Humanomnizhonghua 8 beadchip

Manufactured by Illumina

Sourced in United States, China

The HumanOmniZhongHua-8 BeadChip is a high-density microarray designed for genomic analysis. It features a comprehensive set of genetic markers for detailed interrogation of the human genome.

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39 protocols using humanomnizhonghua 8 beadchip

Genome-wide Linkage Analysis of Family A

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For the genome-wide linkage analysis, approximately 50 ng of genomic DNA of the eight individuals (II3, II7, II9, III8, III18, III22, IV9, and IV12) from Family A was used for the genotyping analysis by Illumina HumanOmniZhongHua-8 BeadChip. Briefly, each sample was whole-genome amplified, fragmented, precipitated, and re-suspended in an appropriate hybridization buffer. Denatured samples were hybridized on prepared Illumina HumanOmniZhongHua-8 BeadChip. After hybridization, the BeadChip oligonucleotides were extended by a single labeled base, which was detected by fluorescence imaging with an Illumina Bead Array Reader. Normalized bead intensity data obtained for each sample was loaded into the Illumina GenomStudio software, which converted fluorescence intensities into SNP genotypes. After quality control filtering, 872,261 SNPs were retained for linkage analysis. A familial relationship check, based on IBD sharing, was carried out to confirm the collected pedigree information. Multipoint parametric linkage analysis was performed in Merlin by using the pruned autosomal SNPs and assuming dominant inheritance with a disease allele frequency of 0.0001 and penetrance rate of 1.

Chen P., Hao X., Li W., Zhao X, & Huang Y. (2016). Mutations in the TMCO3 Gene are Associated with Cornea Guttata and Anterior Polar Cataract. Scientific Reports, 6, 31021.

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Genome-Wide Genotyping of Homosexual and Heterosexual Men

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Genome-wide genotyping of 522 homosexual men and 1294 heterosexual men was performed using the Illumina HumanOmni-Zhonghua-8 Bead Chip according to the manufacturer’s standard instructions. Systemic quality control of 900,015 SNPs in all samples was performed using PLINK 1.90 software^{29 (link)}. A total of 31 samples were removed for the following reasons: (i) discordant sex (n = 1); (ii) call rate <95% (n = 0); and (iii) one of a pair of first- or second-degree relatives (PI_HAT > 0.25) or unexpected duplication (the individual with the lower call rate was removed, n = 30). SNPs were excluded from further analysis if they (i) had a call rate <95% (n = 5061); (ii) had a significant deviation from Hardy-Weinberg equilibrium (P < 1 × 10⁻⁴) in heterosexual men (n = 78); had an MAF < 5% in both homosexual men and heterosexual men (n = 168,917); and (iii) did not map to autosomal or X chromosomes (n = 1409). After quality control, the overall genotyping rate in the remaining individuals and SNPs was 0.9982.

Hu S.H., Li H.M., Yu H., Liu Y., Liu C.X., Zuo X.B., Lu J., Jiang J.J., Xi C.X., Huang B.C., Xu H.J., Hu J.B., Lai J.B., Huang M.L., Liu J.N., Xu D.G., Guo X.C., Wu W., Wu X., Jiang L., Li M., Zhang G.P., Huang J.W., Wei N., Lv W., Duan J.F., Qi H.L., Hu C.C., Chen J.K., Zhou W.H., Xu W.J., Liu C.F., Liang H.Y., Du J., Zheng S.F., Lu Q.L., Zheng L., Hu X.W., Chen F.X., Chen P., Zhu B., Xu L.J., Ni Z.M., Fang Y.Z., Yang Z.K., Shan X.R., Zheng E.D., Zhang F., Zhou Q.Q., Rao Y., Swaab D., Yue W.H, & Xu Y. (2021). Discovery of new genetic loci for male sexual orientation in Han population. Cell Discovery, 7, 103.

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BCL2 Gene Polymorphism Analysis

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The SNPs in the BCL2 gene were selected from the 1000 Genomes Project based on tag SNPs with a minor allele frequency ≥ 0.05 and r² > 0.8, using Haploview software (version 4.2, Broad Institute of MIT and Harvard, Cambridge, MA, USA). These tag SNPs were annotated for their location and predictive functions^{15 (link)}. Study subjects were genotyped using the Illumina HumanOmniZhongHua-8 BeadChip. The analysis was repeated on 5% of the samples to evaluate the reproducibility and quality of genotyping. To exclude possible genotyping errors, we generated genotype cluster plots from the selected SNPs and visually inspected them using GenomeStudio software (version 2.0, Illumina, San Diego, CA, USA).

He J., Liu S., Guo X., Zhang F., Takiff H.E, & Zhao Y. (2022). Polymorphisms of the BCL2 gene associated with susceptibility to tuberculosis. Revista do Instituto de Medicina Tropical de São Paulo, 64, e59.

