Role Of Molecular Markers Research Articles

The mutational analysis in the diagnostic work-up of thyroid nodules: the real impact in a center with large experience in thyroid cytopathology

Fine-needle aspiration (FNA) cytology is a mainstay in the evaluation of thyroid nodules, but fails to reach reliable results in 25-30% of cases. The role of molecular markers in helping clinical decisions has been investigated for the last years, but their clinical usefulness is still unsettled. Mutation analysis of BRAF, RAS genes and TERT promoter was performed in a series of 617 consecutive cytological specimens undergoing FNA. The 617 nodules had the following cytological diagnosis: non diagnostic 22 (3.6%), benign 425 (68.9%), indeterminate 114 (18.5%), suspicious 11 (1.8%) and malignant 45 (7.3%). BRAF mutations were found in 31 cases (5.0%), all but two in suspicious and malignant nodules. RAS mutations were detected in 47 samples (7.6%): 25 benign (5.9%) and 19 indeterminate nodules (16.7%). TERT promoter mutation alone was detected in three samples. Histological outcome was available for 167 nodules, 81 of which proved malignant: all the 48 with suspicious or malignant cytology; 25 out of 56 (44.6%) with indeterminate and 8 out of 57 (14%) with benign cytology. BRAF mutations were associated with worse tumors pathological features. The presence of RAS mutations was indicative of follicular-patterned malignancies in 5 out of 8 benign nodules and 9 out of 11 indeterminate nodules. Our study established mutational rates for BRAF and RAS genes in a large series of FNA specimens. BRAF mutations were confirmed as highly specific but not able to improve cytological diagnosis, while RAS testing proved effective in assessing malignancy in nodules with indeterminate and benign cytology.

Chemotherapy of Oligodendrogliomas.

Oligodendrogliomas are therapy-responsive tumors, which have better prognosis compared to their astrocytic counterparts. The goal of treatment in such cases is not only prolongation of the patients' survival, but maintaining high neurologic functioning and quality of life. Traditionally, after maximal surgical resection fractionated radiation therapy was given. However, prospective randomized trials comparing irradiation alone and its combination with chemotherapy demonstrated strong impact of the latter on prolongation of overall survival in 1p/19q co-deleted anaplastic and "high-risk" low-grade gliomas. In such cases the median survival of patients is well beyond a decade. The optimal chemotherapy regimen (PCV or temozolomide) remains an active clinical trial question, which may be resolved after completion of the ongoing phase III CODEL study (clinicaltrials.gov identifier NCT00887146). Additional investigations should also refine further the prognostic and predictive role of molecular markers in oligodendroglial tumors.

Role of Molecular Markers in Thyroid Nodule Management: Then and Now

To describe the evolution and clinical utility of molecular testing for thyroid nodules and cancer achieved over the last 2 decades. Scientific reports on thyroid cancer genetics and molecular diagnostics in thyroid nodules. Over the last 2 decades, our understanding of the genetic mechanisms of thyroid cancer has dramatically expanded, such that most thyroid cancers now have known gene driver events. This knowledge provides the basis for establishing and further improving molecular tests for thyroid nodules and cancer and for the introduction of new entities such as noninvasive follicular thyroid neoplasm with papillary-like nuclear features. The progress with molecular tests for thyroid nodules started in the 1990s from demonstrating feasibility of detecting various molecular alterations in fine-needle aspiration (FNA) material collected from thyroid nodules. It was followed by the introduction of the first single-gene mutational markers, such as BRAF, and a small mutational panel into clinical practice in the mid 2000s. Currently, several more advanced molecular tests are available for clinical use. They are based on multiple molecular markers and have increasing impact on the clinical management of patients with thyroid nodules. The evolution of molecular tests for thyroid nodules followed the discovery of various diagnostic and prognostic molecular markers of thyroid cancer that can be applied to thyroid FNA samples to inform more individualized management of these patients. FNA = fine-needle aspiration miRNA = micro RNA NGS = next-generation sequencing NIFTP = noninvasive follicular thyroid neoplasm with papillary-like nuclear features NPV = negative predictive value PPV = positive predictive value PTC = papillary thyroid carcinoma RAI = radioactive iodine.

