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The performance of common SNP arrays in assigning African mitochondrial haplogroups

Lankheet, Imke; Vicente, Mário; Barbieri, Chiara; Schlebusch, Carina (2021). The performance of common SNP arrays in assigning African mitochondrial haplogroups. BMC Genomics, 22:43.

Abstract

Background
Mitochondrial haplogroup assignment is an important tool for forensics and evolutionary genetics. African populations are known to display a high diversity of mitochondrial haplogroups. In this research we explored mitochondrial haplogroup assignment in African populations using commonly used genome-wide SNP arrays.

Results
We show that, from eight commonly used SNP arrays, two SNP arrays outperform the other arrays when it comes to the correct assignment of African mitochondrial haplogroups. One array enables the recognition of 81% of the African mitochondrial haplogroups from our compiled dataset of full mitochondrial sequences. Other SNP arrays were able to assign 4–62% of the African mitochondrial haplogroups present in our dataset. We also assessed the performance of available software for assigning mitochondrial haplogroups from SNP array data.

Conclusions
These results provide the first cross-checked quantification of mitochondrial haplogroup assignment performance from SNP array data. Mitochondrial haplogroup frequencies inferred from most common SNP arrays used for human population analysis should be considered with caution.

Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:07 Faculty of Science > Institute of Evolutionary Biology and Environmental Studies
08 Research Priority Programs > Evolution in Action: From Genomes to Ecosystems
Dewey Decimal Classification:570 Life sciences; biology
590 Animals (Zoology)
Scopus Subject Areas:Life Sciences > Genetics
Health Sciences > Health Informatics
Uncontrolled Keywords:Health Informatics, Genetics
Language:English
Date:1 December 2021
Deposited On:28 Oct 2021 07:49
Last Modified:26 Oct 2024 01:37
Publisher:BioMed Central
ISSN:1471-2164
OA Status:Gold
Free access at:PubMed ID. An embargo period may apply.
Publisher DOI:https://doi.org/10.1186/s12863-021-01000-2
PubMed ID:34674637
Project Information:
  • Funder: Uppsala University
  • Grant ID:
  • Project Title:
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  • Licence: Creative Commons: Attribution 4.0 International (CC BY 4.0)

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