Hereditary Gastrointestinal Cancer Panel

39 gene panel that includes assessment of non-coding variants

Ideal for patients with a personal history of a gastrointestinal cancer syndrome and patients with a family history of a gastrointestinal cancer syndrome. This panel is designed to detect heritable germline mutations and should not be used for the detection of somatic mutations in tumor tissue. The genes on this panel are included in the Comprehensive Hereditary Cancer Panel.

Analysis methods Availability Number of genes Test code CPT codes
PLUS
SEQ
DEL/DUP
4 weeks 39 GHC0090 SEQ 81435
DEL/DUP 81436

Summary

Sample requirements:

  • EDTA blood, min. 1 ml
  • Purified DNA, min. 3μg
  • Saliva (Oragene DNA OG-500 kit)

Label the sample tube with your patient’s name, date of birth and the date of sample collection. Note that we do not accept DNA samples isolated from formalin-fixed paraffin-embedded (FFPE) tissue.

About

Gastrointestinal cancers refers to malignant tumors arising from the gastrointestinal tract and accessory organs of digestion including the esophagus, stomach, pancreas, small intestine, large intestine, and rectum. Hereditary diffuse gastric cancer is caused by germline mutations in CDH1. The average age of onset is 38 years and the estimated cumulative risk of gastric cancer by age of 80 years is 80% for both men and women. Women also have a 39%-52% risk for lobular breast cancer. Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors of the human gastrointestinal tract. Germline mutations in KIT have been implicated in inherited susceptibility to GISTs (PMID: 16143141). Familial GIST is characterized by autosomal dominant inheritance and high penetrance. GIST rarely occurs in association with other syndromes such as neurofibromatosis type 1 , caused by germline mutations in NF1. Carney-Stratakis syndrome is characterized by paraganglioma and gastric stromal sarcoma and is caused by germline mutations in SDHB, SDHC, and SDHD (PMID: 17667967). Germline mutations in RHBDF2 have been associated with tylosis esophageal cancer, an autosomal dominant syndrome characterized by palmoplantar keratoderma, oral precursor lesions, and a high lifetime risk of esophageal cancer (PMID: 22265016). Hereditary colorectal cancer syndromes and familial pancreatic cancer are described in the subpanels for these conditions.

Panel Content

Genes in the Hereditary Gastrointestinal Cancer Panel and their clinical significance

