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Bhat A, Bhat GR, Verma S, Sharma B, Bakshi D, Abrol D, Singh S, Qadri RA, Shah R, Kumar R. Evaluation of 17 genetic variants in association with leukemia in the north Indian population using MassARRAY Sequenom. J Biochem Mol Toxicol 2021; 35:e22792. [PMID: 33928715 DOI: 10.1002/jbt.22792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/29/2021] [Accepted: 04/08/2021] [Indexed: 12/24/2022]
Abstract
Leukemia is a heterogeneous disorder, characterized by elevated proliferation of white blood cells. In this study, we explored the association of 17 genetic variants with leukemia patients in the Jammu and Kashmir region of north India. The variants were genotyped by using a high-throughput Agena MassARRAY platform in 758 individuals (166 cases and 592 controls). Of the 17 single-nucleotide polymorphisms (SNPs) studied, five SNPs were showing significant association with the high risk of leukemia in the north Indian population, which includes rs10069690 of telomere reverse transcriptase (TERT) with OR = 0.34 (95% CI, 0.20-0.58; p = .0008), rs2972392 (PSCA) with OR 1.86 (95% CI, 1.04-3.81; p = .035), rs4986764 (BRIP1) with OR 1.34 (95% CI, 1.00-1.80; p = .04), rs6990097 (TNKS) with OR 1.81 (95% CI, 1.2-2.6; p = .001) and rs12190287 (TCF21) with OR 2.87 (95% CI, 1.72-4.7; p = .0001) by allelic association using Plink and analyzed by SPSS. This is the first study to explore these variants with leukemia in the studied population.
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Affiliation(s)
- Amrita Bhat
- Cancer Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Gh Rasool Bhat
- Cancer Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Sonali Verma
- ICMR-CAR, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Bhanu Sharma
- Cancer Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Divya Bakshi
- Cancer Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Deepak Abrol
- Department of Radiotherapy, Government Medical College Kathua, Jammu and Kashmir, India
| | - Supinder Singh
- Department of Medicine, ASCOMS, Sidhra, Jammu and Kashmir, India
| | | | - Ruchi Shah
- ICMR-CAR, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Rakesh Kumar
- Cancer Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
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Shah R, Sharma V, Bhat A, Singh H, Sharma I, Verma S, Bhat GR, Sharma B, Bakshi D, Kumar R, Dar NA. MassARRAY analysis of twelve cancer related SNPs in esophageal squamous cell carcinoma in J&K, India. BMC Cancer 2020; 20:497. [PMID: 32487238 PMCID: PMC7268327 DOI: 10.1186/s12885-020-06991-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 05/21/2020] [Indexed: 02/06/2023] Open
Abstract
Background MassARRAY (Agena Bioscience™) combines competitive PCR with MALDI-TOF mass spectrometry (MS) analysis that gives highly accurate, sensitive, and high-throughput methods for the quantitative analysis of variation of gene expression in multiple samples. SNPs (Single Nucleotide Polymorphisms) have a very high potential of discovering disease-gene relationships. SNP-genotyping through MassARRAY is not only a cost-effective genotyping method but also provides a platform to validate variants observed through a high-throughput Next-generation sequencing (NGS). Methods In the present study, we have incorporated the use of matrix-assisted laser desorption/ionization-time of flight, mass spectrometry (MALDI-TOF) as a tool for differentiating genotypes based on the mass of variant. We have performed multiplex PCR and genotyped 12 SNPs in 758 samples (166 cases and 592 controls). The 12 studied SNPs were chosen with a rationale for their association with multiple cancers in literature. Results This is the first study to explore these SNPs with esophageal cancer within the J&K population. Out of 12 SNPs, two SNPs rs12190287 of TCF21 and rs10046 of CYP19A1 were significantly associated with esophageal cancer with Odds Ratio (OR) 1.412 (1.09–1.8 at 95% CI, p = 0.008) and 1.54 (1.21–2.072 at 95% CI, p = 0.0007) within the population of Jammu and Kashmir. Conclusion We explored 12 SNPs that were found to be associated with multiple cancers in literature with esophageal cancer within the population of J&K. This is the first study to find the relation of these SNPs with ESCC within the studied population. This study explores the relation of genetic and environmental factors with the ESCC susceptibility.
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Affiliation(s)
- Ruchi Shah
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, 182320, India.
| | - Varun Sharma
- Human Genetics Research Group, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, 182320, India
| | - Amrita Bhat
- Cancer Genetics Research Group, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, 182320, India
| | - Hemender Singh
- Human Genetics Research Group, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, 182320, India
| | - Indu Sharma
- Human Genetics Research Group, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, 182320, India
| | - Sonali Verma
- Cancer Genetics Research Group, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, 182320, India
| | - Gh Rasool Bhat
- Cancer Genetics Research Group, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, 182320, India
| | - Bhanu Sharma
- Cancer Genetics Research Group, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, 182320, India
| | - Divya Bakshi
- Cancer Genetics Research Group, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, 182320, India
| | - Rakesh Kumar
- Cancer Genetics Research Group, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, 182320, India
| | - Nazir Ahmed Dar
- Department of Biochemistry, University of Kashmir, Srinagar, Jammu and Kashmir, 180001, India.
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