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Mvp 1.0 genotyping array

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The MVP 1.0 Genotyping Array is a laboratory instrument designed for high-throughput genetic analysis. It allows for the simultaneous detection and identification of multiple genetic variants within a sample. The core function of the MVP 1.0 is to provide a comprehensive and efficient means of genotyping genetic markers of interest.

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Lab products found in correlation

Axiom biobank array, by Thermo Fisher Scientific (3 mentions)

3 protocols using mvp 1.0 genotyping array

1

Genotyping and Imputation of Genetic Variants

Cited 2 times
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DNA extracted from participants’ blood was genotyped using a customized Affymetrix Axiom® biobank array, the MVP 1.0 Genotyping Array. The array was enriched for both common and rare genetic variants of clinical significance in different ethnic backgrounds. Quality-control procedures used to assign ancestry, remove low-quality samples and variants, and perform genotype imputation were previously described47 (link). We excluded: duplicate samples, samples with more heterozygosity than expected, an excess (>2.5%) of missing genotype calls, or discordance between genetically inferred sex and phenotypic gender47 (link). In addition, one individual from each pair of related individuals (more than second degree relatedness as measured by the KING software)48 (link) were removed. Prior to imputation, variants that were poorly called (genotype missingness > 5%) or that deviated from their expected allele frequency observed in the 1000 Genomes reference data were excluded. After pre-phasing using EAGLE v2.449 (link), we then imputed to the 1000 Genomes phase 3 version 5 reference panel (1000 G) using Minimac450 (link). Genotyped SNPs after quality control were interpolated into the imputation file. Imputed variants with poor imputation quality (r2 < 0.3) were excluded from further analyses.
Joseph J., Liu C., Hui Q., Aragam K., Wang Z., Charest B., Huffman J.E., Keaton J.M., Edwards T.L., Demissie S., Djousse L., Casas J.P., Gaziano J.M., Cho K., Wilson P.W., Phillips L.S., O’Donnell C.J, & Sun Y.V. (2022). Genetic architecture of heart failure with preserved versus reduced ejection fraction. Nature Communications, 13, 7753.
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2

Blood DNA Genotyping with Affymetrix Array

Cited 1 time
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DNA extracted from whole blood was genotyped using a customized Affymetrix Axiom biobank array, the MVP 1.0 Genotyping Array. With 723,305 total DNA sequence variants, the array is enriched for both common and rare variants of clinical importance in different ethnic backgrounds (Klarin et al., 2018 (link)).
Chen M.H., Raffield L.M., Mousas A., Sakaue S., Huffman J.E., Moscati A., Trivedi B., Jiang T., Akbari P., Vuckovic D., Bao E.L., Zhong X., Manansala R., Laplante V., Chen M., Lo K.S., Qian H., Lareau C.A., Beaudoin M., Hunt K.A., Akiyama M., Bartz T.M., Ben-Shlomo Y., Beswick A., Bork-Jensen J., Bottinger E.P., Brody J.A., van Rooij F.J., Chitrala K., Cho K., Choquet H., Correa A., Danesh J., Angelantonio E.D., Dimou N., Ding J., Elliott P., Esko T., Evans M.K., Floyd J.S., Broer L., Grarup N., Guo M.H., Greinacher A., Haessler J., Hansen T., Howson J.M., Huang Q.Q., Huang W., Jorgenson E., Kacprowski T., Kähönen M., Kamatani Y., Kanai M., Karthikeyan S., Koskeridis F., Lange L.A., Lehtimäki T., Lerch M.M., Linneberg A., Liu Y., Lyytikäinen L.P., Manichaikul A., Martin H.C., Matsuda K., Mohlke K.L., Mononen N., Murakami Y., Nadkarni G.N., Nauck M., Nikus K., Ouwehand W.H., Pankratz N., Pedersen O., Preuss M., Psaty B.M., Raitakari O.T., Roberts D.J., Rich S.S., Rodriguez B.A., Rosen J.D., Rotter J.I., Schubert P., Spracklen C.N., Surendran P., Tang H., Tardif J.C., Trembath R.C., Ghanbari M., Völker U., Völzke H., Watkins N.A., Zonderman A.B., Wilson P.W., Li Y., Butterworth A.S., Gauchat J.F., Chiang C.W., Li B., Loos R.J., Astle W.J., Evangelou E., van Heel D.A., Sankaran V.G., Okada Y., Soranzo N., Johnson A.D., Reiner A.P., Auer P.L, & Lettre G. (2020). Trans-ethnic and ancestry-specific blood-cell genetics in 746,667 individuals from 5 global populations. Cell, 182(5), 1198-1213.e14.
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3

African American Genetic Analysis of COVID-19 Hospitalization

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The VA Million Veteran Program (MVP) is a US-based longitudinal research program investigating how genes, lifestyle, and military exposures influences health and illness in Veterans, with study recruitment commencing in 201115 (link). Study participants were genotyped using a customized Affymetrix Axiom biobank array (the MVP 1.0 Genotyping Array), containing 723,305 variants16 (link). Imputation was performed to a hybrid imputation panel comprised of the African Genome Resources panel (https://imputation.sanger.ac.uk/?about=1#referencepanels) and 1000G v3p5. COVID-19 cases were identified using an algorithm developed by the VA COVID National Surveillance Tool (NST)17 . COVID-19-related hospitalizations were defined as hospital admissions between 7 days before and 30 days after an individual’s positive SARS-CoV-2 test. The association of hospitalized COVID-19 cases versus all other MVP participants was tested under an additive logistic model and was corrected for age, age2, sex, age-by-sex, and ethnicity-specific PCs. Individuals who died before March 1, 2020 were excluded as was one individual from each related pair. The analysis was restricted to only African American MVP participants (as defined by HARE18 (link)) resulting in 1,300 cases and 98,129 controls.
Huffman J., Butler-Laporte G., Khan A., Drivas T.G., Peloso G.M., Nakanishi T., Verma A., Kiryluk K., Richards J.B, & Zeberg H. (2021). Alternative splicing of OAS1 alters the risk for severe COVID-19. medRxiv.
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