Gene Associated phenotypes Inheritance ClinVar HGMD
APCGardner syndrome, Desmoid disease, hereditary, Familial adenomatous polyposisAD6721907
ATMBreast cancer, Ataxia-TelangiectasiaAD/AR8601026
AXIN2Oligodontia-colorectal cancer syndrome, Oligondontia, isolatedAD1018
BLMBloom syndromeAR91107
BMPR1APolyposis, juvenile intestinalAD87135
BRCA1Pancreatic cancer, Breast-ovarian cancer, familialAD25602361
BRCA2Fanconi anemia, Medulloblastoma, Glioma susceptibility, Pancreatic cancer, Wilms tumor, Breast-ovarian cancer, familialAD/AR29592364
BUB1BMosaic variegated aneuploidy syndrome, Premature chromatid separation traitAD/AR1227
CDH1CDH1-related cancer, Blepharocheilodontic syndrome 1AD152219
CDKN2AMelanoma, familial, Melanoma-pancreatic cancer syndromeAD81230
EPCAMDiarrhea 5, with tufting enteropathy, congenital, Colorectal cancer, hereditary nonpolyposisAD/AR2675
FANCCFanconi anemiaAR7058
GREM1Hereditary mixed polyposis syndromeAD/AR16
KITGastrointestinal stromal tumor, PiebaldismAD75110
MEN1Hyperparathyroidism, familial primary, Multiple endocrine neoplasiaAD239726
MLH1Muir-Torre syndrome, Endometrial cancer, Mismatch repair cancer syndrome, Colorectal cancer, hereditary nonpolyposisAD/AR8291174
MSH2Muir-Torre syndrome, Endometrial cancer, Colorectal cancer, hereditary nonpolyposis,, Mismatch repair cancer syndromeAD/AR8741224
MSH6Endometrial cancer, Mismatch repair cancer syndrome, Colorectal cancer, hereditary nonpolyposisAD/AR580569
MUTYHFamilial adenomatous polyposis,, Colorectal adenomatous polyposis, with pilomatricomasAR118159
NF1Watson syndrome, Neurofibromatosis, Neurofibromatosis-Noonan syndromeAD8102703
NTHL1Familial adenomatous polyposis 3AR43
PALB2Fanconi anemia, Pancreatic cancer, Breast cancerAD/AR422358
PDGFRAGastrointestinal stromal tumorAD2217
PMS2Mismatch repair cancer syndrome, Colorectal cancer, hereditary nonpolyposisAD/AR259324
POLD1Colorectal cancer, Mandibular hypoplasia, deafness, progeroid features, and lipodystrophy syndromeAD329
POLEColorectal cancer, Facial dysmorphism, immunodeficiency, livedo, and short stature syndrome (FILS syndrome)AD/AR750
PTENBannayan-Riley-Ruvalcaba syndrome, Lhermitte-Duclos syndrome, Cowden syndromeAD398627
RHBDF2Tylosis with esophageal cancerAD23
SDHBParaganglioma and gastric stromal sarcoma, Pheochromocytoma, Gastrointestinal stromal tumor, Paragangliomas, Cowden-like syndromeAD138262
SDHCParaganglioma and gastric stromal sarcoma, Gastrointestinal stromal tumor, ParagangliomasAD2657
SDHDParaganglioma and gastric stromal sarcoma, Pheochromocytoma, Paragangliomas, Carcinoid tumors, intestinal, Cowden syndrome, Mitochondrial complex II deficiencyAD62164
SMAD4Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome, Polyposis, juvenile intestinal, Myhre dysplasia, Hereditary hemorrhagic telangiectasiaAD162141
SMARCB1Schwannomatosis, Rhabdoid tumor predisposition syndromeAD31116
STK11Peutz-Jeghers syndromeAD149436
TMEM127PheochromocytomaAD2541
TP53Colorectal cancer, Li-Fraumeni syndrome, Ependymoma, intracranial, Choroid plexus papilloma, Breast cancer, familial, Adrenocortical carcinoma, Osteogenic sarcoma, Hepatoblastoma, Non-Hodgkin lymphomaAD372481
TSC1Lymphangioleiomyomatosis, Tuberous sclerosisAD138346
TSC2Lymphangioleiomyomatosis, Tuberous sclerosisAD3221137
VHLErythrocytosis, familial, PheochromocytomaAD/AR188595

