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Human 610 quad beadchips

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The Illumina human 610-Quad BeadChips are a high-throughput microarray platform designed for genome-wide genotyping. The BeadChips contain more than 620,000 genetic markers and are capable of interrogating single nucleotide polymorphisms (SNPs) across the human genome.

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Lab products found in correlation

Humanomniexpress beadchip, by Illumina (1 mentions) Massarray typer software v4, by Labcorp (1 mentions) Humanhap550 beadchip, by Illumina (1 mentions) Quad 610 chip, by Illumina (1 mentions) Massarray assay, by Labcorp (1 mentions) Taqman, by Thermo Fisher Scientific (1 mentions) Iplex gold chemistry, by Labcorp (1 mentions) Human610 quad, by Illumina (1 mentions) Gentra puregene blood kit, by Qiagen (1 mentions)

6 protocols using human 610 quad beadchips

1

Large-Scale Genotyping of Asian Cohorts

Cited 2 times
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Genotyping of 3,072 and 1,952 samples in SiMES and SCES, respectively, was performed using Illumina Human610-Quad BeadChips (Illumina Inc.). A total of 620,901 SNPs were genotyped in each cohort. An additional 635 samples in SCES was genotyped using Illumina Human OmniExpress BeadChips with a total of 729,698 SNPs. Detailed quality control procedures for sample and SNPs were described elsewhere [20] (link), [21] (link). In brief, samples were excluded based on the following conditions: (1) sample call-rates of less than 95%; (2) excessive heterozygosity; (3) cryptic relatedness; (4) gender discrepancies; and (5) discordant ethnic memberships. We excluded SNPs with (1) high missingness (>5%); (2) gross departure from HWE (p value <10−6) and (3) MAF <1%. Detailed quality control procedures for SCES samples genotyped on OmniExpress chips were provided in the supplementary materials (Text S2). After quality control, we have the following samples and SNPs available for analysis: 2,542 samples and 557,824 SNPs in SiMES, 1,889 samples and 538,408 SNPs in SCES on Illumina Human610-Quad BeadChips, and 615 samples and 633,783 SNPs in SCES on Illumina Human OmniExpress BeadChips.
Liao J., Li X., Wong T.Y., Wang J.J., Khor C.C., Tai E.S., Aung T., Teo Y.Y, & Cheng C.Y. (2014). Impact of Measurement Error on Testing Genetic Association with Quantitative Traits. PLoS ONE, 9(1), e87044.
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2

SSRI Response Pharmacogenomics Analysis

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DNA from PGRN-AMPS SSRI trial patients was genotyped at the RIKEN Center for Genomic Medicine (Yokohama, Japan) using Illumina human 610-Quad BeadChips (Illumina, San Diego, CA, USA), as described previously.11 (link), 37 (link) GWAS were performed using approximately 7.5 million SNPs. Patients were removed from the analysis for non-compliance or non-Caucasian heritage. Baseline analyses were adjusted for age and sex. Metabolite concentrations and changes in metabolite concentrations after SSRI treatment were tested for association with QIDS-C16 percent change, response and remission. See Supplementary Text for details.
Gupta M., Neavin D., Liu D., Biernacka J., Hall-Flavin D., Bobo W.V., Frye M.A., Skime M., Jenkins G.D., Batzler A., Kalari K., Matson W., Bhasin S.S., Zhu H., Mushiroda T., Nakamura Y., Kubo M., Wang L., Kaddurah-Daouk R, & Weinshilboum R.M. (2016). TSPAN5, ERICH3 and selective serotonin reuptake inhibitors in major depressive disorder: pharmacometabolomics-informed pharmacogenomics. Molecular Psychiatry, 21(12), 1717-1725.
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3

Genotyping of Alzheimer's Disease Cohorts

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The France_AD cohort was genotyped with the with Illumina Human 610-Quad BeadChips. The Belgium_AD cohort was genotyped only for markers rs6455128 and rs7989332 by Sequenom MassARRAY assay using iPLEX Gold chemistry (Sequenom, Hamburg, Germany), followed by MALDI-TOF mass spectrometry. Polymerase chain reaction and extension primers were designed using MassARRAY assay Design software v3.0.2.0 (Sequenom). Genotypes were called both automatically using MassARRAY Typer software v4.0 (Sequenom) and manually, blinded for disease status. The USA_AD cohort was genotyped only for markers rs6455128 and rs7989332 using TaqMan (Applied Biosystems) technology, according to established protocols. The GERAD samples (USA2_AD, UK_AD, and Germany_AD cohorts) were genotyped by Illumina 610-quad chip (data for 3333 cases and 1225 elderly screened controls) and by Illumina HumanHap550 Beadchip (data for 5235 population controls).
Gusareva E.S., Carrasquillo M.M., Bellenguez C., Cuyvers E., Colon S., Graff-Radford N.R., Petersen R.C., Dickson D.W., Mahachie Johna J.M., Bessonov K., Van Broeckhoven C., Williams J., Amouyel P., Sleegers K., Ertekin-Taner N., Lambert J.C, & Van Steen K. (2014). Genome-wide association interaction analysis for Alzheimer's disease. Neurobiology of aging, 35(11), 2436-2443.
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4

