Tumor Gene Profiling Research Articles

Compliance with the Current NCCN Guidelines and Its Critical Role in Pancreatic Adenocarcinoma.

Since 2019, the National Comprehensive Cancer Network (NCCN) has recommended genetic testing for patients diagnosed with pancreatic adenocarcinoma that includes universal germline testing and tumor gene profiling for metastatic, locally advanced, or recurrent disease. However, testing compliance with this guideline has not yet been published in the English literature. A quality assurance/quality improvement retrospective review was done to identify patients diagnosed with pancreatic adenocarcinoma from January 2019 to February 2021 to include the patient's clinical status and genetic test results. There were 20 patient cases identified with pancreatic adenocarcinoma. A total of 11 cases had molecular tumor gene profiling and microsatellite instability/mismatch repair (MSI/MMR) testing performed and 1 case had only MSI/MMR testing by immunohistochemistry performed. Only 3 patients of the 20 in total received germline testing. There was a significant number of patients for whom tumor gene profiling or germline testing had never been attempted as per recommended NCCN guidelines.

Identifiable Mutations in Pancreatic Adenocarcinoma in the Veteran Population: Molecular Testing Guidelines by NCCN 2020

Abstract Introduction/Objective In 2019 and 2020, the National Comprehensive Cancer Network (NCCN) advanced a recommendation that all patients with metastatic, recurrent, or locally advanced pancreatic adenocarcinoma should undergo tumor gene profiling (TGP). Prior to these recommendations, TGP in targeted patients have demonstrated a high frequency of KRAS (>90%), TP53 (60-70%), CDKN2A (>50%), SMAD4, TGF- βR1, and TGF- βR2 mutations or alterations. Even less frequent mutations such as the homologous recombination repair (HRR) genes impact treatment by predicting tumor response to platinum-based therapies. However, the literature is sparse for the frequency of these mutations in patients with pancreatic adenocarcinoma undergoing generalized testing as part of the standard of care per NCCN guidance, particularly for veterans. Methods/Case Report For a quality assurance study, a retrospective review was performed to identify patients with pancreatic adenocarcinoma at a tertiary medical center serving veterans from January 2019 to February 2021 with TGP performed as part of their care. All of the TGP had been sent to Foundation Medicine (Cambridge MA), and the identifiable tumor mutations from the test reports were recorded to document the frequency of KRAS, TP53, CDKN2A, SMAD4, TGF- βR1, TGF- βR2 and HRR mutations or alterations. Results (if a Case Study enter NA) There were a total of 11 patients with pancreatic adenocarcinoma who had a tumor specimen for TGP during the study period. All 11 patient tumors had KRAS mutation. 10 out of 11 had a mutation or alteration in TP53. 8 of 11 patients had a CDKN2A mutation or alteration. 7 of 11 patients had a mutation or alteration of SMAD4 though none had TGF- βR1 or TGF- βR2. 2 of 11 patients had HRR mutations (1 with FANCA and 1 with ATM). Conclusion Tumor mutations on generalized gene profiling per NCCN guidelines continue to identify important mutations in pancreatic adenocarcinoma for veteran patients.

Molecular tests and target therapies in oncology: recommendations from the Italian workshop.

Next-generation sequencing (NGS) and liquid biopsy are new technologies that can allow overall tumor profiling in a single analysis and play an important role in the implementation of precision oncology. However, the lack of guidelines in this setting has limited the development of precision oncology in Italy. This articlesummarizes recommendations for the appropriate use of NGS in tumor gene profiling, as well asaccess to tests and target drugs, that were prepared by a group of key opinion leaders and relevant stakeholders. In particular, the need to create laboratory networks capable of carrying out NGS tests in Italy ishighlighted. It also appears necessary to establish an adequate reimbursement system for NGS tests. However, the expert panel recommendsthat the use of NGS tests in clinical practice should be limited to specific tumor types, based on the number and complexity of biomarkers and the availability of treatments.

Breast Cancer Tissue Markers, Genomic Profiling, and Other Prognostic Factors: A Primer for Radiologists.