Non-coding variants covered by the panel

Gene Genomic location HG19 HGVS RefSeq RS-number
APCChr5:112043289c.-125delANM_001127511.2
APCChr5:112043225c.-190G>ANM_001127511.2
APCChr5:112043224c.-191T>CNM_001127511.2
APCChr5:112043223c.-192A>G/TNM_001127511.2
APCChr5:112043220c.-195A>CNM_001127511.2
APCChr5:112043009–112043595
APCChr5:112072710–112073585
APCChr5:112158419c.1408+731C>TNM_000038.5
APCChr5:112158423c.1408+735A>TNM_000038.5
APCChr5:112111315c.423-11A>GNM_000038.5
APCChr5:112111314c.423-12A>GNM_000038.5
APCChr5:112115546c.532-941G>ANM_000038.5rs730881227
APCChr5:112151175c.835-17A>GNM_000038.5
ATMChr11:108093770c.-174A>GNM_000051.3
ATMChr11:108098321c.-30-1G>TNM_000051.3rs869312754
ATMChr11:108094508c.-31+595G>ANM_000051.3
ATMChr11:108121024c.1236-404C>TNM_000051.3
ATMChr11:108138753c.2639-384A>GNM_000051.3
ATMChr11:108141209c.2839-579_2839-576delAAGTNM_000051.3
ATMChr11:108151710c.3403-12T>ANM_000051.3rs201370733
ATMChr11:108158168c.3994-159A>GNM_000051.3rs864622543
ATMChr11:108179837c.5763-1050A>GNM_000051.3rs774925473
BRCA1Chr17:41197588c.*103_*106delTGTCNM_007294.3rs431825382
BRCA1Chr17:41196424c.*1271T>CNM_007294.3
BRCA1Chr17:41197637c.*58C>TNM_007294.3rs137892861
BRCA1Chr17:41196977c.*718A>GNM_007294.3
BRCA1Chr17:41196895c.*800T>CNM_007294.3
BRCA1Chr17:41276134c.-19-2A>GNM_007294.3
BRCA1Chr17:41256984c.213-11T>GNM_007294.3rs80358061
BRCA1Chr17:41256985c.213-12A>GNM_007294.3rs80358163
BRCA1Chr17:41256988c.213-15A>GNM_007294.3
BRCA1Chr17:41209164c.5194-12G>ANM_007294.3rs80358079
BRCA1Chr17:41206122c.5277+2916_5277+2946delAAATTCTAGTGCTTTGGATTTTTTCCTCCATinsGGNM_007294.3
BRCA1Chr17:41199745c.5407-25T>ANM_007294.3rs758780152
BRCA1Chr17:41197859c.5468-40T>ANM_007294.3rs80358151
BRCA2Chr13:32889805c.-40+1G>ANM_000059.3
BRCA2Chr13:32953872c.8954-15T>GNM_000059.3
BRCA2Chr13:32971007c.9502-28A>GNM_000059.3rs397508059
BUB1BChr15:40409289c.-44133G>ANM_001211.5rs576524605
BUB1BChr15:40504689c.2386-11A>GNM_001211.5rs751421137
CDH1Chr16:68842843c.687+92T>ANM_004360.3
CDKN2AChr9:21974860c.-34G>TNM_000077.4rs1800586
CDKN2AChr9:21973573c.150+1104C>ANM_000077.4rs756102261
CDKN2AChr9:21972311c.151-1104C>GNM_000077.4
CDKN2AChr9:21968346c.458-105A>GNM_000077.4
EPCAMChr2:47606078c.556-14A>GNM_002354.2rs376155665
FANCCChr9:98011653c.-78-2A>GNM_000136.2rs587779898
MEN1Chr11:64577626c.-23-22C>ANM_000244.3
MLH1Chr3:37035012c.-27C>ANM_000249.3rs587779001
MLH1Chr3:37034997c.-42C>TNM_000249.3rs41285097
MLH1Chr3:37038099c.117-11T>ANM_000249.3rs267607711
MLH1Chr3:37070436c.1558+13T>ANM_000249.3rs267607834
MLH1Chr3:37050292c.454-13A>GNM_000249.3rs267607749
MLH1Chr3:37053487c.589-9_589-6delGTTTNM_000249.3rs752286654,rs587779026
MLH1Chr3:37061788c.885-9_887dupTCCTGACAGTTTNM_000249.3rs63751620
MSH2Chr2:47630150c.-181G>ANM_000251.2rs786201698
MSH2Chr2:47630106c.-225G>CNM_000251.2rs138068023
MSH2Chr2:47630251c.-78_-77delTGNM_000251.2rs587779182
MSH2Chr2:47635062c.212-478T>GNM_000251.2rs587779138
MSH6Chr2:48034014c.*15A>CNM_000179.2
MUTYHChr1:45797534c.998-13T>GNM_001128425.1
NF1Chr17:29422056c.-272G>ANM_001042492.2
NF1Chr17:29422055c.-273A>CNM_001042492.2
NF1Chr17:29530107c.1260+1604A>GNM_001042492.2
NF1Chr17:29533239c.1261-19G>ANM_001042492.2
NF1Chr17:29534143c.1392+754T>GNM_001042492.2
NF1Chr17:29488136c.288+2025T>GNM_001042492.2
NF1Chr17:29577934c.4110+1802delANM_001042492.2rs863224944
NF1Chr17:29577082c.4110+945A>GNM_001042492.2
NF1Chr17:29580296c.4173+278A>GNM_001042492.2
NF1Chr17:29654479c.5269-38A>GNM_001042492.2
NF1Chr17:29656858c.5610-456G>TNM_001042492.2
NF1Chr17:29657848c.5812+332A>GNM_001042492.2rs863224491
NF1Chr17:29508428c.587-12T>ANM_001042492.2
NF1Chr17:29508426c.587-14T>ANM_001042492.2
NF1Chr17:29664375c.6428-11T>GNM_001042492.2
NF1Chr17:29664618c.6642+18A>GNM_001042492.2
NF1Chr17:29676126c.7190-12T>ANM_001042492.2
NF1Chr17:29685481c.7971-17C>GNM_001042492.2
NF1Chr17:29685177c.7971-321C>GNM_001042492.2
NF1Chr17:29685665c.8113+25A>TNM_001042492.2
NF1Chr17:29510334c.888+651T>ANM_001042492.2
NF1Chr17:29510427c.888+744A>GNM_001042492.2
NF1Chr17:29510472c.888+789A>GNM_001042492.2
PALB2Chr16:23649285c.109-12T>ANM_024675.3rs774949203
PDGFRAChr4:55161473c.*34G>ANM_006206.4rs552950826
PTENChr10:89623226c.-1001T>CNM_000314.4
PTENChr10:89623116c.-1111A>GNM_000314.6
PTENChr10:89623056c.-1171C>TNM_000314.6rs587779981
PTENChr10:89623049c.-1178C>TNM_000314.6
PTENChr10:89622988c.-1239A>GNM_000314.6
PTENChr10:89623462c.-765G>ANM_000314.4
PTENChr10:89623373c.-854C>GNM_000314.4
PTENChr10:89623365c.-862G>TNM_000314.4rs587776675
PTENChr10:89622883–89623482
PTENChr10:89623331c.-896T>CNM_000314.4
PTENChr10:89623306c.-921G>TNM_000314.4
PTENChr10:89623296c.-931G>ANM_000314.4rs587781959
PTENChr10:89692749c.254-21G>CNM_000314.4
SMARCB1Chr22:24176437c.*70C>TNM_003073.3
SMARCB1Chr22:24176449c.*82C>TNM_003073.3
SMARCB1Chr22:24176316c.1119-12C>GNM_003073.3
TMEM127Chr2:96931137c.-18C>TNM_017849.3rs121908813
TP53Chr17:7590694c.-29+1G>TNM_000546.5
TSC2Chr16:2098067c.-30+1G>CNM_000548.3rs587778004
TSC2Chr16:2127477c.2838-122G>ANM_000548.3
TSC2Chr16:2138031c.5069-18A>GNM_000548.3rs45484794
TSC2Chr16:2110656c.976-15G>ANM_000548.3rs45517150
VHLChr3:10183453c.-75_-55delCGCACGCAGCTCCGCCCCGCGNM_000551.3rs727503744

