The Sequencing and Microarray Facility (SMF) offers several microarray services, including:
The SMF’s microarray service offers a comprehensive set of integrated gene expression, genotyping and methylation services that facilitate studying the role of genomic alterations and transcriptional regulation of genes in human, mouse, rat and other species.
The SMF provides complete microarray services including:
- RNA and DNA sample quality check
- Target preparation
- Hybridization Services
- Imaging Services
- Signal quantification
- Gene Expression Profiling
- MicroRNA analysis
- Single Nucleotide Polymorphism (SNP) genotyping, Copy Number Variation (CNV) and Loss of Heterozygosity (LOH)
Our supported applications can be utilized to detect and map chromosomal aberrations and SNPs, profile gene expression patterns, identify differences between two populations of DNA or RNA (i.e., tumor vs. normal cell populations), determine the effect of therapeutic agents on the genome and their effect on gene expression, and determine the effect of genetic alterations on gene expression patterns.
Microarray service pricing
The microarray service offers the Affymetrix platform for Gene Expression and SNP/Genotyping profiling and the Illumina platform for SNP/Genotyping and Methylation profiling. According to the service type, the initial sample quality control (QC) and microarrays may be included in the sample processing cost. The complete service includes target preparation, hybridization, imaging and signal quantification. Investigators may request the complete microarray processing or choose to have the facility perform partial service.
Pricing for microarray services can be found on the service pricing schedule.
A statistical analyst from the Bioinformatics Shared Resource is available once a week to assist new users with experimental design. Workshops are held at FCT5.5049, from 1-3 p.m.
The SMF offers the Microarray Services via an online iLab system. User accounts, project submissions and service requests are managed via iLab for MD Anderson Cancer Center users. Non-MD Anderson users need to fill out a request form and email it with the required PO number and authorizing signatures(s). Please contact the Microarray Service for details.
Access to data
All data generated by the microarray service is stored and accessed via an Institutional Server (gcgserv). Research Information Systems creates a Microarray Data folder for each Principal Investigator as well as a user name and password to access the data for the Principal Investigator and authorized lab members. The SMF uploads the microarray data to the Principal Investigator’s Microarray Data folder. Investigators will be notified via email when data is ready to be downloaded. The microarray data will be copied onto a DVD for non-MD Anderson users.
Please contact Marisela Mendoza for questions related to microarray services and project submission through the iLab system for MD Anderson users as well as submission of requests and samples for non-MD Anderson users.
The SMF performs gene expression microarray services using Affymetrix platform.
Affymetrix gene expression services offer three types of sample processing assays:
- Whole Transcript Plus (good quality Total RNA, ≥33 ng/ul)
- Whole Transcript Pico (degraded or FFPE total RNA, ≤33 ng/ul)
- 3’IVT (total RNA 3’ biased assay)
Pricing for gene exrpression microarray services can be found on the service pricing schedule.
Human, mouse, rat and other eukaryotic organisms can be profiled using the combination of these assays with high density microarrays.
Affymetrix’ whole-transcript analysis approach enables researchers to detect not only the level of expression, but also precisely what is being expressed, including alternative isoforms or genomic deletions. This has opened the door to new insights at a resolution not possible with the classical 3’-based microarrays.
- Affymetrix Exon 1.0 ST whole-transcript (WT) array enables two complementary levels of analysis—gene expression and alternative splicing. Multiple probes per exon enable "exon-level" analysis allowing to distinguish between different isoforms of a gene. The second level is "gene-level" expression analysis, in which multiple probes on different exons are summarized into an expression value of all transcripts from the same gene.
- Affymetrix Gene 1.0 and 2.0 ST whole-transcript arrays include probes to measure both messenger (mRNA) and long intergenic non-coding RNA transcripts (lincRNA). These whole-transcript array designs provide a complete expression profile of mRNA as well as the intermediary lincRNA transcripts that impact the mRNA expression profile.
- Human Transcriptome Array (HTA) 2.0 provides the ability to go beyond gene-level expression profiling by providing the coverage and accuracy required to accurately detect all known transcript isoforms produced by a gene by combining multiple data sources.
- Clariom D Arrays provide a highly detailed view of the transcriptome and offer the fastest path to actionable results. Clariom D Assays allow translational research scientists to generate high-fidelity biomarker signatures quickly and easily. Based on industry-leading microarray technology, the novel design of these assays provides the most intricate transcriptome-wide gene- and exon-level expression profiles, including the ability to detect alternative splicing events of coding and long non-coding (lnc)RNA, in a single three-day experiment.
- The Clariom S Arrays design provides extensive coverage of all known well-annotated genes, compatibility with clinical sample types, scalable formats, and flexible data analysis software. Clariom S Assays are the tools of choice to find expression biomarkers with known function as quickly, easily, and cost-effectively as possible.
- The Affymetrix 3' IVT plus kit is used for visualization of 3' biased eukaryotic expression. This platform utilizes oligo-dT primers to produce cDNA, then in vitro transcription to generate biotin-labeled cRNA, which is hybridized to 3' targeting probes on the array.
- miRNA 3.0 and 4.0 high density arrays provide the most sensitive, accurate and complete measurement of small non-coding RNA transcripts involved in gene regulation. The arrays are designed to interrogate all mature miRNA sequences in miRBase 20, analyze miRNA from all species using the same array format with 3,770 probe sets unique to human, mouse and rat pre-miRNA hairpin sequences and 1,996 human snoRNA and. scaRNA.
The SMF performs SNP genotyping microarray services using Affymetrix and Illumina platforms.
Pricing for SNP profiling microarray services can be found on the service pricing schedule.
