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Verma S, Bakshi D, Bhat GR, Bhat A, Shah R, Sharma B, Wakhloo A, Heer V, Chander G, Kumar R. Genetic analysis of polymorphism rs10937405 of TP63 gene in breast and ovarian cancer patients of North Indian Cohort. J Cancer Res Ther 2023; 19:214-217. [PMID: 37006060 DOI: 10.4103/jcrt.jcrt_1517_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
Abstract
INTRODUCTION Ovarian and breast cancers are highly prevalent in the population of Jammu and Kashmir (J&K). However, case-control association studies on breast and ovarian cancers are lacking in this population. Moreover, no case-control study is available on variant rs10937405 of TP63 in breast and ovarian cancers. Thus, we designed to replicate the cancer susceptible variant rs10937405 of TP63 in ovarian and breast cancers in the population of J&K because the TP63 gene act as a tumor suppressor gene and was previously associated with various cancers. MATERIALS AND METHODS This case-control association study conducted at the Shri Mata Vaishno Devi University, includes 150 breast, 150 ovarian cancer cases, and 210 healthy controls (age and sex-matched). Variant rs10937405 of the TP63 gene was determined by the TaqMan assay. Hardy-Weinberg equilibrium for the variant was assessed using the Chi-square test. The allele and genotype-specific risks were estimated by odds ratios (ORs) with 95% confidence intervals (CI). RESULTS In this study, variant rs10937405 of TP63 gene did not show any risk with ovarian and breast cancer with (P-value = 0.70) having OR 0.94, (0.69-1.28 at 95% CI) and (P-value = 0.16) having OR 0.80, (0.59-1.10). DISCUSSION Our results indicate that the variant rs10937405 of the TP63 gene did not impart any risk of breast and ovarian cancer in the population of J&K. Our results indicate that a larger sample size is needed for further statistical validation. As the study was for a particular variant, it warrants the analysis of other variants of this gene.
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Affiliation(s)
- Sonali Verma
- Scientist "B" at Indian Council of Medical Research-Centre for Advance Research, Katra, Jammu and Kashmir, India
| | - Divya Bakshi
- Research Scholar at School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Gh Rasool Bhat
- Research Scholar at School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Amrita Bhat
- Research Scholar at School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Ruchi Shah
- Department of Biotechnology, Kashmir University, Jammu and Kashmir, India
| | - Bhanu Sharma
- Research Scholar at School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Ajay Wakhloo
- Department of Obstetrics and Gynaecology, Government Medical College Jammu, Jammu and Kashmir, India
| | - Vikas Heer
- Department of Surgical Oncology, Shri Mata Vaishno Devi Super Specialty Narayana Hospital, Katra, Jammu and Kashmir, India
| | - Gresh Chander
- Scientist "B" at Indian Council of Medical Research-Centre for Advance Research, Katra, Jammu and Kashmir, India
| | - Rakesh Kumar
- Scientist "B" at Indian Council of Medical Research-Centre for Advance Research, Katra, Jammu and Kashmir, India
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Sudershan A, Mahajan K, Panjaliya RK, Dhar MK, Kumar P. Algorithm for sample availability prediction in a hospital-based epidemiological study spreadsheet-based sample availability calculator. Sci Rep 2022; 12:1860. [PMID: 35115548 PMCID: PMC8814063 DOI: 10.1038/s41598-021-03399-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 11/25/2021] [Indexed: 11/23/2022] Open
Abstract
Looking at the population's behavior by taking samples is quite uncertain due to its big and dynamic structure and unimaginable variability. All quantitative sampling approaches aim to draw a representative sample from the population so that the results of the studying samples can then be generalized back to the population. The probability of detecting a true effect of a study largely depends on the sample size and if taking small samples will give lowers statistical power, higher risk of missing a meaningful underlying difference. The probability of rejecting the null hypothesis i.e., finding significant difference using the sample largely depends upon the statistical power. There are a lot of online tools used for calculating the sample size, but none tell us about the availability of samples from single site in a fixed span. This study aims to provide an efficient calculation method for the availability of samples during a specific period of a research study which is an important question to be answered during the research study design. So, we have designed a spreadsheet-based sample availability calculator tool implemented in MS-Excel 2007.
