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Infinium arrays

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The Infinium arrays are a suite of high-throughput genotyping platforms developed by Illumina. These arrays are designed to interrogate a large number of genetic variants across the human genome, enabling comprehensive genetic analysis and genome-wide association studies.

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Lab products found in correlation

Omniexpress, by Illumina (1 mentions) Cardio metabochip, by Illumina (1 mentions) Exome chip, by Illumina (1 mentions) Immunochip, by Illumina (1 mentions) X ten, by Illumina (1 mentions) Long ranger pipeline, by 10x Genomics (1 mentions) Genomestudio, by Illumina (1 mentions)

Close spelling variants of this product

Infinium Human Methylation 450 arrays Infinium HumanMethylation27 arrays Infinium Omni2.5Exome-8 SNP arrays Infinium 2.5M bead arrays Brassica 60K Illumina Infinium® HD Assay SNP arrays Infinium Omni 2.5–8 arrays Infinium Methylation 850K/EPIC BeadChip arrays Infinium DNA methylation platform arrays Infinium HumanMethylation450 bead arrays Infinium CoreExome-24 bead arrays

12 protocols using infinium arrays

1

Sardinian Whole-Genome Genotyping and Sequencing

Cited 3 times
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In brief, we genotyped 6,602 individuals from four villages in the Lanusei valley on Sardinia (>60% of the adult population). Each sample was genotyped on four different Illumina Infinium arrays: OmniExpress, Cardio-Metabochip (Voight et al., 2012 (link)), Immunochip (Parkes et al., 2013 (link)), and Exome Chip. We also performed low-depth (~4x coverage) whole-genome sequencing on 3,839 individuals, 2,340 of whom we also genotyped. Study samples, genotyping, sequencing and variant calling have been previously described (Sidore et al., 2015 (link)).
Over 100 traits (e.g. blood lab measurements, anthropometric values) have been measured at 4 to 5 time-points. We looked at 120 traits from the first visit, for which the majority of the individuals have measurements (median number of samples with at least one measurement per trait= 5814, first quartile= 5473, third quartile= 5923). The traits have been previously summarized (Pilia et al., 2006 (link)).
Gagliano S.A., Sengupta S., Sidore C., Maschio A., Cucca F., Schlessinger D, & Abecasis G.R. (2018). Relative impact of indels versus SNPs on complex disease. Genetic Epidemiology, 43(1), 112-117.
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2

Genotype Imputation and Ancestry Adjustment in Cancer GWAS

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The genotype data used in this project was derived from multiple GWAS studies of cancer and other phenotypes in the MEC. For all projects, Illumina Infinium arrays were used, with imputation conducted using Minimac4 and the 1000 Genomes (1000G) Project reference panel (Phase 3 v5). Both subject call rates and variant call rates were ≥ 0.95. Ethnic-specific frequencies were calculated and compared to corresponding ethnic groups in Phase3 1000G for quality control. Infoscore filtering was not implemented in an effort to include all 269 PCa-associated variants (20 (link)), as poor imputation is only likely to introduce non-differential bias. Average r2 was 0.88 and only 2 SNPs (0.7%) had r2 below 0.30. Principal components were calculated using EIGENSTRAT (25 (link)) with 20,202 independent common variants to adjust for potential confounding due to genetic ancestry.
Chou A., Darst B.F., Wilkens L.R., Le Marchand L., Lilja H., Conti D.V, & Haiman C.A. (2022). Association of Prostate-Specific Antigen Levels with Prostate Cancer Risk in a Multiethnic Population: Stability over Time and Comparison with Polygenic Risk Score. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology, 31(12), 2199-2207.
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3

Genome Scanning and HLA Typing

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Illumina Infinium arrays were used for genome scanning, as previously described5 (link). Genotypes of the HLA-B allele were identified by the Luminex microbead method in the NPO HLA laboratory (Kyoto, Japan).
Kadoba K., Watanabe R., Iwasaki T., Nakajima T., Kitagori K., Akizuki S., Murakami K., Nakashima R., Hashimoto M., Tanaka M., Ohmura K., Morinobu A., Terao C, & Yoshifuji H. (2021). A susceptibility locus in the IL12B but not LILRA3 region is associated with vascular damage in Takayasu arteritis. Scientific Reports, 11, 13667.
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4

