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Humanexome 12 v1

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The HumanExome-12 v1.1 is a genetic analysis tool designed for high-throughput genotyping of the human exome. It provides comprehensive coverage of protein-coding regions of the human genome, enabling researchers to investigate genetic variations associated with disease, traits, and other areas of study.

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Lab products found in correlation

Qiaamp dna micro kit, by Qiagen (1 mentions) Humancoreexome 24 v1.0 beadchip, by Illumina (1 mentions) Iscan system, by Illumina (1 mentions) Genomestudio, by Illumina (1 mentions) Humanomniexpress 12v1, by Illumina (1 mentions) Humanomni1 quad, by Illumina (1 mentions) Humancoreexome 24 v 1, by Illumina (1 mentions) Cardio metabochip, by Illumina (1 mentions)

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HumanExome-12 v1.1 or v1.2 DNA Analysis BeadChip (4 citations) HumanExome-12 (3 citations) HumanExome-12 v1 cSNP array (2 citations)

9 protocols using humanexome 12 v1

1

Psoriasis Genetic Profiling in Germans

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All German psoriasis cases (n = 2928) were recruited through local outpatient services at either the Department of Dermatology at Christian-Albrechts-University Kiel, or the Department of Dermatology and Allergy at the Technical University of Munich. The psoriasis cases were genotyped using Illumina HumanExome-12 v1.1, HumanCoreExome-12 v1.1B or HumanCoreExome-24 v1.0 A BeadChips. German healthy control individuals (n = 15 966) were obtained from the PopGen biobank, the KORA S4 survey (an independent population-based sample from the general population living in the region of Augsburg, southern Germany), the Heinz-Nixdorf Recall (HNR) cohort, Bonn, and the SHIP and SHIP-TREND cohorts (56 (link)) (from the Study of Health in Pomerania, a prospective longitudinal population-based cohort study in West Pomerania). German controls were genotyped using Illumina HumanExome-12 v1.0, HumanCoreExome-24 v1.0 A or HumanOmniExpressExome-8 v1.2 A BeadChips (Supplementary Material, Table S1).
Dand N., Mucha S., Tsoi L.C., Mahil S.K., Stuart P.E., Arnold A., Baurecht H., Burden A.D., Callis Duffin K., Chandran V., Curtis C.J., Das S., Ellinghaus D., Ellinghaus E., Enerback C., Esko T., Gladman D.D., Griffiths C.E., Gudjonsson J.E., Hoffman P., Homuth G., Hüffmeier U., Krueger G.G., Laudes M., Lee S.H., Lieb W., Lim H.W., Löhr S., Mrowietz U., Müller-Nurayid M., Nöthen M., Peters A., Rahman P., Reis A., Reynolds N.J., Rodriguez E., Schmidt C.O., Spain S.L., Strauch K., Tejasvi T., Voorhees J.J., Warren R.B., Weichenthal M., Weidinger S., Zawistowski M., Nair R.P., Capon F., Smith C.H., Trembath R.C., Abecasis G.R., Elder J.T., Franke A., Simpson M.A, & Barker J.N. (2017). Exome-wide association study reveals novel psoriasis susceptibility locus at TNFSF15 and rare protective alleles in genes contributing to type I IFN signalling. Human Molecular Genetics, 26(21), 4301-4313.
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2

Serum TSH Association Genetics in Danes

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The biochemical and anthropometric information on and phenotypical characterization of study participants is described in Table S1 and Table S2 and has been presented previously [22] [23] [24] .
Genotyping, variant calling and quality checks DNA extraction, genotyping and genotype call processing has been described previously 21 25 . A total of 8,445 individuals (n Inter99 :5,420, n Health2006 :2,442, n Health2008 :583) with complete phenotype and genotype data participated for the serum TSH association analyses. The genotyping platform was Illumina Human Exome 12v1.0 containing 263.894 SNPs (including 16.024 custom SNPs identified from a recent exome sequencing study in Danes 21 25 ) post quality control.
Ahluwalia T.S., Troelsen J.T., Balslev-Harder M., Bork-Jensen J., Thuesen B.H., Cerqueira C., Linneberg A., Grarup N., Pedersen O., Hansen T, & Dalgaard L.T. (2017). Carriers of a VEGFA enhancer polymorphism selectively binding CHOP/DDIT3 are predisposed to increased circulating levels of thyroid-stimulating hormone. Journal of medical genetics, 54(3).
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3

