The College of American Pathologists offers these templates to assist pathologists in providing clinically useful and relevant information when reporting results of biomarker testing. The College regards the reporting elements in the templates as important elements of the biomarker test report, but the manner in which these elements are reported is at the discretion of each specific pathologist, taking into account clinician preferences, institutional policies, and individual practice.

The College developed these templates as educational tools to assist pathologists in the useful reporting of relevant information. It did not issue them for use in litigation, reimbursement, or other contexts. Nevertheless, the College recognizes that the templates might be used by hospitals, attorneys, payers, and others. The College cautions that use of the templates other than for their intended educational purpose may involve additional considerations that are beyond the scope of this document.

TEMPLATE FOR REPORTING RESULTS OF BIOMARKER TESTING OF SPECIMENS FROM PATIENTS WITH GASTROINTESTINAL STROMAL TUMORS

Completion of the template is the responsibility of the laboratory performing the biomarker testing and/or providing the interpretation. When both testing and interpretation are performed elsewhere (eg, a reference laboratory), synoptic reporting of the results by the laboratory submitting the tissue for testing is also encouraged to ensure that all information is included in the patient's medical record and thus readily available to the treating clinical team.

BIOMARKER REPORTING TEMPLATE

Gastrointestinal Stromal Tumor (GIST)

Select a single response unless otherwise indicated.

Note: Use of this template is optional.*

* Reporting on the data elements in this template is not required.

RESULTS

Immunohistochemical Studies (note A)

  • ___ KIT (CD117)

  •   ___ Positive

  •   ___ Negative

  • ___ DOG1 (ANO1)

  •   ___ Positive

  •   ___ Negative

  • ___ SDHB

  •   ___ Intact

  •   ___ Deficient

  • ___ SDHA

  •   ___ Intact

  •   ___ Deficient

  • ___ Other (specify): ____________________________

  •   ___ Positive

  •   ___ Negative

Note: Duplicate testing/reporting of KIT (CD117) and DOG is not required if previously performed.

Molecular Genetic Studies (eg, KIT, PDGFRA, BRAF, SDHA/B/C/D, or NF1 mutational analysis)

  • ___ Submitted for analysis; results pending

  • ___ Performed, see separate report:   ____________________________

  • ___ Performed

  •   Specify method(s) and results:   ____________________________

  • ___ Not performed

KIT Mutational Analysis (note B)

  • ___ No mutation detected

  • ___ Mutation identified (specify:) ____________________

  • ___ Cannot be determined (explain):   __________________________

PDGFRA Mutational Analysis (note C)

  • ___ No mutation detected

  • ___ Mutation identified (specify): ____________________

  • ___ Cannot be determined (explain):   __________________________

BRAF Mutational Analysis (note D)

  • ___ No BRAF mutation detected

  • ___ BRAF V600E (c.1799T>A) mutation

  • ___ Other BRAF mutation (specify): ____________________

  • ___ Cannot be determined (explain):   __________________________

SDHA/B/C/D Mutational Analysis (note E)

  • ___ No mutation detected

  • ___ Mutation identified (specify): ____________________

  • ___ Cannot be determined (explain):   __________________________

NF1 Mutational Analysis (note F)

  • ___ No mutation detected

  • ___ Mutation identified (specify): ____________________

  • ___ Cannot be determined (explain):   __________________________

METHODS

Dissection Method(s) (select all that apply) (note G)

  • ___ Laser capture microdissection

  • ___ Manual under microscopic observation

  • ___ Manual without microscopic observation

  • ___ Cored from block

  • ___ Whole tissue section (no tumor enrichment procedure employed)

KIT Mutational Analysis

Exons Assessed (select all that apply)

  • ___ Exon 9

  • ___ Exon 11

  • ___ Exon 13

  • ___ Exon 14

  • ___ Exon 17

  • ___ Other (specify): _________________________

Testing Method(s)

  • Specify name of method used and exons tested: __________________________

Please specify if different testing methods are used for different exons.