Haematuria work-up in general care-A German observational study.

Haematuria is a common finding in the population and the diagnostic workflow of this symptom represents a large proportion of "work-load" in the urological outpatient clinic. The intention of this study was to verify if the intensive diagnostic procedures of haematuria patients is justified by detection of a significant proportion of genito-urinary tract cancers. In a retrospective design 1049 consecutive patients, who presented themselves with macro- or microhaematuria in the outpatient clinic PURR in the time from 2011 to 2012, were included in the study and the diagnostic procedures including ultrasound, intravenous urography, computed tomography of the abdomen and urethrocystoscopy as well as therapeutic consequences with its results were analysed. The study group comprised 570 women (54.3%) and 479 men (45.7%) with a median age of 58years and macrohaematuria occurred in 89 patients. Diagnostics revealed seven patients with renal cell cancer, six patients with urothelial cell cancer of the renal pelvis, four patients with urothelial cell cancer of the ureter, 65 patients with urothelial cell cancer of the lower urinary tract and 17 patients with prostate cancer. Age, male gender and macrohaematuria were associated with a higher risk of cancer. The high incidence of urinary tract cancer in the data presented here support the rationale for diagnostic work-up of patients with micro- or macrohaematuria. Prospective randomised trials are necessary to identify index patients for second work-up after a primarily negative investigation as well as the role of molecular markers, which possibly enable to omit invasive work-up.

Role of Molecular Markers in Assessing Genetic Diversity in Mentha: A Review

Morphological, phytochemical and genetic differences were studied to evaluate the level and distribution of diversity among thirteen genotypes of Mentha using both agro-morphological traits and ISSR markers.

EGFR Gene Amplification and KRAS Mutation Predict Response to Combination Targeted Therapy in Metastatic Colorectal Cancer.

Genetic variability in KRAS and EGFR predicts response to cetuximab in irinotecan refractory colorectal cancer. Whether these markers or others remain predictive in combination biologic therapies including bevacizumab is unknown. We identified predictive biomarkers from patients with irinotecan refractory metastatic colorectal cancer treated with cetuximab plus bevacizumab. Patients who received cetuximab plus bevacizumab for irinotecan refractory colorectal cancer in either of two Phase II trials conducted were identified. Tumor tissue was available for 33 patients. Genomic DNA was extracted and used for mutational analysis of KRAS, BRAF, and p53 genes. Fluorescence in situ hybridization was performed to assess EGFR copy number. The status of single genes and various combinations were tested for association with response. Seven of 33 patients responded to treatment. KRAS mutations were found in 14/33 cases, and 0 responded to treatment (p=0.01). EGFR gene amplification was seen in 3/33 of tumors and in every case was associated with response to treatment (p<0.001). TP53 and BRAF mutations were found in 18/33 and 0/33 tumors, respectively, and there were no associations with response to either gene. EGFR gene amplification and KRAS mutations are predictive markers for patients receiving combination biologic therapy of cetuximab plus bevacizumab for metastatic colorectal cancer. One marker or the other is present in the tumor of half of all patients allowing treatment response to be predicted with a high degree of certainty. The role for molecular markers in combination biologic therapy seems promising.

Role of molecular markers in guiding therapy in cancer

Role of molecular markers in guiding therapy in cancer

The utility of molecular markers in pre-operative assessment of thyroid nodules.

The pre-operative diagnosis of thyroid tumors is determined by gold standard fine needle aspiration (FNA) biopsy. This has been widely accepted and offers the most cost-effective approach for evaluation of thyroid nodules. However, its diagnostic accuracy can pose a challenging scenario to surgeons. These diagnostic difficulties may subject patients to unnecessary thyroidectomies for benign thyroid nodules. Thus, additional molecular tests are needed to improve the sensitivity and specificity of FNA. The role of molecular markers is being proposed to predict the type and risk of malignancy to abate the need for diagnostic thyroidectomies. This review discusses their utility and validity in pre-operative diagnosis of thyroid nodules and how these markers can enhance the accuracy of FNA cytology.

New and contemporary markers of prognosis in nonmuscle invasive urothelial cancer.

