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Omniquad array

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The OmniQuad array is a high-throughput genotyping platform designed for large-scale genetic studies. It enables the simultaneous analysis of hundreds of thousands of genetic markers across the human genome.

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Lab products found in correlation

2.5 m array, by Illumina (3 mentions) Ht 12 v3.0 arrays, by Illumina (2 mentions) Infinium human610 quad bead chip, by Illumina (2 mentions) Immunochip, by Illumina (1 mentions) Global screening array, by Illumina (1 mentions)

9 protocols using omniquad array

1

Genome-wide Genotypes and eQTL Analysis

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Whole genome genotypes for the discovery phase were determined by Illumina OmniQuad arrays at Expression Analysis (Durham, NC, USA), and retained where calls were made for 95% of the individuals and Hardy-Weinberg equilibrium observed at P > 0.001. Expression quantitative trait locus (eQTL) analysis was performed only on the Caucasian samples (n = 153) by linear regression against the SNM normalized expression values (similar results were observed for the alternative normalization). Genotypes were excluded if the minor allele frequency was less than 0.1, to avoid rare homozygotes biasing the analysis, and we also required at least two individuals in each genotype class. Only local (cis) associations (SNPs within 250 kb of the probe) were assessed since this analysis is underpowered to assess distal (trans) associations, and in Additional file 2 we report only the strongest association per locus since the study is underpowered to detect multiple associations even in the presence of reduced linkage disequilibrium. In addition, 3,651 probes known to contain common SNPs were removed from the analysis [25 (link)], including 39 putativeeQTL.
Kim J., Ghasemzadeh N., Eapen D.J., Chung N.C., Storey J.D., Quyyumi A.A, & Gibson G. (2014). Gene expression profiles associated with acute myocardial infarction and risk of cardiovascular death. Genome Medicine, 6(5), 40.
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2

Population-based Cohort Study of Genetic and Transcriptomic Profiles

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n = 139 The Center for Health Discovery and Well Being (CD-HWB) Study24 (link) is a population based cohort consisting of 139 individuals of European descent collected in Atlanta USA. Gene expression profiles were generated with Illumina HT-12 V3.0 arrays from peripheral blood collected from Tempus tubes that preserve RNA. Whole genome genotypes were measured using Illumina OmniQuad arrays. Due to the small sample size, most SNP pairs did not pass filtering in this dataset (20 SNP pairs remained) and so we have excluded it from the rest of the analysis.
Hemani G., Shakhbazov K., Westra H.J., Esko T., Henders A.K., McRae A.F., Yang J., Gibson G., Martin N.G., Metspalu A., Franke L., Montgomery G.W., Visscher P.M, & Powell J.E. (2014). Detection and replication of epistasis influencing transcription in humans. Nature, 508(7495), 249-253.
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3

Population-based Cohort Study of Genetic and Transcriptomic Profiles

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n = 139 The Center for Health Discovery and Well Being (CD-HWB) Study24 (link) is a population based cohort consisting of 139 individuals of European descent collected in Atlanta USA. Gene expression profiles were generated with Illumina HT-12 V3.0 arrays from peripheral blood collected from Tempus tubes that preserve RNA. Whole genome genotypes were measured using Illumina OmniQuad arrays. Due to the small sample size, most SNP pairs did not pass filtering in this dataset (20 SNP pairs remained) and so we have excluded it from the rest of the analysis.
Hemani G., Shakhbazov K., Westra H.J., Esko T., Henders A.K., McRae A.F., Yang J., Gibson G., Martin N.G., Metspalu A., Franke L., Montgomery G.W., Visscher P.M, & Powell J.E. (2014). Detection and replication of epistasis influencing transcription in humans. Nature, 508(7495), 249-253.
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4

Genome-Wide Genotyping and Quality Control

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Subjects underwent either genotyping using the Omni-Quad array (Illumina) or a custom genotyping platform designed by a consortium (Immunochip, Illumina), which contained approximately 200,000 SNPs. Quality control protocol was as we have previously described [4 (link), 7 (link)].
Harris V.M., Sharma R., Cavett J., Kurien B.T., Liu K., Koelsch K.A., Rasmussen A., Radfar L., Lewis D., Stone D.U., Kaufman C.E., Li S., Segal B., Wallace D.J., Weisman M.H., Venuturupalli S., Kelly J.A., Alarcon-Riquelme M.E., Pons-Estel B., Jonsson R., Lu X., Gottenberg J.E., Anaya J.M., Cunninghame-Graham D.S., Huang A.J., Brennan M.T., Hughes P., Alevizos I., Miceli-Richard C., Keystone E.C., Bykerk V.P., Hirschfield G., Xie G., Ng W.F., Nordmark G., Bucher S.M., Eriksson P., Omdal R., Rhodus N.L., Rischmueller M., Rohrer M., Wahren-Herlenius M., Witte T., Mariette X., Lessard C.J., Harley J.B., Sivils K.L, & Scofield R.H. (2016). Klinefelter's syndrome (47,XXY) is in excess among men with Sjögren's syndrome. Clinical immunology (Orlando, Fla.), 168, 25-29.
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5

