Transethnic insight into the genetics of glycaemic traits: fine-mapping results from the Population Architecture using Genomics and Epidemiology (PAGE) consortium

• Published in: Diabetologia Vol. 60; no. 12; pp. 2384 - 2398
• Main Authors: Bien, Stephanie A., Pankow, James S., Haessler, Jeffrey, Lu, Yinchang N., Pankratz, Nathan, Rohde, Rebecca R., Tamuno, Alfred, Carlson, Christopher S., Schumacher, Fredrick R., Bůžková, Petra, Daviglus, Martha L., Lim, Unhee, Fornage, Myriam, Fernandez-Rhodes, Lindsay, Avilés-Santa, Larissa, Buyske, Steven, Gross, Myron D., Graff, Mariaelisa, Isasi, Carmen R., Kuller, Lewis H., Manson, JoAnn E., Matise, Tara C., Prentice, Ross L., Wilkens, Lynne R., Yoneyama, Sachiko, Loos, Ruth J. F., Hindorff, Lucia A., Le Marchand, Loic, North, Kari E., Haiman, Christopher A., Peters, Ulrike, Kooperberg, Charles
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01-12-2017; Springer Nature B.V
• Subjects: Blood Glucose - metabolism; Diabetes; Diabetes mellitus; Diabetes Mellitus, Type 2 - blood; Diabetes Mellitus, Type 2 - genetics; Diabetes Mellitus, Type 2 - metabolism; Epidemiology; European Continental Ancestry Group; Fasting; Fasting - blood; Female; Gene mapping; Genetic diversity; Genome-Wide Association Study; Glucose metabolism; Human Physiology; Humans; Insulin; Insulin - blood; Internal Medicine; Laboratory testing; Male; Medicine; Medicine & Public Health; Metabolic Diseases; Polymorphism, Single Nucleotide - genetics; Population; Population genetics; Population studies; Risk factors; Single-nucleotide polymorphism; Statistical analysis; Type 2 diabetes; Fine-mapping; Multiethnic; Glycaemic; Genetic; Page; Glucose; Insulin; Transethnic
• ISSN: 0012-186X; 1432-0428
• DOI: 10.1007/s00125-017-4405-1

Aims/hypothesis
Elevated levels of fasting glucose and fasting insulin in non-diabetic individuals are markers of dysregulation of glucose metabolism and are strong risk factors for type 2 diabetes. Genome-wide association studies have discovered over 50 SNPs associated with these traits. Most of these loci were discovered in European populations and have not been tested in a well-powered multi-ethnic study. We hypothesised that a large, ancestrally diverse, fine-mapping genetic study of glycaemic traits would identify novel and population-specific associations that were previously undetectable by European-centric studies.
Methods
A multiethnic study of up to 26,760 unrelated individuals without diabetes, of predominantly Hispanic/Latino and African ancestries, were genotyped using the Metabochip. Transethnic meta-analysis of racial/ethnic-specific linear regression analyses were performed for fasting glucose and fasting insulin. We attempted to replicate 39 fasting glucose and 17 fasting insulin loci. Genetic fine-mapping was performed through sequential conditional analyses in 15 regions that included both the initially reported SNP association(s) and denser coverage of SNP markers. In addition, Metabochip-wide analyses were performed to discover novel fasting glucose and fasting insulin loci. The most significant SNP associations were further examined using bioinformatic functional annotation.
Results
Previously reported SNP associations were significantly replicated (
p
 ≤ 0.05) in 31/39 fasting glucose loci and 14/17 fasting insulin loci. Eleven glycaemic trait loci were refined to a smaller list of potentially causal variants through transethnic meta-analysis. Stepwise conditional analysis identified two loci with independent secondary signals (
G6PC2
-rs477224 and
GCK-
rs2908290), which had not previously been reported. Population-specific conditional analyses identified an independent signal in
G6PC2
tagged by the rare variant rs77719485 in African ancestry. Further Metabochip-wide analysis uncovered one novel fasting insulin locus at
SLC17A2
-rs75862513.
Conclusions/interpretation
These findings suggest that while glycaemic trait loci often have generalisable effects across the studied populations, transethnic genetic studies help to prioritise likely functional SNPs, identify novel associations that may be population-specific and in turn have the potential to influence screening efforts or therapeutic discoveries.
Data availability
The summary statistics from each of the ancestry-specific and transethnic (combined ancestry) results can be found under the PAGE study on dbGaP here:
https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000356.v1.p1