Our Technology

CAG offers next-generation sequencing (NGS), SNP genome wide association study (GWAS), and a range of other services. The tables below outline the services available, a list of the arrays we utilize, and a brief description of respective capacities. Please note, prices are internal only. For inquiries, please contact co-Director of the Joint Genome Center This email address is being protected from spambots. You need JavaScript enabled to view it. , or Research Lab Manager This email address is being protected from spambots. You need JavaScript enabled to view it. .

Sequencing

Service Coverage Data Produced Comments Price
Human Exome NGS with Standard Bioinformatics Report 30X Clean data: 2.5Gb Sequencing performed on on Illumina® HiSeq 2000.
Data capture on SureSelect 50Mb exome kit (version 4).
$1100/sample
Human Exome NGS with Standard Bioinformatics Report 50X Clean data: 4Gb Sequencing performed on on Illumina® HiSeq 2000.
Data capture on SureSelect 50Mb exome kit (version 4).
$1200/sample
Human Exome NGS with Standard Bioinformatics Report 100X Clean data: 8Gb Sequencing performed on on Illumina® HiSeq 2000.
Data capture on SureSelect 50Mb exome kit (version 4).
Please inquire
100X Paired-End Sequencing One lane Raw data: Up to 37.5Gb depending upon user-prepared and user-quantified library,Sequencing performed on on Illumina® HiSeq 2000. $2050/lane
Human Whole Genome Sequencing 30X Raw data: 100Gb
Clean data: 8Gb
Short insert size library (<500bp).
Sequencing performed on on Illumina® HiSeq 2000.
$4000/sample
Transcriptome Sequencing Please inquire for transcriptome sequencing services - pricing is contingent upon project requirements. NA
Targeted Genome Sequencing Please inquire for targeted sequencing services - pricing is contingent upon project requirements. NA
gDNA Library Construction for Multiplexed Sequencing Short insert size library (<500bp). $320/sample
Sample QC Measured by multiple methods include Qubit/BioTek Synergy HT and gel electrophoresis for DNA. $15/sample
Library QC Caliper GX and qPCR $20/sample
Standard Bioinformatics Analysis Variant-calling and sequence data quality control. $400/sample
Grant Technical Consultation Free
Bioinformatics Consultation $90/hour

NOTE: For large sample sizes, a discount may be available.This email address is being protected from spambots. You need JavaScript enabled to view it. or This email address is being protected from spambots. You need JavaScript enabled to view it. can advise.

GWAS and Methylation

GWAS Array Types Samples Per Chip Markers Per Sample Comments Price
Affymetrix® SNP Array 6.0 1 1,800,000 Includes > 906,600 probes for SNPs and >946,000 for CNV $405
Affymetrix® Axiom 1 600,307 ~90% coverage of markers with 1-5% minor allele frequency $151
Illumina® Human CytoSNP-12 12 300,000 High-throughput analysis of genetic and structural variations that are the most relevant to human disease $255
Illumina® Human OMNI 2.5M 4 2,500,000 Includes markers from HapMap Phases 1-3 and novel data from 1000 Genomes project $450
Illumina® Omni 5M 4 5,000,000 Includes markers from HapMap Phases 1-3 and novel data from 1000 Genomes project. $580
Illumina® OmniExpress 12 700,000 Cost-effective high sample throughput and comprehensive genomic content $240
Illumina® OmniExpress + Exome 12 700,000+ (customizable with up to an additional 200,000 SNPs and markers) Cost-effective high sample throughput and comprehensive genomic content $279
Illumina® Infinium Exome 12 12,000 individual exome and whole-genome sequences on the array. It delivers focused coverage of exonic regions. Exonic variants selected from over 12,000 individual exome and whole-genome sequences. $130
Illumina® Infinium Exome+ 12 Exome chip plus up to 30,000 additional custom markers. Exonic variants selected from over 12,000 individual exome and whole-genome sequences. $130+
Illumina® Infinium™ iSelect HD Custom Genotyping BeadChip 12 90,000-250,000 custom markers. Cost-effective high sample throughput and comprehensive genomic content. $175
Illumina® Infinium™ iSelect HD Custom Genotyping BeadChip 24 3,000-90,000 custom markers. Each Infinium™ HD iSelect Custom BeadChip allows you to choose between 3,000 and 200,000 attempted bead types. $160
Illumina® Infinium™ HumanMethylation450 12 485,000 methylation sites, covering 99% of RefSeq genes*. Covers 99% of RefSeq genes, with an average of 17 CpG sites per gene region. Requires bisulfite conversion (not included in the listed price). $340
Veracode™ 96 486 to 1152 per sample Cost-effective platform for assaying 48 to 1152 SNPs. $26 (standard panel). Customization may incur additional costs.

