-friendly website that allows users to search the MH database (MHBase) based on their research objectives and study population to find suitable loci and provides other functions such as querying reported loci, performing online calculations using the PHASE software, and calculating ancestral-related parameters. The loci in the database are classified as SNP-based MHs, which include only SNPs, and InDel-including MHs, which contain at least one InDel. Here, we provide a detailed overview of the MHBase and an analysis of shared loci at the global and continental levels, ancestral markers, the genetic distance within loci, and mapping with the genome annotation file. The website is an accessible and useful tool for researchers engaged in marker discovery, population studies, assay development, and panel design.
微单倍型 (MHs) 最初是由 Kidd 教授推荐用于法医学的，因为它们可以提高人类识别、亲属关系分析、混合物解析和祖先预测的能力。自引入以来，广泛的研究已经证明了 MHs 在法医学应用中的优势，并为不同人群提供了有用的数据。目前，有两个数据库，ALFRED（Allele FREquency Database）和 MicroHapDB（MicroHaplotype DataBase），存放着已发表的 MH 信息和群体数据。我们之前构建了一个包含 26 个人群全基因组 50bp 内单核苷酸多态性 SNP-SNP MH 数据库 (D-SNPsDB)，整合了物理基因组位置、变体标识符 (rsID) 映射、等位基因频率和基本变体信息等基本数据。在之前的研究基础上，我们进一步从 1000 基因组计划数据集 (第三阶段) 中选择了 26 个人群中短 DNA 片段 (≤50bp) 内至少包含两个变体 (SNP 和/或插入/缺失 [InDels]) 的 MHs，构建了一个更全面的数据库。随后，我们建立了一个用户友好的网站，允许用户根据研究目标和研究人群搜索 MH 数据库 (MHBase)，以找到合适的基因座，并提供其他功能，如查询已报告的基因座、使用 PHASE 软件在线计算和计算祖先相关参数。数据库中的基因座分为 SNP 基 MHs，仅包含 SNP；以及包含至少一个 InDel 的 InDel 基 MHs。在这里，我们详细介绍了 MHBase，并分析了全球和大陆水平的共享基因座、祖先标记、基因座内的遗传距离以及与基因组注释文件的映射。该网站是从事标记发现、群体研究、检测开发和面板设计的研究人员的一种可访问且有用的工具。