GWAS of SSRI Treatment Response

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DNA from PGRN-AMPS SSRI trial patients was genotyped at the RIKEN Center
for Genomic Medicine (Yokohama, Japan) using Illumina human 610-Quad BeadChips
(Illumina, San Diego, CA, USA), as described previously.11 (link), 37 (link) GWAS were performed using approximately 7.5 million
SNPs. Patients were removed from the analysis for non-compliance or
non-Caucasian heritage. Baseline analyses were adjusted for age and sex.
Metabolite concentrations and changes in metabolite concentrations after SSRI
treatment were tested for association with QIDS-C16 percent change, response and
remission. See Supplementary Text for details.
Gupta M., Neavin D., Liu D., Biernacka J., Hall-Flavin D., Bobo W.V., Frye M.A., Skime M., Jenkins G.D., Batzler A., Kalari K., Matson W., Bhasin S.S., Zhu H., Mushiroda T., Nakamura Y., Kubo M., Wang L., Kaddurah-Daouk R, & Weinshilboum R.M. (2016). TSPAN5, ERICH3 and selective serotonin reuptake inhibitors in major depressive disorder: pharmacometabolomics-informed pharmacogenomics. Molecular Psychiatry, 21(12), 1717-1725.
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5

Genetic Profiling of PGRN-AMPS and CO-MED Patients

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PGRN-AMPS patients were genotyped with Illumina human 610-Quad BeadChips (Illumina, San Diego, CA, United States), with quality control and imputation as previously reported (Gupta et al., 2016 (link)). CO-MED patients were genotyped, as previously published, with Illumina Quad, Human Omni 2.5 bead chips (Gadad et al., 2018 (link)). Imputation was performed using the Michigan Imputation Server (Das et al., 2016 (link)). All CO-MED single nucleotide variants (SNVs) included in this analysis met imputation R2 and call rates of >0.95, while genotyped SNVs met LooRsq >0.95.
Grant C.W., Wilton A.R., Kaddurah-Daouk R., Skime M., Biernacka J., Mayes T., Carmody T., Wang L., Lazaridis K., Weinshilboum R., Bobo W.V., Trivedi M.H., Croarkin P.E, & Athreya A.P. (2022). Network science approach elucidates integrative genomic-metabolomic signature of antidepressant response and lifetime history of attempted suicide in adults with major depressive disorder. Frontiers in Pharmacology, 13, 984383.
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6

Genotyping of Recurrent Major Depressive Disorder

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Genotype data was generated for each cohort individually. Human DNA of the MPIP cohort samples was isolated from EDTA blood samples using the Gentra Puregene Blood Kit (Qiagen) with standardized protocols. Genome-wide SNP genotyping was performed using Illumina Human610-Quad (n = 173) and OmniExpress (n = 120) genotyping BeadChips according to the manufacturer's standard protocols. recMDD cohort samples have been genotype on the Illumina-550 BeadChip and details on the genotyping methods have been previously published (Muglia et al., 2010) (link). Quality control was conducted in PLINK 1.90b3s (Chang et al., 2015) (link) Genotyping of the LMU cohort was performed with the Infinium Global Screening Array BeadChip. Genotyping of the recMDD was performed with Illumina Human610-Quad
BeadChips. Further detail on the genotyping and imputation methods used can be found in the individual papers LMU: (Halldorsdottir et al., 2019) (link) and recMDD: (Muglia et al., 2010) (link).
Moore S.R., Halldorsdottir T., Martins J., Lucae S., Müller‐Myhsok B., Mueller N.S., Piechaczek C., Feldmann L., Freisleder F.J., Greimel E., Schulte‐Körne G., Binder E.B., & Arloth J. (2020). Sex differences in the genetic regulation of the blood transcriptome response to glucocorticoid receptor activation.
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