Humanhap 550k

Manufactured by Illumina

Sourced in United States

The HumanHap 550K is a high-density genotyping array developed by Illumina. It is designed to interrogate over 550,000 single nucleotide polymorphisms (SNPs) across the human genome. The HumanHap 550K provides comprehensive genome-wide coverage and enables large-scale genetic association studies.

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Lab products found in correlation

510s beadchips, by Illumina (2 mentions) Humanexon510s duo bead chips, by Illumina (2 mentions) Humanomniexpressexome beadchip, by Illumina (1 mentions) Mega array, by Illumina (1 mentions) Humanomniexpress, by Illumina (1 mentions) Immunochip, by Illumina (1 mentions) U133 plus 2.0 genechip, by Thermo Fisher Scientific (1 mentions) Agilent 2100 bioanalyzer, by Thermo Fisher Scientific (1 mentions) Rneasy mini kit, by Qiagen (1 mentions) Genome wide human snp array 6, by Thermo Fisher Scientific (1 mentions) Hl 60, by American Type Culture Collection (1 mentions) Jurkat cell, by American Type Culture Collection (1 mentions) Human snp array 6, by Thermo Fisher Scientific (1 mentions) Beadstudio software, by Illumina (1 mentions) Beadstation, by Illumina (1 mentions)

10 protocols using humanhap 550k

Genome-Wide Association Study of Participants

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Blood was drawn for participants who provided informed consent; these participants included those from the aforementioned study at the University of Utah, KPMRP, and in the Twin Cities metropolitan area in Minnesota [13 (link)]. GWAS data were obtained using Illumina HumanHap 550K, 610K as part of the GECCO study and has been described previously [18 (link)]. Imputation to HapMap2 Release 24 was performed using MACH which was imputed to HapMap Release 22 using BEAGLE. GWAS samples obtained from Utah and Minnesota are being uploaded in NCBI’s dbGaP (http://www.ncbi.nlm.nih.gov/gap) by the Fred Hutchinson’s Cancer Research Center.

Mullany L.E., Wolff R.K., Herrick J.S., Buas M.F, & Slattery M.L. (2015). SNP Regulation of microRNA Expression and Subsequent Colon Cancer Risk. PLoS ONE, 10(12), e0143894.

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Genotype Imputation and Quality Control

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CARDERA was genotyped on the Immunochip, YEAR on the Immunochip and HumanOmniExpressExome Beadchip, BRASS on the Affymetrix 6.0, Leiden EAC on the Illumina iScan, GENRA on the Illumina MEGA array, NARAC on the Illumina Beadchip (HumanHap 550k), and SLRAS on the Illumina HumanOmniExpress. Prior to imputation all cohorts excluded SNPs with high levels of missingness, low minor allele frequency (MAF), and deviations from Hardy-weinberg equilibrium (HWE). Individuals were removed that did not segregate with reference populations, had high-levels of missingness, or whose phenotypic sex mismatched with sex inferred from genotype data. Genotype phasing and imputation were performed using SHAPEIT and IMPUTE2, respectively. Data were imputed to the 1,000 Genomes Phase 3 Panel, including all samples regardless of ancestry. Post-imputation markers with INFO scores <0.7 or MAF <0.05 were removed (the latter was undertaken as we had limited power to detect associations with low frequency variants). Genotypes were analysed as expected allele “dosages” in all analyses. Genotypes were converted to be reported on the forward strand. The number of variants available post-QC comprised: CARDERA: 3,181,676; YEAR: 6,209,766; Leiden EAC: 674,614; BRASS: 6,059,126; GENRA: 5,662,513; NARAC: 5,373,610; SLRAS: 5,715,821.”

Traylor M., Knevel R., Cui J., Taylor J., Harm-Jan W., Conaghan P.G., Cope A.P., Curtis C., Emery P., Newhouse S., Patel H., Steer S., Gregersen P., Shadick N.A., Weinblatt M.E., Van Der Helm-van Mil A., Barrett J.H., Morgan A.W., Lewis C.M, & Scott I.C. (2019). Genetic associations with radiological damage in rheumatoid arthritis: Meta-analysis of seven genome-wide association studies of 2,775 cases. PLoS ONE, 14(10), e0223246.

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Genome-Wide Association Study of 6-TG and 6-MP Response

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DNA from the Human Variation Panel LCLs had been genotyped in the Mayo Clinic Genotype Shared Resource (GSR) using Illumina HumanHap 550K and 510S BeadChips. The Coriell Institute also genotyped and made available Affymetrix SNP Array 6.0 Chip data for these cell lines. As a result, approximately 1.3 million unique SNPs were available for each cell line. Total RNA was also extracted from each of the LCLs using the Qiagen RNeasy Mini kit (Qiagen, Inc., CA, USA) and RNA quality was tested using an Agilent 2100 Bioanalyzer, followed by hybridization to Affymetrix U133 Plus 2.0 GeneChips. Basal mRNA expression data were normalized using guanine cytosine robust multiarray analysis [36 ]. These data are available in the NCBI database under accession number GSE24277. In an analysis of 1.3 million SNPs one would predict 130 SNPs to be associated with 6-TG or 6-MP IC₅₀ at a 1 × 10⁻⁴ level. No adjustment was made for multiple testing, although a conservative Bonferroni cutoff of p < 7.28 × 10⁻⁵ would account for the 686 SNPs analyzed. For these reasons SNPs with an association <1 × 10⁻⁴ were considered for further study.

