Papers by Arshad A. Pandit
Bangladesh Journal of Medical Science, 2016
Introduction: A genetic polymorphism has been identified inside the CD14 Promoter sequence. It co... more Introduction: A genetic polymorphism has been identified inside the CD14 Promoter sequence. It consists of a C to T transition at base pair -159 from the major transcription site. Subjects carrying the T allele have been shown to have significantly higher soluble CD14 levels than do carriers of the C allele. Consequently, genetic variations in CD14 particularly polymorphism located on the promoter region are thought to have functional effects and increased susceptibility to sepsis.Methods: Our study was a case control study in which a total of 85 samples were included out of which 50 were sepsis free controls and 35 cases of sepsis. Both the cases and controls were selected from Surgical Intensive Care Unit of Sher-i-Kashmir Institute of Medical Sciences (SKIMS), Srinagar. Age more than 80 years, cardiac failure, liver insufficiency and cancer patients were excluded from the study. 5ml of blood from peripheral vein was obtained from each subject in EDTA containing vials and DNA extr...
Revista Argentina de microbiología
Comparison of different methods of DNA extraction from blood to detect fungal DNA by PCR. Invasiv... more Comparison of different methods of DNA extraction from blood to detect fungal DNA by PCR. Invasive fungal infections (IFI) are associated with high mortality by reaching levels of 50%, and also with a significant failure in antifungical treatments. This fact mostly obeys to difficulties in obtaining a fast and accurate mycologic diagnosis due to the low sensitivity of conventional methods, mainly in neutropenic and AIDS patients. Various methods based on fungal DNA study are currently being used for the diagnosis of mycotic infections. We herein evaluated two procedures of extraction and purification of fungal DNA in blood for their use in PCR detection. Both of them showed equal efficiency in obtaining high performance DNA with universal primers ITS land ITS 4 as target.
The Journal of Urology, 2011
Journal of Genetic Syndromes & Gene Therapy, 2015
Ambiguous Genitalia, a rare genetic disorder is caused by defects in the process of fetal sexual ... more Ambiguous Genitalia, a rare genetic disorder is caused by defects in the process of fetal sexual determination and differentiation where a newborn needs prompt evaluation to detect lethal conditions and gender assignment. This genetic screening is taken up with an aim to evaluate the prevalence of the patients born with Ambiguous Genitalia existing in our population.
Journal of Genetic Syndromes & Gene Therapy, 2015
Background: Cystic Fibrosis (CF) one of the most common severe autosomal recessive disorders is c... more Background: Cystic Fibrosis (CF) one of the most common severe autosomal recessive disorders is caused by mutations in CFTR gene. The mutation distributions vary widely between different geographical and ethnic groups. In view of ethnic nature of Kashmiri population (North India), we aim at looking for the 3 common mutations Δ508, 3849+10 kb, C>T and W1282X in CF suspected cases. Method: The mutations were evaluated in 150 highly suspected children with CF, proven by clinical features. ARMS-PCR was used for mutation detection of Δ508 and W1282X while as 3849+10 kb, C>T was assessed by indigenously developed ARMS-PCR and results were confirmed by RFLP. Results: Of the 150 suspected CF cases, one of the three mutations was found in 60 out of the 300 alleles genotyped. Δ508 mutation was found in 36 of 150 (24%) cases, 3849+10 kb, C>T in 24 of 150(16%) cases while as no mutation was observed in W1282X. Interestingly 08 of 09 samples with normal sweat chloride were detected positive for 3849+10 kb, C>T mutation. Conclusion: In this report, frequency of the Δ508 mutation in Kashmiri children with CF is less as compared to the Western Countries. Interestingly, we identified 3849+10 kb, C>T mutation as unique in population under study with much higher frequency as compared to rest of the world. Further we found intron 19, 3849+10 kb, C>T mutation serves as marker in those CF cases having sweat chloride negative.
Cancer biomarkers : section A of Disease markers, Jan 2, 2015
Among various polymorphic variants of TP53 gene, codon 72 polymorphism (Arg72Pro) has been found ... more Among various polymorphic variants of TP53 gene, codon 72 polymorphism (Arg72Pro) has been found to be associated with cancer susceptibility, but only few studies have investigated their effect on thyroid cancer risk. A case control study was conducted to elucidate the possible role of this SNP as risk factor in thyroid cancer development and to examine its correlation with various clinicopathological variables. In this study, we tested the genotype distribution by PCR-RFLP in 140 thyroid cancer patients and 200 cancer-free controls from Kashmir Valley. Genotype frequencies of Arg/Arg (GG), Arg/Pro (GC), and Pro/Pro (CC) genotypes among cases were 0.286, 0.343 and 0.371 while in controls 0.45, 0.37 and 0.18 respectively. Proline allele frequency was significantly higher than arginine frequency in patient group (OR=2.06, 95% C.I=1.5-2.8). Significant association was found between variant genotype of codon 72 of TP53 gene and young age group, female gender, urban dwellers, non-smokers...