Estonian Biobank Psoriasis Study

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All Estonian samples were provided by the population-based biobank of the Estonian Genome Center, University of Tartu. Subjects were recruited by general practitioners (GP) and physicians in the hospitals. Participants in the hospitals were randomly selected from individuals visiting GP offices or hospitals. Diagnosis of psoriasis on the basis of clinical symptoms was posed by a general practitioner and confirmed by a dermatologist (n = 1459). At the time of recruitment, the controls (n = 3167) did not report diagnosis of osteoarthritis, psoriasis, or autoimmune diseases. All Estonian samples were genotyped using Illumina HumanExome-12 v1.1 or HumanCoreExome-24 v1.0 BeadChips (Supplementary Material, Table S1).
Dand N., Mucha S., Tsoi L.C., Mahil S.K., Stuart P.E., Arnold A., Baurecht H., Burden A.D., Callis Duffin K., Chandran V., Curtis C.J., Das S., Ellinghaus D., Ellinghaus E., Enerback C., Esko T., Gladman D.D., Griffiths C.E., Gudjonsson J.E., Hoffman P., Homuth G., Hüffmeier U., Krueger G.G., Laudes M., Lee S.H., Lieb W., Lim H.W., Löhr S., Mrowietz U., Müller-Nurayid M., Nöthen M., Peters A., Rahman P., Reis A., Reynolds N.J., Rodriguez E., Schmidt C.O., Spain S.L., Strauch K., Tejasvi T., Voorhees J.J., Warren R.B., Weichenthal M., Weidinger S., Zawistowski M., Nair R.P., Capon F., Smith C.H., Trembath R.C., Abecasis G.R., Elder J.T., Franke A., Simpson M.A, & Barker J.N. (2017). Exome-wide association study reveals novel psoriasis susceptibility locus at TNFSF15 and rare protective alleles in genes contributing to type I IFN signalling. Human Molecular Genetics, 26(21), 4301-4313.
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4

Genomic DNA Isolation and SNP Analysis

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Genomic DNA was isolated from the FFPE tumor samples using the QIAamp DNA Micro Kit (Qiagen Inc., Valencia, CA, USA) in accordance with the manufacturer’s instructions. The lowest amount of genomic DNA for which the genomic SNP chip analysis was successful was 1 μg. The DNA was extracted from 24 FFPE tissue samples (12 patients), with quality metrics of A260/280 = 1.7–2.0 and A260/230 > 1.6. DNA targets from patients were prepared and hybridized to Infinium HD Assay Super chips following the manufacturer’s recommendations. Quality analysis was performed by importing the CEL files into Illumina Human Exome-12v1.1 according to the “Quality Control Assessment in Genotyping Console”. Association analysis was performed for control versus case with the PLINK (http://pngu.mgh.harvard.edu/~purcell/plink) software, using the Fisher’s exact test, chi-square test and estimated odds ratio. Pearson chi-square values and P-values (chi-square and Fisher’s exact test) were calculated using Haploview 4.2. PLINK data.
Qi Y., Wang N., Pang L.J., Zou H., Hu J.M., Zhao J., Zhang J., Liu C.X., Zhang W.J., Yuan X.L, & Li F. (2015). Identification of potential mutations and genomic alterations in the epithelial and spindle cell components of biphasic synovial sarcomas using a human exome SNP chip. BMC Medical Genomics, 8, 69.
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5

Genome-Wide SNP Genotyping and Imputation

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Genomic DNA was extracted from the frozen cerebellum or occipital cortex, and genotypes were determined using Infinium Human Exome-12 v1.2 and HumanCoreExome-24 v1.0 Beadchip on an iScan system (Illumina, Tokyo, Japan), as described in our previous studies [31 (link), 32 (link), 35 (link)]. Genotyping was conducted in 24 patients with schizophrenia and 48 controls. We used the following criteria to select SNPs: (1) in the autosomal region, (2) with a call rate > 90%, and 3) not duplicated or ambiguous. Ultimately, 217,405 SNPs were included in imputation. Genotype imputation was performed using the Michigan imputation server (https://imputationserver.sph.umich.edu) [36 (link)] with the 1000 Genomes Project Phase 3 dataset of East Asian ancestry [37 (link)] as a reference panel. After imputation, SNPs with low imputation quality (R2 < 0.2) were excluded, leaving 10,256,044 SNPs.
Miyahara K., Hino M., Shishido R., Nagaoka A., Izumi R., Hayashi H., Kakita A., Yabe H., Tomita H, & Kunii Y. (2023). Identification of schizophrenia symptom-related gene modules by postmortem brain transcriptome analysis. Translational Psychiatry, 13, 144.
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6

Exome Genotyping of African Americans

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Genotyping was performed on 2,147 African Americans in HyperGEN using the Illumina exome array HumanExome-12v1-2. Genotype calling was performed by Illumina’s clustering algorithm in Genome Studio [15 (link)]. A total of 19 blind duplicate samples, 17 samples with poor quality (e.g. gender mismatches), and 23 samples from individuals with misreported familial relationship were excluded, leaving 2,088 individuals with genotype data. We removed monomorphic markers, insertion/deletion variants, and single nucleotide polymorphisms (SNPs) with missing rate >5% or Mendelian errors. The number of autosomal SNPs after quality control and exclusion was 100,994. Those SNPs were annotated with the corresponding gene name and SNP function (e.g. amino acid change) by using human genome assembly hg19 and FASTA sequences as reference in ANNOVAR [16 (link)]. After annotation, 86,927 exonic SNPs (including nonsynonymous, stop-gain, and stop-loss variants) were included in the analysis. Additionally, SIFT and PolyPhen values from Combined Annotation Dependent Depletion (CADD) software were used to predict the level of protein damage due to the amino acid change of significant SNPs from gene-based analysis [17 (link)].
Do A.N., Zhao W., Srinivasasainagendra V., Aslibekyan S., Tiwari H.K., Limdi N., Shah S.J., Zhi D., Broeckel U., Gu C.C., Rao D., Schwander K., Smith J.A., Kardia S.L., Arnett D.K, & Irvin M.R. (2017). Whole exome analyses to examine the impact of rare variants on left ventricular traits in African American participants from the HyperGEN and GENOA studies. Journal of hypertension and management, 3(1), 025.
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7

