SNPs, CNVs, and LOH Microarray Profiling Services
Illumina Microarray Platform
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 can 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 including 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 inherent correlation among markers that form haplotype blocks, allowing one highly correlated marker to serve as a proxy for several 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 downstream analysis and includes links to numerous third-party plug-ins for both genotyping and CNV analysis.
CytoSNP 850K: This array contains empirically selected SNPs spanning the entire genome with enriched coverage for 3,262 genes of cytogenetics relevance. It detects chromosomal abnormalities, Copy Number Variants (CNVs), Loss of Heterozygosity (LOH) and Single Nucleotide Polymorphisms (SNPs). We recommend that you submit samples in multiples of 16 as charges apply for empty slots on each array.
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: This beadchip offers a comprehensive set of both common and rare SNPs from the 1000 Genomes project (over 2.3 million fixed 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 can be customized with 200,000 additional markers. We recommend that you submit samples in multiples of 16 as charges apply for empty slots on each array.
Human OmniExpress-Exome-8: Optimized SNP content strategically selected from all 3 HapMap phases (about 960,000 fixed markers) to capture the greatest amount of common SNP variation and drive the discovery of novel association with traits and diseases. The array includes over 274,000 functional exonic markers, delivering coverage of putative exonic variants selected form over 12,000 individual exome and whole-genome sequences. The Beadchip can be used with FFPE samples, and it can be customized with 30,000 additional bead types. We recommend that you submit samples in multiples of 16 as charges apply for empty slots on each array.
Illumina Methylation Microarray Profiling Service
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 ATGC provides DNA Methylation microarray services using 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: This BeadChip provides exceptional coverage (over 935,000 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 profiles regions of chromatin identified by ATAC-seq and ChIP-seq studies. Methylation studies of FFPE samples are enabled with a modified version of the Infinium MethylationEPIC BeadChip protocol. We recommend that you submit samples in multiples of 8 as charges apply for empty slots on each array.
General information links as a reference for minimum number of samples:
|Array Name||Approx. No. of Fixed Markers||Description||Variant Class||DNA Input (ng)||Number of samples required per submission||FFPE or Degraded sample processing by ATGC-Microarray Service|
|Infinium CytoSNP-850K v1.3||850K||It contains empirically selected SNPs spanning the entire genome with enriched coverage for 3,262 genes of known cytogenetics relevance of both constitutional and cancer applications. Each SNP has 15X redundancy to increase the signal-to-noise ratio for making accurate CNV and AOH calls across the genome. Increased sensitivity for low level mosaics and high resolution for copy neutral loss of heterozygosity. Latest generation of Infinium Cytogenetics application arrays.||Chromosomal Abnormalities, Copy Number Variants (CNVs), Loss of heterozygosity, Single Nucleotide Polymorphisms (SNPs).||200ng (50 ng/ul)||8 samples or multiples of 8||Yes|
|Infinium Omni 2.5-8||2.4M||Offers a comprehensive set of both common and rare single nucleotide polymorphism (SNP) for diverse world populations.||Copy Number Variants (CNVs), Germline Variants, Insertions-Deletions (indels), Single Nucleotide Polymorphisms (SNPs), Structural Variants||200ng (50 ng/ul)||16 samples or multiples of 16||No|
|Infinium OmniExpress-Exome-8||960K||The array includes over 274,000 functional exonic markers while delivering high coverage of putative functional exonic variants selected from 12,000 individual exome and whole genome sequences.||Copy Number Variants (CNVs), Germline Variants, Insertions-Deletions (indels), Single Nucleotide Polymorphisms (SNPs), Structural Variants||200ng (50 ng/ul)||16 samples or multiples of 16||No|
|Infinium OmniExpress-24 FFPE||720K||Customizable Beadchip with a add up capacity of 30K custom markers. In addition to large scale genotyping studies the OmniExpress-24 array provides baseline sample data for various downstream applications including common variant, mitochondrial DNA, ancestry, sex determination, loss of variant and insertion-deletion (indel) studies.||Copy Number Variants (CNVs), Germline Variants, Single Nucleotide Polymorphisms (SNPs), Structural Variants||200ng (50 ng/ul)||48 samples or multiples of 48||Yes|
|Infinium MethylationEPIC||935K||Genome-Wide Methylation Screening targeting over 935,000 CpG sites across the genome profiling enhancers and super-enhancers, CTF-binding sites, CNV detection regions, common cancer driver mutations and open regions of chromatin identified by ATAC-seq and ChIP-seq experiments.||Differentially Methylated Cytosines||250ng/ul
|8 samples or multiples of 8||Yes|
Access to Data and Bioinformatics Assistance
Access to data
All data generated by the microarray service is stored and accessed via an Institutional Server for MD Anderson users (gcgserv). Research Information Systems creates a Microarray Data folder for each Principal Investigator as well as a username and password to access the data for the Principal Investigator and authorized lab members. The ATGC 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.
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.
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 ATGC 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.
Microarray Service Pricing
The microarray service offers 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.