Humanomni1 quad v1 0 b beadchip

Manufactured by Illumina

Sourced in United States

The HumanOmni1-Quad_v1-0_B BeadChip is a high-throughput genotyping microarray designed for genome-wide association studies. It features over 1 million genetic markers spanning the entire human genome. The BeadChip is compatible with Illumina's InfiniumTM assay technology, allowing for accurate and reliable genotype data generation.

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Lab products found in correlation

Snplex technology, by Thermo Fisher Scientific (1 mentions) Repli g kit, by Qiagen (1 mentions) 610 quad beadchip, by Illumina (1 mentions)

8 protocols using humanomni1 quad v1 0 b beadchip

Stroke-Associated Genetic Variant Analysis

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We identified 256 SNPs in 115 genes selected from the literature in May 2010 (methods in supplemental data) related to angiogenesis, stroke, hypertension and other pathways associated with stroke (Supplemental Table I).
Genotyping was performed using SNPlex^™ technology (Applied Biosystems, Foster City, California). For quality control, two HapMap samples (NA10860/NA10861) were included, and their genotype concordance was verified. The 256 SNPs reached the minimal call rate.
VISP samples (Cohort-D) were genotyped at the Johns Hopkins Center for Inherited Disease Research, using the Illumina HumanOmni1-Quad_v1-0_B BeadChip (Illumina, San Diego, CA), (methodology in supplemental data).

Fernández-Cadenas I., Mendióroz M., Giralt D., Nafria C., Garcia E., Carrera C., Gallego-Fabrega C., Domingues-Montanari S., Delgado P., Ribó M., Castellanos M., Martínez S., Freijo M.M., Jiménez-Conde J., Rubiera M., Alvarez-Sabín J., Molina C.A., Font M.A., Olivares M.G., Palomeras E., de la Ossa N.P., Martinez-Zabaleta M., Masjuan J., Moniche F., Canovas D., Piñana C., Purroy F., Cocho D., Navas I., Tejero C., Aymerich N., Cullell N., Muiño E., Serena J., Rubio F., Davalos A., Roquer J., Arenillas J.F., Martí-Fábregas J., Keene K., Chen W.M., Worrall B., Sale M., Arboix A., Krupinski J, & Montaner J. (2017). GRECOS project. The use of genetics to predict the vascular recurrence after stroke. Stroke, 48(5), 1147-1153.

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Genome-wide Genotyping and Imputation

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Genomic and whole genome amplified DNA were genotyped on the Human-OMNI1-Quad_v1-0_B BeadChip platform (Illumina, San Diego, California). Initially, 1.2 million SNPs were tested, of which over 900,000 (91%) were successfully genotyped. We employed standard quality control thresholds, and included samples and SNPs with > 97% call rate, while excluding minor allele frequencies < 1%. Additionally, 7.2 million SNPs were imputed against the HapMap 3 cosmopolitan reference panel with Impute2.^{20 (link)} All SNP-gene assignments were made based on the UCSC gene tracks within the GRCh37/hg19 genome build.^{22 23 (link)} Genotypes, and a subset of subject information inclusive of key characteristic and outcome phenotype data have been stored, with no identifying links, in the National Human Genome Research Institute Database of Genotypes and Phenotypes (dbGaP Study Accession: phs000353.v1.p1).^{19 20 (link)}.

Srinivasan L., Page G., Kirpalani H., Murray J.C., Das A., Higgins R.D., Carlo W.A., Bell E.F., Goldberg R.N., Schibler K., Sood B.G., Stevenson D.K., Stoll B.J., Van Meurs K.P., Johnson K.J., Levy J., McDonald S.A., Zaterka-Baxter K.M., Kennedy K.A., Sánchez P.J., Duara S., Walsh M.C., Shankaran S., Wynn J.L, & Cotten C.M. (2017). Genome Wide Association Study of Sepsis in Extremely Premature Infants. Archives of disease in childhood. Fetal and neonatal edition, 102(5), F439-F445.

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Comprehensive Genetic Profiling from Diverse Samples

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Genomic DNA was isolated from a variety of sample types, including cell line (55.2%), whole blood (43.1%), mouthwash (0.4%) and buccal swab (0.05%). Whole genome amplification (Qiagen REPLI-g kit, Valencia, CA, USA) was used to obtain sufficient DNA for genotyping in 1.3% of samples. The genotype data implemented in this study was obtained from two fixed-content SNP panels developed by Illumina (Illumina, San Diego, CA, USA), a genome-wide association (GWA) genotyping array, the HumanOmni1-Quad_v1-0_B BeadChip, and a cardiovascular disease (CVD) SNP panel, the ITMAT-Broad-CARe array, that included THBD and PROCR. Genotyping quality from both arrays was excellent with individual SNP call rates > 98% and a between-panel concordance rate of 99.996% based on study duplicates (for further details please see S1 File) [11 (link)].

Cole J.W., Xu H., Ryan K., Jaworek T., Dueker N., McArdle P., Gaynor B., Cheng Y.C., O'Connell J., Bevan S., Malik R., Ahmed N.U., Amouyel P., Anjum S., Bis J.C., Crosslin D., Danesh J., Engelter S.T., Fornage M., Frossard P., Gieger C., Giese A.K., Grond-Ginsbach C., Ho W.K., Holliday E., Hopewell J., Hussain M., Iqbal W., Jabeen S., Jannes J., Kamal A., Kamatani Y., Kanse S., Kloss M., Lathrop M., Leys D., Lindgren A., Longstreth WT J.r., Mahmood K., Meisinger C., Metso T.M., Mosley T J.r., Müller-Nurasyid M., Norrving B., Parati E., Peters A., Pezzini A., Quereshi I., Rasheed A., Rauf A., Salam T., Shen J., Słowik A., Stanne T., Strauch K., Tatlisumak T., Thijs V.N., Tiedt S., Traylor M., Waldenberger M., Walters M., Zhao W., Boncoraglio G., Debette S., Jern C., Levi C., Markus H., Meschia J., Rolfs A., Rothwell P., Saleheen D., Seshadri S., Sharma P., Sudlow C., Worrall B., Stine O.C., Kittner S.J, & Mitchell B.D. (2018). Genetics of the thrombomodulin-endothelial cell protein C receptor system and the risk of early-onset ischemic stroke. PLoS ONE, 13(11), e0206554.

