Cell-free DNA concentration and integrity as a screening tool for cancer.

AIM OF THE STUDY: This study aims to evaluate cell-free DNA (CFDNA) concentration and integrity in patients with malignant and nonmalignant diseases and in controls to investigate their value as a screening test for cancer, and to correlate them with clinicopathological parameters of cancer patients. MATERIALS AND METHODS: The study included three groups; group I: 120 cancer patients, group II: 120 patients with benign diseases and group III: 120 normal healthy volunteers as control. One plasma sample was collected from each subject. CFDNA was purified from the plasma then its concentration was measured and integrity was assessed by PCR amplification of 100, 200, 400, and 800 bp bands. RESULTS: There was a highly significant difference in CFDNA levels between cancer group and each of benign and control groups. AUC of ROC curve for cancer group versus normal and benign groups were 0.962 and 0.895, which indicated the efficiency of CFDNA as a marker of cancer. As for integrity, normal and benign subjects showed only two bands at 100 and 200 bp, while all cancer patients demonstrated the 400 bp band and 78% of them had the 800 bp whose presence correlated with vascular invasion. CONCLUSION: The combined use of CFDNA concentration and integrity is a candidate for a universal screening test of cancer. Upon setting suitable boundaries for the test it might be applied to identify cancer patients, particularly among subjects with predisposing factors. Being less expensive, CFDNA concentration could be applied for mass screening and for patients with values overlapping those of normal and benign subjects, the use of the more expensive, yet more specific, integrity test is suggested.

Identification of three new mutations in the RB1 gene in patients with sporadic retinoblastoma in Colombia / Identificación de tres nuevas mutaciones en el gen RB1 en pacientes con retinoblastoma esporádico en Colombia

Introduction. Retinoblastoma is a childhood cancer of the retina originated by altered or null retinoblastoma protein (pRb) expression. Genetic alterations in both RB1 alleles in the retinal cells are required for the development of retinoblastoma. In the sporadic form, non-hereditary RB1 gene mutations take place in a single retinoblast cell, and are therefore only present in tumor DNA (somatic mutations). Sporadic retinoblastoma is primarily unilateral, lacks family history and has no risk of transmission to descendants. Genetic tests for detection of RB1 mutation has improved the identification of carriers and facilitated accurate genetic counseling. Objective. To identify mutations in the RB1 gene in Colombian patients with sporadic retinoblastoma by PCR-SSCP followed by sequence. Materials and methods. Four patients with sporadic retinoblastoma were analyzed by PCR-SSCP, followed by DNA sequencing to identify variations in the RB1 gene. Results. We identified five variations in RB1 gene: three new mutations (one germline and two somatic mutations), one new polymorphism and one already reported somatic mutation. Four mutations were found in three patients with unilateral retinoblastoma and one mutation was found in a patient with bilateral retinoblastoma. One of these was a germline mutation in a sporadic unilateral retinoblastoma that was not present in the parents or three siblings analyzed. Conclusions. Our results emphasize the importance of identifying mutations for genetic counseling and clinical management of sporadic retinoblastoma patients. Description of a new RB1 gene variant is interesting since there have been a small number of polymorphisms reported for this gene.

Introducción. El retinoblastoma es un cáncer pediátrico de la retina originado por la expresión alterada o ausente de la proteína del retinoblastoma (pRb). Se requiere la alteración genética de ambos alelos RB1 en las células de la retina para el desarrollo del retinoblastoma. En la forma esporádica, las mutaciones no hereditarias del gen RB1 ocurren en un solo retinoblasto y están presentes sólo en el ADN del tumor (mutaciones somáticas). El retinoblastoma esporádico es generalmente unilateral, no tiene historia familiar y no tiene riesgo de transmisión a la descendencia. Las pruebas genéticas para la detección de mutaciones en RB1 han mejorado la identificación de portadores y han facilitado la precisión de la asesoría genética. Objetivo. Detectar mutaciones en el gen RB1 en pacientes colombianos con retinoblastoma esporádico mediante PCR-SSCP seguido de secuenciación. Materiales y métodos. Se analizaron cuatro pacientes con retinoblastoma esporádico para la detección de variaciones en el gen RB1 mediante PCR-SSCP, seguida de secuenciación. Resultados. Se identificaron cinco variaciones del gen RB1 : tres mutaciones nuevas (una de línea germinal y dos somáticas), un polimorfismo nuevo y una mutación somática ya reportada. Las cuatro mutaciones se encontraron en tres pacientes con retinoblastoma unilateral y uno con bilateral. La mutación germinal se detectó en un paciente con compromiso unilateral y no se encontró en los padres ni en los tres hermanos analizados. Conclusión. Estos resultados enfatizan la importancia, para asesoría genética y manejo clínico, de identificar mutaciones del gen RB1 en pacientes con retinoblastoma esporádico. La descripción de una nueva variante en RB1 es interesante, dado el muy bajo número de polimorfismos reportados para este gen.

