Users should pay close attention to quality control (QC) issues when assembling collections of trait-associated SNPs for PTS calculation. The PTS scores the GADGET computes are very much dependent upon the quality and accuracy of the input data. Specific QC issues that users may want to consider include, but may not be limited to:
AFR - African
AMR - Admixed Americans
EAS - East Asian
EUR - European
SAS - Southeast Asian
Code | Population | Group |
---|---|---|
ACB | African Caribbeans in Barbados | AFR |
ASW | Americans of African Ancestry in SW USA | AFR |
ESN | Esan in Nigeria | AFR |
GWD | Gambian in Western Divisions in the Gambia | AFR |
LWK | Luhya in Webuye Kenya | AFR |
MSL | Mende in Sierra Leone | AFR |
YRI | Yoruba in Ibadan Nigeria | AFR |
CLM | Colombians from Medellin Colombia | AMR |
MXL | Mexican Ancestry from Los Angeles USA | AMR |
PEL | Peruvians from Lima Peru | AMR |
PUR | Puerto Ricans from Puerto Rico | AMR |
CDX | Chinese Dai in Xishuangbanna China | EAS |
CHB | Han Chinese in Bejing China | EAS |
CHS | Southern Han Chinese | EAS |
JPT | Japanese in Tokyo Japan | EAS |
KHV | Kinh in Ho Chi Minh City Vietnam | EAS |
CEU | Utah Residents (CEPH) with Northern and Western European Ancestry | EUR |
FIN | Finnish in Finland | EUR |
GBR | British in England and Scotland | EUR |
IBS | Iberian Population in Spain | EUR |
TSI | Toscani in Italia | EUR |
BEB | Bengali from Bangladesh | SAS |
GIH | Gujarati Indian from Houston Texas | SAS |
ITU | Indian Telugu from the UK | SAS |
PJL | Punjabi from Lahore Pakistan | SAS |
STU | Sri Lankan Tamil from the UK | SAS |
GADGET is intended as a tool for researchers to explore population-specific distributions of genetic variants that have been associated with a wide variety of human traits. Users of this site should treat the results with caution, as the interpretation PTS across populations can be complicated by a number of factors. We provide more detail on these issues on the Learn page and in our manuscript describing the server.
GADGET Compute Source Code: Github