EGAGenomicsN/Ahttps://ega-archive.org/datasets/EGAD00010000652402EGA dataset EGAD00010000652EGAGenetic analyses, including genome-wide association studies and whole exome sequencing (WES), provide powerful tools for the analysis of complex and rare genetic diseases. To date there are no reference data for Aboriginal Australians to underpin the translation of health-based genomic research. Here we provide a catalogue of variants called after sequencing the exomes of 72 Aboriginal individuals to a depth of 20X coverage in ∼80% of the sequenced nucleotides. We determined 320,976 single nucleotide variants (SNVs) and 47,313 insertions/deletions using the Genome Analysis Toolkit. We had previously genotyped a subset of the Aboriginal individuals (70/72) using the Illumina Omni2.5 BeadChip platform and found ~99% concordance at overlapping sites, which suggests high quality genotyping. Finally, we compared our SNVs to six publicly available variant databases, such as dbSNP and the Exome Sequencing Project, and 70,115 of our SNVs did not overlap any of the single nucleotide polymorphic sites in all the databases. Our data set provides a useful reference point for genomic studies on Aboriginal Australians.A body mass index (BMI) >22kg/m2 is a risk factor for type 2 diabetes (T2D) in Aboriginal Australians. To identify loci associated with BMI and T2D we undertook a genome-wide association study using 1,075,436 quality-controlled single nucleotide polymorphisms (SNPs) genotyped (Illumina 2.5M Duo Beadchip) in 402 individuals in extended pedigrees from a Western Australian Aboriginal community. Imputation using the thousand genomes (1000G) reference panel extended the analysis to 6,724,284 post quality-control autosomal SNPs. No associations achieved genome-wide significance, commonly accepted as P<5x10-8. Nevertheless, genes/pathways in common with other ethnicities were identified despite the arrival of Aboriginal people in Australia >45,000 years ago. The top hit (rs10868204 Pgenotyped = 1.50x10-6; rs11140653 Pimputed_1000G = 2.90x10-7) for BMI lies 5' of NTRK2, the type 2 neurotrophic tyrosine kinase receptor for brain-derived neurotrophic factor (BDNF) that regulates energy balance downstream of melanocortin-4 receptor (MC4R). PIK3C2G (rs12816270 Pgenotyped = 8.06x10-6; rs10841048 Pimputed_1000G = 6.28x10-7) was associated with BMI, but not with T2D as reported elsewhere. BMI also associated with CNTNAP2 (rs6960319 Pgenotyped = 4.65x10-5; rs13225016 Pimputed_1000G = 6.57x10-5), previously identified as the strongest gene-by-environment interaction for BMI in African-Americans. The top hit (rs11240074 Pgenotyped = 5.59x10-6, Pimputed_1000G = 5.73x10-6) for T2D lies 5' of BCL9 that, along with TCF7L2, promotes beta-catenin's transcriptional activity in the WNT signaling pathway. Additional hits occurred in genes affecting pancreatic (KCNJ6, KCNA1) and/or GABA (GABRR1, KCNA1) functions. Notable associations observed for genes previously identified at genome-wide significance in other populations included MC4R (Pgenotyped = 4.49x10-4) for BMI and IGF2BP2 Pimputed_1000G = 2.55x10-6) for T2D. Our results may provide novel functional leads in understanding disease pathogenesis in this Australian Aboriginal population.First genome-wide association study in an Australian aboriginal population provides insights into genetic risk factors for body mass index and type 2 diabetes.Reference genotype and exome data from an Australian Aboriginal population for health-based research.Tang Dave D, Anderson Denise D, Francis Richard W RW, Syn Genevieve G, Jamieson Sarra E SE, Lassmann Timo T, Blackwell Jenefer M JMAnderson Denise D, Cordell Heather J HJ, Fakiola Michaela M, Francis Richard W RW, Syn Genevieve G, Scaman Elizabeth S H ES, Davis Elizabeth E, Miles Simon J SJ, McLeay Toby T, Jamieson Sarra E SE, Blackwell Jenefer M JMIllumina Sequencing Technology, Illumina., Illumina SequencingIllumina Sequencing Technology, Illumina., Illumina SequencingGenome-Wide Association, T2DM - Type 2 Diabetes mellitus, Adult-Onset Diabetes Mellitus, Diabetes Type 2, type 2, Noninsulin