Nonmuscle invasive (NMI) urothelial cancer (UC) is associated with varied biological potential. It is characterized by frequent recurrence and progression, which thus worsens the oncological outcome. Nearly three-quarters of NMI UCs recur within 5 years, whereas half can progress during follow-up. Progression is particularly seen in T1 and carcinoma in situ (CIS). Undoubtedly, NMI UC is one of the most expensive cancers to manage. The European Organisation for Research and Treatment of Cancer (EORTC) risk calculator is a commonly used tool for assessing the recurrence and progression potential of a newly diagnosed cancer. The parameters used in the assessment are tumor size and number, pathological stage and grade of the cancer, presence of CIS, and prior recurrence rate. The main advantages of the EORTC tool are its ease of use and the lack of need to run expensive molecular tests. However, reproducibility of pathologic stage and grade is modest, which is a concern to clinicians. Molecular markers have potential for predicting the clinical outcome of NMI UC, given that clinico-pathologic variables are not sufficient for prediction of prognosis in an individual. Significant work has been done in the past 2 decades in understanding the molecular biology of bladder cancer; however, the translational value of this knowledge remains poor. The role for molecular markers in predicting recurrence seems limited because multifocal disease and incomplete treatment are probably more important for recurrence than the molecular features of a resected tumor. Urinary markers have very limited value in prognostication of bladder cancer and are used (mainly as an adjunct to cytology) for detection and surveillance of urothelial cell cancer recurrence. Prediction of progression with molecular markers holds considerable promise. Nevertheless, the contemporary value of molecular markers over clinico-pathologic indexes is limited.

The Role of Molecular Marker in Development of Plant Genetic Resources

Plants are fundamental to life, being the basis of our food production and an essential part of the global ecosystem on which life on earth depends. Plant genetic resources include primitive forms of cultivated plant species and landraces, modern cultivars, breeding lines and genetic stocks, weedy types and related wild species, which provide the building blocks that, allow classical plant breeders and biotechnologists to develop new commercial varieties and other biological products. Detection and analysis of genetic variation can help us to understand the molecular basis of various biological phenomena in plants. Molecular markers for the detection and exploitation of DNA polymorphism is one of the most significant developments in the field of molecular genetics. The presence of various types of molecular markers, and differences in their principles, methodologies, and applications require careful consideration in choosing one or more of such methods. This article describes the advances of molecular marker in present, introduces the molecular basis in development of plant genetic resources and perspectives the important role of molecular marker in development of plant genetic resources in the future.

Is there any diagnostic value of serum protease-activated receptor-1 (PAR1) levels on determination of epithelial ovarian carcinoma?

The role of molecular markers in ovarian cancer is still a matter of debate. Protease-activated receptor-1 (PAR1) might be a good marker in some types of malignant tumors and might provide useful information in diagnosis and prognosis. The objective of this study was to evaluate the serum levels of PAR1 in regard to diagnostic, predictive, and prognostic value in epithelial ovarian cancer (EOC) patients. Forty-four EOC patients were enrolled in this study. Serum PAR1 levels were determined by enzyme-linked immunosorbent assay (ELISA) method. Twenty-five age- and sex-matched healthy controls were included in the analysis. The median age of patients was 58 years old, ranging from 22 to 83 years, where most of them had advanced disease (stage III-IV) (n = 40, 91%). The median serum PAR1 values were significantly elevated in patients compared to healthy controls (1.52 ng/ml vs. 1.13 ng/ml) (p = 0.03), whereas any clinical variables including response to chemotherapy did not associate with serum assay (p > 0.05). Progression-free survival (PFS) and overall survival (OS) of patients who did not respond to chemotherapy nor had platinum resistance in relapsed disease were poorer in the analyses. On the other hand, serum PAR1 levels showed no significant adverse effect on either PFS or OS (p = 0.43 and p = 0.49, respectively). These results proved that baseline serum PAR1 levels of patients with EOC were significantly higher than those of healthy people. However, these assays suggested no predictive or prognostic value in this group of patients.

What is the role of molecular markers in the management of “indeterminate” thyroid nodules?

