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Ghatak S.,Mizoram University | sanga Z.,Mizoram University | Pautu J.L.,Mizoram State Cancer Institute | Kumar N.S.,Mizoram University
Journal of Clinical Laboratory Analysis | Year: 2015

Background: Retrospective studies of archived human specimens, with known clinical follow-up, are used to identify predictive and prognostic molecular markers of disease. Due to biochemical differences, however, formalin-fixed paraffin embedded (FFPE) DNA and RNA have generally been extracted separately from either different tissue sections or from the same section by dividing the digested tissue. Our optimized co-extraction approach provides the option of collecting DNA, which would otherwise be discarded or degraded, for additional or subsequent studies because of the high importance and less availability of clinical FFPE specimen. Methods: Coextraction of DNA and RNA from a single gastric cancer FFPE specimen was optimized by using TRIzol and purifying DNA from the lower aqueous and RNA from the upper organic phases. The protocol involves modification of incubation period for 30 min with proteinase K in glycin-tris-ethylenediamine tetra acetic acid buffer before adding TRIzol. Results: All samples tested successfully performed semiquantitative gene expression by reverse transcriptase PCR. The quantity and quality of DNA from FFPE samples was high which resulted in successful PCR amplification. The isolated DNA also aided in detection of Helicobacter pylori by amplifying the ribosomal 16S gene in a multiplex PCR reaction along with cagA. Conclusion: These results show that the RNA/DNA isolated by this method can be used for easy clinical diagnosis of disease-related gene expression as well as mutation and pathogen detection from a homogenous population of tumor cells. © 2015 Wiley Periodicals, Inc. Source


Mallath M.K.,Tata Medical Center | Taylor D.G.,University College London | Badwe R.A.,Tata Memorial Center | Rath G.K.,All India Institute of Medical Sciences | And 20 more authors.
The Lancet Oncology | Year: 2014

Cancer can have profound social and economic consequences for people in India, often leading to family impoverishment and societal inequity. Reported age-adjusted incidence rates for cancer are still quite low in the demographically young country. Slightly more than 1 million new cases of cancer are diagnosed every year in a population of 1·2 billion. In age-adjusted terms this represents a combined male and female incidence of about a quarter of that recorded in western Europe. However, an estimated 600 000-700 000 deaths in India were caused by cancer in 2012. In age-standardised terms this figure is close to the mortality burden seen in high-income countries. Such figures are partly indicative of low rates of early-stage detection and poor treatment outcomes. Many cancer cases in India are associated with tobacco use, infections, and other avoidable causes. Social factors, especially inequalities, are major determinants of India's cancer burden, with poorer people more likely to die from cancer before the age of 70 years than those who are more affluent. In this first of three papers, we examine the complex epidemiology of cancer, the future burden, and the dominant sociopolitical themes relating to cancer in India. © 2014 Elsevier Ltd. Source


Thapa S.,Mizoram University | Lalrohlui F.,Mizoram University | Ghatak S.,Mizoram University | Zohmingthanga J.,Civil Hospital | And 3 more authors.
Breast Cancer | Year: 2016

Background: Mizoram has the highest incidence of cancer in India. Among women, breast cancer is most prevalent and the state occupies fifth position globally. The reason for high rate of cancer in this region is still not known but it may be related to ethnic/racial variations or lifestyle factors. Methods: The present study aims to identify the candidate mitochondrial DNA (mtDNA) biomarkers—ND1and ATPase for early breast cancer diagnosis in Mizo population. Genomic DNA was extracted from blood samples of 30 unrelated breast cancer and ten healthy women. The mtNDI and mtATP coding regions were amplified by step-down PCR and were subjected to restriction enzyme digestion and direct sequencing by Sanger method. Subsequently, the results of the DNA sequence analysis were compared with that of the revised Cambridge Reference Sequence (rCRS) using Mutation Surveyor and MITOMAP. Results: Most of the mutations were reported and new mutations that are not reported in relationship with breast cancer were also found. The mutations are mostly base substitutions. The effect of non-synonymous substitutions on the amino acid sequence was determined using the PolyPhen-2 software. Statistical analysis was performed for both cases and controls. Odds ratios (ORs) and 95 % confidence intervals (CIs) were estimated from logistic regression. High intake of animal fat and age at menarche was found to be associated with a higher risk of breast cancer in Mizo population. Conclusion: Our results also showed that ATPase6 as compared to ATPase8 gene is far more predisposed to variations in Mizo population with breast cancer and this finding may play an important role in breast cancer prognosis. © 2015, The Japanese Breast Cancer Society. Source