Panel Update

Genes added

  • NTHL1
  • PDGFRA

Genes removed

  • HNF1A

Test strength and Limitations

The strengths of this test include:

  • CAP and ISO-15189 accreditations covering all operations at GHC Genetics including all Whole Exome Sequencing, NGS panels and confirmatory testing
  • CLIA-certified personnel performing clinical testing in a CLIA-certified laboratory
  • Powerful sequencing technologies, advanced target enrichment methods and precision bioinformatics pipelines ensure superior analytical performance
  • Careful construction of clinically effective and scientifically justified gene panels
  • Our Nucleus online portal providing transparent and easy access to quality and performance data at the patient level
  • Our publically available analytic validation demonstrating complete details of test performance
  • ~1,500 non-coding disease causing variants in GHC WES assay (please see below ‘Non-coding disease causing variants covered by this panel’)
  • Our rigorous variant classification based on modified ACMG variant classification scheme
  • Our systematic clinical interpretation workflow using proprietary software enabling accurate and traceable processing of NGS data
  • Our comprehensive clinical statements

Test limitations The following exons are not included in the panel as they are not sufficiently covered with high quality sequence reads: *PPA2* (11, 12). Genes with partial, or whole gene, segmental duplications in the human genome are marked with an asterisk if they overlap with the UCSC pseudogene regions. The technology may have limited sensitivity to detect variants in genes marked with these symbols (please see the Panel content table above).