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Affiliation(s)
- Amrit Sudershan
- Institute of Human Genetics, University of Jammu, Jammu and Kashmir (UT), 180006, India
| | - Kanak Mahajan
- Institute of Human Genetics, University of Jammu, Jammu and Kashmir (UT), 180006, India
| | - Rakesh K Panjaliya
- Department of Zoology, University of Jammu, Jammu and Kashmir (UT), 180006, India
| | - Manoj K Dhar
- Institute of Human Genetics, University of Jammu, Jammu and Kashmir (UT), 180006, India
- School of Biotechnology, University of Jammu, Jammu and Kashmir (UT), 180006, India
| | - Parvinder Kumar
- Institute of Human Genetics, University of Jammu, Jammu and Kashmir (UT), 180006, India.
- Department of Zoology, University of Jammu, Jammu and Kashmir (UT), 180006, India.
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Sharma B, Angurana S, Shah R, Verma S, Bhat A, Bhat GR, Bakshi D, Jamwal RS, Tanwar M, Singh S, Bhat A, Vaishnavi S, Kumar R. Genetic association of ARID5B with the risk of colorectal cancer within Jammu and Kashmir, India. Genes Genet Syst 2021; 96:187-191. [PMID: 34803080 DOI: 10.1266/ggs.21-00010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
Abstract
Colorectal cancer (CRC), which includes the development of cancer from the colon or rectum, is one of the highly prevalent cancers in the populations of Jammu and Kashmir (J&K) in India. However, case-control genetic association studies on CRC are lacking in this population. Various genome-wide association studies have previously shown that single-nucleotide polymorphisms (SNPs) of the AT-rich interaction domain 5B (ARID5B) gene located on chromosome 10q21.2 contribute substantially to the development of colorectal cancer. The association between ARID5B and CRC risk in north Indian population groups is still unknown. To understand the role of ARID5B SNPs in CRC in the population of J&K, we designed a case-control study to investigate the association of the cancer susceptibility variant rs10740055 of ARID5B with CRC in the population of J&K. The study included 180 cases and 390 healthy controls. Genotyping of the rs10740055 variant was performed by RT-PCR using the TaqMan assay technique. Hardy-Weinberg equilibrium of the variant was assessed using the chi-squared test. The allele- and genotype-specific risks were estimated by odds ratios (ORs) with 95% confidence intervals (CIs). The rs10740055 variant showed a higher risk for colorectal cancer with an OR of 3.35 (1.99-5.65 at 95% CI) and P = 0.000005 corrected for age, gender, ethnicity, BMI, alcohol intake and smoking. Our results indicate that the A allele of rs10740055 imparts risk to the population and also that a larger sample size is needed for further statistical validation. The association of other variants in other ARID family genes should also be tested as their role cannot be ruled out.
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Affiliation(s)
- Bhanu Sharma
- School of Biotechnology, Shri Mata Vaishno Devi University
| | | | - Ruchi Shah
- Department of Biotechnology, University of Kashmir
| | - Sonali Verma
- Indian Council of Medical Research-Centre for Advanced Research, School of Biotechnology Shri Mata Vaishno Devi University
| | - Amrita Bhat
- School of Biotechnology, Shri Mata Vaishno Devi University
| | - G R Bhat
- School of Biotechnology, Shri Mata Vaishno Devi University
| | - Divya Bakshi
- School of Biotechnology, Shri Mata Vaishno Devi University
| | | | - Mukesh Tanwar
- Department of Genetics, Maharshi Dayanand University
| | | | - Audesh Bhat
- Centre for Molecular Biology, Central University of Jammu
| | | | - Rakesh Kumar
- School of Biotechnology, Shri Mata Vaishno Devi University.,Indian Council of Medical Research-Centre for Advanced Research, School of Biotechnology Shri Mata Vaishno Devi University
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Jamwal RS, Mahajan N, Bhat GR, Bhat A, Shah R, Verma S, Sharma M, Sharma B, Qadri RA, Kumar R, Bhat A. REV3L single nucleotide variants lead to increased susceptibility towards non-small cell lung cancer in the population of Jammu and Kashmir. Cancer Epidemiol 2021; 75:102047. [PMID: 34655923 DOI: 10.1016/j.canep.2021.102047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 09/16/2021] [Accepted: 10/05/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Non-small cell lung cancer (NSCLC) is the most common lung cancer, accounting for 80-85% of all lung cancer cases. Various genetic studies have associated REV3L (Protein reversion less 3-like) gene mutations, which encodes the catalytic subunit of error prone translesion synthesis polymerase zeta with cancer, including lung cancer; however, no such data is available from any North Indian population. In this study we attempted to screen the North Indian population of Jammu and Kashmir (J&K) for the potential role of REV3L gene