Colorectal cancer (CRC) is one of the most commonly diagnosed malignancies. CRC can be characterized as sporadic cancer or inherited cancer such as Lynch syndrome, familial adenomatous polyposis (FAP) and Mut-Y homolog-associated polyposis (MAP). American Molecular Laboratories has developed a suite of assays that include Next Generation Sequencing, DNA fragment analysis and Immunohistochemistry markers to address sporadic and inherited forms of cancer.

KRAS, NRAS, BRAF, PIK3CA Somatic Mutation Analysis (AmColon™ KRAS, NRAS, BRAF, PIK3CA) NGS Cancer Focus Panel)

This test is indicated for individuals with metastatic colorectal cancer to guide treatment with anti-Epidermal Growth Factor Receptor (EGFR) monoclonal antibodies such as Cetuximab and Panitumumab. Mutations in KRAS, NRAS, BRAF and possibly PIK3CA are associated with resistance to anti-EGFR therapy with Cetuximab and Panitumumab.

The AmColonTM panel tests for somatic mutations in the coding regions of KRAS, NRAS, BRAF, and PIK3CA genes using Next Generation Sequencing technology. The panel covers complete coding regions of KRAS and NRAS genes and 95% of coding regions in BRAF, PIK3CA genes that include BRAF Exon 15 (Codon 600) and PIK3CA Exon 20 (Codon 1047).

AmColon™ Test specifications:

Regions Analyzed Complete coding regions of KRAS, NRAS; >95% of BRAF, PIK3CA genes
Sequencing method PCR Amplification followed Illumina Next Generation Sequencing; 113 amplicons in 7.2 kb region
Sequencing depth >500X
Assay Sensitivity and Specificity >99%
Sample requirement FFPE tumor tissues; 40 ng of DNA
Sample type FFPE tumor tissues
Turn-around time 1 week
Variant frequency >5%

Microsatellite Instability Analysis

Microsatellite Instability (MSI) occurs as a result of germline or somatic inactivation of mismatch repair genes (MSH2, MSH6, MLH1, and PMS2). Loss or downregulation of the expression of the protein products of these genes results in the failure of DNA mismatch repair system.

MSI analysis is a tumor screening test for all newly diagnosed colorectal cancer patients to identify those who may have an inherited form of colorectal cancer (Hereditary Nonpolyposis Colon Cancer, also known ascalled Lynch Syndrome). Family members at risk for the inherited familial mutation can be tested to determine whether they are at risk for developing colorectal cancer due to Lynch Syndrome.

This test is performed by PCR amplification followed by capillary gel electrophoresis using five markers (NR-21, BAT-26, BAT-25, NR-24, and MONO-27) for both normal and tumor tissues.

This test can be performed in conjunction with our immunohistochemistry for MSH2, MSH6, MLH1 and PMS2 proteins.

Microsatellite Instability Test Specifications

Test markers NR-21, BAT-26, BAT-25, NR-24, and MONO-27
Test method PCR and capillary gel electrophoresis
Test sensitivity and specificity >99%
Specimen requirement For matched normal: 1 ml peripheral blood
For tumor tissue: FFPE block or slides.
Turn-around time 1 week

Immunohistochemistry for Gene Expression

Immunohistochemistry (IHC) testing is a complementary testing strategy to Microsatellite Instability (MSI) testing, to identify the gene responsible for the defective DNA mismatch repair within the tumor, since the majority of MSI-H tumors indicate a loss of expression of at least 1 of the 4 MMR genes.

The test will detect the presence or absence of the proteins encoded by mismatch repair (MMR) genes (MLH1, MSH2, MSH6, and PMS2) which are associated with HNPCC/Lynch Syndrome. The antibodies for MLH1, MSH2, MSH6, and PMS2 will identify the tumors that arise in individuals with germline pathogenic variants that inactivate or cause loss of protein expression.

Immunohistochemistry Test Specifications

Test markers MLH1, MSH2, MSH6, and PMS2
Test method Immunohistochemical staining
Test sensitivity and specificity >90%
Specimen requirement For normal tissue: FFPE block or slides.
For tumor tissue: FFPE block or slides.
Turn-around time 3 days


Figure Legend. Lynch syndrome; Immunohistochemical screening for DNA mismatch repair (MMR) proteins in colon cancer. The colon cancer IHC reveals PMS2 positive staining (left panel) and negative MSH2 staining (right panel).

Germline Mutation Analysis for Hereditary Cancer Risk

Patients with hereditary cancer risk have a high risk of developing cancer and require specialized management. The American Molecular Laboratories germline panel analyzes 20 genes, variants in which cause a significantly elevated risk of hereditary colorectal cancer. 

These genes were selected based on published best practice guidelines for evaluation of hereditary colorectal cancer (CRC) risk. The genes included in this panel are medically actionable and have published, evidence-based management and risk-reduction options. 

This test will help guide cancer screening and risk-reduction measures for colorectal cancer prevention. It can also lead to earlier diagnosis, increasing the chances of successful treatment and survival.

List of Genes


Germline Mutation Test Specifications

Regions Analyzed Coding regions of 20 genes
Sequencing method Hybridization-capture followed by Illumina Next Generation Sequencing
Sequencing depth >500X
Assay Sensitivity and Specificity >99%
Sample requirement 200 ng of DNA from blood or saliva
Sample type Blood or saliva samples
Turn-around time 2 weeks