An understanding of prognostic factors in breast cancer is imperative for guiding patient care. Increased tumor size and more advanced nodal status are established independent prognostic factors of poor outcomes and are incorporated into the American Joint Committee on Cancer (AJCC) TNM (primary tumor, regional lymph node, distant metastasis) staging system. However, other factors including imaging findings, histologic evaluation results, and molecular findings can have a direct effect on a patient's prognosis, including risk of recurrence and relative survival. Several microarray panels for gene profiling of tumors are approved by the U.S. Food and Drug Administration and endorsed by the American Society of Clinical Oncology. This article highlights prognostic factors currently in use for individualizing and guiding breast cancer therapy and is divided into four sections. The first section addresses patient considerations, in which modifiable and nonmodifiable prognostic factors including age, race and ethnicity, and lifestyle factors are discussed. The second part is focused on imaging considerations such as multicentric and/or multifocal disease, an extensive intraductal component, and skin or chest wall involvement and their effect on treatment and prognosis. The third section is about histopathologic findings such as the grade and presence of lymphovascular invasion. Last, tumor biomarkers and tumor biology are discussed, namely hormone receptors, proliferative markers, and categorization of tumors into four recognized molecular subtypes including luminal A, luminal B, human epidermal growth factor receptor 2-enriched, and triple-negative tumors. By understanding the clinical effect of these prognostic factors, radiologists, along with a multidisciplinary team, can use these tools to achieve individualized patient care and to improve patient outcomes. ©RSNA, 2018.

Pivotal Role of Liquid Biopsy in Diagnosing, Managing and Monitoring Early and Advanced Stages of Lung Cancer among Asian Population

RATIONALE: Non-small cell lung cancer (NSCLC) remains the leading cause ofcancer-related deaths among Asian population. Liquid biopsy is a new technology thatprovides information on tumor gene profiling through examination of cell-free DNA(CfDNA) in whole blood. This produces data on genetic alterations found in tumortissue that could be used for prompt and effective management of NSCLC. MATERIALS AND METHODS: Between September 2016 and December 2016, weretrospectively collected and reviewed the medical records of thirty-five patients whowere suspected or diagnosed of lung cancer, then underwent serum epidermal growthfactor receptor (EGFR) for further investigation. Liquid biopsy results were comparedwith the subjects’ final diagnosis. RESULTS: The final diagnoses revealed eighteen (51%) benign and seventeen (49%)malignant cases. Fourteen out of seventeen malignant cases were diagnosed asadenocarcinoma. The remaining three out of seventeen subjects’ diagnoses were:anaplastic giant cell, carcinoid tumor and thyroid cancer with lung metastasis. Thesethree were considered as true negative for EGFR liquid biopsy results. The fourteenmalignant cases were divided into two categories which were surgical and chemotherapyor TKI groups. In the surgical group, five were positive for tissue EGFR mutationfollowed by a negative serum EGFR results post-surgery. One out of the five casesreported negative serum EGFR just four days post-operatively.In the chemotherapy or tyrosine kinase inhibitor (TKI) group, four out of nine weretested prior to treatment with three positive results. One was negative serum EGFR buthad positive tissue EGFR. One case out of nine reported positive EGFR followed by anegative EGFR at thirteen days while on treatment. The last four subjects were testedduring prolonged treatment. Two from the four cases reported negative results. Onedetected resistance and the last case was negative EGFR but later deteriorated. CONCLUSION: Liquid biopsy’s roles include lung cancer screening, treatmentevaluation, assessment of recurrence or resistance, an alternative for tissue biopsy anda complementary blood test with radiographic imaging. This test substantially improvespatient care and outcomes at all stages of lung cancer. Keywords: lung cancer diagnosis, Non-small cell lung cancer, liquid biopsy, epidermalgrowth factor receptor

ONCOLOGISTS' BARRIERS AND FACILITATORS FOR ONCOTYPE DX USE: QUALITATIVE STUDY.

Oncotype DX (ODX), a tumor gene profiling test, has been incorporated into clinical guidelines to aid in adjuvant chemotherapy decision making for early-stage, hormone receptor positive breast cancer patients. Despite United States (U.S.) guidelines, less than half of eligible women receive testing. Reasons for low usage are unclear: Our objective was to better understand U.S. oncologists' ODX uptake and how they use ODX during adjuvant chemotherapy decision making. We conducted semi-structured, ~30-minute phone interviews with medical and surgical oncologists in one U.S. State using purposive sampling. Oncologists were included if they saw greater than or equal to five breast cancer patients per week. Recruitment ended upon thematic saturation. Interviews were recorded, transcribed, and double-coded using template analysis. During analysis, themes emerged across three domains. First, organizational factors (i.e., departmental structure, ODX marketing, and medical/insurance guidelines) influenced ease of ODX use. Second, oncologists referenced the influence of interpersonal factors (e.g., normative beliefs and peer use of ODX) over their own practices and recommendations. Third, intrapersonal factors (e.g., oncologist attitudes, perceived barriers, and research gaps) were discussed: although oncologists largely held positive attitudes about ODX, they reported challenges with interpreting intermediate scores for treatment decisions and explaining test results to patients. Finally, oncologists identified several research gaps. As more tumor gene profiling tests are incorporated into cancer care for treatment decision making, it is important to understand their use in clinical practice. This study identified multi-level factors that influence ODX uptake into clinical practice, providing insights into facilitators and modifiable barriers that can be leveraged for improving ODX uptake to aid treatment decision making.

