A newly discovered genetic variant that is associated with type 2 diabetes (T2D) is responsible for almost 7% of all diabetes cases in Greenland, according to a whole-genome sequencing analysis of 448 Greenlandic Inuit individuals.
The variant, identified as c.1108G>T, “has the largest population impact of any previously reported variant” within the HNF1A gene – a gene that can cause maturity-onset diabetes of the young (MODY), reported senior author Torben Hansen, MD, PhD, of the University of Copenhagen, and colleagues in The Lancet Regional Health–Europe. The c.1108G>T variant does not cause MODY, but other variants within the HNF1A gene do. However, carriers of this variant, which is present in 1.9% of the Greenlandic Inuit population and has not been found elsewhere, have normal insulin sensitivity, but decreased beta-cell function and a more than fourfold risk of developing type 2 diabetes. “This adds to a previous discovery that about 11% of all diabetes in Greenlandic Inuit is explained by a mutation in the TBC1D4 variant,” Dr. Hansen told this publication. “Thus 1 in 5 patients diagnosed with type 2 diabetes in Greenland have a specific mutation explaining their diabetes. In European populations only about 1%-2% of patients diagnosed with type 2 diabetes have a known genetic etiology.”
The finding “provides new avenues to subgroup patients, detect diabetes in family members, and pursue precision treatment trials,” noted the authors, although they acknowledged that treatment choices for individuals with this variant still need to be explored. “We know from HNF1A-mutation carriers with European ancestry that they benefit from sulfonylurea treatment,” said Dr. Hansen. “However, we have not yet done treatment studies in Inuit.” The investigators noted that “it is not always the case that variants in HNF1A result in an increased insulin secretory response to sulfonylurea. ... Whether carriers of the c.1108G>T variant could benefit from treatment with sulfonylurea should be pursued within the context of a randomized clinical trial establishing both short- and long-term efficacy of sulfonylurea in these patients.”
A total of 4,497 study participants were randomly sampled from two cross-sectional cohorts in an adult Greenlandic population health survey. Among 448 participants who had whole genome sequencing, 14 known MODY genes were screened for both previously identified as well as novel variants. This identified the c.1108G>T variant, which was then genotyped in the full cohort in order to estimate an allele frequency of 1.3% in the general Greenlandic population, and 1.9% in the Inuit component. The variant was not found in genome sequences of other populations.
The researchers then tested the association of the variant with T2D and showed strong association with T2D (odds ratio, 4.35) and higher hemoglobin A1c levels.
“This is very well-conducted and exciting research that highlights the importance of studying the genetics of diverse populations,” said Miriam Udler, MD, PhD, director of the Massachusetts General Diabetes Genetics Clinic, and assistant professor at Harvard University, both in Boston. “This manuscript builds on prior work from the researchers identifying another genetic variant specific to the Greenlandic Inuit population in the gene TBC1D4,” she added. “About 3.8% of people in this population carry two copies of the TBC1D4 variant and have about a 10-fold increased risk of diabetes. Together the two variants affect 18% of Greenlanders with diabetes.”
Dr. Miriam Udler
With its fourfold increased risk of diabetes, the new variant falls into “an ever-growing category” of “intermediate risk” genetic variants, explained Dr. Udler – “meaning that they have a large impact on diabetes risk, but cannot fully predict whether someone will get diabetes. The contribution of additional risk factors is particularly important for ‘intermediate risk’ genetic variants,” she added. “Thus, clinically, we can tell patients who have variants such as HNF1A c.1108>T that they are at substantial increased risk of diabetes, but that many will not develop diabetes. And for those who do develop diabetes, we are not yet able to advise on particular therapeutic strategies.”
Still, she emphasized, the importance of studying diverse populations with specific genetic risk factors is the end-goal of precision medicine. “An active area of research is determining whether and how to return such information about ‘intermediate risk’ variants to patients who get clinical genetic testing for diabetes, since typically only variants that are very high risk ... are returned in clinical testing reports.” Dr. Udler added that “many more such “intermediate risk’ variants likely exist in all populations, but have yet to be characterized because they are less common than HNF1A c.1108>T; however, ongoing worldwide efforts to increase the sample sizes of human genetic studies will facilitate such discovery.”
The study was funded by Novo Nordisk Foundation, Independent Research Fund Denmark, and Karen Elise Jensen’s Foundation. Dr. Hansen and Dr. Udler had no disclosures.