A set of 192 winter wheat accessions of the 667 accessions in the CAWBIN panel were genotyped using a 35K Affymetrix Axiom SNP array [23 (link)] in this study. The genetic data for the remaining 475 accessions from Europe, the USA, and Australia were obtained from public databases [32 (link)]. Then, the two data sets were merged and further analyzed as described below.
Axiom snp array
Manufactured by Thermo Fisher Scientific
The Axiom SNP array is a high-throughput genotyping platform designed for genome-wide association studies and other genetic research applications. The array enables the simultaneous detection and analysis of thousands of single nucleotide polymorphisms (SNPs) across the human genome.
Automatically generated - may contain errors
Lab products found in correlation
Sureselect xt human all exon 50 mb kit, by Agilent Technologies (1 mentions)
Genetitan system, by Thermo Fisher Scientific (1 mentions)
Affymetrix power tools, by Thermo Fisher Scientific (1 mentions)
Axiom 2.0 assay manual workflow user guide rev3, by Thermo Fisher Scientific (1 mentions)
Axiom analysis suite software, by Thermo Fisher Scientific (1 mentions)
Dneasy blood tissue kit, by Qiagen (1 mentions)
7 protocols using axiom snp array
1
Winter Wheat Genotyping and Analysis
2
Genetic analysis of TET2 and IDH
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Participants were genotyped using a custom content Affymetrix Axiom SNP array, consisting of 770 558 probes, enriched with markers related to immune dysfunction. The Ensembl Gene database, assembly hg19/GRCh37, was used to annotate genes within a 5 kb window of each variant. Genotyping was performed at Advanced BioMedical Laboratories, using standardized quality assurance procedures. As part of SNP-level QC, probes were removed if any of the following applied: probe was duplicate, multiallelic or nonautosomal, missingness >0.03, reproducibility less than 0.90, MAF <1% or deviation from the Hardy–Weinberg equilibrium with P < 1 × 10–6. At sample-level QC, participants were excluded if there was a sex mismatch, duplication or missingness. In order to capture potentially relevant TET2 phenotypes present in related individuals, participants were not excluded due to cryptic relatedness or outlying heterozygosity. After sample and SNP QC SNPs that mapped to TET2 as well as IDH1 and IDH2, (±5 kb) were selected for further analysis. These genes included TET2 as well as IDH1 and IDH2, two regulators of TET2 function [37 (link)].
3
Autozygome-based Exome Sequencing for Rare Variants
4
Wheat Genotyping with High-Density SNP Array
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The 4506 accessions were genotyped using a high-density Affymetrix Axiom SNP array containing 280,226 genic and intergenic SNPs (6 (link)). Genotyping was conducted on the Affymetrix GeneTitan system according to the procedure described by Affymetrix (Axiom 2.0 Assay Manual Workflow User Guide Rev3). Allele calling was carried out using a modified version of the Affymetrix proprietary software packages Affymetrix Power Tools and SNPolisher (www.affymetrix.com/estore/partners_programs/programs/developer/tools/devnettools.affx ) to take into account the specificities of the wheat genome. For all SNPs, HomRO, and HomFLD were calculated (http://media.affymetrix.com/support/developer/downloads/Tools/SNPolisher_User_Guide.pdf ). The HomFLD filter was set to 3.6. As a first step, all the probesets were processed with a mild inbred penalty equal to four on all samples. As a second step, the SNPs failing the quality check criteria (“Other” and “NoMinorHom”) were reprocessed using an inbred penalty of 16. Probesets classified as OTVs by SNPolisher were analyzed with OTV_caller in two steps. SNPs were classified in six main categories according to cluster patterns produced by the Affymetrix software: PHR, OTV, monomorphic high resolution, no minor homozygous, call rate below threshold, and others. For further analyses, only PHRs and OTVs were selected.
5
Comprehensive Lipid and Apolipoprotein Profile
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As described previously,67 (link),70 (link),99 (link),100 at TP0 and at TP1 plasma concentrations of cholesterol, cholesterol precursors (desmosterol, lanosterol, dihydro-lanosterol, lathosterol), the enzymatic metabolites of cholesterol (oxysterols: 24S-OHC, 7α-OHC, and 27-OHC), 5α-cholestanol, and phytosterols (campesterol, 5α-campestanol, stigmasterol, sitosterol, 5α-sitostanol, brassicasterol) were measured by combined gas chromatography-flame ionization mass spectrometry. At TP0, plasma concentrations of triglycerides and HDL-cholesterol were measured on fresh blood samples in the University Hospital Clinical Laboratory (CHUV, Lausanne, Switzerland) using standard analyses.90 (link) Fasting venous blood samples were centrifuged at 4°C aliquoted and frozen at -80°C before analysis.
The APOE haplotypes were determined using nuclear DNA extracted from whole blood obtained from all participants using the Affymetrix Axiom SNP array. Haplotypes were called using BRLMM “http://www.affymetrix.com/support/technical/whitepapers/brlmm_whitepap ”. We analyzed the alleles of two single nucleotide polymorphisms of the APOE gene, rs429358 and rs7412 and defined six haplotypes (e2/e2, e2/e3, e2/e4, e3/e3, e3/e4, and e4/e4. Individuals with at least one e4 allele were considered carriers.
The APOE haplotypes were determined using nuclear DNA extracted from whole blood obtained from all participants using the Affymetrix Axiom SNP array. Haplotypes were called using BRLMM “
6
Genotyping Analysis of Aquaculture Fish
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The genotyped individuals were selected to obtain a balanced number of animals per family (mean = 19, range from 12 to 26) and maintain the phenotypic variance. Genomic DNA was extracted from fin clip samples from 2130 fish (average of 19 fish per family, range from 12 to 26 fish) using a commercial DNeasy Blood & Tissue Kit, Qiagen, following the manufacturer’s instructions. The fish were genotyped using a commercially available 57 K Affymetrix Axiom SNP array, designed by the National Center for Cool and Cold Water Aquaculture at the United States Department of Agriculture (Palti et al. 2015 (link)).
The genotypes were subjected to quality control (QC) using Affymetrix’s Axiom Analysis Suite software, using the default settings (dish QC ≥ 0.82 and genotype call rate ≥ 97% for each sample). Additional QC steps were conducted by filtering out SNPs and samples with a Hardy–Weinberg equilibrium test p-value < 0.00001, SNP call rate lower than 0.90, and minor allele frequency lower than 0.01.
The genotypes were subjected to quality control (QC) using Affymetrix’s Axiom Analysis Suite software, using the default settings (dish QC ≥ 0.82 and genotype call rate ≥ 97% for each sample). Additional QC steps were conducted by filtering out SNPs and samples with a Hardy–Weinberg equilibrium test p-value < 0.00001, SNP call rate lower than 0.90, and minor allele frequency lower than 0.01.
7
Genotyping and HLA Imputation Protocol
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