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

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

doi:10.1007/s00414-016-1524-z

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.

Highlights

Soundararajan et al [1] recently highlighted the limited utility of the many published ancestry informative SNP (AISNP) panels
Soundararajan et al (2016) [1] note that the 128 AISNPs from the Seldin group [2, 3] and our Kidd Lab set of 55 AISNPs [4, 5] at present have the largest numbers of reference populations with the broadest coverage of major world regions
The 55 AISNP panel shows that an additional cluster is defined by the North African populations recently included [5], consistent with the findings based on many more SNPs, that these North African populations form a genetically distinct cluster [11]

Summary

Introduction

Soundararajan et al [1] recently highlighted the limited utility of the many published ancestry informative SNP (AISNP) panels. The development efforts underlying some panels involved examining population samples from only a few very different world regions. The review concluded that there is little need for more new ancestry panels focused on inferring ancestry to a handful of major world geographical regions. What is needed is a coordination of efforts to greatly expand the ethnic populations with published SNP frequency data on the panels with the best worldwide coverage of human diversity. Soundararajan et al (2016) [1] note that the 128 AISNPs from the Seldin group [2, 3] and our Kidd Lab set of 55 AISNPs [4, 5] at present have the largest numbers of reference populations with the broadest coverage of major world regions

Methods

Results

Conclusion