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Infinium coreexome 24 bead arrays

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The Infinium CoreExome-24 bead arrays are a genome-wide genotyping platform designed by Illumina. The arrays provide comprehensive genome coverage, with over 500,000 markers, including common and rare variants. The arrays are suitable for a wide range of genetic research applications.

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Infinium CoreExome 24 array Infinium CoreExome arrays Infinium CoreExome-24 CoreExome-24 array CoreExome-24 Infinium arrays CoreExome

3 protocols using infinium coreexome 24 bead arrays

1

Large-Scale Genetic Analysis of European Ancestry

Cited 3 times
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DNA from 37,412 blood samples was genotyped on customized Illumina Infinium CoreExome-24 bead arrays and subjected to various quality control filters that resulted in a set of 392,323 polymorphic variants. Principal components and ancestry were estimated by projecting all genotyped samples into the space of the principal components of the Human Genome Diversity Project reference panel using PLINK (938 unrelated individuals) [21 (link), 22 (link)]. Pairwise kinship was assessed with the software KING [23 (link)], and the software fastindep was used to reduce the data to a maximal subset that contained no pairs of individuals with 3rd-or closer degree relationship [24 (link)]. We also removed patients not of recent European descent from the analysis, resulting in a final sample of 30,702 unrelated subjects. Additional genotypes were obtained using the Haplotype Reference Consortium panel of the Michigan Imputation Server [25 (link)] and included over 17 million imputed variants with R2 ≥0.3 and minor allele frequency (MAF) ≥0.1%. Genotyping, quality control and imputation are described in detail elsewhere [4 (link)]. Table 1 provides some descriptive statistics of the MGI and UK Biobank samples.
Fritsche L.G., Beesley L.J., VandeHaar P., Peng R.B., Salvatore M., Zawistowski M., Gagliano Taliun S.A., Das S., LeFaive J., Kaleba E.O., Klumpner T.T., Moser S.E., Blanc V.M., Brummett C.M., Kheterpal S., Abecasis G.R., Gruber S.B, & Mukherjee B. (2019). Exploring various polygenic risk scores for skin cancer in the phenomes of the Michigan genomics initiative and the UK Biobank with a visual catalog: PRSWeb. PLoS Genetics, 15(6), e1008202.
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2

Replicating ZNF529 Variant in MGI

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The Michigan Genomics Initiative (MGI) is a repository of electronic medical record and genetic data at Michigan Medicine (N~58,000 participants). MGI participants were enrolled during pre-surgical encounters at Michigan Medicine and provided consent to study genetic and electronic health record data for research. The MGI study was approved by the Institutional Review Board of the University of Michigan Medical School. DNA was extracted from blood samples and participants were genotyped using Illumina Infinium CoreExome-24 bead arrays, which includes the same custom content as the HUNT Study. Genotype data were imputed to the Haplotype Reference Consortium using the Michigan Imputation Server, providing 17 million imputed variants after standard quality control and filtering. Only European individuals were used for analysis. We attempted to replicate the association with ZNF529:p.K405X in 13,319 MGI participants with LDL-C measurements, however, only 1 participant was heterozygous for ZNF529:p.K405X so the power to detect association was near zero. In contrast, we identified 110 heterozygous individuals in the HUNT discovery study.
Nielsen J.B., Rom O., Surakka I., Graham S.E., Zhou W., Roychowdhury T., Fritsche L.G., Gagliano Taliun S.A., Sidore C., Liu Y., Gabrielsen M.E., Skogholt A.H., Wolford B., Overton W., Zhao Y., Chen J., Zhang H., Hornsby W.E., Acheampong A., Grooms A., Schaefer A., Zajac G.J., Villacorta L., Zhang J., Brumpton B., Løset M., Rai V., Lundegaard P.R., Olesen M.S., Taylor K.D., Palmer N.D., Chen Y.D., Choi S.H., Lubitz S.A., Ellinor P.T., Barnes K.C., Daya M., Rafaels N., Weiss S.T., Lasky-Su J., Tracy R.P., Vasan R.S., Cupples L.A., Mathias R.A., Yanek L.R., Becker L.C., Peyser P.A., Bielak L.F., Smith J.A., Aslibekyan S., Hidalgo B.A., Arnett D.K., Irvin M.R., Wilson J.G., Musani S.K., Correa A., Rich S.S., Guo X., Rotter J.I., Konkle B.A., Johnsen J.M., Ashley-Koch A.E., Telen M.J., Sheehan V.A., Blangero J., Curran J.E., Peralta J.M., Montgomery C., Sheu W.H., Chung R.H., Schwander K., Nouraie S.M., Gordeuk V.R., Zhang Y., Kooperberg C., Reiner A.P., Jackson R.D., Bleecker E.R., Meyers D.A., Li X., Das S., Yu K., LeFaive J., Smith A., Blackwell T., Taliun D., Zollner S., Forer L., Schoenherr S., Fuchsberger C., Pandit A., Zawistowski M., Kheterpal S., Brummett C.M., Natarajan P., Schlessinger D., Lee S., Kang H.M., Cucca F., Holmen O.L., Åsvold B.O., Boehnke M., Kathiresan S., Abecasis G.R., Chen Y.E., Willer C.J, & Hveem K. (2020). Loss-of-function genomic variants highlight potential therapeutic targets for cardiovascular disease. Nature Communications, 11, 6417.
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3

Large-Scale Genetic Profiling and Ancestry Analysis

Cited 3 times
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DNA from 47,364 blood samples was genotyped on customized Illumina Infinium CoreExome-24 bead arrays and subjected to various quality-control filters, resulting in a set of 392,323 polymorphic variants. Principal components and ancestry were estimated by projecting all genotyped samples into the space of the principal components of the Human Genome Diversity Project reference panel using PLINK (938 individuals).37 (link),38 (link) Pairwise kinship was assessed with the software KING,39 (link) and the software FastIndep was used to reduce the data to a maximal subset that contained no pairs of individuals with 3rd or closer degree relationship.40 (link) We removed participants without EHR data and participants not of recent European descent from the analysis, resulting in a final sample of 38,360 unrelated subjects. Additional genotypes were obtained using the Haplotype Reference Consortium reference panel of the Michigan Imputation Server41 (link) and included more than 24 million imputed variants with R2 ≥ 0.3 and minor allele frequency (MAF) ≥ 0.01%. Genotyping, quality control, and imputation are described in detail elsewhere.33 (link)
Fritsche L.G., Patil S., Beesley L.J., VandeHaar P., Salvatore M., Ma Y., Peng R.B., Taliun D., Zhou X, & Mukherjee B. (2020). Cancer PRSweb: An Online Repository with Polygenic Risk Scores for Major Cancer Traits and Their Evaluation in Two Independent Biobanks. American Journal of Human Genetics, 107(5), 815-836.
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