Allison M. Cushman-Vokoun

Molecular biomarkers for the evaluation of colorectal cancer: Guideline from The American Society for Clinical Pathology, College of American Pathologists, Association for Molecular Pathology, and the American Society of Clinical Oncology

Purpose Molecular testing of colorectal cancers (CRCs) to improve patient care and outcomes of targeted and conventional therapies has been the center of many recent studies, including clinical trials. Evidence-based recommendations for the molecular testing of CRC tissues to guide epidermal growth factor receptor (EGFR) -targeted therapies and conventional chemotherapy regimens are warranted in clinical practice. The purpose of this guideline is to develop evidence-based recommendations to help establish standard molecular biomarker testing for CRC through a systematic review of the literature. Methods The American Society for Clinical Pathology (ASCP), College of American Pathologists (CAP), Association for Molecular Pathology (AMP), and the American Society of Clinical Oncology (ASCO) convened an Expert Panel to develop an evidence-based guideline to help establish standard molecular biomarker testing, guide targeted therapies, and advance personalized care for patients with CRC. A comprehensive literature search that included over 4,000 articles was conducted to gather data to inform this guideline. Results Twenty-one guideline statements (eight recommendations, 10 expert consensus opinions and three no recommendations) were established. Recommendations Evidence supports mutational testing for genes in the EGFR signaling pathway, since they provide clinically actionable information as negative predictors of benefit to anti-EGFR monoclonal antibody therapies for targeted therapy of CRC. Mutations in several of the biomarkers have clear prognostic value. Laboratory approaches to operationalize molecular testing for predictive and prognostic molecular biomarkers involve selection of assays, type of specimens to be tested, timing of ordering of tests and turnaround time for testing results. Additional information is available at: www.asco.org/CRC-markers-guideline and www.asco.org/guidelineswiki.

Molecular diagnostics of soft tissue tumors.

CONTEXT Soft tissue pathology encompasses a remarkably diverse assortment of benign and malignant soft tissue tumors. Rendering a definitive diagnosis is complicated not only by the large volume of existing histologic subtypes (>100) but also frequently by the presence of overlapping clinical, histologic, immunohistochemical, and/or radiographic features. During the past 3 decades, mesenchymal tumor-specific, cytogenetic and molecular genetic abnormalities have demonstrated an increasingly important, ancillary role in mesenchymal tumor diagnostics. OBJECTIVES To review molecular diagnostic tools available to the pathologist to further classify specific soft tissue tumor types and recurrent aberrations frequently examined. Advantages and limitations of individual approaches will also be highlighted. DATA SOURCES Previously published review articles, peer-reviewed research publications, and the extensive cytogenetic and molecular diagnostic experience of the authors to include case files of The University of Nebraska Medical Center. CONCLUSIONS Cytogenetic and molecular genetic assays are used routinely for diagnostic purposes in soft tissue pathology and represent a powerful adjunct to complement conventional microscopy and clinicoradiographic evaluation in the formulation of an accurate diagnosis. Care should be taken, however, to recognize the limitations of these approaches. Ideally, more than one technical approach should be available to a diagnostic laboratory to compensate for the shortcomings of each approach in the assessment of individual specimens.

Assay Design Affects the Interpretation of T-Cell Receptor Gamma Gene Rearrangements: Comparison of the Performance of a One-Tube Assay with the BIOMED-2-Based TCRG Gene Clonality Assay

Interpretation of capillary electrophoresis results derived from multiplexed fluorochrome-labeled primer sets can be complicated by small peaks, which may be incorrectly interpreted as clonal T-cell receptor-γ gene rearrangements. In this report, different assay designs were used to illustrate how design may adversely affect specificity. Ten clinical cases, with subclonal peaks containing one of the two infrequently used joining genes, were identified with a tri-color, one-tube assay. The DNA was amplified with the same NED fluorochrome on all three joining primers, first combined (one-color assay) and then amplified separately using a single NED-labeled joining primer. The single primer assay design shows how insignificant peaks could easily be wrongly interpreted as clonal T-cell receptor-γ gene rearrangements. Next, the performance of the one-tube assay was compared with the two-tube BIOMED-2-based TCRG Gene Clonality Assay in a series of 44 cases. Whereas sensitivity was similar between the two methods (92.9% vs. 96.4%; P = 0.55), specificity was significantly less in the BIOMED-2 assay (87.5% vs. 56.3%; P = 0.049) when a 2× ratio was used to define clonality. Specificity was improved to 81.3% by the use of a 5× peak height ratio (P = 0.626). These findings illustrate how extra caution is needed in interpreting a design with multiple, separate distributions, which is more difficult to interpret than a single distribution assay.

PU.1 regulates the expression of the vav proto-oncogene.