Whole Genome Sequencing of Tumour and Normal Samples

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The germline and tumour DNA were tested using Illumina Infinium arrays (Illumina, San Diego, CA, USA) according to manufacturer’s instructions. DNA from tumour and matched normal underwent whole-genome paired-end sequencing using an Illumina X-Ten. Sequence reads were trimmed using Cutadapt (version 1.11)28 and aligned to GRCh37 using BWA-MEM (version 0.7.12)29 . Duplicate alignments were marked with Picard (version 1.129, http://picard.sourceforge.net) and BAM files were coordinated-sorted using Samtools (version 1.3)30 (link). Mean coverage was determined using samtools and the following command: samtools depth -a bam_file | awk ‘{sum + =$3} END { print “Average = “,sum/NR}’ > output_coverage. Tumours were sequenced to an average read depth of ~70 × (range of 55X–104X) and normal to ~36 × (range of 28X–44X). The WGS data have been deposited in the European Genome-phenome Archive (EGA) repository under the accession code EGAS000010033031 .
de Luca X.M., Newell F., Kazakoff S.H., Hartel G., McCart Reed A.E., Holmes O., Xu Q., Wood S., Leonard C., Pearson J.V., Lakhani S.R., Waddell N., Nones K, & Simpson P.T. (2020). Using whole-genome sequencing data to derive the homologous recombination deficiency scores. NPJ Breast Cancer, 6, 33.
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5

Illumina Genotyping and Imputation Protocol

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All SardiNIA individuals were typed with four Illumina Infinium arrays. Low pass sequencing, variant calling, genotype imputation and GWAS analysis was conducted as previously described (31 ).
Zoledziewska M., Sidore C., Chiang C.W., Sanna S., Mulas A., Steri M., Busonero F., Marcus J.H., Marongiu M., Maschio A., Ortega Del Vecchyo D., Floris M., Meloni A., Delitala A., Concas M.P., Murgia F., Biino G., Vaccargiu S., Nagaraja R., Lohmueller K.E., Timpson N.J., Soranzo N., Tachmazidou I., Dedoussis G., Zeggini E., Uzzau S., Jones C., Lyons R., Angius A., Abecasis G.R., Novembre J., Schlessinger D, & Cucca F. (2015). Height-reducing variants and selection for short stature in Sardinia. Nature genetics, 47(11), 1352-1356.
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6

Illumina Genotyping and Imputation Protocol

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All SardiNIA individuals were typed with four Illumina Infinium arrays. Low pass sequencing, variant calling, genotype imputation and GWAS analysis was conducted as previously described (31 ).
Zoledziewska M., Sidore C., Chiang C.W., Sanna S., Mulas A., Steri M., Busonero F., Marcus J.H., Marongiu M., Maschio A., Ortega Del Vecchyo D., Floris M., Meloni A., Delitala A., Concas M.P., Murgia F., Biino G., Vaccargiu S., Nagaraja R., Lohmueller K.E., Timpson N.J., Soranzo N., Tachmazidou I., Dedoussis G., Zeggini E., Uzzau S., Jones C., Lyons R., Angius A., Abecasis G.R., Novembre J., Schlessinger D, & Cucca F. (2015). Height-reducing variants and selection for short stature in Sardinia. Nature genetics, 47(11), 1352-1356.
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7

