The rs1801280 SNP is associated with non-small cell lung carcinoma by exhibiting a highly deleterious effect on N-acetyltransferase 2

Lawi, Zahraa Kamil Kadhim; Al-Shuhaib, Mohammed Baqur S.; Amara, Ibtissem Ben

doi:10.1007/s00432-022-04332-3

Cited by 4 publications

(2 citation statements)

References 67 publications

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“…In Iraq, the prevalence of NSCLC has steadily increased. This is due to exposure of Iraqi people the several disastrous wars and the deterioration of health care infrastructures [35] . However, the significance of several TERT SNPs in the development of NSCLC have not been identified in this population.…”

Section: Introductionmentioning

confidence: 99%

Two co-inherited SNPs of the telomerase reverse transcriptase (TERT) gene are associated with Iraqi patients with lung cancer

Lawi,

Alkhammas,

Elerouri

et al. 2023

J Med Biochemistry

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Background: Telomerase reverse transcriptase (TERT) gene is essential for the survival of the vast majority of malignant tumors. This study was conducted to assess the association between TERT gene and non-small cell lung carcinoma (NSCLC) in Iraq. Methods: Genomic DNA samples were extracted from a total of 200 samples of blood. Four specific PCR fragments were designed to amplify four high-frequency rs2735940, rs2736098, rs2736100, and rs10069690 SNPs within the TERT gene. Single-strand conformation polymorphism (SSCP) followed by sequencing reactions were used to genotype and validate the amplified fragments respectively. Results: Individuals with the genotype rs2735940:A/G had a significantly higher risk of developing NSCLC (P=0.0299; OD 2.3158; Cl95% 1.0853 to 4.9414). Individuals with the genotype rs2736098:C/T had also associated with the increased risk of NSCLC (P=0.0363; OD 2.1583; Cl95% 1.0503 to 4.4351). Linkage disequilibrium analysis showed that both SNPs showed a very high level of coinheritance in patients. The LD plot showed that allele T of rs2736098 had collaborated with allele G of rs2735940 to generate TG haplotype in patients. According to our findings, TERT- rs2735940:A/G and TERT- rs2736098:C/T SNPs exhibited significant associations with the increased risk of NSCLC. Both SNPs showed the highest values of co-inheritance in patients. This co-inheritance is mainly represented by allele rs2735940:A and allele rs2736098:C. Both pathogenic T and G alleles have generated TG haplotype that is only available in patients’ samples. Conclusion: This study suggests employing the haplotype TG as a promising biomarker for the early diagnosis of NSCLC. These findings need further validation by large-scale investigation with a larger size of samples in the study population.

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Section: Introductionmentioning

confidence: 99%

Two co-inherited SNPs of the telomerase reverse transcriptase (TERT) gene are associated with Iraqi patients with lung cancer

Lawi,

Alkhammas,

Elerouri

et al. 2023

J Med Biochemistry

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“…Given its pivotal role in subsequent molecular biology experiments, the extensively utilized DNA sequencing methodologies demand vigilant attention to any nucleic acid variations. Owing to its feasibility and cost-effectiveness, Sanger DNA sequencing has found extensive application in pivotal domains other than clinical analysis, spanning biodiversity [14], animal production [15], microbial pathogenesis [16], medical genetics [17], and other recent applications, such as in silico computations [18]. Despite having developed multiple approaches to next-generation sequencing, Sanger biochemistry continues to serve as the foundation for sequencing production in numerous post-PCR genotyping protocols [19].…”

Section: Introductionmentioning

confidence: 99%

Mastering DNA chromatogram analysis in Sanger sequencing for reliable clinical analysis

Al-Shuhaib,

Hashim

2023

Journal of Genetic Engineering and Biotechnology

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Background Sanger dideoxy sequencing is vital in clinical analysis due to its accuracy, ability to analyze genetic markers like SNPs and STRs, capability to generate reliable DNA profiles, and its role in resolving complex clinical cases. The precision and robustness of Sanger sequencing contribute significantly to the scientific basis of clinical investigations. Main body of the abstract Though the reading of chromatograms seems to be a routine step, many errors conducted in PCR may lead to consequent limitations in the readings of AGCT peaks. These errors are possibly associated with improper DNA amplification and its subsequent interpretation of DNA sequencing files, such as noisy peaks, artifacts, and confusion between double-peak technical errors, heterozygosity, and double infection potentials. Thus, it is not feasible to read nucleic acid sequences without giving serious attention to these technical problems. To ensure the accuracy of DNA sequencing outcomes, it is also imperative to detect and rectify technical challenges that may lead to misinterpretation of the DNA sequence, resulting in errors and incongruities in subsequent analyses. Short conclusion This overview sheds light on prominent technical concerns that can emerge prior to and during the interpretation of DNA chromatograms in Sanger sequencing, along with offering strategies to address them effectively. The significance of identifying and tackling these technical limitations during the chromatogram analysis is underscored in this review. Recognizing these concerns can aid in enhancing the quality of downstream analyses for Sanger sequencing results, which holds notable improvement in accuracy, reliability, and ability to provide crucial genetic information in clinical analysis.

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Lung Cancer

Saha,

Majumdar,

Bhattacharyya

2023

Pulmonomics: Omics Approaches for Understanding Pulmonary Diseases

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The rs1801280 SNP is associated with non-small cell lung carcinoma by exhibiting a highly deleterious effect on N-acetyltransferase 2

Cited by 4 publications

References 67 publications

Two co-inherited SNPs of the telomerase reverse transcriptase (TERT) gene are associated with Iraqi patients with lung cancer

Two co-inherited SNPs of the telomerase reverse transcriptase (TERT) gene are associated with Iraqi patients with lung cancer

Mastering DNA chromatogram analysis in Sanger sequencing for reliable clinical analysis

Lung Cancer

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