Asian Pacific Journal of Cancer Prevention Apjcp, 2010
AIM: To assess clinical utility of NMP22 Bladder Check Test and to compare it with voided urine c... more AIM: To assess clinical utility of NMP22 Bladder Check Test and to compare it with voided urine cytology and cystoscopy in early detection of Bladder Cancer.MATERIAL AND METHODS: A total of 115 patients of follow up cases of bladder cancer were enrolled in this study. Urine samples were assayed for the presence of NMP22 using NMP22 Bladder Check Test and cytology was performed by a cytopathologist. The diagnosis, determined from the cystoscopic findings and biopsy findings of the suspicious lesion was considered as the gold standard. For positive biopsies, the results of the NMP22 Test and cytology were also correlated with tumour grade and stage.RESULTS: Mean age of the patients was 57.2 years for males and 55.3 years for females. A total of 59 cases of transitional cell carcinomas (TCCs) were diagnosed among which NMP22 test was positive in 48 cases and cytology in 26 cases. The sensitivity and specificities of NMP22 Test in recurrent bladder cases was 81.3% and 92% which was significantly greater than that of cytology 44% and 96.1% respectively. In non-invasive lesions of TCC, NMP22 Test and cytology was positive in 71.8% and 42.8% of cases respectively. In muscle-invasive lesions, NMP22 Test was positive in 82.2% and 44.4% cases were positive for cytology. The sensitivity of the NMP22 test was 81.3%, which was significantly greater than that of cytology at 44%.CONCLUSION: The NMP22 Bladder Check is a new point of care diagnostic test for urinary bladder cancer. The results of our study have shown that the NMP22 can be used as a substitute for urine cytology as we achieved high sensitivity and specificity with recurrent bladder cases.
Journal of cellular biochemistry, Jan 3, 2015
RET gene polymorphisms act to influence thyroid cancer in a polygenic and low-penetrance manner a... more RET gene polymorphisms act to influence thyroid cancer in a polygenic and low-penetrance manner and no study regarding RET alterations in thyroid cancer has undergone from this part of the world (North India). We evaluated RET G691S (rs1799939), L769L (rs1800861) and S904S (rs1800863) polymorphisms to elucidate their possible role as risk factors in papillary thyroid cancer (PTC) and follicular thyroid cancer (FTC). Polymorphic analysis of RET gene was performed by polymerase chain reaction (PCR), followed by restriction fragment length polymorphism (RFLP). In RET G691S polymorphism, the overall distribution of variant alleles (GA + AA) in cases was 62.9% as against 44.5% in controls (P < 0.05) whereas frequency of RET L769L variant alleles (TG + GG) in cases was 70% versus 88% in controls (P < 0.05). In RET S904S, frequency of variant alleles (CG + GG) in cases was 56% versus 44% in controls (P < 0.05). Interestingly, G691S/L769L variant showed increased risk for the non-s...
