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SNaPshot minisequencing to resolve mitochondrial macro‐haplogroups found in Africa
Author(s) -
Schlebusch Carina M.,
Naidoo Thijessen,
Soodyall Himla
Publication year - 2009
Publication title -
electrophoresis
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.666
H-Index - 158
eISSN - 1522-2683
pISSN - 0173-0835
DOI - 10.1002/elps.200900197
Subject(s) - haplogroup , hypervariable region , subclade , human mitochondrial dna haplogroup , mitochondrial dna , genetics , biology , coding region , mtdna control region , phylogenetic tree , haplotype , evolutionary biology , gene , genotype , clade
African mitochondrial DNA (mtDNA) haplogroups are divided into seven macro‐haplogroups (L0′1′2′3′4′5′6), while the rest of the world's lineages are classified as subgroups of macro‐haplogroups M, N and R. The most common approach to characterizing mtDNA variation is the sequencing of hypervariable segments I and II of the non‐coding control region of the molecule. Given the higher mutation rate within the control region compared with the coding regions of the molecule, recurrent mutations in the former can sometimes hide possible phylogenetic structure. The incorporation of haplogroup‐defining coding region mutations has helped in overcoming this limitation. By judiciously selecting 14 coding region SNPs and incorporating them into a multiplex minisequencing assay we were able to resolve mtDNA sequences from some sub‐Saharan African populations into ten macro‐haplogroups (L0–L6, M, N and R). We tested the efficacy of the panel by screening 699 individuals, consisting mostly of Khoe‐San, Bantu speakers and individuals with mixed ancestries (Coloreds) and found no inconsistencies compared with hypervariable segment sequencing results. The panel provided a fast and efficient means of classifying mtDNA into the ten mitochondrial macro‐haplogroups and provided a reliable screening to distinguish African from non‐African‐derived mtDNA lineages.