Center for Applied Genomics - Core Services

Overview of Services

CAG Biorepository Core

Established in 2006, the CAG Biorepository is one of the largest and most diverse pediatric biobanks in the world. With over 600,000 biological samples, all of which have been genotyped or sequenced at CAG, we offer cutting-edge services for genomic research.

The CAG Biorepository provides logistics, infrastructure and expertise for the collection, production, and storage of high quality human biospecimen and associated data.

The repository boasts two automated systems for sample storage at -20 degrees and -80 degrees, with a collective capacity of over 3 million samples. The CAG Biorepository also supports services for those seeking genotyping and sequencing services, and many other service solutions tailored to suit the needs of your research. 

PBMC isolation, blood/plasma/serum banking, high throughput DNA and RNA extraction, quantification and distribution services are available. 

The CAG Biorepository specializes in difficult or stubborn sample types and can offer solutions for project management and ongoing collection efforts.  The CAG Biorepository uses a customized LIMS system and uses 1 and 2D Barcode technology for sample accuracy, and complete chain of custody records.

Services Offered:

• DNA and RNA Extraction from EDTA Collected Blood, Various tissue types, cells, FFPE, Saliva, Buccal Swabs Blood Spots and Buffy Coat.
• DNA and RNA Quality Control Quantification of DNA/RNA via Nanodrop, E-Gel, Qubit, Pico green and Tape Station technologies.
• Biobanking PBMC isolation and cryopreservation, blood/plasma/serum banking, high throughput DNA and RNA extraction services are available.  Some services require a minimum throughput.  Please inquire for details tailored to your specific project needs.

Contact:

James Snyder
CAG Biorepository Laboratory Manager
snyder3@chop.edu

CAG Sequencing Core

Established in 2012, the CAG Sequencing Laboratory is equipped with state-of-the-art technology and staffed by experts in genomics. Our sequencing operations are fully integrated with the Biorepository and Bioinformatics teams to ensure seamless support throughout all stages of research studies.

Services Offered:

• High-Throughput Sequencing on the Illumina NovaSeq 6000 platform.
• Automated Liquid Handling with Perkin Elmer Sciclone systems.
• mRNA, Total RNAseq, and miRNA Sequencing using Illumina Stranded and low-input kits.
• Whole Exome and Whole Genome Sequencing with Twist Biosciences, including PCR-free options.
• Single-Cell Sequencing using 10x Genomics and Scale Biosciences high-throughput fixation methods.

Contact:

Jonathan Billings
CAG NGS Laboratory Manager
Billingsj@chop.edu

CAG Genotyping Core

Established in 2006, the CAG Genotyping Laboratory is equipped with state-of-the-art technology and staffed by experienced professionals. Our lab works closely with the Biorepository and Bioinformatics teams to ensure seamless integration throughout all stages of research and clinical studies.

Services Offered:

• Genome-Wide Genotyping for broad genetic analysis.
• High-Throughput Genotyping utilizing the Illumina platform for large-scale projects.
• Targeted Genotyping for specific genetic regions.
• SNP and SNV Genotyping to identify genetic variations.
• Copy Number Variation (CNV) Analysis for detecting structural variations.
• Custom Genotyping Services tailored to meet specific research needs.

Contact:

Maria Lemma
CAG Genotyping Laboratory Manager
garrism@chop.edu 

CAG Validation Core

The CAG Validation Core offers high-quality services and expert technical support for a variety of genomic analyses.

Services Offered:

• High-Throughput Gene Expression and SNP Genotyping using Fluidigm's BioMark HD and Juno systems (Standard BioTools).
• Single SNP Genotyping and qPCR on the TaqMan ViiA 7 system.
• Sanger Sequencing, Fragment Analysis, and MLPA with the 3500 Genetic Analyzer.
• Full PCR Sanger Service, including Primer Design, Primer Testing, PCR Amplification, Size Check, PCR Product Clean-Up, and Sanger Sequencing.

Contact:

Maria Lemma
CAG Genotyping Laboratory Manager
garrism@chop.edu

CLIA Tests

CAG has been CLIA-certified since 2016 for the following assays. Each clinical test includes a patient report signed by our board-certified molecular geneticist and physician.

Assays Offered:

• Sanger Sequencing with primer design using AllTaq PCR Mastermix, BigDye Xterminator v3.1, and the 3500 capillary electrophoresis instrument. Analysis performed with Mutation Surveyor software.
• Fragment Analysis for UGT1A1 TA repeat using AllTaq PCR Mastermix, BigDye Xterminator v3.1, and 3500 capillary electrophoresis instrument. Analysis performed with GeneMarker software.
• Genotyping Arrays: GDAcyto, GSAv3.
• DNA Extraction from whole blood and saliva using the Promega kit and Maxwell instrument.
• Next-Generation Sequencing: Whole exome and whole genome sequencing with analysis and interpretation using the TWIST library, NovaSeq 6000, and a custom bioinformatics pipeline.

Contact:

Margaret H. Harr
Program Manager & Genetic Counseling
Email: harrm@chop.edu

CAG Analysis Core

The CAG team is highly equipped with expertise to conduct a broad range of genomic analyses. Our CAG Analysis Core provides comprehensive services, including:

Services Offered:

• Genome-Wide Association Studies (GWAS)
• Plink
• Copy Number Variation (CNV) Analysis
• PennCNV
• Lumpy, Delly, CNVnator, GATK-gCNV, Manta, cn.mops
• SURVIVOR
• Next-Generation Sequencing (NGS) Data Analysis
  (including result generation, interpretation, and analytic reports)
• Whole Genome Sequencing (WGS)
• Whole Exome Sequencing (WES)
• Bulk RNA-seq (Differential Gene Expression Analysis, DGE)
• Single-Cell RNA-seq (scRNA-seq)
• SNP/Indel Genotyping
• Functional Genomics & Pathway Analysis
• Customized analysis on a case-by-case basis
• Clinical Genomics
• Multi-Omics Integration

Contact:

Joseph Glessner
CAG Associate Director
glessner@chop.edu

Contacts