A Modified Extraction Method of Circulating Free DNA for Epidermal Growth Factor Receptor Mutation Analysis

PURPOSE: Circulating free DNA (cfDNA) in plasma is promising to be a surrogate for tumor tissue DNA. However, not all epidermal growth factor receptor (EGFR) mutations in tumor tissue DNA has been detected in matched cfDNA, at least partly due to inefficient cfDNA extraction method. The purpose of this study was to establish an efficient plasma cfDNA extraction protocol. MATERIALS AND METHODS: The yield of plasma cfDNA extracted by our modified phenol-chloroform (MPC) method from non-small-cell lung cancer (NSCLC) patients was compared with that by QIAamp MinElute Virus Spin kit (Qiagen kit) as control, using the Wilcoxon rank-sum test. TaqMan quantitative polymerase chain reaction (qPCR) assays were used to quantify the plasma cfDNA extracted. Both Mutant-enriched PCR (ME-PCR) coupled sequencing and DxS EGFR mutation test kit were used to evaluate the impact of extraction method on EGFR mutation analysis. RESULTS: MPC method extracted more plasma cfDNA than Qiagen kit method (p=0.011). The proportion of longer fragment (> or =202 bp) in cfDNA extracted by MPC method was significantly higher than by Qiagen kit method (p=0.002). In the sequencing maps of ME-PCR products, a higher mutant peak was observed on plasma cfDNA extracted by MPC method than by Qiagen kit method. In DxS EGFR mutation test kit results, plasma cfDNA extracted by MPC method contained more tumor-origin DNA than by Qiagen kit method. CONCLUSION: An improved plasma cfDNA extraction method of MPC is provided, which will be beneficial for EGFR mutation analysis for patients with NSCLC.

Utility of blood DNA levels in diagnosis of breast cancer.

BACKGROUND: Prognostic factors, including both histopathological and biochemical variables, influence the choice of modality and the course of therapy in breast cancer. The biomarkers found in biological fluids, particularly in blood, apparently hold the best promise for the development of screening assays. AIM: To find out if any correlation exists between blood DNA level and tumor stage, size and grade. MATERIALS AND METHODS: This case-control study was carried out on 52 female patients in the age-group of 18-70 years. The cases comprised 25 patients with histopathologically confirmed malignant breast cancer, while 27 patients with benign breast tumors served as the control group. STATISTICAL ANALYSIS: We used the Student's 't' test to compare the differences between the blood DNA levels in the two groups. Pearson's test was performed to find out the correlation between blood DNA levels and the TNM stage, tumor size and grade. RESULTS: It was observed that blood DNA levels showed statistically significant correlation with the TNM stage, tumor size and grade. CONCLUSION: The blood DNA level can be utilized as a noninvasive marker to assess tumor aggressiveness. Thus, it can be useful as a prognostic marker and as a marker of tumor burden.

Role of an androgen receptor gene polymorphism in development of hormone refractory prostate cancer in Indian population.

BACKGROUND: Androgen receptors play critical roles in the development of primary as well as advanced hormone-refractory prostate cancers. Since the growth of prostate cancer is androgen-sensitive, metastatic disease has been treated by hormonal therapy in the form of androgen ablation. Prostate cancer cells rely on androgen receptor (AR) for proliferation and survival. AIM: To evaluate the prognostic significance of androgen receptor polymorphism in patients under hormonal therapy in any form. METHODS: Complete follow up data were available for 87 patients out of 130 patients enrolled for study. DNA was extracted from blood samples using salting out method and then subjected to PCR Genscan for CAG and GGN genotyping. The mean follow up was 10.12+/-8.83 months. RESULTS: Out of 87 patients, 64 experienced clinical as well as biochemical recurrence. The overall hormone refractory rates were 73.4% after one year. We observed a significant shorter median CAG repeats in HRPC patients (20 vs 22). The hazard ratio for HRPCs with the < or =20 CAG repeat genotype was 0.602 (0.33-1.08, p=0.09). Kaplan-Meier analysis showed that HRPC rates were not significantly associated with CAG repeat (p=0.06) but a trend was observed with short CAG repeats. No significant association was observed with AR-GGN repeats. CONCLUSIONS: A trend for association of AR-CAG repeats with HRPC patients in north Indian population was observed, suggesting this to be a prognostic factor for determining the therapeutic regimen.

