Polymorphism in the mitochondrial cytochrome B gene in Koreans

Abstract

Sequencing the mitochondrial control region is very useful for individual identification when conventional DNA typing using autosomal STRs is unavailable. However, low discriminatory power is a problem and another polymorphic locus within the mitochondrial genome is necessary. The cytochrome B (MTCYB) gene, which has undergone several changes during evolution, may be a good candidate for this purpose. Here the sequencing data of the MTCYB gene of 98 unrelated Koreans is presented. A total of 30 polymorphic sites were found which were distributed evenly along the gene. All were nucleotide substitutions and no insertions/deletions were noted. A total of 22 different MTCYB lineages were revealed. Out of 22 different control region lineages with 79 samples which shared the same D-loop sequence with some others within a lineage, 10 lineages with 37 samples could be sub-grouped according to different MTCYB sequences. Some issues concerning the MTCYB gene polymorphism are discussed.

Identification of Native American Founder mtDNAs Through the Analysis of Complete mtDNA Sequences: Some Caveats

“…The three sequences with this motif that appear in the Korean data of Snäll et al (2002), however, tested positively for the RFLP site +4830 HaeII (recognizing a transition at nt 4833) of haplogroup G. We additionally found the 4833 transition (confirmed by +4831 HhaI) in four mtDNAs from China (Table 2). Because all of these mtDNA sequences that belong to haplogroup G have (near-)matches with sequences sampled in Japan (Horai et al 1996;Imaizumi et al 2002;Koyama et al 2002), Korea (Pfeiffer et al 1998;Lee et al 1997Lee et al , 2002, and China (Tsai et al 2001;Yao et al 2000Yao et al , 2003a, it appears that these sequences also belong to haplogroup G. The vast majority of these HVS-I and HVS-II sequences share the 150 polymorphism. In particular, eleven HVS-I and HVS-II sequences from the Korean sample of Lee et al (1997) carry the partial motif 16223-16325; seven of them have the additional part 16362-150 of the motif, Yao et al (2003a) and the data underlying figure 1 of Mishmar et al (2003), respectively; 2 n.d. = not determined.…”

A multiplex allele-specific primer extension assay for forensically informative SNPs distributed throughout the mitochondrial genome

“…For this reason, forensically relevant SNPs in the coding region should be chosen to involve neutral variants. We feel that SNP assays like pyrosequencing that reveal a substantial amount of surrounding sequence variation, or the simple sequencing of coding region genes [17], will not prove wise practical choices for reasons of medical genetic privacy and ethics.…”

Artificial recombination in forensic mtDNA population databases

“…The Korean mtDNA data presented by Lee et al (2002) bear the imprint of several erroneous combinations of the HVR-I and HVR-II sequences with the cytochrome B sequences. Some of the HVR-I and HVR-II sequences were published earlier (Lee et al 1997) but without citation in Lee et al (2002). Alarmingly, some of those recycled HVR-I and HVR-II sequences do not completely match the corresponding ones of the earlier study.…”

“…Alarmingly, some of those recycled HVR-I and HVR-II sequences do not completely match the corresponding ones of the earlier study. With the present knowledge of the East Asian mtDNA phylogeny Kong et al 2003aKong et al , 2003b, one can allocate almost twothirds of the cytochrome B mutations recorded by Lee et al (2002) to specific branches of the mtDNA phylogeny. When comparing the HVR-I and HVR-II motifs with the cytochrome B motifs, we find the following mosaic types (where the first part refers to the control region and the second part to cytochrome B gene): sample F531.2 is an F1b×D4a type, sample H81 an A5×D4a type, sample H84 an M7a1×D4a type, sample H98 an A5×M type (Kong et al 2003a;Bandelt 2004), and sample H75 is an M10×Y1 type.…”