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Genomic Analysis of PUFA Levels

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Study samples were genotyped on the Illumina HumanOmni ZhongHua-8 Bead Chip. After QC [20 (link), 22 (link)–24 (link)] procedures, 711 cases and 638 controls with complete information for both genotypes and plasma PUFA measurement were included in the current study. Imputation for additional autosomal single nucleotide polymorphisms (SNPs) was performed with IMPUTE2 [25 (link)] and genotype calls were based on phase3 1000G cosmopolitan panels.

Chang X., Dorajoo R., Sun Y., Wang L., Ong C.N., Liu J., Khor C.C., Yuan J.M., Koh W.P., Friedlander Y, & Heng C.K. (2020). Effect of plasma polyunsaturated fatty acid levels on leukocyte telomere lengths in the Singaporean Chinese population. Nutrition Journal, 19, 119.

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Genetic Analysis of Thyrotoxic Periodic Paralysis

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Samples from the TPP GWAS (158 patients with TPP and 803 controls) and GD GWAS (17 patients with TPP, 1519 patients with GD and no history of TPP, and 1516 controls) were genotyped using HumanOmniZhonghua-8 BeadChip and Human660-Quad BeadChip kits^{13 (link),14 (link)} (Illumina, Inc), respectively. After robust quality control and imputation analyses (eAppendix and eFigure 1 in the Supplement), association analyses for 2 752 055 SNPs among 175 patients with TPP, 1404 patients with GD and no history of TPP, and 2160 healthy controls were conducted using SNPTEST version 2 software (Oxford University Innovation) (eFigure 2 in the Supplement).^{15 (link)}

Zhao S.X., Liu W., Liang J., Gao G.Q., Zhang X.M., Yao Y., Wang H.N., Yuan F.F., Xue L.Q., Ma Y.R., Zhang L.L., Ye X.P., Zhang Q.Y., Sun F., Zhang R.J., Yang S.Y., Zhan M., Du W.H., Liu B.L., Chen X., Song Z.Y., Li X.S., Li P., Ru Y., Zuo C.L., Li S.X., Han B., Zhu H., Qiao J., Xuan M., Su B., Sun F., Ma J.H., Chen J.L., Tian H.M., Chen S.J, & Song H.D. (2019). Assessment of Molecular Subtypes in Thyrotoxic Periodic Paralysis and Graves Disease Among Chinese Han Adults: A Population-Based Genome-Wide Association Study. JAMA Network Open, 2(5), e193348.

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Genome-wide SNP and CNV Analysis

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Genomic DNA of the family members was prepared from fresh peripheral blood lymphocytes using the standard phenol-chloroform method. SNP array analysis of the extracted DNA was performed using the Human OmniZhongHua-8 Beadchip or HumanCytoSNP-12 BeadChip array (Illumina Inc., San Diego, CA) following the manufacturer’s recommended protocols (www.illumina.com). The two kinds of microarrays contain about 900,000 and 300,000 probes respectively. CNVs were detected with the cnvPartition algorithm and the data including B allele frequency and log R ratio were calculated using GenomeStudio software (cnvPartition Plugin v3.1.6). We picked out CNVs with a call rate >0.99 and a confidence >35 for further analyses.

Ma R., Deng L., Xia Y., Wei X., Cao Y., Guo R., Zhang R., Guo J., Liang D, & Wu L. (2017). A clear bias in parental origin of de novo pathogenic CNVs related to intellectual disability, developmental delay and multiple congenital anomalies. Scientific Reports, 7, 44446.

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Genome-Wide Genotyping for Twin Study

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A genome-wide genotyping scan among 192 pairs was carried out using Illumina HumanOmniZhongHua-8 BeadChip. High-quality genotyping was performed by laboratory specialized in Illumina SNP array genotyping following standard experimental procedures suggested by the manufacturer. A total of 894,956 SNPs were genotyped among 192 paired subjects. SNPs with minor allele frequency <0.05 (169,045 SNPs), Hardy-Weinberg equilibrium P <0.0001(23,170 SNPs), and SNPs call rate<97% (14,138SNPs) were excluded. Twins with a call rate less than 90% and their twin siblings were also ruled out for further zygosity analysis. Genome-wide heterozygosity of each individual was estimated to exclude cross contamination between samples. This test was performed using a subset of 155,588 SNPs pruned for linkage disequilibrium (r² < 0.3). Two samples demonstrated signs of contamination (mean observed heterozygosity = 0.3404, standard deviation = 0.0052), those two samples and their twin siblings were excluded. Finally, 180 pairs of twins with 695,406 SNPs remained after the quality control filters.

Wang B., Gao W., Yu C., Cao W., Lv J., Wang S., Pang Z., Cong L., Wang H., Wu X, & Li L. (2015). Determination of Zygosity in Adult Chinese Twins Using the 450K Methylation Array versus Questionnaire Data. PLoS ONE, 10(4), e0123992.

