Log In Sign up
The largest database of trusted experimental protocols

Humanhap550 chip

Manufactured by Illumina
Visit Supplier
Sourced in United States

The HumanHap550 chip is a genome-wide single nucleotide polymorphism (SNP) genotyping array developed by Illumina. It is designed to interrogate approximately 550,000 genetic markers across the human genome. The chip allows for the high-throughput and cost-effective analysis of genetic variation within a sample.

Automatically generated - may contain errors

Lab products found in correlation

Infinium hd human610 quad beadchip, by Illumina (1 mentions) Human660w quad chip, by Illumina (1 mentions)

Spelling variants of this product

HumanHap550 (58 citations) HumanHap550 quad chip (23 citations) Infinium HumanHap550 genotyping chip (4 citations) Infinium II HumanHap550 SNP chips (2 citations) Illumina HumanHap550 Bead Chips (2 citations) Infinium HumanHap550 chip (2 citations)

9 protocols using humanhap550 chip

1

Genome-wide Genotyping for Clinical Trials

Check if the same lab product or an alternative is used in the 5 most similar protocols
Genome-wide genotyping of the Abbott patients was conducted using the Illumina HumanHap550 chip (Illumina, San Diego, CA, USA). LOCCS and LODO patients were genotyped using the Infinium HD Human610-Quad BeadChip (Illumina). The software PLINK v.1.07 [ref. 22 (link)] was used for quality control (QC) and statistical analysis of genotype data. For QC, SNPs with a study-wise missing data proportion above 0.05 were removed from the analysis. SNPs failing to meet Hardy–Weinberg equilibrium (P<0.0001), in addition to SNPs with >10% missing genotypes were also dropped from the analysis. A total of 542 562 SNPs from the Abbott trials passed QC and were included in the analysis. For LOCCS and LODO, a total of 545 934 SNPs passed QC. To assess population stratification in the primary analysis, the P-values were adjusted for genomic control using PLINK.
Dahlin A., Litonjua A., Irvin C.G., Peters S.P., Lima J.J., Kubo M., Tamari M, & Tantisira K.G. (2015). Genome-wide association study of leukotriene modifier response in asthma. The Pharmacogenomics Journal, 16(2), 151-157.
+ Open protocol
+ Expand
2

Autism Genetic Cohort and Control Study

Cited 1 time
Check if the same lab product or an alternative is used in the 5 most similar protocols
The autism cohort included 3360 cases from Autism Genetics Resource exchange (AGRE), Autism Genome Project (AGP), and Autism Cases recruited and genotyped at CAG [5 (link)]. The control group included children of self-reported Caucasian ancestry, recruited at CHOP. All controls had no history of ASD, or any other central nervous system disorder, chromosomal disorder, syndrome or genetic disorder. All samples were genotyped on the Illumina HumanHap550 chip [5 (link)].
Glessner J.T., Li J., Wang D., March M., Lima L., Desai A., Hadley D., Kao C., Gur R.E., Cohen N., Sleiman P.M., Li Q, & Hakonarson H. (2017). Copy number variation meta-analysis reveals a novel duplication at 9p24 associated with multiple neurodevelopmental disorders. Genome Medicine, 9, 106.
+ Open protocol
+ Expand
3

Genome-wide Genotyping for Genetic Association

Check if the same lab product or an alternative is used in the 5 most similar protocols
Genome-wide genotyping of the LOCCS and LODO trials was conducted using the Illumina HumanHap550 chip (San Diego, CA). For CLIC and PACT, genotyping was performed as described (30, 31), using the Genomewide Affymetrix SNP 6.0 Array (Santa Clara, CA). The software PLINK v.1.07 [32 (link)] was used for QC of genotype data. SNPs with a study-wise missing data proportion above 0.05 were removed from the analysis. SNPs failing to meet Hardy-Weinberg equilibrium (HWE) (P < 0.0001), in addition to SNPs with a minor allele frequency (MAF) < 5% and more than 10% missing genotypes, were also dropped from the analysis. A total of 532,264 SNPs with acceptable quality were genotyped and analyzed in the discovery GWAS for both LOCCS and LODO, and 591,268 SNPs were genotyped and analyzed in both CLIC and PACT.
Dahlin A., Litonjua A., Lima J.J., Tamari M., Kubo M., Irvin C.G., Peters S.P, & Tantisira K.G. (2015). Genome-Wide Association Study Identifies Novel Pharmacogenomic Loci For Therapeutic Response to Montelukast in Asthma. PLoS ONE, 10(6), e0129385.
+ Open protocol
+ Expand
4

