The genetic history of Greenlandic-European contact

The 1919-21 influenza pandemic in Greenland

In Alaska, the 1918-20 influenza pandemic was devastating, with mortality rates up to 90% of the population, while in other arctic regions in northern Sweden and Norway mortality was considerably lower. We investigated the timing and age-patterns in excess mortality in Greenland during the period 1918-21 and compare these to other epidemics and the 1889-92 pandemic. We accessed the Greenlandic National Archives and transcribed all deaths from 1880 to 1921 by age, geography, and cause of death. We estimated monthly excess mortality and studied the spatial-temporal patterns of the pandemics and compared them to other mortality crises in the 40-year period. The 1918-21 influenza pandemic arrived in Greenland in the summer of 1919, one year delayed due to ship traffic interruptions during the winter months. We found that 5.2% of the Greenland population died of the pandemic with substantial variability between counties (range, 0.1% to 11%). We did not see the typical pandemic age-pattern of high young-adult mortality, possibly due to high baseline mortality in this age-group or remoteness. However, despite substantial mortality, the mortality impact was not standing out relative to other mortality crises, or of similar devastation reported in Alaskan populations.

Inuit population have shorter gastric emptying, higher duodenal motility and altered pan-enteric micromilieu: a comparative study between Greenlandic and Danish populations with and without type 2 diabetes

Gastrointestinal function plays a pivotal role in nutrient absorption and overall digestive health. Abnormal gastric emptying is closely linked to type 2 diabetes, impacting blood glucose regulation and causing gastrointestinal symptoms. This study aims to investigate and compare segmental transit times, motility indices, and micromilieu between Greenlandic Inuit and Danish individuals with and without type 2 diabetes. We included forty-four Greenlandic Inuit, twenty-three of whom had type 2 diabetes, and age and gender-matched Danish individuals. Segmental transit time, motility, and luminal environment were measured using the SmartPill®. Greenlandic controls displayed shorter gastric emptying time (GET) (163 min), higher gastric median pH (2.0 pH) and duodenal median contractions (18.2 mm Hg) compared to Greenlanders with type 2 diabetes (GET: 235 min, pH:1.9, median duodenal contraction 18.4 mm Hg) and Danish controls (GET: 190, pH:1.2 median duodenal contraction 17.5 mmHg). Despite similar anti-diabetic management efforts, variations in gastrointestinal physiology were evident, highlighting the complexity of diabetes and its interaction with ethnicity, suggesting potential dietary or even genetic influences, emphasising the necessity for personalised diabetes management approaches. Finally, the study opens possibilities for future research, encouraging investigations into the underlying mechanisms linking genetics, diet, and gastric physiology, as an understanding of factors can lead to more effective, tailored strategies for diabetes care and improved digestive health in diverse populations.

Analysis of admixed Greenlandic siblings shows that the mean genotypic values for metabolic phenotypes differ between Inuit and Europeans

BACKGROUND

Disease prevalence and mean phenotype values differ between many populations, including Inuit and Europeans. Whether these differences are partly explained by genetic differences or solely due to differences in environmental exposures is still unknown, because estimates of the genetic contribution to these means, which we will here refer to as mean genotypic values, are easily confounded, and because studies across genetically diverse populations are lacking.

METHODS

Leveraging the unique genetic properties of the small, admixed and historically isolated Greenlandic population, we estimated the differences in mean genotypic value between Inuit and European genetic ancestry using an admixed sibling design. Analyses were performed across 26 metabolic phenotypes, in 1474 admixed sibling pairs present in a cohort of 5996 Greenlanders.

RESULTS

After FDR correction for multiple testing, we found significantly lower mean genotypic values in Inuit genetic ancestry compared to European genetic ancestry for body weight (effect size per percentage of Inuit genetic ancestry (se), -0.51 (0.16) kg/%), body mass index (-0.20 (0.06) kg/m2/%), fat percentage (-0.38 (0.13) %/%), waist circumference (-0.42 (0.16) cm/%), hip circumference (-0.38 (0.11) cm/%) and fasting serum insulin levels (-1.07 (0.51) pmol/l/%). The direction of the effects was consistent with the observed mean phenotype differences between Inuit and European genetic ancestry. No difference in mean genotypic value was observed for height, markers of glucose homeostasis, or circulating lipid levels.

CONCLUSIONS

We show that mean genotypic values for some metabolic phenotypes differ between two human populations using a method not easily confounded by possible differences in environmental exposures. Our study illustrates the importance of performing genetic studies in diverse populations.

Overview of health research in Greenland from 2001 to 2020

AIMS

Health research in Greenlanders is challenged by a small population, few dedicated researchers and limited funding. Some research areas have proven impactful but gaps in knowledge are unknown. We aimed to quantify health research in Greenland, providing insights for researchers, policymakers and funding agencies to guide future research.

METHODS

We identified all peer-reviewed health research publications with the term 'Greenland***' in title or abstract from 2001 to 2020 through the platform entitled The Lens. Our bibliometric analysis included number of publications, publication rate, research types, research topics, citations and author affiliations, as well as funding.

