Center for Applied Genomics - Core Services

Overview of Services

CAG Biorepository Core:

Established in 2006, the CAG Biorepository is one of the world’s largest and most diverse pediatric biobanks, hosting more than 600,000 biological samples that have been genotyped or sequenced in CAG’s CLIA and CAP-accredited high-throughput centers.

This core provides services in:

-DNA and RNA extraction from blood, tissue, cells, FFPE, saliva, and bloodspots by manually and automatically using BioMek FX and MaxWell

- DNA and RNA QC by NanoDrop, E-Gel, Qubit, and Tape Station

-Aliquot blood, cells in barcoded matrix tubes and properly store them to Ramp

- Isolation of Human PBMC

James Snyder | CAG Biorepository Laboratory Manager
snyder3@chop.edu

CAG Sequencing Core:

Established in 2012, the CAG Sequencing Laboratory is fully equipped with state-of-art technology and experienced staff members. Sequencing operations are integrated with our Biorepository and Bioinformatics teams to keep all stages of a collaborator’s studies connected. The CAG sequencing lab offers cutting edge technologies in the Genomics field:

-High Throughput sequencing on the Illumina Novaseq 6000

-Perkin Elmer Sciclone Automated liquid handlers

-mRNA, Total RNAseq, miRNA seq with Illumina Stranded and low input kits

-Whole Exome and Whole Genome Sequencing with Twist Biosciences also with PCR-Free options

-Single Cell services utilizing 10xGenomics and Scale Biosciences high-throughput fixation process

-Fluidigm confirmation

Jonathan Billings
billingsj@chop.edu 

CAG Genotyping Core:

Established in 2006, the CAG Genotyping Laboratory is fully equipped with state-of-art technology and experienced staff members. Our lab is integrated with our Biorepository and Bioinformatics group, keeping all stages of collaborator’s studies connected.

CAG high-throughput Genotyping Core:

The core established in 2006, it is a large and high-throughput genotyping core all research and clinical using illumina platform. The services include:

- Genome-Wide Genotyping

- High-Throughput Genotyping

- Targeted Genotyping

- SNP and SNV Genotyping

- Copy Number Variation Analysis

- Custom Genotyping

Maria Lemma | CAG Genotyping Laboratory Manager
garrism@chop.edu

CAG Validation Core:

The CAG Validation core provides high-quality services and technical support for

-High Throughput Delta Gene and TaqMan Gene Expression, TaqMan SNP Genotyping, and Digital PCR by BioMark HD and Juno system

-Single SNP Genotyping and qPCR by TaqMan ViiA 7

-Sanger Sequencing, Fragment Analysis, MLPA, and FragileX by 3500 Genetic Analyzer

-Long Range PCR and CNV

-Full PCR Sanger Service including Primer Design, Primer Test, PCR, Size Check, PCR products Clean-Up and Sanger Sequencing

Cuiping Hou / Research Scientist II

houc@chop.edu

CLIA Tests:

CAG has been CLIA certified since 2016 for the assays listed below. Each clinical test comes with a patient report that is signed by our board certified molecular geneticist and physician.

Sanger Sequencing with primer design using AllTaq PCR Mastermix, BigDye Xterminator v3.1, and 3500 capillary electrophoresis instrument. Analysis performed with Mutation Surveyor software.

Fragment analysis for UGT1A1 TA repeat 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 Promega kit and the Maxwell instrument.

Next generation sequencing: whole exome and whole genome sequencing and analysis and interpretation using TWIST library, NovaSeq6000, and a custom bioinformatics pipeline.

Maria Lemma | CAG Genotyping Laboratory Manager

garrism@chop.edu

Leadership

Hakon Hakonarson, MD, PhD | Director, Center for Applied Genomics 

Maria Lemma | CAG Laboratory Manager
garrism@chop.edu

Location and hours of operation

Links and Resources

Genotyping Core:

1. DNA Submission Guidelines

Biorepository Core:

1. Sample Submission and Shipping Instructions

Next Generation Sequencing Core:

1. RNAseq Sample Submission Guidelines

Contacts