polymorphisms in NSCLC. METHODS A total of four REV3L single nucleotide variants were selected for genotyping based on the available literature. The genotyping was carried out by using the TaqMan allele discrimination assay in 500 subjects (200 NSCLC patients and 300 age and sex matched healthy controls). The association of variants with NSCLC was evaluated by logistic regression. RESULTS Out of the four REV3L variants genotyped; rs1002481, rs462779, and rs465646 were found significantly associated with NSCLC risk under the recessive model, with an Odds Ratio (OR) of 3.52(2.14-5.8 at 95% CI, p-value = 0.00000062), 3.7 (1.8-7.6 at 95% CI, p-value = 0.00031), and 2.2 (1.47-3.37 at 95% CI, p-value = 0.0003), respectively. DISCUSSION Our data supports a strong association between variants rs1002481, rs462779, rs465646 and NSCLC, indicating a potential role of these REV3L variants in increasing the risk for the development of NSCLC in the studied population. Although a first report from any Indian population, these variants have been previously reported to be associated with lung and colorectal cancers in different world populations. Our data along with the existing data supports the notation that these variants can be used as potential genetic predisposition markers. AVAILABILITY OF DATA AND MATERIALS Data generated and analysed during study is not available publicly but can be made available from the corresponding author upon reasonable request.
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Affiliation(s)
| | - Nikita Mahajan
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India.
| | - Gh Rasool Bhat
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India.
| | - Amrita Bhat
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India.
| | - Ruchi Shah
- Department of Biotechnology, University of Kashmir, Jammu & Kashmir, India.
| | - Sonali Verma
- Indian Council of Medical Research-Centre for Advanced Research, Shri Mata Vaishno Devi University, Katra, Jammu & Kashmir, India.
| | - Minerva Sharma
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India.
| | - Bhawani Sharma
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India.
| | - Raies A Qadri
- Department of Biotechnology, University of Kashmir, Jammu & Kashmir, India.
| | - Rakesh Kumar
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India; Indian Council of Medical Research-Centre for Advanced Research, Shri Mata Vaishno Devi University, Katra, Jammu & Kashmir, India.
| | - Audesh Bhat
- Centre for Molecular Biology, Central University of Jammu, Jammu & Kashmir, India.
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Sharma B, Angurana S, Bhat A, Verma S, Bakshi D, Bhat GR, Jamwal RS, Amin A, Qadri RA, Shah R, Kumar R. Genetic analysis of colorectal carcinoma using high throughput single nucleotide polymorphism genotyping technique within the population of Jammu and Kashmir. Mol Biol Rep 2021; 48:5889-5895. [PMID: 34319543 DOI: 10.1007/s11033-021-06583-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/20/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND SNP genotyping has become increasingly more common place to understand the genetic basis of complex diseases like cancer. SNP-genotyping through MassARRAY™ is a cost-effective method to quantitatively analyse the variation of gene expression in multiple samples, making it a potential tool to identify the underlying causes of colorectal carcinogenesis. METHODS In the present study, SNP genotyping was carried out using Agena MassARRAY™, which is a cost-effective, robust, and sensitive method to analyse multiple SNPs simultaneously. We analysed 7 genes in 492 samples (100 cases and 392 controls) associated with CRC within the population of Jammu and Kashmir. These SNPs were selected based on their association with multiple cancers in literature. RESULTS This is the first study to explore these SNPs with colorectal cancer within the J&K population.7 SNPs with a call rate of 90% were selected for the study. Out of these, five SNPs rs2234593, rs1799966, rs2229080, rs8034191, rs1042522 were found to be significantly associated with the current study under the allelic model with an Odds Ratio OR = 2.981(1.731-5.136 at 95% CI); p value = 4.81E-05 for rs2234593,OR = 1.685(1.073-2.647 at 95% CI);; p value = 0.02292 for rs1799966, OR = 1.5 (1.1-2.3 at 95% CI), p value = 0.02 for rs2229080, OR = 1.699(1.035-2.791 at 95% CI); p value = 0.03521 for rs8034191, OR = 20.07 (11.26-35.75); p value = 1.84E-34 for rs1042522 respectively. CONCLUSION This is the first study to find the relation of Genetic variants with the colorectal cancer within the studied population using high throughput MassARRAY™ technology. It is further anticipated that the variants should be evaluated in other population groups that may aid in understanding the genetic complexity and bridge the missing heritability.