RESULTS

From 2001 to 2020, a total of 640 health research publications concerning Greenland or Greenlanders were identified, with an average annual publication growth rate of 2.9%. The major health research topics studied in Greenland were infectious diseases, environmental health and general health. Several research fields, including rheumatology, nephrology and dermatology among others proved understudied at best. Three Danish universities contributed with 33% of all publications, with the International Journal of Circumpolar Health (N=176, 28%) being the top journal destination. The most productive author had 119 article authorships during the period.

CONCLUSION

During the past 20 years, Greenland's annual publication rate has been steadily increasing, with an average of 32 articles about health research published each year, which is a higher publication rate than world average. The health research in Greenland is primarily epidemiologic with infectious disease being the most studied research area. Most publications were anchored in Denmark and centred around a few highly productive authors.

A novel 193-plex MPS panel integrating STRs and SNPs highlights the application value of forensic genetics in individual identification and paternity testing

Massively parallel sequencing (MPS) has emerged as a promising technology for targeting multiple genetic loci simultaneously in forensic genetics. Here, a novel 193-plex panel was designed to target 28 A-STRs, 41 Y-STRs, 21 X-STRs, 3 sex-identified loci, and 100 A-SNPs by employing a single-end 400 bp sequencing strategy on the MGISEQ-2000™ platform. In the present study, a series of validations and sequencing of 1642 population samples were performed to evaluate the overall performance of the MPS-based panel and its practicality in forensic application according to the SWGDAM guidelines. In general, the 193-plex markers in our panel showed good performance in terms of species specificity, stability, and repeatability. Compared to commercial kits, this panel achieved 100% concordance for standard gDNA and 99.87% concordance for 14,560 population genotypes. Moreover, this panel detected 100% of the loci from 0.5 ng of DNA template and all unique alleles at a 1:4 DNA mixture ratio (0.2 ng minor contributor), and the applicability of the proposed approach for tracing and degrading DNA was further supported by case samples. In addition, several forensic parameters of STRs and SNPs were calculated in a population study. High CPE and CPD values greater than 0.9999999 were clearly demonstrated and these results could be useful references for the application of this panel in individual identification and paternity testing. Overall, this 193-plex MPS panel has been shown to be a reliable, repeatable, robust, inexpensive, and powerful tool sufficient for forensic practice.

Estimating admixture pedigrees of recent hybrids without a contiguous reference genome

The genome of recently admixed individuals or hybrids has characteristic genetic patterns that can be used to learn about their recent admixture history. One of these are patterns of interancestry heterozygosity, which can be inferred from SNP data from either called genotypes or genotype likelihoods, without the need for information on genomic location. This makes them applicable to a wide range of data that are often used in evolutionary and conservation genomic studies, such as low-depth sequencing mapped to scaffolds and reduced representation sequencing. Here we implement maximum likelihood estimation of interancestry heterozygosity patterns using two complementary models. We furthermore develop apoh (Admixture Pedigrees of Hybrids), a software that uses estimates of paired ancestry proportions to detect recently admixed individuals or hybrids, and to suggest possible admixture pedigrees. It furthermore calculates several hybrid indices that make it easier to identify and rank possible admixture pedigrees that could give rise to the estimated patterns. We implemented apoh both as a command line tool and as a Graphical User Interface that allows the user to automatically and interactively explore, rank and visualize compatible recent admixture pedigrees, and calculate the different summary indices. We validate the performance of the method using admixed family trios from the 1000 Genomes Project. In addition, we show its applicability on identifying recent hybrids from RAD-seq data of Grant's gazelle (Nanger granti and Nanger petersii) and whole genome low-depth data of waterbuck (Kobus ellipsiprymnus) which shows complex admixture of up to four populations.

A novel splice-affecting HNF1A variant with large population impact on diabetes in Greenland

Background

The genetic disease architecture of Inuit includes a large number of common high-impact variants. Identification of such variants contributes to our understanding of the genetic aetiology of diseases and improves global equity in genomic personalised medicine. We aimed to identify and characterise novel variants in genes associated with Maturity Onset Diabetes of the Young (MODY) in the Greenlandic population.

Methods

Using combined data from Greenlandic population cohorts of 4497 individuals, including 448 whole genome sequenced individuals, we screened 14 known MODY genes for previously identified and novel variants. We functionally characterised an identified novel variant and assessed its association with diabetes prevalence and cardiometabolic traits and population impact.

Findings

We identified a novel variant in the known MODY gene HNF1A with an allele frequency of 1.9% in the Greenlandic Inuit and absent elsewhere. Functional assays indicate that it prevents normal splicing of the gene. The variant caused lower 30-min insulin (β = -232 pmol/L, β_SD = -0.695, P = 4.43 × 10^-4) and higher 30-min glucose (β = 1.20 mmol/L, β_SD = 0.441, P = 0.0271) during an oral glucose tolerance test. Furthermore, the variant was associated with type 2 diabetes (OR 4.35, P = 7.24 × 10^-6) and HbA1c (β = 0.113 HbA1c%, β_SD = 0.205, P = 7.84 × 10^-3). The variant explained 2.5% of diabetes variance in Greenland.

