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Omni1m

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The Omni1M is a high-throughput genotyping array designed for genome-wide association studies (GWAS) and large-scale genetic research. The core function of the Omni1M is to enable efficient and comprehensive genome-wide genotyping of single nucleotide polymorphisms (SNPs) across the human genome.

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Lab products found in correlation

Humanhap300 beadchip, by Illumina (1 mentions) Cnv370v1, by Illumina (1 mentions) Cnv370 quadv3, by Illumina (1 mentions) Human610 quad beadchip, by Illumina (1 mentions) Omniexpress, by Illumina (1 mentions) Axiom, by Illumina (1 mentions)

6 protocols using omni1m

1

Genome-Wide Association Study of POAG

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In total 1,155 glaucoma cases and 1,992 controls, genotyped on Illumina Omni1M or OmniExpress arrays and imputed to the 1000 Genomes Phase 1 Europeans panel, were used as discovery cohort in this study to perform a genome-wide association study for Primary Open Angle Glaucoma (POAG) (stage 1). The association results for the top SNPs from the discovery cohort were replicated in stage 2 and then stage 3 replication cohorts. The cohort details, genotyping platforms for each cohort and diagnostic criteria are listed in the Supplementary Notes. In addition, we performed a meta-analysis for the top SNPs in the discovery and replication cohorts. In this method section we have described the methods used for imputation and statistical analysis for the discovery cohort. Methods used for each replication cohort are present in the Supplementary Notes.
Gharahkhani P., Burdon K.P., Fogarty R., Sharma S., Hewitt A.W., Martin S., Law M.H., Cremin K., Bailey J.N., Loomis S.J., Pasquale L.R., Haines J.L., Hauser M.A., Viswanathan A.C., McGuffin P., Topouzis F., Foster P.J., Graham S.L., Casson R.J., Chehade M., White A.J., Zhou T., Souzeau E., Landers J., Fitzgerald J.T., Klebe S., Ruddle J.B., Goldberg I., Healey P.R., Mills R.A., Wang J.J., Montgomery G.W., Martin N.G., Radford-Smith G., Whiteman D.C., Brown M.A., Wiggs J.L., Mackey D.A., Mitchell P., MacGregor S, & Craig J.E. (2014). Common variants near ABCA1, AFAP1 and GMDS confer risk of primary open-angle glaucoma. Nature genetics, 46(10), 1120-1125.
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2

Genetic Variant Analysis in Diverse Populations

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GoDARTS participants were genotyped using the Affymetrix 6.0 (n=927) and Illumina Human Omni Express (n=809) platforms. ORCADES samples were genotyped with either the Illumina HumanHap300 bead chip (n=890) or the Illumina Omni1M (n=304) or Illumina Omni Express bead chips (n=1073). Genotype data quality was assessed and imputed on the basis of 1000 Genome Projects reference panel. Imputed genotypes for 658, 1078, 1358 individuals from the GoDARTS data set 1, GoDARTS data set 2, and ORCADES cohorts, respectively, were used for the three independent GWAS analysis.
LBC1936 samples were genotyped using the Illumina Human 610Quad BeadChip. A total of 1398 participants from the 2 independent Croatian replication cohorts were available for the analysis, and subjects were genotyped on different genotyping platforms including Illumina CNV370v1 and CNV370-Quadv3 for Croatia-Korčula (n=378), and Illumina CNV370-Quadv3 and IlluminaOmniExpressExome-8v1_A for Croatia-Split (n=376). More details on QC, imputation, and processing can be found in the online-only Data Supplement.
Veluchamy A., Ballerini L., Vitart V., Schraut K.E., Kirin M., Campbell H., Joshi P.K., Relan D., Harris S., Brown E., Vaidya S.S., Dhillon B., Zhou K., Pearson E.R., Hayward C., Polasek O., Deary I.J., MacGillivray T., Wilson J.F., Trucco E., Palmer C.N, & Doney A.S. (2019). Novel Genetic Locus Influencing Retinal Venular Tortuosity Is Also Associated With Risk of Coronary Artery Disease. Arteriosclerosis, Thrombosis, and Vascular Biology, 39(12), 2542-2552.
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3

