Control region sequences for East Asian individuals in the Scientific Working Group on DNA Analysis Methods forensic mtDNA data set

Abstract

The Scientific Working Group on DNA Analysis Methods (SWGDAM) mitochondrial DNA (mtDNA) population data set is used to infer the relative rarity of mtDNA profiles obtained from evidence samples and of profiles used to identify missing persons. In this study, the East Asian haplogroup patterns in the SWGDAM data sets were analyzed in a phylogenetic context to determine relevant single nucleotide polymorphisms (SNPs) and to describe haplogroup distributions for Asians ( n=753; with a breakdown of individuals from China n=356, Korea n=182, Japan n=163, and Thailand n=52). We focus on the patterns observed in the SWGDAM Chinese data set and refer to interesting differences in the smaller subgroup data sets for the other East Asian populations (Japanese, Korean, and Thai). A total of 218 SNPs were observed in the data set, including 37 observed positions not previously reported. In the largest of the East Asian SWGDAM data sets (Chinese), these SNPs ranged from having 1 to 29 changes in the phylogenetic tree, with site 16519 being the most variable. On average there were 4.5 changes for a character on the tree. The most variable sites (with 14 or more changes each listed from fastest to slowest) observed were 16519 ( L=29), 16311 ( L=27), 152 ( L=24), 146 ( L=21), 16172 ( L=17), 16189 ( L=17), 195 ( L=16), 16362 ( L=15), 16093 ( L=14), 16129 ( L=14), and 150 ( L=14). These rapidly changing sites are consistent with other published analyses. Only 28 SNPs are needed to identify all clusters containing 1% ( n=7) or more individuals in the East Asian data set. All 36 haplogroups previously observed in East Asian populations were also seen in the SWGDAM data sets and include: A, B, B4, B4a, B4b, B5a, B5b, C, D, D4, D4a, D4b, D5, D5a, F, F1, F1a, F1b, F1c, F2a, G2, G2a, M, M7a1, M7b, M7b1, M7b2, M7c, M8a, M9, M10, N9a, R, R9a, Y, and Z. Haplogroups A, B4a, D4, and F1a were the most commonly observed clusters in the Chinese data set (the largest of the data sets) with each of these occurring in more than 6% of the samples in the data set. The next most common haplogroups in the Chinese data set include the clusters C, M7b1, and N9a with each observed at frequencies greater than or equal to 4%. European Caucasian, and African haplogroups were rarely observed within the East Asian data sets. The various analyses revealed that the data set was similar to published East Asian data sets such as those from Han Chinese.