Gene profiling and circulating tumor cells as biomarker to prognostic of patients with locoregional breast cancer.

The gene profile of primary tumors, as well as the identification of circulating tumor cells (CTCs), can provide important prognostic and predictive information. In this study, our objective was to perform tumor gene profiling (TGP) in combination with CTC characterization in women with nonmetastatic breast cancer. Biological samples (from peripheral blood and tumors) from 167 patients diagnosed with stage I, II, and III mammary carcinoma, who were also referred for adjuvant/neoadjuvant chemotherapy, were assessed for the following parameters: (a) the presence of CTCs identified by the expression of CK-19 and c-erbB-2 in the peripheral blood mononuclear cell (PBMC) fraction by quantitative reverse transcription PCR (RT-PCR) and (b) the TGP, which was determined by analyzing the expression of 21 genes in paraffin-embedded tissue samples by quantitative multiplex RT-PCR with the Plexor® system. We observed a statistically significant correlation between the progression-free interval (PFI) and the clinical stage (p = 0.000701), the TGP score (p = 0.006538), and the presence of hormone receptors in the tumor (p = 0.0432). We observed no correlation between the PFI and the presence or absence of CK-19 or HER2 expression in the PBMC fraction prior to the start of treatment or in the two following readouts. Multivariate analysis revealed that only the TGP score significantly correlated with the PFI (p = 0.029247). The TGP is an important prognostic variable for patients with locoregional breast cancer. The presence of CTCs adds no prognostic value to the information already provided by the TGP.

Application of immunohistochemistry in thyroid pathology.

Accurate classification of follicular-patterned thyroid lesions is not always an easy task on routine surgical hematoxylin-eosin-stained or cytologic fine-needle aspiration specimens. The diagnostic challenges are partially due to differential diagnostic criteria that are often subtle and subjective. In the past decades, tremendous advances have been made in molecular gene profiling of tumors and diagnostic immunohistochemistry, aiding in diagnostic accuracy and proper patient management. To evaluate the diagnostic utility of the most commonly studied immunomarkers in the field of thyroid pathology by review of the literature, using the database of indexed articles in PubMed (US National Library of Medicine) from 1976-2013. Literature review, authors' research data, and personal practice experience. The appropriate use of immunohistochemistry by applying a panel of immunomarkers and using a standardized technical and interpretational method may complement the morphologic assessment and aid in the accurate classification of difficult thyroid lesions.

Chimiothérapie ciblée du cancer du sein basée sur une analyse génomique de la tumeur

The purpose of this review of the literature is to document how breast cancer patients perceive the use of tumor gene profiling approaches to better adapt treatments, and to identify the features of these approaches that may impact their clinical application. In general, the use of tumor genomic analysis was perceived by patients as an approach facilitating personalized medicine and received considerable support. Nevertheless, a number of confusions and worries about these practices were also identified. Improving the quality of provider/patient communications should enable patients to play a more active part in the decision-making about their treatment. This will ensure that those who agree to their tumor gene analysis have realistic expectations and sound deductions of the final result disclosure process.

Everolimus post-progression on tyrosine kinase inhibitors in metastatic renal cell carcinoma: A clinical review of patients demonstrating a durable response and the effective management of treatment toxicity.

449 Background: The mammalian target of rapamycin (mTOR) inhibitor everolimus has been licensed as a second line treatment in metastatic renal cell carcinoma (mRCC) following treatment failure with a tyrosine kinase inhibitor (TKI). A randomised placebo control trial of everolimus used in this setting demonstrated only a modest median progression free survival of 4.9 months (Motzer RJ, et al. Phase 3 trial of everolimus for metastatic renal cell carcinoma: final results and analysis of prognostic factors. Cancer 2010;116:4256-65). Methods: We present 2 patients with a prolonged treatment response - both encountered mTOR inhibitor specific adverse events, the management of which will be discussed. Results: Patient 1: A 47 year old man with mRCC, previously treated with the Atzpodien regimen followed by sunitinib. A radiological response was seen after 2 treatment cycles of Everolimus and has remained stable for 25 months to date. A triglyceride level of 32.2 mmol/l has responded to a 50% dose reduction, dietary advice and the addition of a fibrate without loss of disease control. Patient 2: A 62 year old man with mRCC initially treated with Interferon followed by sunitinib. He developed radiological evidence of pneumonitis after 2 months of everolimus but did not experience (G3) symptoms until 2 months later. Pneumonitis responded to treatment deferral and corticosteroids and did not recur when everolimus was reintroduced. He achieved 18 months of PFS. Conclusions: Everolimus can initiate prolonged periods of progression free survival when used after progression on a TKI. The treatment is well tolerated and adverse events can be easily managed to allow ongoing therapy. Our further investigation, including tumor gene profiling, of such patients will allow a more personalised approach in the management of mRCC and improved prognostication in the clinic.