POAG Genetic Consortium Datasets

Cited 2 times
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The US data are derived from the National Eye Institute Glaucoma Human Genetics Collaboration Heritable Overall Operational Database (NEIGHBORHOOD), a genetic consortium that includes the following eight independent datasets: Massachusetts Eye and Ear Infirmary; National Eye Institute Glaucoma Human Genetics Collaboration; Iowa; Marshfield; the Ocular Hypertension Treatment Study; the Women's Genome Health Study; and two datasets from the Glaucoma Genes and Environment Study: one genotyped on the Affymetrix platform and the other genotyped on the Illumina HapMap Series.16 (link) The NEIGHBORHOOD dataset has a total of 3853 POAG cases and 33,480 controls. The Australian and New Zealand data are derived from the Australian and New Zealand Registry of Advanced Glaucoma (ANZRAG) and consist of 1115 advanced POAG cases and 1992 controls genotyped on the Illumina Omni 1M or the OmniExpress array. Cases and controls were drawn from Southern Adelaide Health Service/Flinders University, University of Tasmania, Queensland Institute of Medical Research, and the Royal Victorian Eye and Ear Hospital.17 (link) All participants in both datasets were of European ancestry. The institutional review boards of all participating institutions approved this study.
Cooke Bailey J.N., Gharahkhani P., Kang J.H., Butkiewicz M., Sullivan D.A., Weinreb R.N., Aschard H., Allingham R.R., Ashley-Koch A., Lee R.K., Moroi S.E., Brilliant M.H., Wollstein G., Schuman J.S., Fingert J.H., Budenz D.L., Realini T., Gaasterland T., Scott W.K., Singh K., Sit A.J., Igo RP J.r., Song Y.E., Hark L., Ritch R., Rhee D.J., Vollrath D., Zack D.J., Medeiros F., Vajaranant T.S., Chasman D.I., Christen W.G., Pericak-Vance M.A., Liu Y., Kraft P., Richards J.E., Rosner B.A., Hauser M.A., Craig J.E., Burdon K.P., Hewitt A.W., Mackey D.A., Haines J.L., MacGregor S., Wiggs J.L, & Pasquale L.R. (2018). Testosterone Pathway Genetic Polymorphisms in Relation to Primary Open-Angle Glaucoma: An Analysis in Two Large Datasets. Investigative Ophthalmology & Visual Science, 59(2), 629-636.
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4

Genotyping and Imputation Pipeline for NTR

Cited 1 time
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Genotyping in children (YNTR) and adults (ANTR) was done on multiple platforms over time including Perlegen-Affymetrix, Affymetrix 6.0, Affymetrix Axiom, Illumina Human Quad Bead 660, Illumina Omni 1M and Illumina GSA. Quality control and processing of the genotype data was performed on the complete dataset of all genotyped participants from the NTR. Quality control was carried out and haplotypes were estimated in PLINK. CEU population outliers, based on per platform 1000 Genomes PC projection with the Smartpca software (50 (link)), were excluded. Data were phased per platform using Eagle, and then imputed to 1000 Genomes using Minimac, following the Michigan imputation server protocols. For the polygenic scoring imputed data were converted to best guess genotypes, and filtered to include only ACGT SNPs, SNPs with MAF > 0.01, HWE p > 10−5 and genotype call rate > 0.98, and exclude SNPs with more than 2 alleles. All Mendelian errors were set to missing. Principal components (PCs) were calculated with Smartpca using linkage-disequilibrium-pruned (LD-pruned) 1000 Genomes–imputed SNPs that were also genotyped on at least one platform, had MAF > 0.05 and were not present in the long-range LD regions.
Odintsova V.V., Rebattu V., Hagenbeek F.A., Pool R., Beck J.J., Ehli E.A., van Beijsterveldt C.E., Ligthart L., Willemsen G., de Geus E.J., Hottenga J.J., Boomsma D.I, & van Dongen J. (2021). Predicting Complex Traits and Exposures From Polygenic Scores and Blood and Buccal DNA Methylation Profiles. Frontiers in Psychiatry, 12, 688464.
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5