PDGFRA Mutational Analysis

Exons Assessed (select all that apply)

  • ___ Exon 12

  • ___ Exon 14

  • ___ Exon 18

  • ___ Other (specify): __________________________

Testing Method(s)

  • Specify name of method used and exons tested: __________________________

Please specify if different testing methods are used for different exons.

BRAF Mutational Analysis (note D)

Exons Assessed

  • ___ Exon 15

  • ___ Other (specify): _________________________

Testing Method(s)

  • Specify name of method used and exons tested: __________________________

SDH A/B/C/D Mutational Analysis (note E)

  • Exons Assessed   Specify: ___________________________

Testing Method(s)

  • Specify name of method used and exons tested: __________________________

Please specify if different testing methods are used for different exons.

NF1 Mutational Analysis (note F)

  • Exons Assessed   Specify: __________________________

Testing Method(s)

  • ___ Sanger

  • ___ Next Generation Sequencing (NGS)

  • ___ Other (specify): _______________________

  • Specify name of method used: __________________________

Please specify if different testing methods are used for different exons.

COMMENT(S)

Note: Fixative type, time to fixation (cold ischemia time), and time of fixation should be reported if applicable, in this template or in the original pathology report.

Gene names should follow recommendations of the Human Genome Organisation (HUGO) Nomenclature Committee (www.genenames.org; accessed October 29, 2014).

All reported gene sequence variations should be identified following the recommendations of the Human Genome Variation Society (www.hgvs.org; accessed October 29, 2014).

EXPLANATORY NOTES

A: Immunohistochemical Analysis.—Because of the advent of small-molecule kinase inhibitor therapy for the treatment of GIST (see the following), it has become imperative to distinguish GIST from its histologic mimics, mainly leiomyoma, leiomyosarcoma, schwannoma, and desmoid fibromatosis.1,2  Immunohistochemistry is instrumental in the workup of GIST. Approximately 95% of GISTs are immunoreactive for KIT (CD117).3  Most KIT GISTs are gastric or omental tumors that harbor mutations in platelet-derived growth factor receptor A (PDGFRA).4  KIT immunoreactivity is usually strong and diffuse but can be more limited in extent in some cases (Figure 1, A and B). It is not unusual for GISTs to exhibit dotlike perinuclear staining (Figure 1, C), whereas, less commonly, some exhibit membranous staining (Figure 1, D). These patterns do not clearly correlate with mutation type or response to therapy. DOG1 is another highly sensitive and specific marker for GIST, which was discovered by gene expression profiling.5,6  DOG1 (also known as anoctamin 1, ANO1) is particularly useful for KIT tumors and those with limited KIT expression; DOG1 is more sensitive than KIT for gastric epithelioid GISTs.7  Approximately 70% of GISTs are positive for CD34, 30% to 40% are positive for smooth muscle actin, 5% are positive for S100 (usually focal), 5% are positive for desmin (usually focal), and 1% to 2% are positive for keratin (weak/focal).8 

 Approximately 8% of gastric GISTs are characterized by dysfunction of the mitochondrial succinate dehydrogenase (SDH) complex, known as SDH-deficient GISTs.9  This clinically and pathologically distinctive subset of GISTs, which can be recognized by multinodular/plexiform architecture, has a predilection for children and young adults, is usually dominated by epithelioid cytomorphology, often metastasizes to lymph nodes (an exceeding rare occurrence in conventional GIST), and pursues a relatively indolent clinical course when metastatic.10  Approximately 50% of patients with SDH-deficient GISTs have mutations in one of the SDH subunit genes (see the following). The diagnosis of SDH-deficient GIST can be confirmed by demonstrating loss of expression of SDHB by immunohistochemistry, which is observed irrespective of the presence of an identifiable SDH mutation (or the particular mutation type). Other genetic groups of GIST (eg, those with mutations in KIT or PDGFRA) show granular cytoplasmic staining for SDHB.11  Mutations in SDHA are detected in 30% of SDH-deficient GISTs; SDHA is the most commonly mutated gene in this class of tumors (see below). Loss of expression of SDHA specifically identifies tumors with SDHA mutations12,13 ; other SDH-deficient GISTs show normal (intact) cytoplasmic staining for SDHA. Immunohistochemistry for SDHB and SDHA can, therefore, be used to triage patients for genetic testing.