Breast Cancer

The mortality rate due to breast cancer has declined over the preceding decades to a great extent, secondary to the development and use of effective adjuvant therapy. Tamoxifen remains the standard of care in premenopausal women, whereas aromatase inhibitors have become standard therapy after menopause for women with hormone-sensitive disease. Tumor gene profiling assays are being increasingly used to identify women with hormone-sensitive disease, who would benefit from adjuvant chemotherapy. For those women with hormone negative cancer, systemic chemotherapy provides substantial reduction in the risk of disease recurrence and death.

Prognostic Role of a Gene Signature in Breast Cancer

Just a few years ago, the idea of gene profiling of tumors was viewed as a futuristic concept that would change our approach to patient prognosis and

RB1 gene mutation up-date, a meta-analysis based on 932 reported mutations available in a searchable database

BackgroundRetinoblastoma, a prototype of hereditary cancer, is the most common intraocular tumour in children and potential cause of blindness from therapeutic eye ablation, second tumours in germ line carrier's survivors, and even death when left untreated. The molecular scanning of RB1 in search of germ line mutations lead to the publication of more than 900 mutations whose knowledge is important for genetic counselling and the characterization of phenotypic-genotypic relationships.ResultsA searchable database (RBGMdb) has been constructed with 932 published RB1 mutations. The spectrum of these mutations has been analyzed with the following results: 1) the retinoblastoma protein is frequently inactivated by deletions and nonsense mutations while missense mutations are the main inactivating event in most genetic diseases. 2) Near 40% of RB1 gene mutations are recurrent and gather in sixteen hot points, including twelve nonsense, two missense and three splicing mutations. The remainder mutations are scattered along RB1, being most frequent in exons 9, 10, 14, 17, 18, 20, and 23. 3) The analysis of RB1 mutations by country of origin of the patients identifies two groups in which the incidence of nonsense and splicing mutations show differences extremely significant, and suggest the involvement of predisposing ethnic backgrounds. 4) A significant association between late age at diagnosis and splicing mutations in bilateral retinoblastoma patients suggests the occurrence of a delayed-onset genotype. 5) Most of the reported mutations in low-penetrance families fall in three groups: a) Mutations in regulatory sequences at the promoter resulting in low expression of a normal Rb; b) Missense and in-frame deletions affecting non-essential sequence motifs which result in a partial inactivation of Rb functions; c) Splicing mutations leading to the reduction of normal mRNA splicing or to alternative splicing involving either true oncogenic or defective (weak) alleles.ConclusionThe analysis of RB1 gene mutations logged in the RBGMdb has shown relevant phenotype-genotype relationships and provided working hypothesis to ascertain mechanisms linking certain mutations to ethnicity, delayed onset of the disease and low-penetrance. Gene profiling of tumors will help to clarify the genetic background linked to ethnicity and variable expressivity or delayed onset phenotypes.

DNA Array-Based Gene Profiling

Cancer is a heterogeneous disease in most respects, including its cellularity, different genetic alterations, and diverse clinical behaviors. Traditional molecular analyses are reductionist, assessing only 1 or a few genes at a time, thus working with a biologic model too specific and limited to confront a process whose clinical outcome is likely to be governed by the combined influence of many genes. The potential of functional genomics is enormous, because for each experiment, thousands of relevant observations can be made simultaneously. Accordingly, DNA array, like other high-throughput technologies, might catalyze and ultimately accelerate the development of knowledge in tumor cell biology. Although in its infancy, the implementation of DNA array technology in cancer research has already provided investigators with novel data and intriguing new hypotheses on the molecular cascade leading to carcinogenesis, tumor aggressiveness, and sensitivity to antiblastic agents. Given the revolutionary implications that the use of this technology might have in the clinical management of patients with cancer, principles of DNA array-based tumor gene profiling need to be clearly understood for the data to be correctly interpreted and appreciated. In the present work, we discuss the technical features characterizing this powerful laboratory tool and review the applications so far described in the field of oncology.