One hundred and eleven individuals (57 with AD from the E280A pedigree and 54 individuals with sAD) were whole-exome genotyped using Illumina HumanExome BeadChip-12v1_A. This SNP-chip covers putative functional exonic variants selected from over 12 000 individual exome and whole-genome sequences, and consists of ~250 000 markers representing diverse populations (including European, African, Chinese and Hispanic individuals), and a range of common conditions such as type 2 diabetes, cancer, metabolic and psychiatric disorders. In addition to pure exonic variation, the HumanExome BeadChip-12v1_A (Illumina, San Diego, CA, USA) chip covers single-nucleotide polymorphisms (SNPs) in splice sites, in stop variants, in promoter regions and genome-wide association study tag markers, among other potentially functional variation. Samples with calls below Illumina's expected 99% SNP call rates were excluded.
Humanexome beadchip 12v1 a
Manufactured by Illumina
Sourced in United States
The HumanExome BeadChip-12v1_A is a high-throughput genotyping array designed for comprehensive coverage of human exonic regions. It targets over 240,000 genetic variants found primarily in protein-coding regions of the genome. This product is intended for research use only.
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20 protocols using humanexome beadchip 12v1 a
1
Whole-Exome Genotyping of Alzheimer's Cohorts
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Genotyping Protocol Using Illumina Exome Beadchips
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Genotyping was conducted using Illumina HumanExome-12v1_A Beadchips in accordance with the manufacturer's recommendations (Illumina). Calling of genotypes was performed using Illumina GenomeStudio version 2011.1 software. Cluster boundaries were determined by calling study samples simultaneously. Probes were excluded if monomorphic in all datasets, had a call rate <0.99 in cases/controls in a series, the difference in uncalled genotypes between cases and controls was statistically significant (P<0.05), if Hardy–Weinberg in controls P<0.001, or if non-autosomal (Supplementary Table 1 ). Samples were excluded if the call rate was <0.99, outlying heterozygosity (>3 SD), or if a discrepancy was observed between manifest sex and X-chromosome genotype. To assess the fidelity of genotyping we examined the concordance in 493 individuals from the 1958BC,15 (link) which had also been sequenced18 (link) using TruSeq capture in conjunction with Illumina HiSeq2000 technology, and a GATK2 ref. 19 (link) pipeline according to best practices.20 (link), 21 Genotypes were compared at genomic positions for which allele codings could be unambiguously assigned, excluding 257A/T and C/G SNPs with MAF>0.40.
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Genotyping with Illumina HumanExome-12v1_A Beadchips
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Whole-Exome Genotyping of Diverse Populations
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Genomic DNA from 60 participants was whole-exome genotyped by the Australian Genome Facility (Melbourne, VIC, Australia), an Illumina Certified Service Provider for the Infinium Genotyping Service. Briefly, DNA was whole-genome amplified, fragmented, hybridized, fluorescently tagged, and scanned [20 (link)]. Whole-exome genotyping was conducted using Illumina's HumanExome 12v1_A BeadChip. This chip covers regions with putative functional exonic variants selected from exome- and whole-genome sequences of >12,000 individuals. The exonic content consists of >250,000 markers representing diverse populations (including European, African, Chinese, and Hispanic individuals) in addition to common conditions (such as type 2 diabetes, cancer, and metabolic and psychiatric disorders). In order to test genotyping reliability and quality, one individual was duplicated. The identity by descent (IBD) matrix between all pairs of individuals was used for quality control and for subsequent analyses concerning the mixed model (see below). Entries of the IBD matrix contain the probability that a particular allele is inherited from a common ancestor [21 (link)].
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Illumina HumanExome-12v1_A Beadchip Protocol
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Exome Array Genotyping of HUNT Cohort
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Illumina HumanExome-12v1_A Beadchip Protocol
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Briefly, the Illumina HumanExome-12v1_A Beadchip (Illumina, San Diego, CA, USA) includes 247 870 markers focused on protein-altering variants identified from whole-exome sequencing DNA from >12 000 individuals of multiple ethnicities and with multiple diseases/traits. In addition to 203 310 PAVs, the array also features 4761 GWAS trait-associated SNPs, 2061 HLA tags, 3015 ancestry-informative markers, 4896 identity-by-descent estimation markers and 4139 random synonymous SNPs. Comprehensive details about the exome array are available at http://genome.sph.umich.edu/wiki/Exome_Chip_Design .
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Exome Genotyping and Imputation of T2D
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From this cross-sectional study of Finnish men [47 (link)], we analyzed data from 487 individuals with T2D previously ascertained for genotyping as part of the T2D-GENES initiative [48 (link)]. Genotyping was performed using Illumina HumanExome-12v1_A Beadchip, and imputation was performed using the Haplotype Consortium Reference Panel [49 (link)] using the Michigan Imputation Server [50 (link)]. Written consent was provided by all study participants.
9
Exome Array Genotyping of HUNT Cohort
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We attempted genotyping of 5,771 HUNT individuals at the Genomic Core Facility, Norwegian University of Science and Technology, Norway, using the HumanExome-12v1_A Beadchip (Illumina, CA) and the Infinium HD ultra protocol. The exome array includes 247,870 markers focused on protein-altering variants (nonsynonymous, splicing, and stop-altering) selected from >12,000 exome and genome sequences, including variants associated with complex traits in previous GWAS, HLA tags, ancestry-informative markers, markers for identity-by-descent estimation, and random synonymous SNPs. Details about SNP content and selection strategies can be found at the exome array design webpage.
10
Genotype Calling and Quality Control
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Presence of variants and their mode of inheritance was confirmed using the ExomeChip data for those available. Those variants of interest not on the ExomeChip were confirmed using Sanger sequencing. Samples were genotyped using the Illumina HumanExome-12v1_A Beadchip, containing 247,870 SNVs, at the CGT at the HIHG. Genotype calling was performed using Illumina's GenTrain version 1.0 clustering algorithm in GenomeStudio version 2011.1 and a GenCall cutoff score of 0.15 was used. To improve genotype calling, the data ware re-clustered within the study sample. Genotypes were then extracted and quality control procedures performed. All samples had call rate > 95% and self-reported sex matched the genetically-determined sex in all samples.
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