Genome-Wide Imputation using 1000 Genomes

Cited 1 time
Check if the same lab product or an alternative is used in the 5 most similar protocols
To compare whole-genome sequencing to imputation from the 1000 genomes reference panel we used haplotypes from the 1000 Genomes Phase I integrated (version 3) release with singletons removed (30 061 896 variants; 28 681 763 SNPs and 1 380 133 indels). Genotype data captured on the Illumina HumanHap550 chip were phased using MACH 1.0.16 (29 (link),30 (link)). Subsequent imputation was performed using Minimac (version 2012.10.9) (31 (link)). We used a multi-ethnic haplotype reference panel that included 1092 individuals including 379 Europeans (including 98 Tuscans), 181 Americans, 246 Africans and 289 Asians, in an attempt to capture variants that may be rare in Europeans but more common on haplotypes from different ethnic backgrounds.
Wood A.R., Tuke M.A., Nalls M., Hernandez D., Gibbs J.R., Lin H., Xu C.S., Li Q., Shen J., Jun G., Almeida M., Tanaka T., Perry J.R., Gaulton K., Rivas M., Pearson R., Curran J.E., Johnson M.P., Göring H.H., Duggirala R., Blangero J., Mccarthy M.I., Bandinelli S., Murray A., Weedon M.N., Singleton A., Melzer D., Ferrucci L, & Frayling T.M. (2014). Whole-genome sequencing to understand the genetic architecture of common gene expression and biomarker phenotypes. Human Molecular Genetics, 24(5), 1504-1512.
+ Open protocol
+ Expand
5

Genome-Wide Association Study of SLE

Check if the same lab product or an alternative is used in the 5 most similar protocols
We analyzed data from a previous genome-wide association study of SLE (the Hom et al. study), which comprised 1,165 cases following our QC analysis (see Supplementary Text). We used a further 2,107 previously genotyped controls from the NIH CGEMS study, which were genotyped using the Illumina HumanHap550 chip. Owing to the lower density of genotyping, in some cases data imputed to the density of the 1000 Genomes (1KG) study were used in the analysis of the Hom et al. study and the subsequent meta-analysis. Imputed data are identified in tables.
Bentham J., Morris D.L., Graham D.S., Pinder C.L., Tombleson P., Behrens T.W., Martín J., Fairfax B.P., Knight J.C., Chen L., Replogle J., Syvänen A.C., Rönnblom L., Graham R.R., Wither J.E., Rioux J.D., Alarcón-Riquelme M.E, & Vyse T.J. (2015). Genetic association analyses implicate aberrant regulation of innate and adaptive immunity genes in the pathogenesis of systemic lupus erythematosus. Nature genetics, 47(12), 1457-1464.
+ Open protocol
+ Expand
6