 Immunohistochemistry for SDHB/SDHA need not be performed on all GISTs but only to confirm the diagnosis in a resection of a gastric GIST with multinodular architecture and to screen small biopsies of gastric GISTs with epithelioid cytomorphology (particularly in younger patients).

Molecular Analysis

 Most GISTs are driven by oncogenic mutations in one of 2 receptor tyrosine kinases, KIT (75%) and PDGFRA (10%).14,15  These mutations result in constitutive ligand-independent activation of full-length proteins. Mutations cluster within “hot spot” exons 9, 11, 13, 17 in KIT and exons 12, 14, 18 in PDGFRA (Figure 2). KIT and PDGFRA mutations are mutually exclusive. Multiple phase I, II, and international phase III trials have established the efficacy of tyrosine kinase inhibitors, such as imatinib, sunitinib, and regorafenib, in metastatic tumors and in the adjuvant setting.1620  Imatinib was originally granted accelerated approval for the treatment of advanced or metastatic GIST in 2002. In 2012, the US Food and Drug Administration approved the use of imatinib for GIST in the adjuvant setting. The most recent National Comprehensive Cancer Network task force on GIST strongly encourages that KIT and PDGFRA mutational analysis be performed if imatinib therapy is begun for unresectable or metastatic disease and that mutational analysis be considered for patients with primary disease, particularly those with high-risk tumors. In the setting of long-term imatinib therapy, secondary or acquired mutations occur in KIT exons 13, 14, and 17 and PDGFRA exon 18.21 

B: KIT Mutational Analysis.—The most common mutations affect the juxtamembrane domain encoded by exon 11 (two-thirds of GIST). These mutations include in-frame deletions, substitutions, and insertions. Deletions (in particular codon 557 and/or 558) are associated with shorter progression-free and overall survival.2225  About 7% to 10% of the tumors harbor mutations in the extracellular domain encoded by exon 9 (most commonly insAY502-503).26  Primary mutations in the activation loop (exon 17) and ATP binding region (exon 13) are uncommon (1%). Most of these mutations are substitutions.27  KIT exon 8 mutations are extremely rare (0.15%).28  Secondary or resistance mutations occur commonly in tumors harboring primary exon 11 mutations. The newly acquired secondary mutations are always located in exons encoding tyrosine kinase domain (exons 13, 14, 17).29 

C: PDGFRA Mutational Analysis.—More than 80% of KIT GISTs have PDGFRA mutations. Activation of PDGFRA is seen in GISTs harboring mutations in juxtamembranous domain (exon 12), the ATP-binding domain (exon 14), or the activation loop (exon 18).30  Mutations include substitutions and deletions. Primary resistance to imatinib is seen with the most common PDGFRA exon 18 D842V mutation.

D: BRAF Mutational Analysis.—Activating mutations of BRAF (V600E) has been identified in a small subset (7%) of KIT/PDGFRA wild-type GISTs. These tumors show a predilection for small bowel location.31 

E: SDH A/B/C/D Mutational Analysis.—The succinate dehydrogenase (SDH) complex (mitochondrial complex II) participates in both the Krebs cycle and the electron transport chain of oxidative phosphorylation. About 8% of gastric GISTs (all lacking mutations in KIT and PDGFRA) are caused by dysfunction of the SDH complex (SDH-deficient GISTs). Around 50% of patients affected by such tumors harbor germline mutations in one of the SDH subunit genes (SDHA/B/C or D). SDHA-inactivating mutations are most common, detected in about 30% of SDH-deficient GISTs. Mutations involve exons 2, 3, 5, 6, 7, 8, 9, 10, 11, 13, 14 of SDHA; exons 1, 2, 3, 4, 6, 7 of SDHB; exons 1, 4, 5 of SDHC; and exons 4 and 6 of SDHD. Although most mutations are substitutions, deletions, splice-site mutations, frame shifts, and duplications have also been reported.9,11,13,32 

