Table 2 Description of the reference panels used by the different methods. We list a summary of the sample sizes and the total variants across the available populations
From: PRED-LD: efficient imputation of GWAS summary statistics
Reference panel | Label | population sample | Number of samples | Total Variants |
|---|---|---|---|---|
TOP-LD \((r^{2}\) \(\ge\) 0.2) | EUR | European | 13,160 | 69,524,944 |
AFR | African | 1,335 | 60,392,677 | |
SAS | South Asian | 239 | 22,309,649 | |
EAS | East Asian | 844 | 35,538,656 | |
Pheno scanner (MAF > 1% and \(r^{2}\) > 0.8,1000 Genomes project—Phase 3, hg19 and hg38) | EUR | European | 503 | 11,159,862 |
AFR | African | 661 | 11,159,862 | |
SAS | South Asian | 489 | 11,159,862 | |
EAS | East Asian | 504 | 11,159,862 | |
AMR | American | 347 | 11,159,862 | |
HapMap | ASW | African ancestry in Southwest USA | 90 | 1,561,113 |
CEU | Utah residents with Northern and Western European ancestry from the CEPH collection | 180 | 1,412,161 | |
CHB | Han Chinese in Beijing, China | 90 | 1,328,283 | |
CHD | Chinese in Metropolitan Denver, Colorado | 100 | 1,305,880 | |
GIH | Gujarati Indians in Houston, Texas | 100 | 1,407,540 | |
JPT | Japanese in Tokyo, Japan | 91 | 1,296,969 | |
LWK | Luhya in Webuye, Kenya | 100 | 1,529,438 | |
MEX | Mexican ancestry in Los Angeles, California | 90 | 1,409,947 | |
MKK | Maasai in Kinyawa, Kenya | 180 | 1,419,626 | |
TSI | Toscans in Italy | 100 | 1,419,920 | |
YRI | Yoruba in Ibadan, Nigeria | 180 | 1,501,085 | |
RAISS (1000 Genomes Project Phase 3, hg38) | EUR | European | 632 | 8,193,280 |
AFR | African | 893 | 13,876,891 | |
SAS | South Asian | 601 | 8,579,150 | |
EAS | East Asian | 585 | 7,245,426 | |
AMR | American | 490 | 9,347,814 | |
SSIMP & FAPI (1000 Genomes Project Phase 3, hg19) | EUR | European | 503 | 81,271,745 |
AFR | African | 661 | 81,271,745 | |
SAS | South Asian | 489 | 81,271,745 | |
EAS | East Asian | 504 | 81,271,745 | |
AMR | American | 347 | 81,271,745 |