What is the role of molecular markers in the management of “indeterminate” thyroid nodules?

Overview of Myelodysplastic Syndromes

Myelodysplastic syndromes (MDS) were first presented as a separate entity in hematology in 1982 by the French-American-British (FAB) group. Although widely accepted, this classification was revised in 2001 and again in 2008 by the World Health Organization (WHO). During that time, a great effort was made by diagnostic entities of world renown as well as by other research groups and individuals to establish a reliable prognostic system. Today, two systems are accepted by the hematologic community: the International World Prognostic Scoring System (IPSS) and the WHO Prognostic Scoring System (WPSS). Almost from the beginning, it was assumed that MDS are clonal disorders. Cytogenetics not only proved the clonality in the majority of cases but also greatly contributed to the stratification of patients into risk categories. With the progress made in treatment for MDS, comorbidities became an important part of the integral pretreatment consideration, as patients with a high index of comorbidity evaluation very often do not benefit from treatment. Recent advances in the diagnostic and prognostic evaluation of MDS patients were achieved by studying the effect of age in different MDS subgroups and the role of molecular markers in predicting clinical evolution.

313 Role of molecular markers in nephrectomy specimen as prognosticators for patients with metastatic renal cell carcinoma in the era of targeted therapy

313 Role of molecular markers in nephrectomy specimen as prognosticators for patients with metastatic renal cell carcinoma in the era of targeted therapy

The Role of Molecular Markers and Tumor Histological Type in Central Lymph Node Metastasis of Papillary Thyroid Carcinoma

To look for genetic mutations that might predict central compartment lymph node metastasis (LNM) in papillary thyroid carcinoma (PTC) using strict criteria for N0 and N1 disease. We identified patients with PTC from our institution's pathology archives. Strict criteria were used for assessing the presence or the absence of central neck LNM. Disease was classified as N0 only if a comprehensive ipsilateral and pretracheal central neck dissection was performed and if pathological analysis revealed no evidence of LNM. Primary tumor samples were analyzed for a panel of known or suspected PTC-associated molecular markers, including BRAF, RET -PTC, KRAS, NRAS, HRAS, PIK3CA, and their variants. Academic medical center. Three hundred eighty-nine patients with PTC. Molecular mutations in tumors with and without LNM. Of 389 identified cases, 209 fit the inclusion criteria, with 158 classified as node positive (N1) and 51 as node negative (N0). The follicular variant histological type was present in 7 of 158 N1 tumors (4.4%) and 24 of 51 N0 tumors (47.1%) and thus was strongly associated with lack of central neck metastasis in this study (odds ratio, 0.05; 95% CI, 0.02-0.14). Predictive factors for central LNM included extracapsular extension, angiolymphatic invasion, and higher T stage (T3 and T4). The BRAF mutation was more prevalent in the classic PTC histological type than the follicular variant. None of the molecular marker mutations that were analyzed in this study, including the BRAF mutation, predicted LNM in classic PTC. Positive risk factors for central LNM include male sex, extracapsular extension, angiolymphatic invasion, and advanced T stage. The follicular variant histological type has a significantly lower incidence of central neck metastasis. In contrast to recent studies, the BRAF mutation was not significantly associated with central neck LNM from PTC when using a strict definition of a central neck dissection.

Correlation between loss of heterozygosity on chromosome 1p and 19q and expression of MGMT, p53 and Ki-67 proteins in gliomas

