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infinium humanhap550  (INFINIUM Inc)

 
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    Structured Review

    INFINIUM Inc infinium humanhap550
    Data are from (a) Agilent Human Genome CGH Microarray 244A (Memorial Sloan-Kettering Cancer Center), (b) Affymetrix Genome-Wide Human SNP Array 6.0 (Broad Institute of MIT and Harvard), (c) Illumina 550 K Infinium <t>HumanHap550</t> SNP Chip (HudsonAlpha Institute for Biotechnology) platforms (chr 1–23). Green bars represent amplification and red bars represent deletion. The height of each bar represents the frequency of the alteration in the group. The differentially amplified genes are in chromosome 7 and differentially deleted genes are in chromosome 10.
    Infinium Humanhap550, supplied by INFINIUM Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/244+k+microarray+data/humanhap300+duo+array/pmc03639162-70-15-14
    Average 90 stars, based on 1 article reviews
    infinium humanhap550 - by Bioz Stars, 2026-10
    90/100 stars

    Images

    1) Product Images from "Age-Specific Signatures of Glioblastoma at the Genomic, Genetic, and Epigenetic Levels"

    Article Title: Age-Specific Signatures of Glioblastoma at the Genomic, Genetic, and Epigenetic Levels

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0062982

    Data are from (a) Agilent Human Genome CGH Microarray 244A (Memorial Sloan-Kettering Cancer Center), (b) Affymetrix Genome-Wide Human SNP Array 6.0 (Broad Institute of MIT and Harvard), (c) Illumina 550 K Infinium HumanHap550 SNP Chip (HudsonAlpha Institute for Biotechnology) platforms (chr 1–23). Green bars represent amplification and red bars represent deletion. The height of each bar represents the frequency of the alteration in the group. The differentially amplified genes are in chromosome 7 and differentially deleted genes are in chromosome 10.
    Figure Legend Snippet: Data are from (a) Agilent Human Genome CGH Microarray 244A (Memorial Sloan-Kettering Cancer Center), (b) Affymetrix Genome-Wide Human SNP Array 6.0 (Broad Institute of MIT and Harvard), (c) Illumina 550 K Infinium HumanHap550 SNP Chip (HudsonAlpha Institute for Biotechnology) platforms (chr 1–23). Green bars represent amplification and red bars represent deletion. The height of each bar represents the frequency of the alteration in the group. The differentially amplified genes are in chromosome 7 and differentially deleted genes are in chromosome 10.

    Techniques Used: Microarray, Genome Wide, Amplification

    Related Articles

    Ii Assay:

    Article Title: Gene-based elevated triglycerides and T2D risk in the Women’s Genome Health Study
    Article Snippet: .. Genotyping and Genetic Risk Score In the WGHS, genotyping was performed with the HumanHap300 Duo array using the Infinium II assay 19 , 20 . ..

    Article Title: Gene-based elevated triglycerides and T2D risk in the Women’s Genome Health Study
    Article Snippet: .. In the WGHS, genotyping was performed with the HumanHap300 Duo array using the Infinium II assay 19 , 20 . ..

    Gene Expression:

    Article Title: Exploiting expression patterns across multiple tissues to map expression quantitative trait loci
    Article Snippet: .. Genotyping was done on Infinium HumanHap550 Beadchips to assay genotypes for 561,466 SNPs, from the cerebellum tissue samples while gene expression profiling of 22,184 mRNA transcripts was performed using Illumina HumanRef-8 Expression BeadChips. ..

    Expressing:

    Article Title: Exploiting expression patterns across multiple tissues to map expression quantitative trait loci
    Article Snippet: .. Genotyping was done on Infinium HumanHap550 Beadchips to assay genotypes for 561,466 SNPs, from the cerebellum tissue samples while gene expression profiling of 22,184 mRNA transcripts was performed using Illumina HumanRef-8 Expression BeadChips. ..

    other:

    Article Title: Causal graph-based analysis of genome-wide association data in rheumatoid arthritis
    Article Snippet: Out of these SNPs, only 20 are assayed in NARAC cohort using Infinium HumanHap550 platform.

    Article Title: Gene-Based Elevated Triglycerides and Type 2 Diabetes Mellitus Risk in the Women’s Genome Health Study
    Article Snippet: In the WGHS, genotyping was performed with the HumanHap300 Duo array using the Infinium II assay.19,20 Imputation for the singlenucleotide polymorphisms (SNPs) that were not present in the genotyping array was performed using MACH (v. 1.0.16) using the 1000 genomes phase I v. 3 (March 2012) cosmopolitan reference panel.



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    Image Search Results


    a TCGA matched samples (520 from BRCA, 150 from GBM) run on both microarray and RNA-seq were split into a training set (2/3) and test set (1/3). b RNA-seq samples were titrated into each training set, 10% at a time (0–100%), resulting in eleven training sets for each normalization method. Each RNA-seq sample replaces its matched microarray sample. Cross-platform normalization methods were applied to each training set independently. c We used three supervised algorithms to train classifiers (molecular subtype and mutation status of TP53 and PIK3CA in both BRCA and GBM) on each training set and tested on the microarray and RNA-seq test sets. The test sets were projected onto and back out of the training set space using unsupervised Principal Components Analysis to obtain reconstructed test sets. The subtype classifiers trained in step 3A were used to predict on the reconstructed test sets. Pathways regulating gene expression were identified using the unsupervised method PLIER.

    Journal: Communications Biology

    Article Title: Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously

    doi: 10.1038/s42003-023-04588-6

    Figure Lengend Snippet: a TCGA matched samples (520 from BRCA, 150 from GBM) run on both microarray and RNA-seq were split into a training set (2/3) and test set (1/3). b RNA-seq samples were titrated into each training set, 10% at a time (0–100%), resulting in eleven training sets for each normalization method. Each RNA-seq sample replaces its matched microarray sample. Cross-platform normalization methods were applied to each training set independently. c We used three supervised algorithms to train classifiers (molecular subtype and mutation status of TP53 and PIK3CA in both BRCA and GBM) on each training set and tested on the microarray and RNA-seq test sets. The test sets were projected onto and back out of the training set space using unsupervised Principal Components Analysis to obtain reconstructed test sets. The subtype classifiers trained in step 3A were used to predict on the reconstructed test sets. Pathways regulating gene expression were identified using the unsupervised method PLIER.

    Article Snippet: For BRCA (520 pairs of matched samples), we used log 2 -transformed, lowess normalized Agilent 244 K microarray data and RSEM (RNA-seq by Expectation Maximization) gene-level count RNA-seq data .

    Techniques: Microarray, RNA Sequencing Assay, Mutagenesis, Expressing