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The performance of ...
The performance of common SNP arrays in assigning African mitochondrial haplogroups
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- Lankheet, Imke (författare)
- Uppsala universitet,Människans evolution
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- Vicente, Mário (författare)
- Uppsala universitet,Evolution och utvecklingsbiologi,Människans evolution,Uppsala Univ, Dept Organismal Biol, Human Evolut, Norbyvagen 18C, SE-75236 Uppsala, Sweden.;Ctr Palaeogenet, Svante Arrhenius Vagen 20C, SE-10691 Stockholm, Sweden.
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- Barbieri, Chiara (författare)
- Univ Zurich, Dept Evolutionary Biol & Environm Studies, Winterthurerstr 190, CH-8057 Zurich, Switzerland.;Max Planck Inst Sci Human Hist MPI SHH, Dept Linguist & Cultural Evolut DLCE, Kahlaische Str 10, D-07745 Jena, Germany.
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- Schlebusch, Carina, 1977- (författare)
- Uppsala universitet,Evolutionsbiologi,Evolution och utvecklingsbiologi,Människans evolution,Science for Life Laboratory, SciLifeLab,Uppsala Univ, Dept Organismal Biol, Human Evolut, Norbyvagen 18C, SE-75236 Uppsala, Sweden.;Univ Johannesburg, Palaeores Inst, POB 524, ZA-2006 Auckland Pk, South Africa.;SciLifeLab, Uppsala, Sweden.
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(creator_code:org_t)
- 2021-10-21
- 2021
- Engelska.
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Ingår i: BMC GENOMIC DATA. - : BioMed Central (BMC). - 2730-6844. ; 22:1
- Relaterad länk:
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https://doi.org/10.1...
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https://uu.diva-port... (primary) (Raw object)
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https://bmcgenomdata...
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
Ämnesord
Stäng
- 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.
Ämnesord
- NATURVETENSKAP -- Biologi -- Genetik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Genetics (hsv//eng)
Nyckelord
- SNP array
- Haplogroup assignment
- mtDNA
- Africa
- HaploGrep
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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