To study the correlation of loss of heterozygosity (LOH) on chromosome 1p and 19q with the expression of MGMT, p53 and Ki-67 proteins in gliomas. One hundred and forty six cases of gliomas (45 oligodendrogliomas, 42 oligodendroastrocytomas, and 59 astrocytomas) were included in this study. Their tissue and blood samples were retrospectively analyzed by PCR-denaturing high-performance liquid chromatography (DHPLC) for 1p and 19q status and by immunohistochemistry for MGMT, p53 and Ki-67 expression patterns. The correlation among them and with clinicopathological characteristics were analyzed by chi-square test and t-test. In the oligodendrogliomas, the positive rate of 1p LOH was 59.8%, significantly higher than 33.9% in astrocytomas (P = 0.002), and 1p and 19q LOH was 42.5%, significantly higher than 16.9% in astrocytomas (P = 0.001). Combined with LOH on 1p and 19q, low MGMT expression (65.5%), and high Ki-67 expression (54%) were more frequent in oligodendrogliomas, whereas high p53 expression was more frequent in astrocytomas and mixed tumors (75.2%). 1p LOH (72.5%) and low MGMT (87.5%) expressions were more frequent in grade II oligodendrogliomas, whereas high expressions of p53 (83.0%) and Ki-67 (76.6%) were more frequent in grade III oligodendrogliomas. In addition, high Ki-67 expression was more frequent in grade III astrocytomas. LOH on 1p and 19q LOH was more frequent in nontemporal oligodendrogliomas (55.6%) than that in temporal ones (22.2%, P = 0.002). Non-random associations were found between LOH 1p and 19q LOH, MGMT and p53 protein expressions, and MGMT and Ki-67 protein expressions (all P < 0.05), whereas mutual exclusions were found between LOH on 1p and 19q and p53 expression, and LOH 1p and Ki-67 expression. There is a significant interrelationship of the investigated molecular markers and clinicopathological features of gliomas, which support a promising role of molecular markers in guiding diagnostic assessment and clinical management of gliomas.

Myeloproliferative Neoplasms: The Role of Molecular Markers

1. LeiLani Collins, MS, MT(ASCP)SH[⇑][1] 1. University of Tennessee Health Science Center, Memphis, TN 1. Address for Correspondence: LeiLani Collins, MS, MT(ASCP)SH , University of Tennessee Health Science Center, 930 Madison Ave., Ste. 670, Memphis, TN 38163, 901-448-6299, Fax: 901-448-7545, lcollins{at}uthsc.edu After reading this article, the reader will be able to: 1. Describe the fusion gene formed as a result of the translocation t(9;22)(q34;q11) in chronic myelogenous leukemia. 2. Describe common symptoms of Philadelphia chromosome negative myeloproliferative neoplasms. 3. State the frequency of the occurrence of the JAK2 V617F mutation in PV, ET, and PMF. 4. Describe the significance of the JAK2 mutation in the diagnosis of PV, ET, and PMF. 5. Describe the significance of tyrosine kinase inhibitors on the treatment of MPNs. 6. Define current treatment for Philadelphia chromosome negative MPNs. 7. Describe the significance of imatinib treatment for CML on treatment for the other MPNs. The myeloproliferative neoplasms (MPN), formerly known as the myeloproliferative disorders (MPD), are a group of clonal disorders involving hyperproliferation of one or more of the myeloid cell lines (erythrocytic, granulocytic, megakaryocytic). The most common disorders traditionally classified as MPNs are chronic myelogenous leukemia (CML), polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF). Other, less common disorders in this group include chronic neutrophilic leukemia (CNL), chronic eosinophilic leukemia (CEL), mastocytosis, and myeloproliferative neoplasm, unclassifiable (MPN,U).1 All of these neoplasms are most common in people with a median age of 65 years at diagnosis but have been diagnosed in all age groups. Common presenting signs are fatigue, splenomegaly, and elevated cell counts. Often, there are bleeding or thrombotic symptoms. Chronic Myelogenous Leukemia (CML)— BCR/ABL1 -Positive MPN CML is a disease of “firsts” that has led the way for diagnostic, treatment, and prognostic factors for the other MPNs. It is the first disorder for which the term “leukemia” was used; the first malignancy associated with a recurring chromosomal abnormality (Philadelphia chromosome); the first disease in which the chromosomal abnormality formed a fusion gene ( BCR/ABL1 ); the first disease in which a protein fundamental to the pathogenesis of the disease was identified; and, the first disorder in which a therapeutic agent specifically targeted the molecular defect to effectively treat the disorder.1 Historically, CML was the first MPN to have a known acquired chromosomal abnormality, a reciprocal translocation between the long arms of chromosomes 9 and 22 known as the Philadelphia chromosome (Ph1) and designated as… After reading this article, the reader will be able to: 1. Describe the fusion gene formed as a result of the translocation t(9;22)(q34;q11) in chronic myelogenous leukemia. 2. Describe common symptoms of Philadelphia chromosome negative myeloproliferative neoplasms. 3. State the frequency of the occurrence of the JAK2 V617F mutation in PV, ET, and PMF. 4. Describe the significance of the JAK2 mutation in the diagnosis of PV, ET, and PMF. 5. Describe the significance of tyrosine kinase inhibitors on the treatment of MPNs. 6. Define current treatment for Philadelphia chromosome negative MPNs. 7. Describe the significance of imatinib treatment for CML on treatment for the other MPNs. [1]: #corresp-1