Bladder cancer is the fourth most incident cancer in males and ninth most in females. In the Unit... more Bladder cancer is the fourth most incident cancer in males and ninth most in females. In the United States, over 67,000 new cases are diagnosed per year, and over 350,000 1 cases diagnosed worldwide. Men have a higher risk of bladder cancer than women transitional cell carcinoma (3:1). Urothelium cancers account for 5.6% of male and 1.8% of female cancers in India, with actual crude rate incidence of 2 about 1 in 174 and 1 in 561 women, respectively. We conducted a detailed study of the bladder cancer cases registered from 2005 to 2010 in the only tertiary care hospital in India. This study revealed that bladder cancer ranks as the 7th leading cancer and accounts for 5.9% of all prevalent cancers in the Kashmiri population (data accepted). Bladder cancer arises primarily from transitional cells of the bladder mucosal epithelium (90% of cases) and may present as a noninvasive, papillary tumor protruding from the mucosal surface, which is readily resectable. This stark difference in morphology and survival implicates separate oncogenic pathways for noninvasive compared to muscle-3,4 invasive cancer. The incidence of bladder cancer was strongly associated with occupational exposure to aromatic amines used in the dye industry, before their potent
Biology and Medicine, 2015
Background: Studies have demonstrated that the mutant *2 and*3 allele of the CYP2C19 loss-of-func... more Background: Studies have demonstrated that the mutant *2 and*3 allele of the CYP2C19 loss-of-function polymorphism is associated with diminished metabolization of clopidogrel and an attenuated platelet response to clopidogrel treatment. Since no such study has been conducted in this region, we examined CYP2C19 polymorphism in Acute Coronary Syndrome (ACS) patients on clopidogrel treatment, and its effect on the cardiovascular outcomes. Material and Methods: A total of 100 samples of ACS were included in this study and genotyping of CYP2C19 *2 and *3 gene polymorphisms was performed by a Polymerase chain reaction-Restriction fragment length polymorphism (PCR-RFLP). Results: The distribution of CYP2C19*2 allele wild *1/*1, Heterozygous *1/*2 and homozygous mutant *2/*2 genotypes was 56%, 34% and 10% respectively while for CYP2C19*3 wild*1/*1 and heterozygous *1/*3 genotypes was 84% and 16% respectively. The frequency of compound heterozygotes (*2/*3) was found in 9% (9 of 100 patients). CYP2C19 *1/*2 allele was found in 03 of 34 (8.8%) patients who had CV events followed by 2 of 10 (20%) patients with mutant genotype CYP2C19*2 (*2/*2) on follow up. In the CYP2C19*3, 31.2% having heterozygous genotype (*1/*3) had CV events as compared to 11.9% with *1/*1 (31% v/s 11.9% p> 0 .05). In the poor-metabolizer group (*2/*2 or *2/*3), 20.1% of patients had CV events on follow up compared to 15.6% in the extensive metabolizer group (*1/*1), whereas in the intermediate group only 10% of patients had CV events (p>0.05). Conclusion: We conclude that patients carrying CYP2C19 loss-of-function alleles had a higher rate of subsequent cardiovascular events as against those with normal allele. Lack of significant events even in presence of variant alleles justifies us to some extent to continue clopidogrel in our patients. B io lo g y and M e d ic in e
Asian Pacific Journal of Cancer Prevention Apjcp, 2010
The focus of the study was to investigate the frequencies of homozygous deletions and mutations o... more The focus of the study was to investigate the frequencies of homozygous deletions and mutations of p16 gene in gastric carcinomas in the Kashmiri population. A total of 84 gastric carcinoma patients were screened by the single strand conformation polymorphism (SSCP) technique and later by DNA sequencing to detect mutations of the p16 gene. Also PCR was applied further to further detect any homozygous deletions. SSCP and DNA sequencing performed encompassing all the three exons of p16 gene could not detect any mutations in any ofl 84 cases. Though we could observe mobility shifts in SSCP of two samples, subsequent DNA sequencing did not show any mutation. Further PCR could not detect any homozygous deletion in P16 in any case. Though Kashmir is a high incidence area of gastric carcinomas, p16gene mutations /or deletions do not appear to be involved.
Egyptian Journal of Medical Human Genetics, 2016
Background: Primary amenorrhea (PA) is proposed to have multiple etiological factors that include... more Background: Primary amenorrhea (PA) is proposed to have multiple etiological factors that include genetic factors, intrauterine malformations, endocrine dysfunction and environmental factors, as revealed by previous studies pertaining to amenorrhea. However, among the various proposed etiologies, genetic factors appear to be highly associated with PA as approximately 40% of PA cases have been found to have genetic causes. Aim of the study: The present study was proposed to establish the frequency and pattern of chromosomal abnormalities in PA cases of Kashmir. Subjects and methods: A total of 108 females within the age group of 14-33 years and having a history of amenorrhea were included in the study. Peripheral blood lymphocyte cultures were set for each subject according to standard protocol and chromosomal analysis was carried out on well spread metaphases by the help of Cytovision software Version 3.9. Results: The results of the present study reveal that the incidence of chromosomal abnormalities in PA cases of this region is almost similar with those of many reports around the world. However, we report two unique chromosomal alterations viz., 46,XX, dup2q(13) and 46,XX, t(2,5)(p11.2;q34) that have not been found elsewhere in the literature. Conclusion: The results of the present study indicate that chromosomal analysis of females with PA, after the exclusion of non-genetic causes, should be essentially considered for the precise diagnosis and the development of more successful treatment. The study being the first of its kind in this part of the world forms the basis for further studies of the PA cases of this region. The precise molecular characterization of the unique breakpoint regions reported in our study can possibly help in the identification of new genes involved in primary amenorrhea.