Harmonized Genetic Data Processing in ADNI

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In ADNI-1, genotyping was performed using the Illumina Infinium Human-610-Quad BeadChip. In ADNI-2/GO, genotyping was performed on the Illumina OmniQuad array. Quality control (QC) and statistical analyses were performed using PLINK software (version 1.07; Purcell et al., 2007 (link)). During QC, we excluded Single Nucleotide Polymorphisms (SNPs) with a genotyping efficiency <90%, a minor allele frequency (MAF) < 5%, or deviation from Hardy-Weinberg Equilibrium (p < 1 × 10−6). This left 515,383 SNPs in ADNI-1 and 605,317 SNPs in ADNI-2/GO. Finally, we merged the two genotyping files for our analyses and again applied a genotyping efficiency <90%. This left a total of 296,267 SNPs for data analysis.
Hohman T.J., Koran M.E, & Thornton-Wells T.A. (2014). Genetic variation modifies risk for neurodegeneration based on biomarker status. Frontiers in Aging Neuroscience, 6, 183.
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6

Genotyping in ADNI Cohorts

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In ADNI-1, genotyping was performed using the Illumina Infinium Human-610-Quad BeadChip. In ADNI-2/GO, genotyping was performed on the Illumina OmniQuad array. After quality control (QC) procedures using PLINK,22 256,790 SNPs remained for data analysis (Appendix A).
Hohman T.J., Koran M.E, & Thornton-Wells T.A. (2014). Genetic Modification of the Relationship between Phosphorylated Tau and Neurodegeneration. Alzheimer's & dementia : the journal of the Alzheimer's Association, 10(6), 637-645.e1.
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7

Genotypic Quality Control of ADNI Cohorts

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The single-nucleotide polymorphisms (SNPs) data of ADNI-1, ADNI-GO, and ADNI-2 cohorts were collected from either the Illumina 2.5-M array or the Illumina OmniQuad array (Saykin et al., 2010 (link); Shen et al., 2010 (link)). The SNPs shown in both arrays were used for the following analyses.
Quality control (QC) analysis was conducted by using R package snpStats (Clayton, 2012 ) in R software (R Core Team, 2013 ). In the QC, we excluded any SNPs that did not meet any of the following criteria: (1) SNPs on chromosome 1-22; (2) call rate per SNP > 95%; (3) Hardy-Weinberg equilibrium (HWE) test of p-value >10–6 (absolute value of z-score <4.753424). After QC analysis, 2,379,855 SNPs remained for the subsequent analyses.
Liu C, & Yu J. (2019). Genome-Wide Association Studies for Cerebrospinal Fluid Soluble TREM2 in Alzheimer’s Disease. Frontiers in Aging Neuroscience, 11, 297.
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8

APOE Genotyping in Alzheimer's Cohorts

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ADNI samples were genotyped using either the Illumina 2.5-M array (a byproduct of the ADNI whole-genome sequencing sample) or the Illumina OmniQuad array [29 (link)] APOE genotype was assessed with two SNPs (rs429358, rs7412) that define the epsilon 2, 3, and 4 alleles, using DNA extracted by Cogenics from a 3 mL aliquot of EDTA blood. In EMIF, APOE genotypes were measured using genome-wide SNP genotyping with Global Screening Array (Illumina Inc., San Diego, CA, USA) [29 (link)].
Tijms B.M., Gobom J., Teunissen C., Dobricic V., Tsolaki M., Verhey F., Popp J., Martinez-Lage P., Vandenberghe R., Lleó A., Molinuévo J.L., Engelborghs S., Freund-Levi Y., Froelich L., Bertram L., Lovestone S., Streffer J., Vos S., A., Blennow K., Scheltens P., Zetterberg H, & Visser P.J. (2021). CSF Proteomic Alzheimer’s Disease-Predictive Subtypes in Cognitively Intact Amyloid Negative Individuals. Proteomes, 9(3), 36.
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9

ADNI SNP Data Quality Control

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The SNP data of ADNI-1, ADNI-GO, and ADNI-2 cohorts were collected from either the Illumina 2.5-M array or the Illumina OmniQuad array (Saykin et al., 2010 (link)). The SNPs shown in both arrays were used for the following analysis.
Quality control (QC) analysis was conducted by using R package snpStats (Clayton, 2012 ) in R software (R Core Team, 2013 ). In the QC, we excluded any SNPs that did not meet any of the following criteria: (1) SNPs on chromosome 1-22; (2) call rate per SNP > 95%; (3) minor allele frequency (MAF) > 5%; (4) Hardy-Weinberg equilibrium (HWE) test of p-value > 10-6 (absolute value of z-score < 4.753424). After QC analysis, 575353 SNPs remained for the subsequent analysis.
Liu C., Chyr J., Zhao W., Xu Y., Ji Z., Tan H., Soto C, & Zhou X. (2018). Genome-Wide Association and Mechanistic Studies Indicate That Immune Response Contributes to Alzheimer’s Disease Development. Frontiers in Genetics, 9, 410.
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