This test does not detect the following:
  • Complex inversions
  • Gene conversions
  • Balanced translocations
  • Mitochondrial DNA variants
  • Repeat expansion disorders unless specifically mentioned
  • Non-coding variants deeper than ±20 base pairs from exon-intron boundary unless otherwise indicated (please see above Panel Content / non-coding variants covered by the panel).

This test may not reliably detect the following:
  • Low level mosaicism
  • Stretches of mononucleotide repeats
  • Indels larger than 50bp
  • Single exon deletions or duplications
  • Variants within pseudogene regions/duplicated segments

The sensitivity of this test may be reduced if DNA is extracted by a laboratory other than GHC Genetics.

For additional information, please refer to the Test performance section and see our Analytic Validation.

Test Performance

The GHC Genetics panel covers classical genes associated with Brugada syndrome, catecholaminergic polymorphic ventricular tachycardia (CPVT), cardiac arrest underlying cardiac condition, cardiac arrest cause unspecified, syncope and collapse, abnormal ECG, Long QT syndrome, arrhythmogenic right ventricular cardiomyopathy (ARVC) and Short QT syndrome. The genes on the panel have been carefully selected based on scientific literature, mutation databases and our experience.

Our panels are sliced from our high-quality whole exome sequencing data. Please see our sequencing and detection performance table for different types of alterations at the whole exome level (Table).

Assays have been validated for different starting materials including EDTA-blood, isolated DNA (no FFPE), saliva and dry blood spots (filter card) and all provide high-quality results. The diagnostic yield varies substantially depending on the assay used, referring healthcare professional, hospital and country. GHC Genetics’ Plus Analysis (Seq+Del/Dup) maximizes the chance to find a molecular genetic diagnosis for your patient although Sequence Analysis or Del/Dup Analysis may be a cost-effective first line test if your patient’s phenotype is suggestive of a specific mutation type.

Performance of GHC Genetics Whole Exome Sequencing (WES) assay.
All individual panels are sliced from WES data.

Sensitivity % (TP/(TP+FN) Specificity %
Single nucleotide variants 99.65% (412,456/413,893) >99.99%
Insertions, deletions and indels by sequence analysis
1-10 bps 96.94% (17,070/17,608) >99.99%
11-50 bps 99.07% (957/966) >99.99%
Copy number variants (exon level dels/dups)
Clinical samples (small CNVs, n=52)
1 exon level deletion 92.3% (24/26) NA
2 exons level deletion/duplication 100.0% (11/11) NA
3-7 exons level deletion/duplication 93.3% (14/15) NA
Microdeletion/-duplication sdrs (large CNVs, n=37))
Size range (0.1-47 Mb) 100% (37/37)
Simulated CNV detection
2 exons level deletion/duplication 90.98% (7,357/8,086) 99.96%
5 exons level deletion/duplication 98.63% (7,975/8,086) 99.98%
The performance presented above reached by WES with the following coverage metrics
Mean sequencing depth at exome level 174x
Nucleotides with >20x sequencing coverage (%) 99.4%

Our mission is to improve the quality of the sequencing process and each modification is followed by our standardized validation process. Detection of Del/Dup of several genes is by MLPA analysis (MS Holland). All genes are performed by CNV analysis through the genome depending on exon size, sequencing coverage and sequence content. We have validated the assays for different starting materials including isolated DNA from EDTA blood that provide high-quality results.

Bioinformatics & clinical interpretation

The sequencing data generated in our laboratory is analysed by our bioinformatic pipeline, integrating state-of-the art algorithms and industry-standard software solutions. We use also JSI medical systems software for sequencing data analysis. JSI medical systems is a certified system offering sophisticated bioinformatic software solutions covering a wide field of sequencing techniques.

Incorporation of rigorous quality control steps throughout the workflow of the pipeline ensures the consistency, validity and accuracy of results.

Every pathogenic or probably pathogenic variant is confirmed by the Sanger sequencing method. Sanger sequencing is also used occasionally with other variants reported in the statement. In the case of variant of uncertain significance (VUS) we do not recommend risk stratification based on the genetic finding. The analysis of detected variants was performed on the basis of the reference database of polymorphisms and international mutation databases: UMD, LOVD and ClinVar.