Genome-Wide Association Study of SLE

Check if the same lab product or an alternative is used in the 5 most similar protocols
We analyzed data from a previous genome-wide association study of SLE (the Hom et al. study), which comprised 1,165 cases following our QC analysis (see Supplementary Text). We used a further 2,107 previously genotyped controls from the NIH CGEMS study, which were genotyped using the Illumina HumanHap550 chip. Owing to the lower density of genotyping, in some cases data imputed to the density of the 1000 Genomes (1KG) study were used in the analysis of the Hom et al. study and the subsequent meta-analysis. Imputed data are identified in tables.
Bentham J., Morris D.L., Graham D.S., Pinder C.L., Tombleson P., Behrens T.W., Martín J., Fairfax B.P., Knight J.C., Chen L., Replogle J., Syvänen A.C., Rönnblom L., Graham R.R., Wither J.E., Rioux J.D., Alarcón-Riquelme M.E, & Vyse T.J. (2015). Genetic association analyses implicate aberrant regulation of innate and adaptive immunity genes in the pathogenesis of systemic lupus erythematosus. Nature genetics, 47(12), 1457-1464.
+ Open protocol
+ Expand
7

ALSPAC Longitudinal Cohort Study

Cited 1 time
Check if the same lab product or an alternative is used in the 5 most similar protocols
The ALSPAC (Avon Longitudinal Study of Parents and Children) is a longitudinal cohort study covering the area of the former county of Avon, UK [18 (link),19 (link)]. Women who were pregnant, living in the study area and had an expected delivery date between 1 April 1991 and 31 December 1992 were eligible for inclusion in the study. Birth weight and related data were abstracted from medical records. Children were genotyped on the Illumina HumanHap550 chip and mothers were genotyped using the Illumina human660W quad chip. Quality Control (QC) was undertaken as described previously [16 (link)] and imputation was to the HRC reference panel yielding data available for 8884 mothers and 8860 children with genotype data available. Of these, 4570 mother-child pairs with phenotype data were available for analysis.
Beaumont R.N., Kotecha S.J., Wood A.R., Knight B.A., Sebert S., McCarthy M.I., Hattersley A.T., Järvelin M.R., Timpson N.J., Freathy R.M, & Kotecha S. (2020). Common maternal and fetal genetic variants show expected polygenic effects on risk of small- or large-for-gestational-age (SGA or LGA), except in the smallest 3% of babies. PLoS Genetics, 16(12), e1009191.
+ Open protocol
+ Expand
8

Genetic Enrichment Analysis for HIV Risk

Cited 1 time
Check if the same lab product or an alternative is used in the 5 most similar protocols
Enrichment analysis was applied to investigate whether the genes in pathogen-interaction networks and under positive selection were also associated with HIV risk and host control. For this analysis, the maximum absolute iHS value in any population was utilized for each SNP. To test for enrichment, p-value cutoffs were chosen for eight published HIV GWAS datasets [36 (link)–43 (link)]. Enrichment analyses were based on Fisher’s exact test, and fold enrichment was calculated based on observed vs. expected overlap. The total number of SNPs was based on the overlap between the Illumina HumanHap550 chip (commonly used in HIV GWAS) and the set of independent HIV-interactome SNPs referred to as Set B in Methods above.
Corona E., Wang L., Ko D, & Patel C.J. (2018). Systematic detection of positive selection in the human-pathogen interactome and lasting effects on infectious disease susceptibility. PLoS ONE, 13(5), e0196676.
+ Open protocol
+ Expand
9

ADHD Genome-Wide Association Study

Cited 1 time
Check if the same lab product or an alternative is used in the 5 most similar protocols
The 1013 ADHD cases of European descent were recruited and genotyped at CHOP; additional cases were from NIMH and The University of Utah [7 (link)]. The control group included healthy children aged 6–18 years old, with no serious underlying medical disorder, including but not limited to neurodevelopmental disorders, cancer, chromosomal abnormalities, and known metabolic or genetic disorders [7 (link)]. Samples were genotyped on the Illumina HumanHap 550 chip [7 (link)].
Glessner J.T., Li J., Wang D., March M., Lima L., Desai A., Hadley D., Kao C., Gur R.E., Cohen N., Sleiman P.M., Li Q, & Hakonarson H. (2017). Copy number variation meta-analysis reveals a novel duplication at 9p24 associated with multiple neurodevelopmental disorders. Genome Medicine, 9, 106.
+ Open protocol
+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!