ArticleBMC genomics2014
Evaluating the accuracy of AIM panels at quantifying genome ancestry.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 35 citations in OpenAlex.
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- Reliability of phenotype estimation and extended classification of ancestry using decedent samples.International journal of legal medicine · 2021Article
- Pitfalls of barcodes in the study of worldwide SARS-CoV-2 variation and phylodynamics.Zoological research · 2021Article
- Ancestry patterns inferred from massive RNA-seq data.RNA (New York, N.Y.) · 2019Article
- Selection of Optimal Ancestry Informative Markers for Classification and Ancestry Proportion Estimation in Pigs.Frontiers in genetics · 2019Article
- Human ancestry indentification under resource constraints -- what can one chromosome tell us about human biogeographical ancestry?BMC medical genomics · 2018Article
- An Ancestry Informative Marker Set Which Recapitulates the Known Fine Structure of Populations in South Asia.Genome biology and evolution · 2018Article
- Developing reduced SNP assays from whole-genome sequence data to estimate introgression in an organism with complex genetic patterns, the Iberian honeybee (Evolutionary applications · 2018Article
- Genetic Ancestry for Sleep Research: Leveraging Health Inequalities to Identify Causal Genetic Variants.Chest · 2018Review
- A 2-transcript host cell signature distinguishes viral from bacterial diarrhea and it is influenced by the severity of symptoms.Scientific reports · 2018Article
- Robust inference of population structure from next-generation sequencing data with systematic differences in sequencing.Bioinformatics (Oxford, England) · 2018Article
- Ancestry inference using principal component analysis and spatial analysis: a distance-based analysis to account for population substructure.BMC genomics · 2017Article
- Genomic insights on the ethno-history of the Maya and the 'Ladinos' from Guatemala.BMC genomics · 2015Article
- Reduced SNP panels for genetic identification and introgression analysis in the dark honey bee (Apis mellifera mellifera).PloS one · 2015Article
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3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThere is a growing interest among geneticists in developing panels of Ancestry Informative Markers (AIMs) aimed at measuring the biogeographical ancestry of individual genomes. The efficiency of these panels is commonly tested empirically by contrasting self-reported ancestry with the ancestry estimated from these panels.
resultsUsing SNP data from HapMap we carried out a simulation-based study aimed at measuring the effect of SNP coverage on the estimation of genome ancestry. For three of the main continental groups (Africans, East Asians, Europeans) ancestry was first estimated using the whole HapMap SNP database as a proxy for global genome ancestry; these estimates were subsequently compared to those obtained from pre-designed AIM panels. Panels that consider >400 AIMs capture genome ancestry reasonably well, while those containing a few dozen AIMs show a large variability in ancestry estimates. Curiously, 500-1,000 SNPs selected at random from the genome provide an unbiased estimate of genome ancestry and perform as well as any AIM panel of similar size. In simulated scenarios of population admixture, panels containing few AIMs also show important deficiencies to measure genome ancestry.
conclusionsThe results indicate that the ability to estimate genome ancestry is strongly dependent on the number of AIMs used, and not primarily on their individual informativeness. Caution should be taken when making individual (medical, forensic, or anthropological) inferences based on AIMs.
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