Egyptian Journal of Medical Human Genetics, 2016
There are several syndromes in which specific mitotic chromosomal abnormalities can be seen, like... more There are several syndromes in which specific mitotic chromosomal abnormalities can be seen, like premature centromere separation, premature (sister) chromatid separation, and somatic aneuploidies. Identifications of such specific cytogenetic findings can be the key factor that leads towards the diagnosis of syndromes like Roberts SC phocomelia. The case presented here as Roberts SC phocomelia syndrome was identified as a child with multiple congenital anomalies and dysmorphic features. Conventional cytogenetic analysis of the case revealed premature sister chromatid separation. The premature centromeric separation was also confirmed by C banding analysis of the child. It is the first and the only case of Roberts SC phocomelia diagnosed from this part of the world. The present case report emphasizes the importance of conventional cytogenetics in the diagnosis of such syndromes.
Journal of Cancer Research and Experimental Oncology, 2011
Ethanolic herbal extract residue of the seeds of Annona squamosa Linn. were tested against Dalton... more Ethanolic herbal extract residue of the seeds of Annona squamosa Linn. were tested against Dalton's Lymphoma Ascites (DLA) tumour cells. Then its effect on the increased lifespan of mice with DLA tumour cells was studied. At high and low dosages, it exhibited 66.67 and 56.25% increase in the lifespan. Percentage of haemoglobin (Hb) and red blood cell (RBC) counts of treated were higher than that of tumour bearing mice. The white blood cell (WBC) counts of treated were lower than that of tumour bearing mice. This is a good index of tumour recovery. Further studies were focused on mice induced with solid tumour to record the tumour volume and lifespan. It is learnt from the UV-Vis, IR, 1 H and 13 C NMR spectra analyses that annoglacin-B, an acetogenin, present in the extract residue of A. squamosa may be responsible for the biological activity.
International Journal of Research in Medical Sciences, 2015
Renal stone formation (or nephrolithiasis) is a common problem worldwide with an increasing incid... more Renal stone formation (or nephrolithiasis) is a common problem worldwide with an increasing incidence in Westernized societies. Urinary stones have plagued humans since the earliest records of civilization. Calcium oxalate stones, or stones which contain calcium phosphate, are the most common type of urolithiasis, occurring in 70-80% of stone sufferers the majority are ABSTRACT Background: Inflammation may be one cause of nephrolithiasis and the interleukin-18 (IL-18) encoding gene polymorphisms at +105 A>C has been implicated in several inflammation related diseases. The aim of this study was to test whether IL-18+105 A>C polymorphisms could act as genetic marker for renal stone disease. A case-control study was conducted to observe the genotype distribution of IL-18+105 A>C, to elucidate the possible role of this SNP as risk factor in renal stone development and to examine its correlation with the clinico-pathologic variables. Methods: Using the Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) technique, we tested the genotype distribution of 160 nephrolithiasis patients in comparison with 200 disease free controls from the same geographical region. Results: We observed significant differences of IL-18+105 A to C between the controls and patients with odds ratio 5.4 (P = 0.001). The prevalence of the variant genotypes AC + CC in the patients was higher than that in the controls (45% v/s 30%) and showed a significant association (P = 0.003). Moreover, the frequency per copy of the C allele of IL-18+105 A>C was found to be implicated more in patient group 0.27 as against only 0.16 in controls (P = 0.0003). Further, males and subjects with <45 years of age in patient group were significantly associated with variant genotype (P <0.05). Conclusion: Thus, it is evident from our study that IL-18+105 A>C is implicated in renal stone disease, and that the rare, C related allele is connected with higher susceptibility to nephrolithiasis.
Cancer biomarkers : section A of Disease markers, Jan 2, 2015
Among various polymorphic variants of TP53 gene, codon 72 polymorphism (Arg72Pro) has been found ... more Among various polymorphic variants of TP53 gene, codon 72 polymorphism (Arg72Pro) has been found to be associated with cancer susceptibility, but only few studies have investigated their effect on thyroid cancer risk. A case control study was conducted to elucidate the possible role of this SNP as risk factor in thyroid cancer development and to examine its correlation with various clinicopathological variables. In this study, we tested the genotype distribution by PCR-RFLP in 140 thyroid cancer patients and 200 cancer-free controls from Kashmir Valley. Genotype frequencies of Arg/Arg (GG), Arg/Pro (GC), and Pro/Pro (CC) genotypes among cases were 0.286, 0.343 and 0.371 while in controls 0.45, 0.37 and 0.18 respectively. Proline allele frequency was significantly higher than arginine frequency in patient group (OR=2.06, 95% C.I=1.5-2.8). Significant association was found between variant genotype of codon 72 of TP53 gene and young age group, female gender, urban dwellers, non-smokers...