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Genotyping and Controlled-Access Data of VISP Study

Cited 2 times

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Previously, 2100 VISP participants were genotyped on the Illumina HumanOmni1-Quad_v1-0_B BeadChip (Illumina, Inc) [9 (link), 15 (link)]. We selected 556 variants spanning ±10 kb of 24 genes associated with sphingolipid metabolism and the sphingomyelinase pathway (S3 Table). Individual level VISP genetic, metabolomics, and epigenetics data is considered sensitive controlled data and cannot be shared publicly, as specified by the IRBs of Wake Forest University School of Medicine, the University of North Carolina at Chapel Hill School of Medicine, and the University of Virginia School of Medicine, along with the NIH Data Access Committee. Controlled-access data can only be obtained if a user has been authorized by the appropriate Data Access Committee (DAC). The individual level Genomics and Randomized Trials Network (GARNET) VISP data are available in the database of Genotypes and Phenotypes (dbGaP) (Accession: phs000343.v3.p1) and can be requested through the dbGaP Authorized Access System (https://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?page=login), the Cerebrovascular Disease Knowledge Portal (https://cd.hugeamp.org/), and the Coriell Institute for Medical Research (https://catalog.coriell.org/). The authors will also share the data on request.

Davis Armstrong N.M., Spragley K.J., Chen W.M., Hsu F.C., Brewer M.S., Horn P.J., Williams S.R., Sale M.M., Worrall B.B, & Keene K.L. (2021). Multi-omic analysis of stroke recurrence in African Americans from the Vitamin Intervention for Stroke Prevention (VISP) clinical trial. PLoS ONE, 16(3), e0247257.

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DNA Extraction and Genotyping Protocol

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DNA was extracted from the earliest age blood spot collected on filter paper. Whole genome amplification was used for samples that did not provide adequate genomic DNA. Genotyping was done on the Illumina HumanOmni1-Quad_v1-0_B BeadChip.

Jilling T., Ambalavanan N., Cotten C.M., Martin C.A., Maheshwari A., Schibler K., Levy J, & Page G.P. (2018). Surgical Necrotizing Enterocolitis in Extremely Premature Neonates is Associated with Genetic Variations in an Intergenic Region of Chromosome Eight. Pediatric research, 83(5), 943-953.

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VISP Genetic Analysis Protocol

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A subset of VISP participants provided consent for inclusion in genetic studies. These participants were included in the GWAS component of VISP, supported by the National Human Genome Research Institute (NHGRI), Grant U01 HG005160, as part of the Genomics and Randomized Trials Network (GARNET); dbGaP Study Accession: phs000343.v3.p1. Samples were genotyped at the Johns Hopkins Center for Inherited Disease Research (CIDR), using the Illumina HumanOmni1-Quad_v1-0_B BeadChip (Illumina, San Diego, CA, USA). Individuals were excluded if they were unexpected duplicates or had gender discrepancies. A total of 2,100 individuals were included in the final genetic analyses; summary statistics are provided in Table 1. These subjects consisted of 1,725 individuals of European descent, 258 individuals of African descent, and 117 individuals classified as others.

Keene K.L., Chen W.M., Chen F., Williams S.R., Elkhatib S.D., Hsu F.C., Mychaleckyj J.C., Doheny K.F., Pugh E.W., Ling H., Laurie C.C., Gogarten S.M., Madden E.B., Worrall B.B, & Sale M.M. (2014). Genetic Associations with Plasma B12, B6, and Folate Levels in an Ischemic Stroke Population from the Vitamin Intervention for Stroke Prevention (VISP) Trial. Frontiers in Public Health, 2, 112.

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Genetic Imputation and Analysis of PD Risk

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The UDALL data set was genotyped using Illumina 610-quad BeadChip (Illumina, San Diego, CA).^{25 (link)} The NGRC data set was genotyped using Illumina HumanOmni1-Quad_v1-0_B BeadChip (Illumina).^{26 (link)} Final marker sets after quality control (described in detail in these previous publications) were used for the imputation of untyped SNPs separately in each of the 2 data sets. Imputation allowed us to obtain genetic information on additional variants through the genome for a more thorough investigation. Both data sets were imputed up to 38 million SNPs using IMPUTE2 and the 1000 Genomes reference panel (phase 1, March 2012).^{27 (link)} During quality control, SNPs that had low imputation quality (info score <0.4) and low minor allele frequency (less than 1%) were removed from further analysis. SNPs within the 5-kb flanking regions of the start and end of CACNA1C and CACNA1D were examined for interaction with vitamin D status and association with PD.

Wang L., Maldonado L., Beecham G.W., Martin E.R., Evatt M.L., Ritchie J.C., Haines J.L., Zabetian C.P., Payami H., Pericak-Vance M.A., Vance J.M, & Scott W.K. (2016). DNA variants in CACNA1C modify Parkinson disease risk only when vitamin D level is deficient. Neurology: Genetics, 2(3), e72.

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DNA Extraction and Genotyping Protocol

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