PGS Publication: PGP000062

Publication Information (EuropePMC)
Title Genetics of Type 2 Diabetes in U.S. Hispanic/Latino Individuals: Results From the Hispanic Community Health Study/Study of Latinos (HCHS/SOL).
PubMed ID 28254843(Europe PMC)
doi 10.2337/db16-1150
Publication Date March 2, 2017
Journal Diabetes
Author(s) Qi Q, Stilp AM, Sofer T, Moon JY, Hidalgo B, Szpiro AA, Wang T, Ng MCY, Guo X, MEta-analysis of type 2 DIabetes in African Americans (MEDIA) Consortium, Chen YI, Taylor KD, Aviles-Santa ML, Papanicolaou G, Pankow JS, Schneiderman N, Laurie CC, Rotter JI, Kaplan RC.
Released in PGS Catalog: March 27, 2020

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
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Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
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Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution PGS Scoring File (FTP Link)
PGS000125
(Qi_T2D_2017)
PGP000062 |
Qi Q et al. Diabetes (2017)
Type 2 Diabetes type II diabetes mellitus 80
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000125/ScoringFiles/PGS000125.txt.gz

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM)
Evaluated Score PGS Sample Set ID
(PSS)
Performance Source Trait PGS Effect Sizes
(per SD change)
Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM000404 PGS000125
(Qi_T2D_2017)
PSS000232|
Hispanic or Latin American Ancestry|
7,746 individuals
PGP000062 |
Qi Q et al. Diabetes (2017)
Reported Trait: Type 2 Diabetes OR (Odds Ratio, per risk allele): 1.07 [1.06, 1.08] center, age, sex, 5 PCs of ancestry Covariance matrices corresponding to genetic relatedness (kinship), household, and census block group were included as random effects in the mixed model analysis

Evaluated Samples

PGS Sample Set ID
(PSS)
Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000232 Individuals with T2D were defined as those with fasting time >8 h and fasting glucose levels ≥126 mg/dL, fasting ≤8 h and fasting glucose ≥200 mg/dL, post–oral glucose tolerance test glucose ≥200 mg/dL, HbA1c ≥6.5% (48 mmol/mol), or on current treatment with antihyperglycemia medications.
[
  • 2,499 cases
  • , 5,247 controls
]
,
39.65 % Male samples
Hispanic or Latin American
(Central American, Cuban, Dominican, Mexican, Puerto Rican, South American)
Ancestry groups were defined based on a combination of self-identified Hispanic/Latino background and genetic similarity HCHS, SOL