Genome-wide Genotyping and Imputation for NSPHS

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DNA samples from the NSPHS individuals were genotyped using the Illumina HumanExome-12v1 and either Illumina Infinium HumanHap300v2.0 or Illumina HumanOmniExpress-12v1 bead microarrays [14 (link)]. Analysis of genotype raw data and quality control (QC) were performed using GenABEL package [39 (link)]. A total of 556,432 and 979,343 genotypes passed the QC in the samples collected in 2006 and 2009 respectively, and were used to impute unassayed genetic variants. Genotype data were imputed with a pre-phasing approach implemented in SHAPEIT version 2.5 (r790)) [40 (link)] and IMPUTE2 (version 2.3.2) [41 (link)] in the two sub-cohorts separately, using the 1000 Genomes Phase 3 integrated variant set (released October 2014) as the reference panel. Quality control (QC) were performed using GTOOL (v0.7.5) [42 ]. First, IMPUTE’s ‘info’ score >0.3 were required in both sub-cohorts prior to merging. The merged data were filtered using a Bonferroni-corrected Hardy–Weinberg cutoff of 0.05, combined info score >0.3 and a minor-allele frequency (MAF) > 0.0001, corresponding to at least one chromosome in the whole material. Only autosomal SNPs were included in the analyses. After QC of imputed autosomal data 11,901,484 SNPs and a total of 1,033 individuals remained (S2 Table). All genomic positions have been reported according to GRCh37.
Ahsan M., Ek W.E., Rask-Andersen M., Karlsson T., Lind-Thomsen A., Enroth S., Gyllensten U, & Johansson Å. (2017). The relative contribution of DNA methylation and genetic variants on protein biomarkers for human diseases. PLoS Genetics, 13(9), e1007005.
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8

Comprehensive Trio Exome Sequencing

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The 124 patients underwent one of proband-only ES (available since December 2011), trio ES (available since October 2014), or critical-trio ES (an expedited test available since April 2015), all of which were performed by Baylor Genetics as clinical assays. Trio ES involves sequencing the proband and both parents, allowing variants to be described as inherited or de novo, and in cis or trans. Critical-trio ES is analytically identical to trio ES, but follows an expedited schedule and is most often used for critically ill patients. A few patients included in this study had Total Blueprint panels, which encompass roughly 5,000 genes associated with Mendelian disease. In some cases parental samples were provided and used to phase and determine inheritance of significant variants identified with proband-only ES. All samples were concurrently analyzed by Illumina HumanOmni1-Quad, HumanExome-12v1 or HumanCoreExome-24v1 chromosomal microarrays to exclude large copy number variants. Exome data were interpreted according to ACMG guidelines and variant interpretation guidelines of Baylor Genetics as previously described [Lalani et al., 2016 (link)].
Kumar R.D., Meng L., Liu P., Miyake C.Y., Worley K.C., Bi W, & Lalani S.R. (2022). Clinical exome sequencing uncovers a high frequency of Mendelian disorders in infants with stroke: a retrospective analysis. American journal of medical genetics. Part A, 188(11), 3184-3190.
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9

Validation of sCD163 Genetic Loci

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Loci with P<5×10−8 in the EA cohort were validated in the ADDITION‐PRO cohort for association with sCD163 levels. The ADDITION‐PRO cohort, a longitudinal cohort study nested in the Danish arm of the Anglo‐Danish‐Dutch study of Intensive Treatment Intensive Treatment In peOple with screeNdetcted Diabetes in Primary Care is a population‐based, longitudinal study of Danish participants at high risk for diabetes.39 sCD163 was measured with an in‐house ELISA assay,40 which correlates well with the assay used in the CHS (r2=0.97). Genotyping was performed with the Illumnia Cardio‐Metabochip and Illumina Human Exome 12v1 arrays. Analyses were performed on 939 participants with both sCD163 measurements and genotype data adjusting for age, sex, and principal components 1 to 4, with a significance threshold (P<0.05) when corrected for multiple testing at 3 loci.
Durda P., Raffield L.M., Lange E.M., Olson N.C., Jenny N.S., Cushman M., Deichgraeber P., Grarup N., Jonsson A., Hansen T., Mychaleckyj J.C., Psaty B.M., Reiner A.P., Tracy R.P, & Lange L.A. (2022). Circulating Soluble CD163, Associations With Cardiovascular Outcomes and Mortality, and Identification of Genetic Variants in Older Individuals: The Cardiovascular Health Study. Journal of the American Heart Association: Cardiovascular and Cerebrovascular Disease, 11(21), e024374.
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