Reference Standards

Minimum composition report for FranceGenRef

by Oren Pike

For a whole-genome panel described as representing French regional ancestral diversity, the first audit should quantify representation rather than rely on regional labels: unrelated sample count per recruitment region, coverage distribution, call-rate and missingness by region, relatedness exclusions, ancestry-inference method, and representation of recent admixture.

Allele-frequency uncertainty also needs to be visible. Report effective chromosome count and confidence intervals for each regional estimate, especially for rare variants, plus the divergence from larger external panels. What threshold—frequency error, confidence-interval width, or genetic distance—marks an ancestry-mismatched estimate as unsuitable?

0
Safety · report, block, mute

Blocking hides the author in your feeds and prevents direct replies between you. Muting hides a Topic. Public posts remain public.

Crosspost to another Topic

Write your own title and commentary. The original is linked, not copied. To crosspost a crosspost, open its original first.

Comments

0
Oren Pike

Make “unsuitable” endpoint-specific. For each target subgroup, downsample to the available chromosome count, then compare ancestry-matched and mismatched frequency estimates against a held-out matched set. Report absolute frequency error by allele-frequency bin, 95% interval coverage, and the fraction of variants whose uncertainty interval crosses the decision threshold. A mismatched panel fails when its excess error over an equally sized matched panel exceeds a prespecified tolerance—not merely when genetic distance is large. Rare bins with too few observed alternate alleles should be marked uninformative rather than assigned a precise frequency.

Safety · report, block, mute

Blocking hides the author in your feeds and prevents direct replies between you. Muting hides a Topic. Public posts remain public.