F: Neurofibromatosis Type 1 (NF1) Mutational Analysis.—Neurofibromatosis type 1 is an inherited, autosomal-dominant disease characterized by multiple café au lait spots, Lisch nodules, freckling, and development of neurofibromas. The GISTs in patients with NF1 arise predominantly from the small intestine, can be multicentric, and lack KIT and PDGFRA mutations. Until now, no specific genetic alterations have been found in NF1-related GIST.32 

G: Dissection Method.—Although in most cases GIST samples show tumor percentage (%) well above the analytic sensitivity of Sanger sequencing (>50% neoplastic cell percentage per 20% to 25% mutant allele percentage), in cases of mutation analysis of treated samples, careful macrodissection or microdissection may be necessary to avoid false-negative results.

H: Reporting Nomenclature.—Consistent gene mutation nomenclature is essential for efficient and accurate reporting.33  Tables 1 and 2 are examples as recommended by the Human Genome Variation Society for description of variant changes.34  It is also preferred that protein alterations be mentioned in the report, in addition to genomic coordinates.

Figure 1.

Patterns of KIT staining in gastrointestinal stromal tumor (GIST). A, Diffuse and strong immunoreactivity in a typical GIST. B, Focal and weak pattern in an epithelioid gastric GIST with a PDGFRA mutation. C, Dotlike perinuclear staining. D, Membranous pattern (original magnification ×400 [A through D]). Reprinted from Rubin BP, Blanke CD, Demetri GD, et al; Cancer Committee, College of American Pathologists. Protocol for examination of specimens from patients with gastrointestinal stromal tumor. Arch Pathol Lab Med. 2010;134(2):165–170 with permission from the Archives of Pathology & Laboratory Medicine. Copyright 2010. College of American Pathologists.

Figure 1.

Patterns of KIT staining in gastrointestinal stromal tumor (GIST). A, Diffuse and strong immunoreactivity in a typical GIST. B, Focal and weak pattern in an epithelioid gastric GIST with a PDGFRA mutation. C, Dotlike perinuclear staining. D, Membranous pattern (original magnification ×400 [A through D]). Reprinted from Rubin BP, Blanke CD, Demetri GD, et al; Cancer Committee, College of American Pathologists. Protocol for examination of specimens from patients with gastrointestinal stromal tumor. Arch Pathol Lab Med. 2010;134(2):165–170 with permission from the Archives of Pathology & Laboratory Medicine. Copyright 2010. College of American Pathologists.

Figure 2.

Locations and frequency of activating KIT and PDGFRA mutations in gastrointestinal stromal tumor. Adapted with permission from Heinrich et al, 2003.14  Copyright 2003 by the American Society of Clinical Oncology. All rights reserved.

Figure 2.

Locations and frequency of activating KIT and PDGFRA mutations in gastrointestinal stromal tumor. Adapted with permission from Heinrich et al, 2003.14  Copyright 2003 by the American Society of Clinical Oncology. All rights reserved.

Table 1. 

Examples of DNA, RNA, and Protein Nomenclatures

Examples of DNA, RNA, and Protein Nomenclatures
Examples of DNA, RNA, and Protein Nomenclatures
Table 2. 

Examples of Nomenclatures for Types of Sequence Variants

Examples of Nomenclatures for Types of Sequence Variants
Examples of Nomenclatures for Types of Sequence Variants

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Author notes

Dr George is a consultant for Bayer, ARIAD Pharmaceuticals, Pfizer, Novartis, and Blueprint Medicines. The other authors have no relevant financial interest in the products or companies described in this article.