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PIMA: A population informative multiplex for the Americas.

C Carvalho Gontijo1, L G Porras-Hurtado2, A Freire-Aradas3

  • 1Forensic Genetics Unit, University of Santiago de Compostela, Spain; Human Genetics Laboratory, Institute of Biological Sciences, University of Brasília, Brazil.

Forensic Science International. Genetics
|November 25, 2019
PubMed
Summary

A new SNP panel, PIMA (Population Informative Multiplex for the Americas), efficiently identifies Indigenous American ancestry. Combined with an existing panel, it offers powerful genetic analysis for diverse American populations.

Keywords:
AIMAncestryHGDP-CEPHIndigenous AmericanPopulation admixtureSNPSNaPshot

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Area of Science:

  • Population Genetics
  • Forensic Genetics
  • Human Ancestry

Background:

  • Assessing genetic variability in indigenous American populations is crucial for understanding historical demography.
  • Existing genetic markers may not fully capture the nuanced ancestry of admixed populations in the Americas.
  • A need exists for efficient, small-scale genetic tools to complement uniparental markers.

Purpose of the Study:

  • To develop and validate a novel, small-scale autosomal SNP multiplex for ancestry inference in the Americas.
  • To select SNPs with high allele frequency differentiation between continental populations.
  • To create a flexible tool that complements existing genetic markers for population and forensic analyses.

Main Methods:

  • Selection of 26 autosomal SNPs and 1 X-chromosome SNP based on allele frequencies and informativeness.
  • Development of the PIMA (Population Informative Multiplex for the Americas) panel using SNaPshot technology.
  • Combined analysis of PIMA with a 34plex forensic ancestry panel (PIMA+34plex) and comparison with a larger SNP panel (LACE).

Main Results:

  • The PIMA+34plex panel demonstrated equivalent power to a 314-SNP panel for ancestry estimation with reduced genotyping effort.
  • Genetic structure and ancestry profiles of 22 diverse American populations were successfully estimated.
  • Results showed efficient detection of the American genetic component, consistent with historical and demographic data.

Conclusions:

  • The PIMA panel, especially when combined with the 34plex panel, provides a powerful and practical tool for analyzing American populations.
  • This approach effectively detects Indigenous American ancestry in contemporary populations.
  • The PIMA+34plex system is suitable for both population genetic studies and forensic DNA analyses in the Americas.