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Robust Genotyping and Quality Control Across Cohorts

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SCHS, SCES, SiMES, SINDI and SP2 were genotyped on different arrays, with SCHS on Illumina HumanOmniZhongHua-8 BeadChip (San Diego, California, the United States), 1/3 SCES, SiMES, SINDI and 1,467 samples of SP2 on the Human610-Quad BeadChip, 2/3 SCES on Illumina OminiExpress, and 1,016 samples of SP2 on the Human 1M-Duo v3 BeadChip. The quality control of SCES, SiMES SINDI and SP2 have been described elsewhere (Dorajoo et al., 2013 (link), Liao et al., 2014 (link)). Chip-wise quality control procedures have been conducted following standard criteria in all studies (Supplementary Table I and II). Briefly, SNP quality control was conducted based on allele frequency (MAF < 0.01), call-rates (< 0.95) and deviations from Hardy-Weinberg Equlibrium (P < 10⁻⁰⁴). Sample quality control was conducted based on sample call rates (< 0.98), heterozygosity (> 3S.D), first degree relateness and discordant ethnic relationship based on Principle component analyses. After quality control, 2003 samples and 802,635 SNPs remained in SCHS. Linkage disequilibrium (LD) based pruning (r² < 0.2) was applied on the genome-wide autosomal SNPs using PLINK (version 1.07) in SCHS. Finally, 142,208 independent SNPs remained in SCHS for further analysis.

Ke T., Dorajoo R., Han Y., Khor C.C., van Dam R.M., Yuan J.M., Koh W.P., Liu J., Teo Y.Y., Goh D.Y., Tai E.S., Wong T.Y., Cheng C.Y., Friedlander Y, & Heng C.K. (2016). Interaction between peroxisome proliferator activated receptor δ and epithelial membrane protein 2 polymorphisms influences HDL-cholesterol levels in the Chinese population. Annals of human genetics, 80(5), 282-293.

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Genetic Variation Study of Primary Biliary Cholangitis in Han Chinese

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The PBC patients recruited in this study have been reported previously.6 The PBC patients were recruited with the approval of the research ethics boards of Southeast University and Jiaotong University and in accordance with the guidelines of the Declaration of Helsinki (2008). Informed consent was obtained from all subjects recruited. In brief, all patients self‐reported Han Chinese origin and were diagnosed based on the criteria recommended by the American Association for the Study of Liver Diseases.22 SNP genotyping was performed using Han Chinese population–specific HumanOmniZhongHua‐8 BeadChip (Illumina, San Diego, CA). The quality control of genotyping results was detailed in our GWA report.6 We removed SNPs with a call rate of <90%, a minor allele frequency (MAF) < 1%, and a Hardy‐Weinberg equilibrium P value < 1 × 10⁻⁴. Potential genetic relatedness based on pairwise identity by descent for all of the successfully genotyped individuals was examined using PLINK 1.07 software.23 If first‐degree or second‐degree relative pairs were identified (PI‐HAT value > 0.25), we removed the samples with the lower genotyping call rates of the related individuals. SNPs located on the X, Y, or mitochondrial chromosomes and all copy number variation probes were excluded.

Wang C., Zheng X., Jiang P., Tang R., Gong Y., Dai Y., Wang L., Xu P., Sun W., Wang L., Han C., Jiang Y., Wei Y., Zhang K., Wu J., Shao Y., Gao Y., Yu J., Hu Z., Zang Z., Zhao Y., Wu X., Dai N., Liu L., Nie J., Jiang B., Lin M., Li L., Li Y., Chen S., Shu L., Qiu F., Wu Q., Zhang M., Chen R., Jawed R., Zhang Y., Shi X., Zhu Z., Pei H., Huang L., Zhao W., Tian Y., Zhu X., Qiu H., Gershwin M.E., Chen W., Seldin M.F., Liu X., Sun L, & Ma X. (2019). Genome‐wide Association Studies of Specific Antinuclear Autoantibody Subphenotypes in Primary Biliary Cholangitis. Hepatology (Baltimore, Md.), 70(1), 294-307.

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Comprehensive Genetic Testing Protocol for Epilepsy

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Genetic testing was carried out using chromosome karyotype analysis, CNV analysis, mitochondrial genome sequencing, epilepsy gene panels and WES. CNV analysis was performed with the Illumina HumanOmniZhonghua-8 Bead Chip; Mitochondrial genome sequencing was subsequently performed on an Illumina HiSeq 2000 platform (Illumina, San Diego, CA, USA); details were provided by our team previously^{29 (link)}. The epilepsy gene panel contained 265 epilepsy-associated genes was performed on methods previously reported by Lemke et al^{30 (link)}. WES was also performed based on methods previously reported by our team^{29 (link)} by using Illumina HiSeq X Ten (Illumina, San Diego, CA, USA) with 150-bp paired-end reads.

Yang H., Yang X., Cai F., Gan S., Yang S, & Wu L. (2022). Analysis of clinical phenotypic and genotypic spectra in 36 children patients with Epilepsy of Infancy with Migrating Focal Seizures. Scientific Reports, 12, 10187.

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