Services offered by CMDL

Sample processing

Whole blood processing for isolation of:

Plasma
Serum
Buffy coat
PBMCs
Granulocytes

Processing of other body fluids, including:

Saliva
Ascites
Urine
Bone marrow aspirate
Pleural fluid

Nucleic acid extraction

Manual and automated (QIAsymphony, Maxwell RSC 48, Biomek FXP) nucleic acid extractions, genomic DNA (gDNA), circulating cell free DNA (ccfDNA) and RNA, from:

Plasma
Serum
Bone marrow aspirate
Buffy coat
Granulocytes
Fresh frozen tissue
PBMCs
Ascites
Pleural fluid
Urine
Saliva
FFPE tissue slides/scrolls

Quantification and viability

Nucleic acid quantification: Qubit, Fluoroskan, qPCR
Nucleic acid fragment size analysis: 2100 Bioanalyzer, 4200 TapeStation
Cellular quantification and viability: LUNA FL

Validated NGS panels

We offer a spectrum of validated NGS approaches.

We are always open to trialling and adopting new approaches to accommodate a study.

Currently available panels validated for gDNA, FFPE gDNA and ccfDNA:

350 gene pan-cancer panel (Twist Bioscience Custom Capture Panel)
110 gene lymphoid malignancy panel (Twist Bioscience Custom Capture Panel)
56 gene myeloid panel for myeloid malignancies and clonal haematopoesis (Twist Bioscience Custom Capture Panel)
Shallow whole genome sequencing (sWGS)
T cell receptor (TCR) sequencing (QIAseq Immune Repertoire RNA Library Kit)
Ampliseq Cancer Hotspot Panel (commercial Illumina amplicon based panel for actionable variants in hotspot regions of oncogenes)

Library preparation is performed at CMDL and sequencing is performed by SMCL.

Bioinformatics analysis

For all our NGS workflows, we offer an in-house bioinformatics analysis which includes quality control and variant calling as standard, following Genome Analysis Toolkit's Best Practices.

Data transfer

Standard fastq files are generated from the internal bcl Illumina files using Illumina’s own bcl2fastq package with all the recommended settings. Data is then returned via a password protected https link.

Molecular assays

We currently offer assays for:

Real-time PCR approaches including methylation analysis of the MGMT gene promoter
QX200 Droplet Digital PCR system for variant detection and copy number analysis assays, among many
NanoString nCounter assays on request (mainly gene expression and CNV analysis from RNA)

Buffy coat production training video

This video explains the steps required to process whole blood samples into buffy coat and double-spun plasma samples. This process is routinely followed in the CMDL to generate blood product samples for cancer research.

This video is intended as a visual training aide alongside full procedure documentation, risk assessment, and in-person training. No liability is accepted when following this training video alone. Please always follow the appropriate safety precautions when handling sharps, blood, and blood products.

Address:
Cancer Molecular Diagnostics Laboratory, University of Cambridge, Clifford Allbutt Building, Hills Road, Cambridge, CB2 0AH.

Telephone: 01223 762074

General enquiries:
CMDL@medschl.cam.ac.uk