*Information provided by Illumina® (www.illumina.com)
NOTE: For large sample sizes, a discount may be available.This email address is being protected from spambots. You need JavaScript enabled to view it. or This email address is being protected from spambots. You need JavaScript enabled to view it. can advise.

Sample Management

REMP Sample Storage and Management

To ensure integrity, highest quality and full utility of genomic data, CAG operates a robotic-based sample storage system from REMP (Oberdiessbach, Switzerland), where all internal and external biological samples are stored. Two CAG technicians are employed full-time to maintain the repository, which comprises a fully-automated infrastructure to store and track specimens. The REMP repository resides in a dedicated 15,000 square feet space. Our -20C robotic freezer REMP module can house more than 12 million samples and is complemented by twenty -80°C freezers, ten -140°C freezers and a walk-in 4°C refrigerated cold box, all in a contained secured facility.

Receiving External DNA/biological samples are accepted into the REMP facility through a receiving dock which is located internally in a highly restricted secure environment. Placements of sample into the storage module (e.g. blood, sera, and DNA stored at -20C), does not involve any manual handling. Furthermore the system supports pre-orders that dramatically speed up the retrieval process. Sample batches can be consolidated within the freezer. Samples are delivered through a gateway hatch and no humans ever enter the freezer (except for robotic maintenance).

Security CAG offers one of the most sophisticated sample management systems in the world. We have security alarms on all freezers and refrigerators which are linked to the hospital security alarm system (monitored by staff 24-hours-a-day). In the event of any failures occurring, CHOP security is instructed to go through emergency contacts for the first 10 CAG employees listed until one is available to address the issue at source. In the event of local disaster/failure, our disaster contingency plan encompasses extra freezers and liquid nitrogen tanks and we also have multiple geographical sites for data back-up.

Inquiries

To learn more about what CAG has to offer in terms of sample storage and management, please contact This email address is being protected from spambots. You need JavaScript enabled to view it. .

The REMP in action

Background & Inquiries

Background

GWAS: The genotyping yield of the Illumina Infinium chemistry exceeds 99.4 percent and allele-calling accuracy exceeds 99.99 percent. In addition to the Illumina® genotyping workflow, CAG offers the Affymetrix® SNP 6.0 and Axiom PEG panels that are run on our Biomek FX in combination with the Gene Titan instrument. The two systems allow flexibility to internal and collaborative projects.

Sequencing: CAG offers NGS services by harnessing the power and flexibility of two major platforms, Hi-Seq (Illumina®, Inc) and SOLiD 5500 (Life®). We operate the former in partnership with BGI America.

Based on the specific needs of our collaborators, we can employ a variety of library preparation and custom targeted enrichment approaches. The different platforms require the construction of platform-specific DNA libraries, which can be generated in-house or by the collaborator. Each library can be tagged with a different index, allowing a flow cell lane to have multiple libraries sequenced at the same time. The number of reads varies from tens of thousands to hundreds of millions depending on the platform, number of partitions and type of library.

Robotics, LIMS and QC: The Center's equipment includes multiple Tecan liquid handling systems and scanning instruments with integrative Laboratory Information Management System (LIMS) and automated allele-calling software allowing for genotyping throughput of hundreds of DNA samples per day. The workflow in the Center is robotic-based for DNA isolation and processing and includes automated algorithms for quality control (QC) of the genotypes produced. The workflow is entirely automated with respect to allele-calling, data-processing and genotype QC measures; however, the genotyping workflow within CAG has multiple checkpoints to ensure high-quality data is produced.

Inquiries

Contact Information: To learn more about what CAG has to offer researchers, please contact This email address is being protected from spambots. You need JavaScript enabled to view it. . Please provide the email address and phone number of your Lab's contact person. In addition, providing the following information will allow us to respond to your requests more efficiently:

Project Information: Please provide a brief description of the experimental design. The following information should include

  • Number of Samples
  • Type of Library Preparation
  • Multiplexing Plans
  • Number of Flow Cell Lanes
  • Number of Sequencing Cycles
  • Data Analysis Plans

Sample Names: Verify that each sample has a unique name and that the sample tubes submitted have the correct sample identification clearly written on each tube.

Sample Volumes: Accurately measure each sample volume with a pipet.

Sample Preparation Protocol: Identify sample preparation protocol used. Please provide a copy of the protocol.

Sample Concentrations (ng/uL): Measure each sample concentration using a fluorometer/pico gree-based assay. Accurate measurements are crucial for success of the labeling procedure.

260/280 Ratios: This ratio indicates the quality of the DNA. Agarose Gel Electrophoresis Image – Provide the gel image with the sample wells and ladder sizes clearly labeled. The image will be used to confirm sample quality and size.