Matimba A., Li F., Livshits A., Cartwright C.S., Scully S., Fridley B.L., Jenkins G., Batzler A., Wang L., Weinshilboum R, & Lennard L. (2014). Thiopurine pharmacogenomics: association of SNPs with clinical response and functional validation of candidate genes. Pharmacogenomics, 15(4), 433-447.

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Comprehensive Genotyping of LCLs

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DNA from all of the LCLs was genotyped using Illumina HumanHap 550K and 510S BeadChips as described previously 29 (SuperSeries accession no. GSE24277). We also obtained publicly available Affymetrix SNPArray 6.0 Chip SNP data for the same cell lines 57, which involved 643,600 SNPs unique to the Affymetrix SNP array. SNPs that deviated from Hardy–Weinberg equilibrium (HWE) based on the minimum P‐value from an exact test for HWE 58 and the stratified test for HWE (P < 0.001); SNPs with call rates < 95%; or SNPs with minor allele frequencies (MAFs) < 5% were removed from the analysis.

Cairns J., Fridley B.L., Jenkins G.D., Zhuang Y., Yu J, & Wang L. (2018). Differential roles of ERRFI1 in EGFR and AKT pathway regulation affect cancer proliferation. EMBO Reports, 19(3), e44767.

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Genotyping of Lymphoblastoid Cell Lines

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287 lymphoblastoid cell lines (LCLs) were obtained from the Coriell Institute. DNA from these 287 LCLs was genotyped with the Affymetrix Human SNP Array 6.0 at the Coriell Institute, and with the Illumina HumanHap550K and HumanExon510S-Duo Bead Chips in our laboratory. The genotype data were deposited in the National Center for Biotechnology Information Gene Expression Omnibus (GEO accession: GSE23120) (20 (link)).

Nguyen T.T., Gao H., Liu D., Philips T.J., Ye Z., Lee J.H., Shi G.X., Copenhaver K., Zhang L., Wei L., Yu J., Zhang H., Barath A., Luong M., Zhang C., Gaspar-Maia A., Li H., Wang L., Ordog T, & Weinshilboum R.M. (2022). Glucocorticoids unmask silent non-coding genetic risk variants for common diseases. Nucleic Acids Research, 50(20), 11635-11653.

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Genetic and Expression Profiling of Human Cell Lines

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The HL-60 and Jurkat cell lines were obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA). The “Human Variation Panel” of lymphoblastoid cell lines (LCLs) was obtained from the Coriell Institute (Camden, NJ). DNA from these 287 LCLs had been genotyped in the Coriell Institute using the Affymetrix Genome-Wide Human SNP Array 6.0 (Affymetrix, Santa Clara, CA), and in our laboratory using Illumina HumanHap 550K and HumanExon 510S-Duo BeadChips (Illumina, San Diego, CA). Imputation was then performed using 1000 Genomes data (http://www.1000genomes.org/data). We also generated gene expression data for these LCLs with Affymetrix U133/2.0/Plus GeneChip expression arrays, as described previously (16 (link)). Jurkat cells were cultured in Roswell Park Memorial Institute (RPMI) media with 10% fetal bovine serum (FBS), and the HL-60 and LCL cells were cultured in the same media with 15% FBS.

Fasching P.A., Liu D., Scully S., Ingle J.N., Lyra PC J.r., Rack B., Hein A., Ekici A.B., Reis A., Schneeweiss A., Tesch H., Fehm T.N., Heinrich G., Beckmann M.W., Ruebner M., Huebner H., Lambrechts D., Madden E., Shen J., Romm J., Doheny K., Jenkins G.D., Carlson E.E., Li L., Fridley B.L., Cunningham J.M., Janni W., Monteiro A.N., Schaid D.J., Häberle L., Weinshilboum R.M, & Wang L. (2022). Identification of Two Genetic Loci Associated with Leukopenia after Chemotherapy in Breast Cancer Patients. Clinical cancer research : an official journal of the American Association for Cancer Research, 28(15), 3342-3355.