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Affiliation(s)
- Bhanu Sharma
- School of Biotechnology, Shri Mata Vaishno Devi University, Jammu and Kashmir 182320, Katra, India
| | | | - Amrita Bhat
- School of Biotechnology, Shri Mata Vaishno Devi University, Jammu and Kashmir 182320, Katra, India
| | - Sonali Verma
- School of Biotechnology, Shri Mata Vaishno Devi University, Jammu and Kashmir 182320, Katra, India
| | - Divya Bakshi
- School of Biotechnology, Shri Mata Vaishno Devi University, Jammu and Kashmir 182320, Katra, India
| | - Ghulam Rasool Bhat
- School of Biotechnology, Shri Mata Vaishno Devi University, Jammu and Kashmir 182320, Katra, India
| | - Rajeshwer Singh Jamwal
- School of Biotechnology, Shri Mata Vaishno Devi University, Jammu and Kashmir 182320, Katra, India
| | - Asif Amin
- Department of Biotechnology, University of Kashmir, Srinagar, 190006, India
| | - Raies Ahmed Qadri
- Department of Biotechnology, University of Kashmir, Srinagar, 190006, India
| | - Ruchi Shah
- Department of Biotechnology, University of Kashmir, Srinagar, 190006, India.
| | - Rakesh Kumar
- School of Biotechnology, Shri Mata Vaishno Devi University, Jammu and Kashmir 182320, Katra, India.
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Zhou J, Gou H, Zhang L, Wang X, Ye Y, Lu X, Ying B. ARID5B Genetic Polymorphisms Contribute to the Susceptibility and Prognosis of Male Acute Promyelocytic Leukemia. DNA Cell Biol 2019; 38:1374-1386. [PMID: 31599655 DOI: 10.1089/dna.2019.4926] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
This study was conducted using TagSNPs to systematically explore the relationship between ARID5B polymorphisms and the occurrence, clinical characterization, and prognosis of acute myeloid leukemia (AML). A total of 569 unrelated AML patients and 410 healthy individuals from West China were recruited, and ARID5B TagSNPs were genotyped using iMLDR® (improved multiplex ligation detection reaction). It was found that the association of ARID5B polymorphisms with AML was most significant in acute promyelocytic leukemia (APL), and exclusively in males, the mutant alleles of rs6415872, rs2393726, rs7073837, rs10821936, and rs7089424 were found to increase the risk of developing APL in men, the odds ratio (OR) were 1.36, 1.74, 1.45, 1.53, and 1.56 (all p < 0.05), respectively. Haplotype analysis revealed that haplotype [AACCG] increased the risk of male APL with an OR of 1.53 (95% confidence interval: 1.10-2.14, p = 0.012). Besides, there was a strong positive additive interaction between rs6415872 and rs10821936, rs7089424, respectively, and cases attributed to the interaction of rs6415872, rs10821936, and rs7089424 accounted for 100%. Furthermore, ARID5B single nucleotide polymorphisms were found associated with clinical features of AML, and rs6415872 was shown to be an independent prognosis factor in APL patients. Besides, dual luciferase report assay showed that rs6415872 may affect the binding activity of PPARG with ARID5B. ARID5B polymorphisms contribute to male APL risk, clinical feature, and prognosis, suggesting the importance of ARDI5B in AML pathogenesis and development, and the gender and subtype preference may prompt some specific mechanisms of ARID5B. Besides, ARID5B polymorphisms might be a potential prognosis biomarker.
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Affiliation(s)
- Juan Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Haimei Gou
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, P.R. China
| | - Li Zhang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Xinyi Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Yuanxin Ye
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Xiaojun Lu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, P.R. China
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