SNVstory: inferring genetic ancestry from genome sequencing data

Bollas, Audrey E.; Rajkovic, Andrei; Ceyhan, Defne; Gaither, Jeffrey B.; Mardis, Elaine R.; White, Peter

doi:10.1186/s12859-024-05703-y

BMC Bioinformatics

Table 2 Genetic ancestry versus self-reported ethnicity and race

From: SNVstory: inferring genetic ancestry from genome sequencing data

Model labels	Ethnicity	Race	Counts
(A) gnomAD
afr	Non-Hispanic or Latino	Black or African American	20
	Non-Hispanic or Latino	Bi-racial/multi-racial	10
	Unknown/not reported ethnicity	Bi-racial/multi-racial	3
	Hispanic or Latino	Bi-racial/multi-racial	2
	Hispanic or Latino	White	1
	Non-Hispanic or Latino	White	1
amr	Hispanic or Latino	White	8
		Unknown/unspecified	5
		Black or African American	2
	Non-Hispanic or Latino	White	1
	Hispanic or Latino	Bi-racial/multi-racial	1
asj	Non-Hispanic or Latino	White	1
eas	Non-Hispanic or Latino	Asian	3
	Non-Hispanic or Latino	White	2
	Hispanic or Latino	Bi-racial/multi-racial	1
eur	Non-Hispanic or Latino	White	210
	Non-Hispanic or Latino	Bi-racial/multi-racial	5
	Hispanic or Latino	Bi-racial/multi-racial	5
	Hispanic or Latino	White	3
	Unknown/not reported ethnicity	White	3
	Unknown/not reported ethnicity	Bi-racial/multi-racial	1
	Hispanic or Latino	Unknown/unspecified	1
sas	Non-Hispanic or Latino	Asian	3
sas	Non-Hispanic or Latino	White	1
(b) 1kGP
afr	Non-Hispanic or Latino	Black or African American	19
	Non-Hispanic or Latino	Bi-racial/multi-racial	2
	Hispanic or Latino	Bi-racial/multi-racial	1
	Unknown/not reported ethnicity	Bi-racial/multi-racial	1
amr	Hispanic or Latino	White	12
	Non-Hispanic or Latino	Bi-racial/multi-racial	10
	Hispanic or Latino	Bi-racial/multi-racial	8
	Non-Hispanic or Latino	White	8
	Hispanic or Latino	Unknown/unspecified	6
	Hispanic or Latino	Black or African American	2
	Unknown/not reported ethnicity	Bi-racial/multi-racial	2
	Non-Hispanic or Latino	Black or African American	1
eas	Non-Hispanic or Latino	Asian	3
eur	Non-Hispanic or Latino	White	207
	Unknown/Not Reported Ethnicity	White	3
	Non-Hispanic or Latino	Bi-racial/multi-racial	3
	Unknown/not reported ethnicity	Bi-racial/multi-racial	1
sas	Non-Hispanic or Latino	Asian	3
sas	Non-Hispanic or Latino	White	1
(C) SGDP
Africa	Non-Hispanic or Latino	Black or African American	20
	Non-Hispanic or Latino	Bi-racial/multi-racial	9
	Hispanic or Latino	Bi-racial/multi-racial	3
	Unknown/not reported ethnicity	Bi-racial/multi-racial	3
	Hispanic or Latino	Black or African American	2
	Non-Hispanic or Latino	White	1
CentralAsiaSiberia	Hispanic or Latino	Unknown/unspecified	3
CentralAsiaSiberia	Hispanic or Latino	White	1
EastAsia	Non-Hispanic or Latino	Asian	3
SouthAsia	Hispanic or Latino	White	4
	Non-Hispanic or Latino	Asian	3
	Non-Hispanic or Latino	White	3
WestEurasia	Non-Hispanic or Latino	White	212
	Hispanic or Latino	White	7
	Non-Hispanic or Latino	Bi-racial/multi-racial	6
	Hispanic or Latino	Bi-racial/multi-racial	6
	Hispanic or Latino	Unknown/unspecified	3
	Unknown/not reported ethnicity	White	3
	Unknown/not reported ethnicity	Bi-racial/multi-racial	1

Value counts of genetic ancestry model predictions trained using gnomad (A), 1kGP (B), and SGDP (C) compared to self-reported ethnicity and race

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