Dependent, Genome Wide Association Analysis, Whole Genome Association Study, Type 2 Diabetes Mellitus, Risk Factor Score, DIABETES MELLITUS TYPE 02, diabetes mellitus type 2, Maturity-onset diabetes, School-Age, Risk Factors, GWA Studies, Body Mass, Non-Insulin-Dependent, Studies, Non-Insulin Dependent Diabetes Mellitus, Maturity Onset Diabetes, non-insulin-dependent diabetes mellitus, Slow Onset, Risk Factor, Correlates, Maturity-Onset Diabetes, Quetelet Index, T2DM, School-Age Populations, GWA Study, Populations at Risk, Non-Insulin-Dependent Diabetes Mellitus, GWA, Risk Score, Maturity Onset Diabetes Mellitus, Population, adult-onset, Stable Diabetes Mellitus., Population at Risk, Genome Wide Association Scan, Genome-Wide Association Studies, BMI, Ketosis-Resistant Diabetes Mellitus, NIDDM, genetic, Social, Study, Noninsulin-Dependent, Diabetes mellitus, Maturity-onset diabetes mellitus, Noninsulin Dependent Diabetes Mellitus, Stable, Health Correlates, Quetelet, MODY (Maturity-onset diabetes of the young), Diabetes Mellitus, Social Risk Factor, Ketosis-Resistant, School Age Population, constitutitional genetic, Non Insulin Dependent, Diabetes, Adult Onset, Type 2 diabetes, Index, Adult-onset diabetes, Type 2 diabetes mellitus, Adult-onset diabetes mellitus, familial, MODY, Factor, Risk Factor Scores, Genome-Wide, Noninsulin-dependent diabetes mellitus, Adult-Onset, T2D, Genome Wide Association Study, Adult-Onset Diabetes, School Age, Quetelet's Index, Slow-Onset Diabetes Mellitus, Maturity-Onset, Score, Type 2 Diabetes Mellitus Non-Insulin Dependent, Ketosis Resistant, Whole Genome Association Analysis, Maturity-Onset Diabetes Mellitus, Populations, Type 2 Diabetes, Factors, Social Risk Factors, Risk, Type II Diabetes, Type 2, School Age Populations, Genome Wide Association Studies, Risk Scores, Noninsulin-Dependent Diabetes Mellitus, Social Risk, type II, Quetelets Index, Health, non-insulin-dependent, Non-Insulin Dependent Diabetes, Association Studies, inherited genetic, Association Study, School-Age Population, Type II, hereditary, Slow-Onset, Maturity OnsetGenome-Wide Association, protein translation, other disease, 0998/12, Activity, determination, Complete Exome, Laboratory, PNT-P1, Genome Wide Association Analysis, Whole Genome Association Study, ETS2, Ets2, DmelCG17077, EY3-1, Pnt, Normalcies, CG8705., DMPOINT1A, pntegfr, GWA Studies, 0608/07, png, diseases, Studies, disease or disorder, diseases and disorders, Whole Transcriptome, Transcriptome Sequencing, Research Activity, D-ets-2, 3520, Laboratory Research, Pnt-P1, Normalities, Priorities, average, GWA Study, WES, human disease, Complete, Exome Sequencings, pointed-RC, Genomes, Research, Complete Exome Sequencing, Whole Transcriptome Sequencing, GWA, Sequencing, EK3-2, Genome Wide Association Scan, Genome-Wide Association Studies, genetic, non-neoplastic, Study, l(3)07825, Whole Exome, Whole, disorder, Homo sapiens disease, CG17077, Development and Research, Research Priority, Nucleotide, constitutitional genetic, l(3)j1B7, Individual Health, protein anabolism, Ets, protein biosynthetic process, Complete Exome Sequencings, Data Set, Exome, familial, disorders, Research Priorities, D-Ets-2, ets94F, medical condition, 0123/09, Normalcy, Genome-Wide, Exome Sequencing, Priority, Genome Wide Association Study, chemical analysis, Diseases, Research Activities, protein formation, condition, protein biosynthesis, overlap, rare (European definition), Whole Genome Association Analysis, Individual, pnt-P1, pnt-P2, l(3)s118306, nucleotides, Research and Development, Complete Transcriptome, pntP2, Complete Transcriptome Sequencing, Pointed-P1, Normality, Ets94F, Exomes, whole genome, Genome Wide Association Studies, Activities, ptd, disease, PntP2, Health, Ets58AB, protein synthesis, PntP1, E(E2F)3D, Whole Exome Sequencing, Association Studies, inherited genetic, PNTP2, Association Study, assay, hereditary, Transcriptome Sequencings, PNTP1, POINTfalseIllumina_HumanOmni2.5 - samplesGenotyped samples using Illumina HumanOmni2.52017-07-26 15:39:25EGAD0001000065296062707011425760438EGAC00001000261EGAS00001001004