The consequence of variants in coding and splice regions are estimated using Alamut software. The Alamut database contains more than 28000 coding genes, non-protein coding genes and pseudogenes. This database (shared with the high throughput annotation engine for NGS data, Alamut Batch) is frequently updated. Information comes from different public databases such as NCBI, EBI, and UCSC, as well as other sources including gnomAD, ESP, Cosmic, ClinVar, or HGMD and CentoMD (for those a separate subscription from Qiagen/Biobase and Centogene respectively is required). Alamut Visual finds information about nucleotide conservation data through many vertebrates’ species, with the phastCons and phyloP scores, amino acid conservation data through orthologue alignments and information on protein domains.

Moreover, we integrate several missense variant pathogenicity prediction tools and algorithms such as SIFT, PolyPhen, AlignGVGD or MutationTaster. It also offers a window dedicated to the in silico study of variants’ effect on RNA splicing, allowing the assessment of their potential impact on splice junctions and visualization of cryptic or de novo splice sites. Impact on splicing regulation is also assessed.


Clinical interpretation

At GHC Genetics our geneticists and clinicians, who together evaluate the results from the sequence analysis pipeline in the context of phenotype information provided in the requisition form, prepare the clinical report. We recommend an interpretation of the findings of this molecular genetic analysis, including subsequent oncological consultation for the patient in the context of genetic counselling for the patient.

We strive to continuously monitor current genetic literature identifying new relevant information and findings and adapting them to our diagnostics. This enables relevant novel discoveries to be rapidly translated and adopted into our ongoing diagnostics development without delay. The undertaking of such comprehensive due diligence ensures that our diagnostic panels and clinical statements are the most up-to-date on the market.

Variant classification is the corner stone of clinical interpretation and resulting patient management decisions. Minor modifications were made to increase reproducibility of the variant classification and improve the clinical validity of the report. Our experience with tens of thousands of clinical cases analysed at our laboratories enables us to further develop the industry standard.

The final step in the analysis of sequence variants is confirmation of variants classified as pathogenic or likely pathogenic using bi-directional Sanger sequencing. Variant(s) fulfilling all of the following criteria are not Sanger confirmed: 1) the variant quality score is above the internal threshold for a true positive call, 2) an unambiguous IGV in-line with the variant call and 3) previous Sanger confirmation of the same variant three times at GHC Genetics. Reported variants of uncertain significance (VUS) are confirmed with bi-directional Sanger sequencing only if the quality score is below our internally defined quality score for true positive call. Reported copy number variations with a size >10 exons are confirmed by orthogonal methods such as qPCR if the specific CNV has been seen less than three times at GHC Genetics.

Our clinical statement includes tables for sequencing and copy number variants that include basic variant information (genomic coordinates, HGVS nomenclature, zygosity, allele frequencies, in silico predictions, OMIM phenotypes and classification of the variant). In addition, the statement includes detailed descriptions of the variant, gene and phenotype(s) including the role of the specific gene in human disease, the mutation profile, information about the gene’s variation in population cohorts and detailed information about related phenotypes. We also provide links to the references used, and mutation databases to help our customers further evaluate the reported findings if desired. The conclusion summarizes all of the existing information and provides our rationale for the classification of the variant.

Identification of pathogenic or likely pathogenic variants in dominant disorders or their combinations in different alleles in recessive disorders are considered molecular confirmation of the clinical diagnosis. In these cases, family member testing can be used for risk stratification within the family. In the case of variants of uncertain significance (VUS), we do not recommend family member risk stratification based on the VUS result. Furthermore, in the case of VUS, we do not recommend the use of genetic information in patient management or genetic counselling.

Our Clinical interpretation team analyses millions of variants from thousands of individuals with rare diseases. Thus, our database, and our understanding of variants and related phenotypes, is growing by leaps and bounds. Our laboratories are therefore well positioned to re-classify previously reported variants as new information becomes available. If a variant previously reported by GHC Genetics is re-classified, our laboratories will issue a follow-up statement to the original ordering health care provider at no additional cost.