43:["$","title",null,{"children":"2021 Ancestry Inference Papers | lorenasandoval88 | Observable"}] 4b:T1683,

Two 2021 studies of genetic ancestry

Different purposes: VISAGE developed a compact ancestry test. Padakanti and colleagues investigated how ancestry-related PCA patterns are distributed across the genome.

Feature	VISAGE Basic Tool	Padakanti PCA study
Main aim	Infer broad ancestry using a small laboratory assay.	Connect PCA population patterns to informative DNA locations.
Data	1000 Genomes, HGDP-CEPH, and additional reference datasets.	2,504 people from 26 populations in 1000 Genomes.
Marker selection	Combine established ancestry markers; balance population informativeness and laboratory performance.	Rank markers by PCA weights; add or subtract their contributions to test preservation of the pattern.
Marker numbers	115 ancestry SNPs.	2,000 loci in a PC1 example; millions in the main dense-marker analyses.
Population coverage	African, European, East Asian, South Asian, Indigenous American, and Oceanian references.	Continental patterns and finer differences within Africa, East Asia, and Europe; no Oceanian panel.
Main outputs	Reference-group likelihoods and model-based ancestry mixture estimates.	PCA scores, informative genomic regions, local ancestry, and demographic analyses.

The 2,000-SNP clarification: The top 1,000 positive-weight and 1,000 negative-weight loci closely reproduced PC1 scores. This demonstrated a sufficient subset, not a universal 2,000-SNP ancestry panel. The main necessary informative loci analyses used millions of loci.

What did their results measure?

Study	Reported result	Correct interpretation
VISAGE	All 520 reference profiles were correctly classified in leave-one-out testing.	Successful group assignment in that evaluation; not guaranteed accuracy for every population.
PCA study	Full and 2,000-locus PC1 scores correlated at r ≥ 0.99.	Close agreement between scores; not 99% ancestry-classification accuracy.

These statistics measure different outcomes. A fair accuracy comparison would require the same test samples, ancestry targets, and evaluation measures.

References: de la Puente et al. (2021), VISAGE Basic Tool · Padakanti et al. (2021), informative loci and PCA

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