Asian Pacific journal of cancer prevention : APJCP, 2010
The focus of the study was to investigate the frequencies of homozygous deletions and mutations o... more The focus of the study was to investigate the frequencies of homozygous deletions and mutations of p16 gene in gastric carcinomas in the Kashmiri population. A total of 84 gastric carcinoma patients were screened by the single strand conformation polymorphism (SSCP) technique and later by DNA sequencing to detect mutations of the p16 gene. Also PCR was applied further to further detect any homozygous deletions. SSCP and DNA sequencing performed encompassing all the three exons of p16 gene could not detect any mutations in any ofl 84 cases. Though we could observe mobility shifts in SSCP of two samples, subsequent DNA sequencing did not show any mutation. Further PCR could not detect any homozygous deletion in P16 in any case. Though Kashmir is a high incidence area of gastric carcinomas, p16gene mutations /or deletions do not appear to be involved.
Asian Pacific journal of cancer prevention : APJCP, 2013
The DNA repair gene XRCC1 Arg399Gln gene polymorphism has been found to be implicated in the deve... more The DNA repair gene XRCC1 Arg399Gln gene polymorphism has been found to be implicated in the development of various cancers, including colorectal cancer (CRC), in different populations. We aimed to determine any association of this polymorphism with the risk of CRC in Kashmir. A total of 120 confirmed cases of CRC and 146 healthy cancer free controls from the Kashmiri population were included in this study. Genotyping was carried out by the polymerase chain reaction- restriction fragment length polymorphism (PCR-RFLP) method. Genotype frequencies of XRCC1 Arg399Gln observed in controls were 34.2%, 42.5% and 23.3% for GG (Arg/Arg), GA (Arg/Gln), AA( Gln/Gln), respectively, and 28.3%, 66.7% and 5% in cases, with an odds ratio (OR)=5.7 and 95% confidence interval (CI) =2.3-14.1 (p=0.0001). No significant association of Arg399Gln SNP with any clinicopathological parameters of CRC was found. We found the protective role of 399Gln allele against risk to the development of CRC. The XRCC1 h...
Asian Pacific journal of cancer prevention : APJCP, 2010
To assess clinical utility of NMP22 Bladder Check Test and to compare it with voided urine cytolo... more To assess clinical utility of NMP22 Bladder Check Test and to compare it with voided urine cytology and cystoscopy in early detection of Bladder Cancer. A total of 115 patients of follow up cases of bladder cancer were enrolled in this study. Urine samples were assayed for the presence of NMP22 using NMP22 Bladder Check Test and cytology was performed by a cytopathologist. The diagnosis, determined from the cystoscopic findings and biopsy findings of the suspicious lesion was considered as the gold standard. For positive biopsies, the results of the NMP22 Test and cytology were also correlated with tumour grade and stage. Mean age of the patients was 57.2 years for males and 55.3 years for females. A total of 59 cases of transitional cell carcinomas (TCCs) were diagnosed among which NMP22 test was positive in 48 cases and cytology in 26 cases. The sensitivity and specificities of NMP22 Test in recurrent bladder cases was 81.3% and 92% which was significantly greater than that of cyt...
Asian Pacific journal of cancer prevention : APJCP, 2009
The objective of this study was to assess the frequency of specific-point mutations in N-ras of t... more The objective of this study was to assess the frequency of specific-point mutations in N-ras of the RAS gene family in a group of Kashmiri patients with bladder cancer and to observe any association with clinicopathological parameters. Paired tumor and normal tissue specimens of 55 consecutive patients with urothelial cell carcinoma were screened and DNA was extracted for detection of N-ras activating mutations in exons 1 and 2. In addition, blood was also collected from all the cases to rule out any germ line mutation. Specific point mutations of activated N-ras were detected in 9% (5 of 55) of the bladder cancer patients, all being missense. The base substitutions identified included three transversions (two G toT and one A to T) and two transitions ( A-G). Sixty % of the mutations were detected in codon 61 and 40% in codon 12. No significant correlations were found between the mutations and clinical features. Although N-ras gene mutation might be one of the mechanisms underlying ...
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Papers by Arshad A. Pandit