Colorectal Cancer Panel Sequencing

Description of Colorectal Cancer

Colorectal Cancer Panel Sequencing

Colorectal cancer (CRC) is a common malignancy of the digestive tract that occurs in the colon. It usually occurs at the junction of the rectum and the sigmoid colon. Hereditary colorectal cancer is associated with specific genetic abnormalities. With the appreciation and deep understanding of the genetic basis of colorectal cancer, more genes that make people susceptible to CRC may be discovered. Hereditary colorectal cancer includes the following syndromes: hereditary nonpolyposis colon cancer (HNPCC), also known as Lynch syndrome, familial adenomatous polyposis (FAP) and attenuated familial adenomatous polyposis (AFAP), and certain other rare syndromes, such as Cowden syndrome, juvenile polyposis syndrome and Peutz-Jeghers syndrome.

Microsatellite instability (MSI) is an important reason for the occurrence of HNPCC and partial sporadic colorectal cancer. MSI is caused by defecting of the mismatch repair (MMR) genes. MMR genes (mainly MLH1, MSH2, PMS2, and MSH6) may lose function due to mutation, deletion or apparent silencing, thus cannot repair mismatches that occur during DNA replication, resulting in an MSI phenotype. FAP mediates an autosomal dominant inherited disease that usually has mutations of the same gene, and practically all mutations result in C-terminally truncated proteins. The pathogenic variants in the adenomatous polyposis coli (APC) gene, mapped on the long arm of chromosome 5, are responsible for FAP by causing intestinal wall dynamics disorder. When other epithelial cells proliferate abnormally, the APC gene will stabilize the total number of cells, so that would not lead to a sustainable growth perturbation. When the APC gene mutates, the balance between cell division and cell death will be broken permanently, leading to tumor formation. MUTYH protein is involved in the base excision repair (BER) pathway. The MUTYH double allele mutations with different types (nonsense, missense, frameshift and cleavage site mutations, or truncated proteins) are confirmed associated with the occurrence of colorectal cancer.

To support clinical researches, CD-Genomics offers a colorectal cancer panel library related to the genes with increased risk for hereditary colorectal cancer. If necessary, you can choose genes that fit your requirements.


Gene List of Colorectal Cancer Panel Sequencing

APC AXIN2 BLM BMPR1A CDH1 CHEK2 EPCAM FAN1 GALNT12 GREM1
MLH1 MLH3 MSH6 MUTYH NTHL1 PMS2 POLD1 POLE PTEN SMAD4
STK11 TP53                

Highlights of Colorectal Cancer Panel Sequencing Service

  • Target-enrichment sequencing by Illumina provides extremely high depth (average depth > 1000x) with lower costs.
  • High coverage uniformity ensures the sequencing data more efficiency.
  • SNVs, indels, and even low frequency variations can be detected.
  • Strict quality control throughout the pipeline workflow to ensure the accuracy and repeatability of the sequencing.
  • Fast turnaround time.

Applications of Colorectal Cancer Panel Sequencing

  • Cancer related mechanism studies
  • Biomarker discovery
  • Therapeutic target discovery
  • Drug target discovery
  • Discover rare mutations and detect low frequency mutations

Service Specifications

Service Specifications

Sample Requirements

  • Sample types for genome DNA from tissues, whole blood, cultured cells, and formalin-fixed paraffin-embedded (FFPE) tissues.
  • Recommended amount: 2μg
  • Minimum amount: 200ng
  • Collection: DNA samples are stored in TE buffer or equivalent. Blood is collected by routine blood collection kits.
Service Specifications

Sequencing

  • Illumina PE150
  • Enrichment Method: Amplicon sequencing
  • More than 80% of bases with a ≥Q30 quality score
  • Recommended sequencing depth: ≥ 500x
Service Specifications

Bioinformatics Analysis

We provide customized bioinformatics analysis including:

  • Read alignment
  • Variant calling/Annotation

Gene Panel Workflow

CD Genomics provides the accurate and cost-effective colorectal cancer panel sequencing and bioinformatics analysis. Our professional expert team executes quality management, following every procedure to ensure confident and unbiased results. The general workflow for colorectal cancer panel sequencing is outlined below.

Gene Panel Workflow

Deliverables

Raw sequencing data (FASTQ). Mutation discovery and related data analysis can be delivered on request.

For more information about the colorectal cancer panel or need other amplification requirements, please contact us.

References:

  1. Kinzler K W, et al. Vogelstein B. Lessons from hereditary colorectal cancer. Cell, 1996, 87(2): 159-170.
  2. Fishel R, et al. The human mutator gene homolog MSH2 and its association with hereditary nonpolyposis colon cancer. Cell, 1993, 75(5): 1027-1038.
  3. Rustgi A K, et al. The genetics of hereditary colon cancer. Genes & development, 2007, 21(20): 2525-2538.
* For Research Use Only. Not for use in diagnostic procedures.

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