Increasing the reference populations for the 55 AISNP panel: the need and benefits

Andrew J Pakstis; Longli Kang; Lijun Liu; Zhiying Zhang; Tianbo Jin; Elena L Grigorenko; Frank R Wendt; Bruce Budowle; Sibte Hadi; Mariam Salam Al Qahtani; Niels Morling; Helle Smidt Mogensen; Goncalo E Themudo; Usha Soundararajan; Haseena Rajeevan; Judith R Kidd; Kenneth K Kidd

doi:10.1007/s00414-016-1524-z

Increasing the reference populations for the 55 AISNP panel: the need and benefits

Andrew J Pakstis, Longli Kang, Lijun Liu, Zhiying Zhang, Tianbo Jin, Elena L Grigorenko, Frank R Wendt, Bruce Budowle, Sibte Hadi, Mariam Salam Al Qahtani, Niels Morling, Helle Smidt Mogensen, Goncalo E Themudo, Usha Soundararajan, Haseena Rajeevan, Judith R Kidd, Kenneth K Kidd

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Abstract

Ancestry inference for an individual can only be as good as the reference populations with allele frequency data on the SNPs being used. If the most relevant ancestral population(s) does not have data available for the SNPs studied, then analyses based on DNA evidence may indicate a quite distantly related population, albeit one among the more closely related of the existing reference populations. We have added reference population allele frequencies for 14 additional population samples (with >1100 individuals studied) to the 125 population samples previously published for the Kidd Lab 55 AISNP panel. Allele frequencies are now publicly available for all 55 SNPs in ALFRED and FROG-kb for a total of 139 population samples. This Kidd Lab panel of 55 ancestry informative SNPs has been incorporated in commercial kits by both ThermoFisher Scientific and Illumina for massively parallel sequencing. Researchers employing those kits will find the enhanced set of reference populations useful.

Original language	English
Journal	International Journal of Legal Medicine
Volume	131
Issue number	4
Pages (from-to)	913–917
ISSN	0937-9827
DOIs	https://doi.org/10.1007/s00414-016-1524-z
Publication status	Published - 1 Jul 2017

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Increasing the reference populations for the 55 AISNP panel: the need and benefitsFinal published version, 564 KBLicence: CC BY

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Pakstis, A. J., Kang, L., Liu, L., Zhang, Z., Jin, T., Grigorenko, E. L., Wendt, F. R., Budowle, B., Hadi, S., Al Qahtani, M. S., Morling, N., Mogensen, H. S., Themudo, G. E., Soundararajan, U., Rajeevan, H., Kidd, J. R., & Kidd, K. K. (2017). Increasing the reference populations for the 55 AISNP panel: the need and benefits. International Journal of Legal Medicine, 131(4), 913–917. https://doi.org/10.1007/s00414-016-1524-z

Pakstis, AJ, Kang, L, Liu, L, Zhang, Z, Jin, T, Grigorenko, EL, Wendt, FR, Budowle, B, Hadi, S, Al Qahtani, MS, Morling, N , Mogensen, HS, Themudo, GE, Soundararajan, U, Rajeevan, H, Kidd, JR & Kidd, KK 2017, 'Increasing the reference populations for the 55 AISNP panel: the need and benefits', International Journal of Legal Medicine, vol. 131, no. 4, pp. 913–917. https://doi.org/10.1007/s00414-016-1524-z

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title = "Increasing the reference populations for the 55 AISNP panel: the need and benefits",

abstract = "Ancestry inference for an individual can only be as good as the reference populations with allele frequency data on the SNPs being used. If the most relevant ancestral population(s) does not have data available for the SNPs studied, then analyses based on DNA evidence may indicate a quite distantly related population, albeit one among the more closely related of the existing reference populations. We have added reference population allele frequencies for 14 additional population samples (with >1100 individuals studied) to the 125 population samples previously published for the Kidd Lab 55 AISNP panel. Allele frequencies are now publicly available for all 55 SNPs in ALFRED and FROG-kb for a total of 139 population samples. This Kidd Lab panel of 55 ancestry informative SNPs has been incorporated in commercial kits by both ThermoFisher Scientific and Illumina for massively parallel sequencing. Researchers employing those kits will find the enhanced set of reference populations useful.",

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AU - Kang, Longli

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AU - Jin, Tianbo

AU - Grigorenko, Elena L

AU - Wendt, Frank R

AU - Budowle, Bruce

AU - Hadi, Sibte

AU - Al Qahtani, Mariam Salam

AU - Morling, Niels

AU - Mogensen, Helle Smidt

AU - Themudo, Goncalo E

AU - Soundararajan, Usha

AU - Rajeevan, Haseena

AU - Kidd, Judith R

AU - Kidd, Kenneth K

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N2 - Ancestry inference for an individual can only be as good as the reference populations with allele frequency data on the SNPs being used. If the most relevant ancestral population(s) does not have data available for the SNPs studied, then analyses based on DNA evidence may indicate a quite distantly related population, albeit one among the more closely related of the existing reference populations. We have added reference population allele frequencies for 14 additional population samples (with >1100 individuals studied) to the 125 population samples previously published for the Kidd Lab 55 AISNP panel. Allele frequencies are now publicly available for all 55 SNPs in ALFRED and FROG-kb for a total of 139 population samples. This Kidd Lab panel of 55 ancestry informative SNPs has been incorporated in commercial kits by both ThermoFisher Scientific and Illumina for massively parallel sequencing. Researchers employing those kits will find the enhanced set of reference populations useful.

AB - Ancestry inference for an individual can only be as good as the reference populations with allele frequency data on the SNPs being used. If the most relevant ancestral population(s) does not have data available for the SNPs studied, then analyses based on DNA evidence may indicate a quite distantly related population, albeit one among the more closely related of the existing reference populations. We have added reference population allele frequencies for 14 additional population samples (with >1100 individuals studied) to the 125 population samples previously published for the Kidd Lab 55 AISNP panel. Allele frequencies are now publicly available for all 55 SNPs in ALFRED and FROG-kb for a total of 139 population samples. This Kidd Lab panel of 55 ancestry informative SNPs has been incorporated in commercial kits by both ThermoFisher Scientific and Illumina for massively parallel sequencing. Researchers employing those kits will find the enhanced set of reference populations useful.

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DO - 10.1007/s00414-016-1524-z

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SP - 913

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JO - International Journal of Legal Medicine

JF - International Journal of Legal Medicine

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ER -

Increasing the reference populations for the 55 AISNP panel: the need and benefits

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