Vav is a guanine nucleotide exchange factor for the rho/rac GTPases that is upregulated in the embryo during the transition from primitive to definitive hematopoiesis. It is one of several genetic markers that correlates with the differentiation of the intraembryonic definitive hematopoietic stem cell. Subsequently, in the adult, vav is expressed predominantly in cells of the hematopoietic system. A heat‐resistant protein complex that bound to a 23‐bp segment, which is essential for vav promoter activity, was found to be present in myeloid cells but not T‐cells. The complex was absent in non‐hematopoietic cells which normally do not express vav. Using a saturation mutagenesis method, Mutex, a “footprint” of the protein binding site (AGAGGAAGT) was obtained that was consistent with the consensus binding site for PU.1. A specific antibody to PU.1 supershifted the complex and identified the presence of PU.1 within the complex. A GST fusion protein of the human PU.1 bound to the same consensus sequence as the heat‐resistant complex from myeloid lineages. Specific mutation of the GGAA PU.1 core binding site silenced vav promoter activity and a dominant negative PU.1 inhibited the transactivation of PU.1 at the vav promoter as measured by the expression of the EGFP reporter gene. In addition, PCR analysis of immunoprecipitated chromatin using specific antibodies for PU.1 detected the co‐immunoprecipitation of DNA containing the vav promoter. These results suggest that PU.1 is essential for transcriptional activity of the vav promoter in myeloid cells. J. Cell. Biochem. 84: 772–783, 2002.

Comparison Study of the Performance of the QIAGEN EGFR RGQ and EGFR Pyro Assays for Mutation Analysis in Non–Small Cell Lung Cancer

OBJECTIVES To compare 2 laboratory assays commonly used in the evaluation of epidermal growth factor receptor (EGFR) mutations in non-small cell lung cancer (NSCLC). METHODS Fifty-three formalin-fixed, paraffin-embedded NSCLC specimens were selected. Extracted DNA was analyzed using the EGFR RGQ Amplification Refractory Mutation System Scorpions probe-based real-time polymerase chain reaction (PCR) assay and the EGFR Pyro pyrosequencing assay. RESULTS Fourteen EGFR mutations were identified in 13 specimens using at least 1 of the assays, with a mutation concordance rate of 92.9%. Using dideoxy sequencing as the gold standard, clinical sensitivity was 73.7% and 68.4% by the RGQ and Pyro assays, respectively, but 100% by both for common drug sensitivity mutations. Performance observations included the following: the RGQ system requires higher DNA input, the RGQ system is a single-step procedure, the EGFR Pyro assay is a 2-step procedure, only the RGQ system can identify exon 20 insertions, the RGQ system is more sensitive, and the Pyro system can specify exact mutations for all interrogated sites. CONCLUSIONS Both the RGQ real-time PCR and Pyro assays adequately detect common EGFR mutations; however, the RGQ system is more clinically and analytically sensitive. Performance characteristics should be considered when evaluating these EGFR mutation assays for clinical adoption.

Regulation of the vav proto-oncogene by LKLF

The transcriptional induction of the vav proto-oncogene coincides with the first appearance of the definitive hematopoietic stem cell in the aorta-gonad-mesonephros region. Vav promoter activity was dependent on a previously identified 23 bp DNA segment containing PU.1 and Runx1/AML-1 binding sites and on a newly identified, highly conserved, 12 bp DNA segment (Box B). The sequence of Box B was identical in the human, mouse and rat species. Mutation of the CACCC core sequence led to diminished vav promoter activity. A protein complex which bound to Box B was found in hematopoietic cells but not in cells which did not express vav. A double-stranded oligonucleotide containing a mutation of the CACCC core was less effective in electro-mobility shift assay competitions than the wild-type sequence. UV crosslinking studies identified a 37 kDa DNA binding protein which interacted with Box B in U937 cells. Antibody supershift assays identified this protein as lung Krüppel-like factor (LKLF). LKLF, expressed as a glutathione S-transferase fusion protein, was capable of binding to Box B. A dominant-negative LKLF was able to inhibit the expression of enhanced green fluorescent protein by the vav promoter and chromatin immunoprecipitations detected LKLF bound to the vav promoter in U937 but not HeLa cells. These in vitro results suggest future in vivo experiments to examine the role of LKLF, a gene required for vasculogenesis, in the induction of vav during the genesis of the definitive hematopoietic stem cell from the vascular endothelium.