Genome-Wide Association Study of POAG

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In total 1,155 glaucoma cases and 1,992 controls, genotyped on Illumina Omni1M or OmniExpress arrays and imputed to the 1000 Genomes Phase 1 Europeans panel, were used as discovery cohort in this study to perform a genome-wide association study for Primary Open Angle Glaucoma (POAG) (stage 1). The association results for the top SNPs from the discovery cohort were replicated in stage 2 and then stage 3 replication cohorts. The cohort details, genotyping platforms for each cohort and diagnostic criteria are listed in the Supplementary Notes. In addition, we performed a meta-analysis for the top SNPs in the discovery and replication cohorts. In this method section we have described the methods used for imputation and statistical analysis for the discovery cohort. Methods used for each replication cohort are present in the Supplementary Notes.
Gharahkhani P., Burdon K.P., Fogarty R., Sharma S., Hewitt A.W., Martin S., Law M.H., Cremin K., Bailey J.N., Loomis S.J., Pasquale L.R., Haines J.L., Hauser M.A., Viswanathan A.C., McGuffin P., Topouzis F., Foster P.J., Graham S.L., Casson R.J., Chehade M., White A.J., Zhou T., Souzeau E., Landers J., Fitzgerald J.T., Klebe S., Ruddle J.B., Goldberg I., Healey P.R., Mills R.A., Wang J.J., Montgomery G.W., Martin N.G., Radford-Smith G., Whiteman D.C., Brown M.A., Wiggs J.L., Mackey D.A., Mitchell P., MacGregor S, & Craig J.E. (2014). Common variants near ABCA1, AFAP1 and GMDS confer risk of primary open-angle glaucoma. Nature genetics, 46(10), 1120-1125.
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6

Cognitive Impairment Genetics and Memory

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A sample of 209 elderly patients (n=91 males, n=118 females) with cognitive impairments (n=59 mild cognitive impairment, n=150 dementia) was investigated. The participants were recruited within the early diagnostic and prognostic program of the Competence Network on Dementia (CND) at each of the 13 participating sites in Germany with the diagnosis of mild J o u r n a l P r e -p r o o f cognitive impairment or Alzheimer's disease (Kornhuber et al., 2009; Jessen et al., 2009) .
Participants were between 50-90 years old (71.4+0.6; mean+SEM). All patients were tested for logical memory subtest of the Wechsler Memory Scale (WMS) for immediate and delayed retrieval of a verbal story (Abikoff et al., 1987) .
All patients were genotyped using the Illumina Omni-1M rs6873782, rs2286643, rs11950723, rs6869180, rs882663, rs10053906, rs12109550) or a significant deviation from Hardy-Weinberg equilibrium (HWE) (rs3806948) leaving 34 SNPs (Fig. 1). In addition, five SNPs were excluded because of linkage disequilibrium (LD) of R²≥0.8 (rs17111051, rs7732895, kgp9208102, rs17656349, rs6885505) . MAFs, HWE and LD structure were analyzed using Haploview version 4.2 (https://www.broadinstitute.org/haploview/haploview/; LD plot; Fig. 1). In the end, we tested 29 SNPs for their associations with logical memory performance and hippocampal volumes.
Rhein C., Mühle C., Lenz B., Richter-Schmidinger T., Kogias G., Boix F., Lourdusamy A., Dörfler A., Peters O., Ramirez A., Jessen F., Maier W., Hüll M., Frölich L., Teipel S., Wiltfang J., Kornhuber J, & Müller C.P. (2020). Association of a CAMK2A genetic variant with logical memory performance and hippocampal volume in the elderly. Brain research bulletin, 161.
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