Role of molecular markers in the management of head and neck cancers

Head and neck squamous cell carcinoma (HNSCC) is the fifth most common cancer worldwide. Despite advances in treatment, the prognosis remains poor. HNSCC comprise a wide spectrum of neoplasms with different tumor biologies, prognosis and response to therapies. Current tumor classification is based on morphology and anatomic distribution, which leads to a homogeneous treatment for different diseases. Moreover, traditional diagnostic methods such as clinical assessment, histopathological examination, and imaging techniques are limited in their capacity to provide information on prognosis and decision making. Molecular markers have increased the understanding of the pathogenesis of head and neck cancer because they give increasing insight into tumor biology, prognosis, and response to therapy. The practical application of these discoveries is beginning to assist greatly in the evaluation and treatment of HNSCC to achieve a more personalized and effective approach. This article focuses on the molecular markers that have already been extensively studied such as epidermal growth factor receptor and human papillomavirus as well as those that offer potential for personalized therapy such as HIF-1 and ERCC-1. The ideal biomarker should be assayed accurately and easily, highly specific, and cost effective. Thus, a validation is required before their implementation into clinical guidelines.

The role of Molecular Markers in Improvement of Fruit Crops

Markers have been used over the years for the classification of plants. Markers are any trait of an organism that can be identified with confidence and relative easy, and can be followed in a mapping population on another hand markers be defined as heritable entities associated with the economically important trait under the control of polygenes. Morphological markers can be detected with naked eye (naked eye polymorphism) or as difference in physical or chemical properties of the macromolecules. In other words, there are two types of genetic markers viz. morphological markers or naked eye polymorphism and non-morphological markers or molecular markers. Morphological markers include traits such as plant height, disease response, photoperiod, sensitivity, shape or colour of flowers, fruits or seeds etc. Molecular markers include biochemical constituents. Morphological markers have many limitations for being used as markers particularly in fruit crops because of long generation time and large size of fruit trees besides being influenced by environment. Consequently, molecular markers could be appropriate choice to study and preserve the diversity in any germplasm. Molecular markers have diverse applications in fruit crop improvement, particularly in the areas of genetic diversity and varietal identification studies, gene tagging, disease diagnostics, pedigree analysis, hybrid detection, sex differentiation and marker assisted selection.

The role of molecular markers and marker assisted selection in breeding for organic agriculture

Plant geneticists consider molecular marker assisted selection a useful additional tool in plant breeding programs to make selection more efficient. Standards for organic agriculture do not exclude the use of molecular markers as such, however for the organic sector the appropriateness of molecular markers is not self-evident and is often debated. Organic and low-input farming conditions require breeding for robust and flexible varieties, which may be hampered by too much focus on the molecular level. Pros and contras for application of molecular markers in breeding for organic agriculture was the topic of a recent European plant breeding workshop. The participants evaluated strengths, weaknesses, opportunities, and threats of the use of molecular markers and we formalized their inputs into breeder’s perspectives and perspectives seen from the organic sector’s standpoint. Clear strengths were identified, e.g. better knowledge about gene pool of breeding material, more efficient introgression of new resistance genes from wild relatives and testing pyramided genes. There were also common concerns among breeders aiming at breeding for organic and/or conventional agriculture, such as the increasing competition and cost investments to get access to marker technology, and the need for bridging the gap between phenotyping and genotyping especially with complex and quantitative inherited traits such as nutrient-efficiency. A major conclusion of the authors is that more interaction and mutual understanding between organic and molecular oriented breeders is necessary and can benefit both research communities.