Epidermal Growth Factor Receptor Mutational Status and Brain Metastases in Non–Small-Cell Lung Cancer

Introduction Epidermal growth factor receptor (EGFR) mutations in non–small-cell lung cancers (NSCLC) may be more common in patients with brain metastases. Previous studies, however, did not adjust for effects of confounding variables. Methods This retrospective study included 1,522 consecutive patients with NSCLC, whose tumors were diagnosed and tested for EGFR mutations at the University of Nebraska Medical Center (Omaha, NE) and Tata Memorial Hospital (Mumbai, India). Multivariate logistic regression was used to identify any association between EGFR status and clinical factors. Results EGFR mutations were more common in females than males (38.7% v 24.8%), Asians than whites (31.3% v 13.4%), nonsmokers than smokers (40.2% v 14.6%), alcohol nonconsumers than users (32.4% v 15.8%), adenocarcinoma than other histology types (32.7% v 10.3%), and patients with brain metastases than extracranial or no metastases (39.4% v 29.8% v 15.1%; P < .001 for all comparisons). There was a higher likelihood of an EGFR mutation among patients with brain metastases (odds ratio, 1.8; P < .001). The median overall survival (OS) was 19.8 months. Patients with brain metastases had a shorter median OS (15 v 20.6 months; P = .02). However, in the cohort of EGFR mutation–positive patients, there was no difference in median OS between patients with and without brain metastases (20.8 v 25.1 months; P = .11). Conclusion There is a nearly two-fold higher incidence of EGFR mutations in NSCLC among patients with brain metastases at diagnosis. EGFR mutations did not predict for outcomes from brain metastases.

Standards for Clinical Grade Genomic Databases.

CONTEXT Next-generation sequencing performed in a clinical environment must meet clinical standards, which requires reproducibility of all aspects of the testing. Clinical-grade genomic databases (CGGDs) are required to classify a variant and to assist in the professional interpretation of clinical next-generation sequencing. Applying quality laboratory standards to the reference databases used for sequence-variant interpretation presents a new challenge for validation and curation. OBJECTIVES To define CGGD and the categories of information contained in CGGDs and to frame recommendations for the structure and use of these databases in clinical patient care. DESIGN Members of the College of American Pathologists Personalized Health Care Committee reviewed the literature and existing state of genomic databases and developed a framework for guiding CGGD development in the future. RESULTS Clinical-grade genomic databases may provide different types of information. This work group defined 3 layers of information in CGGDs: clinical genomic variant repositories, genomic medical data repositories, and genomic medicine evidence databases. The layers are differentiated by the types of genomic and medical information contained and the utility in assisting with clinical interpretation of genomic variants. Clinical-grade genomic databases must meet specific standards regarding submission, curation, and retrieval of data, as well as the maintenance of privacy and security. CONCLUSION These organizing principles for CGGDs should serve as a foundation for future development of specific standards that support the use of such databases for patient care.

Molecular Biomarkers for the Evaluation of Colorectal Cancer

Abstract Objectives: To develop evidence-based guideline recommendations through a systematic review of the literature to establish standard molecular biomarker testing of colorectal cancer (CRC) tissues to guide epidermal growth factor receptor (EGFR) therapies and conventional chemotherapy regimens. Methods: The American Society for Clinical Pathology, College of American Pathologists, Association for Molecular Pathology, and American Society of Clinical Oncology convened an expert panel to develop an evidence-based guideline to establish standard molecular biomarker testing and guide therapies for patients with CRC. A comprehensive literature search that included more than 4,000 articles was conducted. Results: Twenty-one guideline statements were established. Conclusions: Evidence supports mutational testing for EGFR signaling pathway genes, since they provide clinically actionable information as negative predictors of benefit to anti-EGFR monoclonal antibody therapies for targeted therapy of CRC. Mutations in several of the biomarkers have clear prognostic value. Laboratory approaches to operationalize CRC molecular testing are presented.

QIAGEN Therascreen KRAS RGQ Assay, QIAGEN KRAS Pyro Assay, and Dideoxy Sequencing for Clinical Laboratory Analysis of KRAS Mutations in Tumor Specimens

OBJECTIVE To compare the performance of assays used to assess KRAS mutations in tumor specimens. METHODS We analyzed DNA extracted from 30 formalin-fixed paraffin-embedded (FFPE) tumor specimens using the QIAGEN Therascreen KRAS RGQ and QIAGEN Pyro reagents, with dideoxy sequencing (colloquially considered to be the gold standard) as the reference method. RESULTS We detected 22 codon 12 or 13 KRAS mutations using the Pyro assay, whereas the RGQ assay detected 19 mutations. For mutation detection, the clinical sensitivity was 86% for the RGQ assay compared with 100% for the Pyro but 100% for the KRAS mutations that the RGQ was predesigned to detect. The Pyro could detect rare mutations. The RGQ demonstrated a lower limit of detection compared with the Pyro; However, the Pyro required less DNA input than the RGQ. CONCLUSION The 2 assays that we tested yielded comparable performance in detecting KRAS mutations, as we had expected based on assay design. Overall, the Pyro assay detects more mutations and requires less DNA input but is less analytically sensitive, compared with the RGQ assay.