GSCT - QG Analytics

Genomic Scores

Genomic scores play a central role in precision health providing information about genetic risk that can improve decision making in health care systems.

We apply a powerful computational framework for genomic scoring of complex traits. A key feature of this modeling approach is a higher prediction accuracy achieved by better accounting for linkage disequilibrium among markers and the genetic architecture of the traits and using information across the traits analyzed.

We have provided examples of how to use this computational framework for genomic scoring in R Tutorials. Further details about the statistical models and methods used for computing genomic scores can be found in QG Notes, Polygenic Scores – Wikipedia, and in the presentation below:

Genomic_Scores

GSCT database

Below we provide a database for Genomic Scoring of Complex Traits (GSCT). Using our computational framework we have computed and assessed the genomic scores for a range of complex traits and diseases in humans. The prediction accuracy of the genomic scores (R2 or AUC) are provided in the table below. The genomic scores have been further biologically validated by identifying genomic features (such as genes, pathways, protein and chemical complexes) underpinning the scores (see further details here: GACT).

GSCT ID	Trait	Gender	Study	Population	Type	Model	Accuracy
GSCT00001	BMI	Males	UK Biobank	EUS	Quantitative	ST-PT	0.0718
GSCT00002	BMI	Females	UK Biobank	EUS	Quantitative	ST-PT	0.075
GSCT00003	Height	Males	UK Biobank	EUS	Quantitative	ST-PT	0.2154
GSCT00004	Height	Females	UK Biobank	EUS	Quantitative	ST-PT	0.224
GSCT00005	BMI	Males	UK Biobank	EUS	Quantitative	MT-PT	0.0894
GSCT00006	BMI	Females	UK Biobank	EUS	Quantitative	MT-PT	0.091
GSCT00007	Height	Males	UK Biobank	EUS	Quantitative	MT-PT	0.2534
GSCT00008	Height	Females	UK Biobank	EUS	Quantitative	MT-PT	0.2568
GSCT00009	BMI	Males	UK Biobank	EUS	Quantitative	ST-BLR	0.0902
GSCT00010	BMI	Females	UK Biobank	EUS	Quantitative	ST-BLR	0.0894
GSCT00011	Height	Males	UK Biobank	EUS	Quantitative	ST-BLR	0.304
GSCT00012	Height	Females	UK Biobank	EUS	Quantitative	ST-BLR	0.3158
GSCT00013	BMI	Males	UK Biobank	EUS	Quantitative	MT-BLR	0.1208
GSCT00014	BMI	Females	UK Biobank	EUS	Quantitative	MT-BLR	0.1148
GSCT00015	Height	Males	UK Biobank	EUS	Quantitative	MT-BLR	0.3578
GSCT00016	Height	Females	UK Biobank	EUS	Quantitative	MT-BLR	0.3564