Interpretation

The reported variant has the largest population impact of any previously reported variant within a MODY gene. Together with the recessive TBC1D4 variant, we show that close to 1 in 5 cases of diabetes (18%) in Greenland are associated with high-impact genetic variants compared to 1-3% in large populations.

Funding

Novo Nordisk Foundation, Independent Research Fund Denmark, and Karen Elise Jensen's Foundation.

Simultaneous inference of parental admixture proportions and admixture times from unphased local ancestry calls

Population genetic analyses of local ancestry tracts routinely assume that the ancestral admixture process is identical for both parents of an individual, an assumption that may be invalid when considering recent admixture. Here, we present Parental Admixture Proportion Inference (PAPI), a Bayesian tool for inferring the admixture proportions and admixture times for each parent of a single admixed individual. PAPI analyzes unphased local ancestry tracts and has two components: a binomial model that leverages genome-wide ancestry fractions to infer parental admixture proportions and a hidden Markov model (HMM) that infers admixture times from tract lengths. Crucially, the HMM accounts for unobserved within-ancestry recombination by approximating the pedigree crossover dynamics, enabling inference of parental admixture times. In simulations, we find that PAPI's admixture proportion estimates deviate from the truth by 0.047 on average, outperforming ANCESTOR and PedMix by 46.0% and 57.6%, respectively. Moreover, PAPI's admixture time estimates were strongly correlated with the truth (R=0.76) but have an average downward bias of 1.01 generations that is partly attributable to inaccuracies in local ancestry inference. As an illustration of its utility, we ran PAPI on African American genotypes from the PAGE study (N = 5,786) and found strong evidence of assortative mating by ancestry proportion: couples' ancestry proportions are highly correlated (R = 0.87) and are closer to each other than expected under random mating (p < 10-6). We anticipate that PAPI will be useful in studying the population dynamics of admixture and will also be of interest to individuals seeking to learn about their personal genealogies.

Thyroid autoimmunity in Greenlandic Inuit

Objective

This study aimed to provide the first data on the occurrence of thyroid autoimmunity among Inuit in Greenland, a distinct ethnic group who is not iodine deficient.

Design

This study is a population-based cross-sectional study.

Methods

Data were collected in Nuuk in West Greenland and in Ammassalik district in East Greenland. Information on lifestyle, diet and diseases was obtained using questionnaires. Thyroid peroxidase antibody (TPOAb), thyroglobulin antibody (TGAb) and thyroid-stimulating hormone (TSH) were measured in serum. Iodine and creatinine were measured in spot urine samples.

Results

The participation rate was 95% with 434 Inuit participants; 75% were smokers. Iodine excretion was 169 µg/24 h in urban West Greenland, 224 µg/24 h in the main town and 228 µg/24 h in settlements in rural East Greenland. TPOAb, TgAb or either of these was measured in the serum from 3.7, 5.9 and 8.3% of participants, respectively. TPOAb or TgAb was found in 9.3% of Inuit women and 7.5% of men and more frequently, in East Greenland Inuit with the higher iodine excretion (P = 0.02). There was some evidence suggesting that thyroid autoimmunity was more frequent among non-smokers (12.5%) compared to smokers (7.0%). Harbouring a thyroid autoantibody was most frequent in participants with TSH above 3.6 mIU/L (P < 0.001).

Conclusion

Thyroid autoantibodies were rare among Greenland Inuit. While iodine nutrition was associated with autoimmunity similarly to other ethnic groups, the influence of sex and smoking was limited. This could suggest genetic component in Inuit, but the impact of cold, selenium and persistent organic pollutants needs to be elucidated.

Hand grip strength and chair stand test amongst Greenlandic Inuit: reference values and international comparisons

Muscle strength is an important predictor for function and mortality among older adults. We measured hand grip strength among 1442 participants aged 15+ years and carried out a 30 second chair stand test among 786 participants aged 55+ years. Neither test has been carried out among the Inuit before. We present reference values for men and women as means with standard deviations and medians with 10^th, 25^th, 75^th and 90^th percentiles. Hand grip strength was higher among men than among women (means 45.2 kg and 25.8 kg; p < 0.0001), in linear regression analyses it increased with height (β_men = 0.69; β_women = 0.46), weight (β_men = 0.24; β_women = 0.08) and body mass index (β_men = 0.56; β_women = 0.24), and decreased with age (β_men = −0.49; β_women = −0.29) and Inuit genetic ancestry (β_men = −0.96; β_women = −0.59). Chair stand score showed similar associations with sex (mean score for men and women 13.8 and 11.5; p < 0.0001), age (β_men = −0.22; β_women = −0.20) and Inuit genetic ancestry (β_men = −0.38; β_women = −0.41). The hand grip strength of the Inuit was at the same level as in European and North American populations whereas chair stand score was lower than that of a mostly white US population.