Hereditary Gastrointestinal Cancer Panel, Sequencing and Deletion/Duplication

Associated Disorders

Lynch Syndrome

• Caused by a single pathogenic variant in one of the mismatch repair (MMR) genes (MLH1, MSH2, MSH6, PMS2) or EPCAM exon 9 deletions
• Individuals are at an increased risk for colorectal, uterine, and other cancers
• The Lynch syndrome genes are also offered through the Lynch Syndrome Panel (3001605); for more information, see the Lynch Syndrome Panel, Sequencing and Deletion/Duplication Test Fact Sheet.

Others

• Other associated disorders on this panel include Cowden syndrome, familial adenomatous polyposis (FAP), Li-Fraumeni syndrome (LFS), Peutz-Jeghers syndrome (PJS), and others. Please see Genes Tested table for more information.

Genetics

Genes

See Genes Tested table for genes included in the panel.

Etiology

Greater than 2-4% of colorectal cancers are associated with a hereditary cause. 

Prevalence

1/279 individuals from the general population are estimated to have Lynch syndrome. 

Inheritance

• All genes tested on the Hereditary GI Cancer Panel are autosomal dominant with the exception of the following:

• Some genes are associated with autosomal recessive childhood cancer predisposition or other syndromes.
• See Genes Tested table for additional details.

Contraindications for Ordering

• Should not be ordered to detect somatic variants associated with malignancy as sensitivity for mosaic variants is low with methodology used for germline assays
• Individuals with hematologic malignancy and/or a previous allogenic bone marrow transplant should not undergo molecular genetic testing on peripheral blood specimen.
  • Testing of cultured fibroblasts is required for accurate interpretation of test results.
• When a relative has a previously identified pathogenic variant, see Familial Mutation, Targeted Sequencing (2001961).

Methodology

This test is performed using the following sequence of steps:

• Selected genomic regions, primarily coding exons and exon-intron boundaries, from the targeted genes are isolated from extracted genomic DNA using a probe-based hybrid capture enrichment workflow.
• Enriched DNA is sequenced by massively parallel sequencing (MPS; also known as next generation sequencing [NGS]) followed by paired-end read alignment and variant calling using a custom bioinformatics pipeline. The pipeline includes an algorithm for detection of large (single exon-level or larger) deletions and duplications.
• Sanger sequencing is performed as necessary to fill in regions of low coverage and in certain situations, to confirm variant calls.
• Large deletion/duplication calls made using MPS are confirmed by an orthogonal exon-level microarray when sample quality and technical conditions allow.
• Long-range PCR followed by nested Sanger sequencing is performed on the following gene and exons:
  • PMS2 (NM_000535) 11, 12, 13, 14, 15
• Bidirectional Sanger sequencing is performed on the following genes and exons:
  • MSH2 (NM_000251) 5
  • PTEN (NM_000314) 9
• Multiplex ligation-dependent probe amplification (MLPA) is performed on the following gene to call exon-level deletions and duplications:
  • PMS2 (NM_000535)

Clinical Sensitivity

Variable, dependent on phenotype/condition

Analytic Sensitivity

Limitations

• A negative result does not exclude a heritable form of cancer.
• Diagnostic errors can occur due to rare sequence variations.
• Interpretation of this test result may be impacted if this individual has had an allogeneic stem cell transplantation.
• The following will not be evaluated:
  • Variants outside the coding regions and intron-exon boundaries of the targeted genes
  • Regulatory region variants and deep intronic variants
  • Breakpoints of large deletions/duplications
  • Deletions/duplications in AXIN2 and MSH3
  • Sequence variants in EPCAM
  • The following exons are not sequenced due to technical limitations of the assay:
    • APC (NM_001354896) 12; (NM_001354898, NM_001354904) 2; (NM_001354900) 11
    • CHEK2 (NM_001005735) 3; (NM_001349956) 4
    • PDGFRA (NM_001347827) 17; (NM_001347828) 2; (NM_001347830) 1
    • SDHA (NM_004168) 14; (NM_001294332) 13; (NM_001330758) 12
    • SDHC (NM_001035511) partial exon 5 (Chr1:161332225-161332330); (NM_001278172) partial exon 4 (Chr1:161332225-161332330)
    • SDHD (NM_001276506) 4
• The following may not be detected:
  • Deletions/duplications/insertions of any size by massively parallel sequencing
  • Large duplications less than 3 exons in size
  • Noncoding transcripts
  • Single exon deletions/duplications may not be detected based on the breakpoints of the rearrangement
  • Some variants due to technical limitations in the presence of pseudogenes and/or repetitive/homologous regions
  • Low-level somatic variants
  • Deletions/duplications in the following exons:
    • APC (NM_001354896) 12; (NM_001354898, NM_001354904) 2; (NM_001354900) 11
    • BMPR1A (NM_004329) 12-13
    • CDH1 (NM_001317185) 10
    • CHEK2 (NM_007194) 11-15; (NM_001005735) 3,12-16; (NM_001257387) 12-16; (NM_001349956) 4,10-14; (NM_145862) 10-14
    • MLH3 (NM_001040108) 7-8; (NM_014381) 7
    • PDGFRA (NM_001347827) 17; (NM_001347828) 2; (NM_001347830) 1
    • PTEN (NM_000314, NM_001304718) 9; (NM_001304717) 1,10
    • SDHA (NM_004168) 1,10-15; (NM_001294332) 1,9-14; (NM_001330758) 1,10-13
    • SDHD (NM_001276506) 4

Genes Tested