Ghatak S.,Mizoram University | Lallawmzuali D.,Mizoram State Cancer Institute | Lalmawia,Mizoram University | Sapkota R.,Mizoram University | And 4 more authors.
Current Genetics | Year: 2014

Mitochondrial DNA (mtDNA) is known for its high frequencies of polymorphisms and mutations as it is prone to oxidative stress. The aim of the present study is to assess the novel mutations in mitochondrial genes from blood samples among the breast cancer patients from a less studied Northeast Indian population. D, B, L haplogroups were observed in the cancer samples and a total of 44 mtDNA D-loop sequence variations at 42 distinct nucleotide positions were found. All the sequence variations were transitional substitutions and 6 were heteroplasmic states, except for a cytosine copy number change (9C/8C) at np 303e309 in three samples examined. A total of 88 Cytochrome Oxidase C subunit I (COXI) sequence differences with respect to the Revised Cambridge Reference Sequence (rCRS) were identified including 20 missense variants with 100 % sample mutation frequency. All 20 missense mutations are highly conserved with a Cumulate Index of 100 %. Among 88 COXI mutations, 24 (13 were Non-Synonymous and 11 were Synonymous) were not previously reported (novel mutation) in the literature or the public mtDNA mutation databases. Analysis of three-dimensional structure of COXI open reading frame (ORF) predicted the effect of one single codon (96R > C, 217T > I, 224-225GG > EE and 227D > T) mutations located in the signal peptide binding position. Analysis of mitochondrial DNA mutations, as a viable alternative, has the advantage of being capable of detecting inherent risk factors for breast cancer development. © 2014 Springer-Verlag. Source


Kimi L.,Mizoram University | Ghatak S.,Mizoram University | Yadav R.P.,Mizoram University | Chhuani L.,Mizoram University | And 3 more authors.
Biochemical Genetics | Year: 2016

The enzymes encoded by glutathione S-transferase mu 1 (GSTM1) and theta 1 (GSTT1) genes are involved in the metabolism of wide range of carcinogens that are ubiquitous in the environment. Homozygous deletions of the GSTM1 and GSTT1 genes are commonly found and result in lack of enzyme activity. This study was undertaken to evaluate the association between GSTM1, GSTT1 and GSTP1 gene polymorphism and breast cancer risk in Mizoram population. Odd ratio (OR) and 95% confidence interval (CI) from conditional logistic regression model were used to estimate the association between genetic polymorphism and breast cancer risk. The GSTM1 and GSTT1 null genotypes were associated with an increased risk of breast cancer [OR = 10.80 (95% CI 1.16–100.43)]. The risk of breast cancer associated with the GSTT1 null genotype was observed to be low among postmenopausal women. When considered together, GSTM1 and GSTT1 genotypes were found to be associated with an increased risk of breast cancer. The relationship between GSTM1 and GSTT1 gene deletions and breast cancer risk was substantially altered by consumption of Smoked Meat/Vegetable. In the present study, GSTP1Ile105Val (rs1695) polymorphism was related to breast cancer susceptibility or phenotype. Our data provides evidence for substantially increased risk of breast cancer associated with GSTM1 and/or GSTT1 homozygous gene deletions in Mizoram population. © 2015, Springer Science+Business Media New York. Source

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