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Large-Scale Lymphoblastoid Cell Genotyping

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Three hundred lymphoblastoid cell lines were obtained from the Coriell Institute and were genotyped with the Illumina HumanHap550K and HumanExon510S‐Duo Bead Chips in our laboratory, information that was combined with data generated at the Coriell Institute using the Affymetrix Human SNP Array 6.0. The genotype data were deposited in the National Center for Biotechnology Information Gene Expression Omnibus under accession number GSE23120.²²

Nguyen T.T., Liu D., Gao H., Ye Z., Lee J., Wei L., Yu J., Zhang L., Wang L., Ordog T, & Weinshilboum R.M. (2022). Glucocorticoids mediate transcriptome‐wide alternative polyadenylation: Potential mechanistic and clinical implications. Clinical and Translational Science, 15(11), 2758-2771.

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Genome-wide SNP data for LCLs

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Expression array data were obtained for all 174 lymphoblastoid cell lines (LCLs) as previously described [17 (link)]. Illumina HumanHap550K and 510S BeadChips, which assayed 561,298 and 493,750 SNPs, respectively, were used to obtain genome-wide SNP data for these LCLs [23 (link)]. Genotyping was performed in the Genotype Shared Resource (GSR) at the Mayo Clinic, Rochester, MN. We also obtained publicly available Affymetrix SNP Array 6.0 Chip SNP data which involved 643,600 SNPs unique to the Affymetrix SNP array for the same cell lines. After quality control (QC), SNPs with call rates <0.95, Hardy-Weinberg Equilibrium (HWE) P values < 0.001, or MAFs <5% were excluded, as were DNA samples with call rates <0.95. A total of 1,348,798 SNPs that passed QC were used to perform the association studies.

Li L., Fridley B.L., Kalari K., Niu N., Jenkins G., Batzler A., Abo R.P., Schaid D, & Wang L. (2014). Discovery of genetic biomarkers contributing to variation in drug response of cytidine analogues using human lymphoblastoid cell lines. BMC Genomics, 15, 93.

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Large-Scale Nordic Multiple Sclerosis Genotyping

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In all, 2106 MS patients of Nordic origin from Sweden (n=713), Norway (n=1030) and Denmark (n=363), and 624 controls matched on the Swedish sample were genotyped on the Illumina Human Quad 660 chip (Illumina, San Diego, CA, USA) and quality controlled as described elsewhere^{6 (link)} (data accessible at https://www.ebi.ac.uk/ega/studies/EGAS00000000101). From this quality control, 91 individuals were excluded due to genotyping error and/or close relationship.
An additional 678 controls for breast cancer patients treated in the Stockholm area,^{15 (link)} typed on Illumina 1M (Illumina), and 674 controls for Swedish patients with myocardial infarction,^{16 (link), 17 (link)} typed on Illumina HumanHap 550k (Illumina), were also added. The data are available upon request from http://www.karmastudy.org (breast cancer) and http://procardis.org (myocardial infarction), respectively.
An additional quality control, after re-calling the genotypes for the additional controls and combining the two data sets, was performed with PLINK using a minor allele frequency of 0.05, Hardy–Weinberg equilibrium of 1e-6, a missingness per individual of 0.07, as required by Beagle,^{14 (link)} and a missingness per marker of 0.1, left 441 731 markers in the analysis.

Westerlind H., Imrell K., Ramanujam R., Myhr K.M., Celius E.G., Harbo H.F., Oturai A.B., Hamsten A., Alfredsson L., Olsson T., Kockum I., Koski T, & Hillert J. (2014). Identity-by-descent mapping in a Scandinavian multiple sclerosis cohort. European Journal of Human Genetics, 23(5), 688-692.

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Fibroblast Chromosome FISH Analysis

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Chromosome preparations from cultured fibroblasts were analyzed by FISH using a chromosome 12p specific DNA probe. The probe was labeled by nick translation with spectrum green. FISH was done according to standard protocol [15] (link). To validate the level of mosaicism in the probands 2 ml of cell culture from the flasks used for RNA and DNA isolation were cultured on flaskettes (Thermo scientific, Waltham, MA, USA). Slides were prepared for chromosome (interphase) analysis using standard cytogenetic protocols. For each proband 200 cells were analyzed.
We also used genome-wide single nucleotide polymorphism (SNP) arrays (Illumina HumanHap 550K; Illumina, San Diego, CA, USA) to detect percentage of mosaicism in all seventeen probands with PKS as described previously [12] (link). For this analysis DNA was isolated from the cultured fibroblasts (OD₂₆₀/OD₂₈₀ 1.8–2.0 and OD₂₆₀/OD₂₃₀>2.0, respectively). The samples were genotyped on the Illumina Bead Station (Illumina, San Diego, CA, USA). Analysis of all copy number variation calls was detected using Illumina Bead Studio software. The degree of mosaicism in all the probands were detected by assessing probe intensities measured by log R ratios, along with shifts in genotype frequencies of SNP probes measured by B allele frequencies [16] (link).

Kaur M., Izumi K., Wilkens A.B., Chatfield K.C., Spinner N.B., Conlin L.K., Zhang Z, & Krantz I.D. (2014). Genome-Wide Expression Analysis in Fibroblast Cell Lines from Probands with Pallister Killian Syndrome. PLoS ONE, 9(10), e108853.

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