Humanexome beadchip genotyping array, by Illumina - Product details

1

Mitochondrial DNA Copy Number Estimation

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The ARIC study recruited 15,792 individuals between 1987 and 1989 aged 45 to 65 years from 4 US communities. DNA for mtDNA-CN estimation was collected from different visits and was derived from buffy coat using the Gentra Puregene Blood Kit (Qiagen). Relevant covariates were derived from the same visit in which DNA was collected. Our analyses were limited to 1,085 individuals with mtDNA-CN data available across all four platforms performed within ARIC: Affymetrix Genome-Wide Human SNP Array 6.0, Illumina HumanExome BeadChip genotyping array, WES and WGS. Eighty-eight percent of our final ARIC participants were Black.
The MESA study recruited 6,814 individuals free of prevalent clinical CVD from 6 US communities across 4 ethnicities. Age range at baseline was 45 to 84 and the baseline exam occurred between 2000 and 2002. DNA for mtDNA-CN analyses was isolated from exam 1 peripheral leukocytes using the Gentra Puregene Blood Kit. Our analyses were restricted to 3,489 White and Black (36%) individuals with mtDNA-CN data available across the three platforms with mtDNA-CN data available at the time of analysis: qPCR, Affymetrix Genome-Wide Human SNP Array 6.0 and Illumina HumanExome BeadChip genotyping array. Exam 1 DNA for the exploratory dPCR pilot study was derived from packed red blood cells.

Longchamps R.J., Castellani C.A., Yang S.Y., Newcomb C.E., Sumpter J.A., Lane J., Grove M.L., Guallar E., Pankratz N., Taylor K.D., Rotter J.I., Boerwinkle E, & Arking D.E. (2020). Evaluation of mitochondrial DNA copy number estimation techniques. PLoS ONE, 15(1), e0228166.

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Replication analysis of erythrocyte and leukocyte variants

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We conducted follow-up replication analysis in 18,018 independent EA samples from the Women’s Health Initiative (WHI) and 5,261 Han Chinese individuals from the Shijingshan district of Beijing that participated in the Peking University – University of Michigan Study of Atherosclerosis (PUUMA) (Supplementary Note). Both studies were genotyped using an Illumina HumanExome BeadChip genotyping array and had erythrocyte and WBC traits available.^{16 (link)} All novel, significant (pHFE and PIGM/DARC since these loci have previously well-defined, known signals and were also seen in the single variant analyses. In the case where an association was identified in the discovery analysis with an erythrocyte trait other than Hb or Hct, we analyzed the association with Hb and Hct in the replication analysis. Similarly, in the case where a leukocyte subtype association was found in the discovery analyses, we analyzed those variants’ association with total WBC in the replication analysis. We applied a Bonferroni correction to the number of replication tests we conducted for the single variant analyses (p-value = 0.05 / 19 = 0.003) and for the gene-based tests (p-value = 0.05 / 10 = 0.005).

Pankratz N., Schick U.M., Zhou Y., Zhou W., Ahluwalia T.S., Allende M.L., Auer P.L., Bork-Jensen J., Brody J.A., Chen M.H., Clavo V., Eicher J.D., Grarup N., Hagedorn E.J., Hu B., Hunker K., Johnson A.D., Leusink M., Lu Y., Lyytikäinen L.P., Manichaikul A., Marioni R.E., Nalls M.A., Pazoki R., Smith A.V., van Rooij F.J., Yang M.L., Zhang X., Zhang Y., Asselbergs F.W., Boerwinkle E., Borecki I.B., Bottinger E.P., Cushman M., de Bakker P.I., Deary I.J., Dong L., Feitosa M.F., Floyd J.S., Franceschini N., Franco O.H., Garcia M.E., Grove M.L., Gudnason V., Hansen T., Harris T.B., Hofman A., Jackson R.D., Jia J., Kähönen M., Launer L.J., Lehtimäki T., Liewald D.C., Linneberg A., Liu Y., Loos R.J., Nguyen V.M., Numans M.E., Pedersen O., Psaty B.M., Raitakari O.T., Rich S.S., Rivadeneira F., Di Sant A.M., Rotter J.I., Starr J.M., Taylor K.D., Thuesen B.H., Tracy R.P., Uitterlinden A.G., Wang J., Wang J., Dehghan A., Huo Y., Cupples L.A., Wilson J.G., Proia R.L., Zon L.I., O’Donnell C.J., Reiner A.P, & Ganesh S.K. (2016). Meta-analysis of rare and common exome chip variants identifies S1PR4 and other loci influencing blood cell traits. Nature genetics, 48(8), 867-876.

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3

Replication analysis of erythrocyte and leukocyte variants

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

We conducted follow-up replication analysis in 18,018 independent EA samples from the Women’s Health Initiative (WHI) and 5,261 Han Chinese individuals from the Shijingshan district of Beijing that participated in the Peking University – University of Michigan Study of Atherosclerosis (PUUMA) (Supplementary Note). Both studies were genotyped using an Illumina HumanExome BeadChip genotyping array and had erythrocyte and WBC traits available.^{16 (link)} All novel, significant (pHFE and PIGM/DARC since these loci have previously well-defined, known signals and were also seen in the single variant analyses. In the case where an association was identified in the discovery analysis with an erythrocyte trait other than Hb or Hct, we analyzed the association with Hb and Hct in the replication analysis. Similarly, in the case where a leukocyte subtype association was found in the discovery analyses, we analyzed those variants’ association with total WBC in the replication analysis. We applied a Bonferroni correction to the number of replication tests we conducted for the single variant analyses (p-value = 0.05 / 19 = 0.003) and for the gene-based tests (p-value = 0.05 / 10 = 0.005).

Pankratz N., Schick U.M., Zhou Y., Zhou W., Ahluwalia T.S., Allende M.L., Auer P.L., Bork-Jensen J., Brody J.A., Chen M.H., Clavo V., Eicher J.D., Grarup N., Hagedorn E.J., Hu B., Hunker K., Johnson A.D., Leusink M., Lu Y., Lyytikäinen L.P., Manichaikul A., Marioni R.E., Nalls M.A., Pazoki R., Smith A.V., van Rooij F.J., Yang M.L., Zhang X., Zhang Y., Asselbergs F.W., Boerwinkle E., Borecki I.B., Bottinger E.P., Cushman M., de Bakker P.I., Deary I.J., Dong L., Feitosa M.F., Floyd J.S., Franceschini N., Franco O.H., Garcia M.E., Grove M.L., Gudnason V., Hansen T., Harris T.B., Hofman A., Jackson R.D., Jia J., Kähönen M., Launer L.J., Lehtimäki T., Liewald D.C., Linneberg A., Liu Y., Loos R.J., Nguyen V.M., Numans M.E., Pedersen O., Psaty B.M., Raitakari O.T., Rich S.S., Rivadeneira F., Di Sant A.M., Rotter J.I., Starr J.M., Taylor K.D., Thuesen B.H., Tracy R.P., Uitterlinden A.G., Wang J., Wang J., Dehghan A., Huo Y., Cupples L.A., Wilson J.G., Proia R.L., Zon L.I., O’Donnell C.J., Reiner A.P, & Ganesh S.K. (2016). Meta-analysis of rare and common exome chip variants identifies S1PR4 and other loci influencing blood cell traits. Nature genetics, 48(8), 867-876.

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Humanexome beadchip genotyping array

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3 protocols using humanexome beadchip genotyping array

Mitochondrial DNA Copy Number Estimation

Replication analysis of erythrocyte and leukocyte variants

Replication analysis of erythrocyte and leukocyte variants

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