Quantification of Plasma DNA as a Tumor Marker in Patients with Pancreatic Cancer / 대한소화기학회지

BACKGROUND/AIMS: The plasma DNA concentration of patients with cancer is known to be higher than normal controls. Increased DNA concentration and tumor-specific genes in plasma can be used as tumor markers in some cancers. This study was designed to evaluate whether quantification of plasma DNA concentration by using real-time PCR is useful as a tumor marker in the diagnosis of pancreatic cancer. METHODS: Twenty-four patients (M:F=16:8, mean age; 60.5+/-11.5 years) with pancreatic cancer were recruited for this study. Fifteen patients with chronic pancreatitis and fifteen healthy persons were selected as controls (M:F=26:4, 53.5+/-11.2 years). The concentration of plasma DNA was determined by real-time PCR for telomerase reverse transcriptase gene. RESULTS: Plasma DNA concentration in patients with pancreatic cancer (46.4+/-63.2 ng/mL) was higher than that of chronic pancreatitis (p=0.041) and normal controls (p=0.030). The sensitivity and specificity in detecting pancreatic cancer were 75% and 70% respectively when the cut-off value of plasma DNA concentration was set at 46.9 ng/mL. CONCLUSIONS: Plasma DNA concentration in patients with pancreatic cancer was higher than that of controls. However, its sensitivity and specificity is not high enough to be used as a tumor marker for pancreatic cancer.

NAT2 gene polymorphism in bladder cancer: a study from North India

PURPOSE: This study was conducted to examine: 1) whether the NAT2 genotypes are risk factors for bladder cancer, 2) to study possible association of tobacco usage with NAT2 genotype of these patients. MATERIALS AND METHODS: This case control study was undertaken over a period of 19 months and included 101 bladder cancer patients and 110 controls. The NAT2 genotypes were identified by PCR-RFLP method in peripheral blood DNA samples. Genotypes frequencies and the association of the genotypes among patients and controls group were assessed by chi2 test and Fisher exact test. RESULTS: The NAT2 fast acetylator genotype frequency of slow or fast acetylator genotypes was not significant in bladder cancer patients alone (OR = 1.18, 95 percent CI: 0.69 - 2.03, p value = 0.583) or combination with tobacco users (OR = 0.84, 95 percent CI: 0.328 - 2.125, p value = 0.813) when compared with controls. CONCLUSION: These data demonstrate that the NAT2 fast or slow acetylators genotype did not associated with the risk of developing bladder cancer in North Indian population when compared with controls.

Circulating DNA in plasma or serum

Small amounts of DNA circulate in both healthy and diseased human plasma/serum, and increased concentrations of DNA are present in the plasma of cancer patients. Characteristics of tumor DNA have been found in genetic material extracted from the plasma of cancer patients. These features include decreased strand stability, the presence of specific oncogene or tumor suppressor gene mutations, microsatellite alterations, Ig rearrangements and hypermethylation of several genes. The results obtained in many different cancers have opened a new research area indicating that plasma DNA might eventually be a suitable target for the development of noninvasive diagnostic, prognostic and follow-up tests for cancer. Following the discovery of tumor derived DNA in plasma or serum, cell-free fetal DNA has also been found in maternal plasma and serum. This discovery provides an easily accessible source of fetal genetic material for prenatal diagnosis.

Diagnostico precoz de neoplasia endocrina multiple tipo 2 (MEN 2) por la deteccion de portadores de mutaciones en el proto-oncogen RET / Early diagnosis of multiple endocrine neoplasia type 2 by detection of matated RET proto-oncogene carriers

El MEN 2 es un síndrome hereditario autosómico dominante, en el cual mutaciones del RET dan origen a tres fenotipos diferentes: carcinoma medular de tiroides familiar (CMTF), MEN 2A y MEN 2B. La identificación de mutaciones en el proto-oncogen RET predice el desarrollo de la enfermedad antes de las evidencias clínicas y bioquímicas. En este trabajo se identificaron portadores del RET por caracterización de mutaciones en pacientes y sus familiares. Se estudiaron 21 familias con CMTF (5 y 6 miembros), 4 con MEN 2A (dos de 5, una de 4 y otra de 3 miembros) y 2 con MEN 2B (5 y 1 miembros). Se obtuvieron muestras de ADN de sangre, en todos los casos y de tejido de feocromocitoma y/o tejido tiroideo en los operados. Se utilizó PCR para amplificar los exones 10, 11 y 16 con oligonucleótidos específicos, realizándose secuenciación directa de los fragmentos. En las familias con CMTF y con MEN 2A se encontraron mutaciones en el codón 634 del exón 11 en 16 sujetos, dectándose 9 casos con la mutación TGC r CGC (cisteína a arginina), 3 con TGC r TAC (cisteína a tirosina) y 4 con TGC r TTC (cisteína a fenilalanina). En los pacientes con MEN 2 B se encontró una mutación en el codón 918 del exón 16 ATG r ACG (meitonina a treonina). En tejido tumoral se detectó la misma mutación que en sangre periférica. El diagnóstico de MEN 2 fue confirmado en los 8 pacientes y detectado en 10 familiares. En los 5 portadores tiroidectomizados se encontró hiperplasia de células C o microcarcinoma in situ en 2 niños (9 y 12 años) y CMT en 3 adultos. La detección temprana de mutaciones del RET, especialmente en familiares seguida por tiroidectomía total, podría prevenir el desarrollo de CMT, modificado el desenlace fatal que ocurre cuando es diagnosticado tardíamente.