Samples were genotyped on the Illumina Human 1 M beadchip at the Center for Inherited Diseases Research at Johns Hopkins University. Details of quality control procedures have been previously reported [25 (link)]. Analysis was restricted to SNPs with minor allele frequency ≥ 1%, call rate ≥ 98% and Hardy-Weinberg Equilibrium p-value ≥ 10−5. IMPUTE2 was used to phase the observed genotypes and impute unobserved genotypes [28 (link), 29 (link)] using the 1000 Genomes phase 1 reference panel (release June 2011, b37) [30 (link)] separately by ancestry. To minimize effects of population stratification, 577,039 SNPs were used to generate ten principal components (PC) using EIGENSOFT 3.0 [31 (link)] and SMARTPCA [32 (link)]. To circumvent over-fitting only PCs that were associated with BMI and indicative of ancestral background were used in subsequent analyses [31 (link)–33 (link)]. The software Quanto was used to assess the power of the SAGE sample (n = 2,348) to detect known BMI/obesity genetic variants [34 ]. These calculations were computed using descriptive statistics reported in original papers, which included variant frequency, effect size, odds-ratio and percent variance accounted for.
Human1m beadchip
Manufactured by Illumina
Sourced in United States
The Illumina Human1M BeadChip is a high-throughput genotyping microarray designed to interrogate approximately 1 million genetic variants across the human genome. The device is used for genome-wide association studies and other large-scale genomic research applications.
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10 protocols using human1m beadchip
1
Quality Control and Imputation for Genotypic Data
2
Genome-Wide Imputation for Genetic Analyses
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Participants were genotyped on the Illumina Human 1M BeadChip (San Diego, CA, USA); detailed genotyping and quality control information for this sample can be found in Edenberg et al.20 (link) The European-American and African-American participants in the case–control sample were imputed together (n=1884). Prior to imputation, monomorphic SNPs (that is, SNPs with a minor allele frequency <0.0001), SNPs with missingness >2%, SNPs with Hardy–Weinberg equilibrium P<1 × 10−6 and SNPs that did not map to the Hg19 reference genome were filtered out, leaving 936 240 SNPs. Phasing of entire chromosomes or chromosome arms was performed using SHAPEIT.23 (link), 24 (link) Genotype imputation of additional SNPs was carried out with IMPUTE2 v.2.031 using the March 2012 release (v3) of the 1000 Genomes Project data (www.1000genomes.org 25 (link)). Imputation analysis was performed for genomic windows of 5 Mb with an overlap interval of 500 kb between adjacent segments. Following the recommendations of the authors of IMPUTE2, we did not limit our imputation procedure to European reference samples. Monomorphic sites were excluded.
3
GLP1R Genotyping Protocol for Genetic Studies
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Genotyping for Studies 1, 3 and 4 was performed at the National Institute on Alcohol Abuse and Alcoholism Laboratory of Neurogenetics. Genomic DNA was extracted from whole blood using standard protocols. DNA samples were genotyped using the Illumina OmniExpress BeadChip array (Illumina, San Diego, CA, USA) including more than 700 000 SNPs. The average genotype reproducibility was 0.99994. GLP1R SNPs, locations spanning from the 5′ to the 3′ flanking regions, were selected from the Illumina data set for analysis. The LCTS sample was split according to self-reported ancestry and deviation from Hardy–Weinberg Equilibrium was assessed only in control subjects for all 40 SNPs located in GLP1R. SNPs with a Hardy–Weinberg Equilibrium P-value <0.01 and a minor allele frequency of ⩽5% in Caucasian and/or African Americans were excluded from the analysis. We also excluded rs10305518 as this SNP was in perfect linkage disequilibrium (r2=1) with rs10305514 leaving a total of 26 SNPs (Supplementary Table S1 ). For Study 2, samples were genotyped on the Illumina Human 1 M Beadchip by the Center for Inherited Disease Research at Johns Hopkins University.11 (link)
4
Genetic Profiling for Clinical Research
5
Genome-wide SNP Association Analysis
6
Rigorous Quality Control in Genetic Association
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All subjects were genotyped on the Illumina Human 1M beadchip. Phenotype and
genotype data were rigorously cleaned before association analysis. Subjects with
poor genotypic data, allele discordance, problematic sample identification
(relatedness, misidentification, misspecification), duplicated identifiers,
gender or chromosomal anomalies, ethnicity issues (including missing
information, non-EA or AA, mismatch between self- and genetically-inferred
ethnicity), or with a missing genotype call rate ≥2% across all SNPs were
excluded. Furthermore, SNPs with allele discordance, chromosomal anomalies or
batch effect, SNPs with an overall missing genotype call rate ≥2%, monomorphic
SNPs, SNPs with minor allele frequencies <0.01 in either EAs or AAs, and SNPs
that deviated from HardyWeinberg equilibrium
(p<10−4) within EA or AA controls were also
excluded. This selection process yielded 805,814 SNPs in EAs and 895,714 SNPs in
AAs.[11 (link),12 (link)]
genotype data were rigorously cleaned before association analysis. Subjects with
