Longitudinal Genomic Study of Sardinian Cohort

The SardiNIA study is a longitudinal population-based health study including 6,602 individuals from the Lanusei valley on Sardinia. The participants have been genotyped on four different Illumina Infinium arrays, OmniExpress, Cardio-Metabochip^{85 (link)}, Immunochip^{86 (link)}, and Exome Chip). Samples with low call rate or with discrepancies between inferred and reported sex and/or relationships were excluded. After genotyping, variants with low call rates, large discordance among duplicate or identical twin genotypes, excess Mendelian inconsistencies, deviations from Hardy–Weinberg equilibrium, or MAF = 0 were excluded. Variants were then imputed from a SardiNIA-specific sequencing panel (~4× coverage) of 3839 individuals, using Minimac3^{87 (link)}. Markers with imputation quality R² > 0.3 (or >0.6 in variants with MAF < 1%) were retained, resulting in a total of ~19 million genetic variants.

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Moksnes M.R., Graham S.E., Wu K.H., Hansen A.F., Gagliano Taliun S.A., Zhou W., Thorstensen K., Fritsche L.G., Gill D., Mason A., Cucca F., Schlessinger D., Abecasis G.R., Burgess S., Åsvold B.O., Nielsen J.B., Hveem K., Willer C.J, & Brumpton B.M. (2022). Genome-wide meta-analysis of iron status biomarkers and the effect of iron on all-cause mortality in HUNT. Communications Biology, 5, 591.

Publication 2022

Infinium arrays

Chip Exome Genetic variants Genotypes Identical twin Population health

Corresponding Organization : Norwegian University of Science and Technology

Other organizations : Michigan Medicine, University of Michigan–Ann Arbor, Université de Montréal, Massachusetts General Hospital, St Olav's University Hospital, Imperial College London, British Heart Foundation, University of Cambridge, Institute of Genetic and Biomedical Research, National Institutes of Health, National Institute on Aging, Montreal Heart Institute

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independent variables

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Samples with low call rate or with discrepancies between inferred and reported sex and/or relationships were excluded
Variants with low call rates, large discordance among duplicate or identical twin genotypes, excess Mendelian inconsistencies, deviations from Hardy–Weinberg equilibrium, or MAF = 0 were excluded
Markers with imputation quality R^2 > 0.3 (or >0.6 in variants with MAF < 1%) were retained

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