Hereditary Gastrointestinal Cancer Panel, Sequencing and Deletion/Duplication

  • Recommended test to confirm a diagnosis of hereditary GI cancer in individuals with a personal or family history of GI cancer and/or polyposis.
  • When a relative has a previously identified pathogenic sequence variant, see Familial Mutation, Targeted Sequencing (2001961).
  • Testing minors for adult-onset conditions is not recommended and will not be performed on minors without prior approval; for additional information, please contact an ARUP genetic counselor (800-242-2787).
  • Recommended test if there is a known familial sequence variant previously identified in a family member.
  • A copy of the family member’s test result documenting the familial variant is required.

Pathogenic germline variants in multiple genes have been implicated in hereditary gastrointestinal (GI) cancer. Hereditary cancer predisposition is often characterized by early age of onset (typically before age 50) and multiple, multifocal, and/or related cancers in a single individual or in closely related family member(s). Pathogenic variants in the genes analyzed by this panel cause variable phenotypes and cancer risks, including non-GI cancers. See Genes Tested table below for more details regarding the genes and syndromes included on the Hereditary GI Cancer Panel. Genes included on this panel are also included on other related tests (see Related Tests section and Hereditary Cancer Genetic Testing - Germline Testing for Inherited Cancer Syndromes).

Disease Overview

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:
Gene Inheritance Pattern

SDHD

Autosomal dominant with paternal parent-of-origin effect

MLH3

Autosomal recessive

MSH3

Autosomal recessive

NTHL1

Autosomal recessive

MUTYH

Autosomal recessive but may also have autosomal dominant risks that are not well defined

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

Test Interpretation

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

Variant Class Analytic Sensitivity (PPA) Estimatea (%)
and 95% Credibility Region (%)
Analytic Specificity (NPA) Estimate (%)

SNVs

>99 (96.9-99.4)

>99.9

Deletions 1-10 bpb

93.8 (84.3-98.2)

>99.9

Insertions 1-10 bpb

94.8 (86.8-98.5)

>99.9

Exon-levelc deletions

97.8 (90.3-99.8) [2 exons or larger]

62.5 (38.3-82.6) [single exon]

>99.9

Exon-levelc duplications

83.3 (56.4-96.4) [3 exons or larger]

>99.9

Exon-level deletions/duplications (MLPA)

>99

>99

aPPA values are derived from larger methods-based MPS and/or Sanger validations. These values do not apply to testing performed by multiplex ligation-dependent probe amplification (MLPA) unless otherwise indicated.

bVariants greater than 10 bp may be detected, but the analytical sensitivity may be reduced.

cIn most cases, a single exon deletion or duplication is less than 450 bp and 3 exons span a genomic region larger than 700 bp.

bp, base pairs; NPA, negative percent agreement; PPA, positive percent agreement; SNVs, single nucleotide variants

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

Gene MIM Number Disorder/Associated Cancer(s)/Tumor(s) Inheritance

APC

611731

 

FAP

AFAP

GAPPS

Colorectal adenomas and cancer, duodenal adenomas and cancer, gastric fundic gland polyps, medulloblastoma, osteomas, pancreas, thyroid, and others

AD

AXIN2

604025

ODCRCS

Colorectal,a polyposis

AD

BMPR1A

601299

JPS

Colorectal, juvenile polyps, small intestine, stomach

AD

CDH1

192090

HDGC

Diffuse gastric, lobular breast

AD

CHEK2

604373

Breast, colorectal, prostate, thyroida

AD

EPCAM

(Exon 9 deletions/duplications only)

185535

Lynch syndrome/HNPCC

Brain, colorectal, endometrial, ovarian, pancreas, prostate, renal pelvis and/or ureter, stomach, and others

AD
KIT 164920 GIST AD

MLH1

120436

Lynch syndrome/HNPCC

Brain, colorectal, endometrial, ovarian, pancreas, prostate, renal pelvis and/or ureter, stomach, and others

AD

CMMRD

AR

MLH3 604395

MLH3-associated polyposis

Breast,a colorectal,a polyposis

AR
MSH2

609309

Lynch syndrome/HNPCC

Brain, colorectal, endometrial, ovarian, pancreas, prostate, renal pelvis and/or ureter, stomach, and others

AD

CMMRD

AR

MSH3

600887

Colorectal,a polyposis

AR

MSH6

600678

Lynch syndrome/HNPCC

Brain, colorectal, endometrial, ovarian, pancreas, prostate, renal pelvis and/or ureter, stomach, and others

AD

CMMRD

AR

MUTYH

604933

Breast,a colorectala

AD

MAP

Colorectal adenomas and cancer, duodenal adenomas and cancer

AR

NTHL1

602656

Colorectal,a polyposis

AR

PDGFRA 173490 GIST, inflammatory fibroid polyp, fibroid tumor AD

PMS2

600259

Lynch syndrome/HNPCC

Brain, colorectal, endometrial, ovarian, pancreas, prostate, renal pelvis and/or ureter, stomach, and others

AD

CMMRD

AR

POLD1

174761

PPAP

Colorectal,a polyposis

AD

POLE

174762

PPAP

Colorectal,a polyposis

AD

PTEN

601728

Cowden syndrome/PTEN hamartoma tumor syndrome

Breast, colorectal, endometrial, Lhermitte-Duclos disease (cerebellar dysplastic gangliocytoma), melanoma, renal cell carcinoma, thyroid, and others

AD

SDHA 600857

HPP syndromes

GIST, paraganglioma, pheochromocytoma, pulmonary chondroma, renal clear cell carcinoma
AD

SDHB

185470

HPP syndromes

GIST, paraganglioma, pheochromocytoma, pulmonary chondroma, renal clear cell carcinoma

AD

SDHC

602413

HPP syndromes

GIST, paraganglioma, pheochromocytoma, pulmonary chondroma, renal clear cell carcinoma

AD

SDHD

602690

HPP syndromes

GIST, paraganglioma, pheochromocytoma, pulmonary chondroma, renal clear cell carcinoma

ADb

SMAD4

600993

JPS, HHT syndrome

Colorectal, juvenile polyps, small intestine, stomach

AD

STK11

602216

PJS

Breast, cervix, colorectal, endometrial, lung, ovarian (sex cord with annular tubules), pancreas, Peutz-Jeghers-type hamartomatous polyps, small intestine, stomach, testes

AD

TP53

191170

LFS

Adrenocortical carcinoma, breast, choroid plexus carcinoma, CNS, colorectal, melanoma, osteosarcoma, pancreas, prostate, renal, rhabdomyosarcoma, soft tissue sarcoma, stomach, thyroid, and others

AD

aAssociation is suggested but not well-established at this time.

bPaternal parent-of-origin effect.

AD, autosomal dominant; AFAP, attenuated familial adenomatous polyposis; AR, autosomal recessive; CMMRD, constitutional mismatch repair deficiency; CNS, central nervous system; FAP, familial adenomatous polyposis; GAPPS, gastric adenocarcinoma and proximal polyposis of the stomach; GIST, gastrointestinal stromal tumors; HDGC, hereditary diffuse gastric cancer; HHT, hereditary hemorrhagic telangiectasia; HNPCC, hereditary nonpolyposis colorectal cancer; HPP, hereditary paraganglioma-pheochromocytoma; JPS, juvenile polyposis syndrome; LFS, Li-Fraumeni syndrome; MAP, MUTYH-associated polyposis; ODCRCS, oligodontia-colorectal cancer syndrome; PJS, Peutz-Jeghers syndrome; PPAP, polymerase proofreading-associated polyposis

References

Additional Resources