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DNA Extraction

Automated DNA extraction from buccal brushes, small volumes of blood, blood spots, and various tissues (such as cell cultures and mouse tails), located in a separate pre-PCR room. The Qiagen BioRobot M48 system performs 48 individual extractions in 2-6 hours using a magnetic bead separation process.

Sequencing and Fragment Analysis

Illumina's BeadArray technology provides quality and sensitivity due to a 30-fold redundancy and a 100% QC on every feature. The BeadStation's core component, the BeadArray Reader, scans 3-micron features assembled into the highest-density arrays available for genetic analysis. This technology together with Illumina's novel assays enables reduced sample and reagent input requirements. GoldenGate genotyping: standard & custom content panels (96 well) from 96- to 1536-plex Infinium whole-genome genotyping: Integrated solutions for 100, 300, and 500K SNP loci Direct hybridization gene expression: Whole-genome and focused array solutions DASL gene expression: Standard and custom panels of up to 1,536 genes for RNA from multiple sources including FFPE tissues Methylation profiling: Custom panels of up to 1,536 genes for samples using the GoldenGate Assay for Methylation

The Beckman Coulter SNPstream is utilized to genotype from 4,000 up to 3 million genotypes per day. This automated, multiplexed system can process up to 48 SNPs in each well of a 384-well plate. The SNPstream operates at a consistent cost per genotype or per sample, regardless of run throughput, allowing users to cost-effectively pinpoint targets with low-throughput studies as well as conduct high-throughput analyses. The SNPstream features a single-based primer extension technology and operates at over 99% accuracy. The system’s high sensitivity delivers accurate results using as little as 2 ng of genomic DNA. The plates are compatible with the existing Biomek® series liquid handlers, for fast pre-and post-PCR setup. Multiplexing within the system’s 384-well plate enables the user to run a range of genomic samples on the same plate. The system can accommodate up to 72 plates a day. The data collection, analysis and QC from raw data to genotype are highly automated and a complete summary report is provided. The SNPstream Genotyping Systems are validated on multiple sources and species, including genomic DNA from blood, tissue (including FFPE), cell culture or buccal swab and from human, mouse, cow, microbial and plant species.

The ABI 7900 fast real-time PCR System is a real-time quantitative PCR system that combines 96- and 384-well plate compatibility with fully automated robotic loading. Key applications include gene expression quantitation and the detection of single nucleotide polymorphisms (SNPs) using the fluorogenic 5' nuclease assay.

The ABI 3100 is a multi-color fluorescence-based DNA analysis system using the technology of capillary electrophoresis with 16 capillaries operating in parallel. This fully automated system separates amplified fragments of varying sizes for analysis of short tandem repeats (STRs) among individuals and extended pedigrees. Raw DNA sequence is retrieved from the 3100 and imported into Applied Biosystems SEQSCAPE, v.2.0, a sequence comparison tool designed to determine the quality of the DNA nucleotide calls and to identify nucleotide and amino acid variants.

The ABI TaqMan 7000 is a complete end point and real-time PCR system that detects and quantitates nucleic acid sequences. In real-time PCR, cycle-by-cycle detection of accumulated PCR product is made possible by combining thermal cycling, fluorescence detection, and application-specific software in a single instrument. Quantitative results are available immediately after PCR without additional purification or analysis The system uses a Peltier-based, 96-well block thermal cycling system with standard 96-well plates or 0.2 mL tubes. Multicolor detection provides flexibility for multiplex quantitation assays, allelic discrimination assays, and plus/minus assays. The machine uses Sequence Detection System 1.1 software.

The Tecan Freedom EVO 150 is a versatile liquid handling platform and flexible robotic workstation with two pipetting heads and one robotic arm serving a full range of life science applications. The Freedom EVO platform is used to perform routine liquid transfers, such as the transfer of DNA from individual vials into the 96-well storage and amplification plates required by downstream applications.

The Beckman Biomek FX instrument is used to perform routine liquid transfers, such as the transfer of DNA from individual vials into the 96-well storage and amplification plates required by downstream applications. The Biomek FX is utilized to prepare a plate to determine the concentration of the extracted DNA and then using the concentrations obtained to create a normalized plate of samples to be used for amplification and sequencing. The Biomek FX can also create mother-daughter replica plates, transfer individual samples into a new plate or vial and prepare and dispense the necessary reagents for DNA amplification. This system is also located in pre-amplification space.

By incorporating a wide range of next-generation features into a small-footprint design, the Biomek NX sets a new standard for flexible laboratory solutions. It puts every aspect of liquid handling – including pipetting, dilution, dispensing, and integrations – into a single, automated system. It is used for Post-PCR liquid handling needs.

Biobanking

• Sample storage and tracking throughout their entire life – barcoding
  
• Views/Folders and Filters to query the database
  
• Roles and securities
  
• Racks and rack storage (Fill, move, delete and split samples within racks)
  
• Customizable racks and plates (different dimensions)
  
• Customized workflows created for every project
  
• Functionality to import different sample types and sample data, in a high throughput capacity using a CSV formatted file (electronic manifest)
  
• Functionality to export sample sheet to ABI 3100, ABI 3730 and ABI 7000.
  
• Ability to update volume and concentration details associated to samples already logged into the LIMS

• Web-based data management tool for genetics studies
  
• Allows CMG collaborators to view/download data with a simple web browser
  
• Main functions
  
• Data Repository
  
• Genetics Statistical analysis tools
  
• Data quality checks (Mendelian errors, HWE)
  
• Haplotyping (with or without pedigree data)
  
• Association and LD
  
• TDT and quantitative TDT
  
• Sib-pair analysis
  
• Nonparametric linkage analysis
  
• Parametric linkage analysis
  
• Quantitative linkage
  
• Can subset and combine data sets
  
• Security includes password controlled privilege system
  
• Types of datasets include:
  
• Genotype (SNP, microsatellite)
  
• Phenotype
  
• Affection status
  
• Pedigree
  
• Map Frequency

CMG also has access to:

Automated DNA extraction from fresh and frozen cells as well as large volume blood samples can yield up to 500 µg DNA per 10 ml blood. Located in pre-PCR room, allows for walk-away purification. Beeps a lot.

The Biotage PSQ96 Pyrosequencer is a multi-application, quantitative genetic analysis system based on Pyrosequencing technology. It can be used for sequencing and genetic analysis for microbiological species identification, resistance typing, DNA methylation analysis and studying pharmacogenetic markers. It is capable of rapidly reading typically 50 to 100 bases, genotyping virtually any SNP, performing InDel analysis, and quantitatively measuring alleles in haploid as well as polyploid genomes, It gives rapid access to true sequencing information. Preparation and sequencing 50 bases takes less than 1 hour. Sample preparation for Pyrosequencing requires only 10 minutes. Up to 96 samples can be prepared and sequenced in parallel.