poor genotypic data, allele discordance, problematic sample identification
(relatedness, misidentification, misspecification), duplicated identifiers,
gender or chromosomal anomalies, ethnicity issues (including missing
information, non-EA or AA, mismatch between self- and genetically-inferred
ethnicity), or with a missing genotype call rate ≥2% across all SNPs were
excluded. Furthermore, SNPs with allele discordance, chromosomal anomalies or
batch effect, SNPs with an overall missing genotype call rate ≥2%, monomorphic
SNPs, SNPs with minor allele frequencies <0.01 in either EAs or AAs, and SNPs
that deviated from HardyWeinberg equilibrium
(p<10−4) within EA or AA controls were also
excluded. This selection process yielded 805,814 SNPs in EAs and 895,714 SNPs in
AAs.[11 (link),12 (link)]
7
Genomic DNA Profiling of TILs
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Genomic DNA was isolated from tumour infiltrating lymphocyte samples using the QIAmp DNA Mini Kit (Qiagen, Germantown, MD) according to the manufacturers guidelines. DNA quality and quantity was assessed using Nanodrop (ThermoScientific, Pittsburgh, PA). Samples were genotyped using Illumina Human 1 M Beadchip. Samples have been processed according to the Illumina procedure for the Infinium II assay. Data was extracted by the Illumina BeadArray reader. Samples and markers with call rate below 95% were excluded from analysis and a GenCall cutoff score of 0.15 was used for all Infinium II products. The SNP data was filtered by GenTrain score with a hard cut off of < 0.5 being excluded from further analysis. Heterozygous SNP calls for each sample were exported and subsequently compared to the genotype derived from the RNA-seq data.
8
Copy Number Variation Analysis Protocol
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CNV analysis was performed using cnvPartition CNV Analysis Plug-in for GenomeStudio [48] . This program identifies regions of CNV in a project's samples based on allele frequency (B allele frequency [BAF]) and signal intensity (log R ratio [LRR]) data derived from the project. The cnvPartition algorithm estimates copy number by comparing the observed BAF and LRR for each locus to predict BAFs and LRRs of different copy number scenarios [57, 58] . For regions with copy numbers other than two, the algorithm also assigns a confidence score for the copy number that is called. The confidence threshold allows users to filter out CNV regions that have low confidence values. The default value of 35 was determined empirically using normal HapMap samples on the Illumina Human1M BeadChip [57] . The current study used a more stringent cutoff value of 100 for the confidence threshold and ten for the minimum probe count (default value three). In addition, the authors excluded sex chromosomes and did not include copy-neutral loss of heterozygosity (a phenomenon whereby one of two homologous chromosomal regions is lost, but various mechanisms have ensured the presence of two identical copies of such region in the genome) in the final results.
9
Genome-Wide Association Study of Serious Adverse Drug Reactions
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We analyzed previously published GWAS results from 72 Caucasian SJS cases and 461 matched controls [10 ] genotyped with Illumina’s Human 1M BeadChip (see S1 File ). Low quality SNPs were eliminated using standard quality control procedures (excluding markers with MAF < 0.01 and GenTrain score < 0.6). The association of SNPs to the ADR phenotype was calculated by logistic regression, using the top four principal components as covariates to account for population structure. Details of all analysis steps are available in [10 ].
10
Genome-wide SNP Genotyping and Quality Control
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In GeneSTAR, genome-wide SNP genotyping was performed at deCODE Genetics, Inc. using the Human 1Mv1_C array from Illumina, Inc. with an average call rate per sample of 99.65 % (overall missing data rate = 0.35 %). Using 25 duplicate pairs, the reproducibility rate was >99.95 %. Samples that showed Mendelian errors > 5 % were excluded. We also excluded SNPs with call rate < 90 %, MAF <5 % and/or severe deviation from Hardy Weinberg equilibrium (p-value < 10−6) in the discovery sample.
In PGAP, genotyping was performed using the Illumina Human1M BeadChip at Baylor College of Medicine. Individuals with greater than 3 % missing genotypes, or average heterozygosity greater than 2 standard deviations from the mean were excluded. Any SNP locus with >5 % missing genotypes or deviation from Hardy Weinberg Equilibrium (p-value < 10−6) was removed. In the final analysis, only those SNPs were included in the analysis for which data were available in both the discovery and replication samples.
In PGAP, genotyping was performed using the Illumina Human1M BeadChip at Baylor College of Medicine. Individuals with greater than 3 % missing genotypes, or average heterozygosity greater than 2 standard deviations from the mean were excluded. Any SNP locus with >5 % missing genotypes or deviation from Hardy Weinberg Equilibrium (p-value < 10−6) was removed. In the final analysis, only those SNPs were included in the analysis for which data were available in both the discovery and replication samples.
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