Colorectal Cancer Genetics Study in Scotland

Cited 2 times
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Main analyses were replicated using the Study of Colorectal Cancer in Scotland (SOCCS), a population-based case-control study conducted between 1996 and 2006. Details of study recruitment and data collection have been previously described in detail (19 (link)). The study included 1,556 incident CRC cases, and 2,201 adult cancer-free controls, identified from the Community Health Index in Scotland. Genotyping was conducted using custom Illumina Infinium arrays and OmniExpressExome BeadChip arrays. Detailed descriptions of genotyping and imputation of common genetic variants are presented in previous reports (20 (link),21 (link)). The study was approved by the Multicenter Research Ethics Committee for Scotland (reference number: 01/0/05) and by the Research and Development Office of NHS Lothian (reference number: 2003/W/GEN/05).
Weigl K., Hsu L., Knebel P., Hoffmeister M., Timofeeva M., Farrington S., Dunlop M, & Brenner H. (2019). Head-to-Head Comparison of Family History of Colorectal Cancer and a Genetic Risk Score for Colorectal Cancer Risk Stratification. Clinical and Translational Gastroenterology, 10(12), e00106.
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8

Integrated Multi-Omics Analysis Pipeline

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Linked-read WGS data was processed and phased using the Long Ranger pipeline from 10x Genomics (v1.2.0 for GemCode and v2.1.6 for Chromium) with the hg19/GRCh37 reference genome. Data were visualized using the Loupe Genome Browser v2.1.1. SVs called by Long Ranger were manually reviewed against karyotype data, CNA data from Illumina Infinium arrays, and fusion genes detected by RNA-sequencing. Genomic copy number levels were estimated by chromosomal segmentation read-depth analysis in 10 Kb windows using the CNVnator software40 (link). B-allele frequencies were calculated from VCF files using the VariantAnnotation package and custom scripts in R41 (link). Ideograms of derivative chromosomes were drawn to scale with the CyDAS software42 (link).
Nordlund J., Marincevic-Zuniga Y., Cavelier L., Raine A., Martin T., Lundmark A., Abrahamsson J., Norén-Nyström U., Lönnerholm G, & Syvänen A.C. (2020). Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole-genome sequencing. Scientific Reports, 10, 2512.
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9

Longitudinal Genomic Study of Sardinian Cohort

Cited 2 times
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The SardiNIA study is a longitudinal population-based health study including 6,602 individuals from the Lanusei valley on Sardinia. The participants have been genotyped on four different Illumina Infinium arrays, OmniExpress, Cardio-Metabochip85 (link), Immunochip86 (link), and Exome Chip). Samples with low call rate or with discrepancies between inferred and reported sex and/or relationships were excluded. After genotyping, variants with low call rates, large discordance among duplicate or identical twin genotypes, excess Mendelian inconsistencies, deviations from Hardy–Weinberg equilibrium, or MAF = 0 were excluded. Variants were then imputed from a SardiNIA-specific sequencing panel (~4× coverage) of 3839 individuals, using Minimac387 (link). Markers with imputation quality R2 > 0.3 (or >0.6 in variants with MAF < 1%) were retained, resulting in a total of ~19 million genetic variants.
Moksnes M.R., Graham S.E., Wu K.H., Hansen A.F., Gagliano Taliun S.A., Zhou W., Thorstensen K., Fritsche L.G., Gill D., Mason A., Cucca F., Schlessinger D., Abecasis G.R., Burgess S., Åsvold B.O., Nielsen J.B., Hveem K., Willer C.J, & Brumpton B.M. (2022). Genome-wide meta-analysis of iron status biomarkers and the effect of iron on all-cause mortality in HUNT. Communications Biology, 5, 591.
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10

Illumina Genotyping of Study Participants

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DNA of studied individuals were genotyped at the iGE3 Platform of the University of Geneva, Switzerland, using Illumina Infinium arrays (San Diego, USA; GSAMD-24v2.0, GSA-24v2.0, CoreExome-24v1.1, and CoreExome-24v1.2). Genotypes values were obtained with GenomeStudio (Illumina).
Quinodoz M., Peter V.G., Bedoni N., Royer Bertrand B., Cisarova K., Salmaninejad A., Sepahi N., Rodrigues R., Piran M., Mojarrad M., Pasdar A., Ghanbari Asad A., Sousa A.B., Coutinho Santos L., Superti-Furga A, & Rivolta C. (2021). AutoMap is a high performance homozygosity mapping tool using next-generation sequencing data. Nature Communications, 12, 518.
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