The Genome-Wide Human SNP Array 6.0 contains more than 1.8 million markers of genetic variation. Approximately half of the markers include single nucleotide polymorphism (SNPs) detection probes while the other half detects copy number variation (CNV). The SNP Array 6.0 allows researchers to perform association studies with large sample sizes. These markers have a better representation of SNPs on chromosomes X and Y, mitochondrial SNPs, SNPs in recombination hotspots and new SNPs added to the dbSNP database after completion of the GeneChip Human Mapping 500k arry set.
CytoScan HD Array provides the broadest coverage and highest performance for detecting chromosomal aberrations with a greater than 99% sensitivity. It can reliably detect 25-50kb copy number changes across the genome at high specificity with single-nucleotide polymorphism (SNP) allelic corroboration. With more than 2.6 million copy number markers, CytoScan HD Suite covers all OMIM™ and RefSeq genes. Enables low-level mosaicism visualization, absence of heterozygosity (AOH) and acquired UPD (aUPD) detection, copy number change confirmation, triploidy detection, allelic imbalance pattern visualization, genomic contamination identification, trio consistency checking, and parent-of-origin analysis.
The OncoScan Array delivers an entirely new perspective on the cancer genome from even the most challenging solid formalin-fixed paraffin embedded (FFPE) tumor samples. The OncoScan assay utilizes molecular inversion probes that generate multiplexed array hybridization targets from as short as 40 base-pairs of sequence. The Oncoscan array utilizes SNP probes to provide genomic information that includes copy number variations (CNVs) loss of heterozygosity (LOH) and cancer-related somatic mutations.
Illumina's Genotyping Infinium BeadChips offer researchers the flexibility to genotype samples with hundreds of thousands to millions of markers that deliver genome-wide coverage with the most up-to-date content.
The Illumina Omni family of genotyping microarrays is able to detect up to 5 million markers per sample and offers customizability of array content. These arrays are designed from next-generation sequencing data from international projects such as the 1000 Genomes Project.
Omni microarrays offer unparalleled genomic coverage using intelligently selected tag SNPs that maximize the likelihood of finding true associations for a given phenotype. The power of a tag SNP approach stems from the in¬herent correlation among markers that form haplotype blocks, allowing one highly correlated marker to serve as a proxy for a number of others across the genome. This approach allows for the broadest selection of maximally informative markers, resulting in the best genome-wide coverage of both common and rare variants.
Illumina also has modified protocols for handling partially degraded samples from archival tissues including FFPE tissues.Illumina’s GenomeStudio® software offers the ability to jointly analyze SNPs and CNV probes for down¬stream analysis, and includes links to numerous third-party plug-ins for both genotyping and CNV analysis.
Human CytoSNP-12: Twelve (12) samples per chip. Single Nucleotide Polymorphism (SNP) coverage across the entire genome. The Beadchip can be used with FFPE samples. Content includes about 300,000 SNPs targeting regions to be important for cytogenetic analysis. Generated data can be used to characterize common congenital disorders and profile reported copy number variation (CNV) regions, while providing dense coverage for novel CNVs discovery.
Human OmniExpress-24: Twenty-four (24) samples per chip. Optimized SNP content strategically selected from all 3 HapMap phases (710,000 markers) to capture the greatest amount of common SNP variation and drive the discovery of novel association with traits and diseases. The Beadchip can be used with FFPE samples and it could be customized with 30,000 additional bead types.
Human Omni 5-4: Four (4) samples per chip. It delivers a comprehensive SNP coverage across world super populations (4.3 million markers). This high density array provides exceptional coverage of common, intermediate and rare SNPs and harnesses tag SNPs selected from the International HapMap project and 1000 project, offering optimized content for whole-genome genotyping and copy number variation (CNV), germline variants, insertions-deletions (indels) and SNPs structural variants.
Human Omni 2.5-8: Eight (8) samples per chip. The beadchip offers a comprehensive set of both common and rare SNPs from the 1000 Genomes project (2.3 million markers), generating high quality data for Copy Number Variants (CNVs), germline variants, insertions-deletions (indels) and SNPs structural variants. The Beadchip can be used with FFPE samples and it could be customized with 200,000 additional markers.
Human OmniExpress-Exome-8: Eight (8) samples per chip. Optimized SNP content strategically selected from all 3 HapMap phases (960,000 markers) to capture the greatest amount of common SNP variation and drive the discovery of novel association with traits and diseases. The array includes 274,000 functional exonic markers, delivering coverage of putative exonic variants selected form over 12,000 individual exome and hole-genome sequences. The Beadchip can be used with FFPE samples and it could be customized with 30,000 additional bead types.
DNA methylation plays a role in the regulation of gene expression and has been implicated in many human diseases including cancer. The effect of aberrant methylation (either hypermethylation or hypomethylation) can be analyzed using DNA Methylation microarray analysis for a variety of applications.
Pricing for methylation array services can be found on the service pricing schedule.
The SMF provides DNA Methylation microarray services through the Illumina platform.
Illumina has developed a robust BeadArray methylation platform that provides quantitative methylation measurements for the detection of epigenetic changes at the single-CpG-site level of several thousand genes at one time. The arrays are capable of profiling 8 samples in parallel while minimizing the cost per sample making it ideal for screening genome-wide association study (GWAS) populations.
Infinium MethylationEPIC: Eight (8) samples per chip. The BeadChip provides exceptional coverage (over 859,000 methylation sites per sample at single nucleotide resolution) of CpG islands, RefSeq Genes, ENCODE open Chromatin, ENCODE transcription factor binding sites, and FANTOM5 enhancers. It contains about 90% of the original InfiniumMethylation 450 BeadChip content to provide a broad, comprehensive view of the methylome. Methylation studies of FFPE samples are enabled with a modified version of the Infinium MethylationEPIC BeadChip protocol.