Genotyping:The predictive power of haplotypes in clinical response

Judson, Richard S.; Jc, Stephens; Windemuth, Andreas

doi:10.1517/14622416.1.1.15

Cited by 121 publications

(86 citation statements)

References 29 publications

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“…Moreover, haplotype analysis offers the advantages of not assuming that any of the genotyped polymorphisms is functional, and it allows for the possibility of an ungenotyped functional variant to be in LD with the genotyped polymorphisms. [24][25][26][27] Therefore, we conducted a subsequent analysis on CDK5 haplotypes consisting of À904 G4A, À270 C4G and À238 A4C polymorphisms, which are in strong LD. In the dominant haplotype analysis, the A-G-C haplotype of the three polymorphic sites was shown to be related to the higher risk of lung cancer (overall OR¼1.59, 95% CI¼1.16-2.18).…”

Section: Discussionmentioning

confidence: 99%

Single-nucleotide polymorphisms in the promoter of the CDK5 gene and lung cancer risk in a Korean population

et al. 2009

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Cyclin-dependent kinase 5 (CDK5), a proline-directed serine/threonine kinase, which was originally known for its regulatory role in neuronal activities, has recently been suggested to play a role in extraneuronal activities. For example, a recent study detected overexpression of the CDK5 gene in non-small-cell lung cancer. Therefore, in order to explore the association of the CDK5 gene with lung cancer risk in a Korean population, the genotypes of the CDK5 promoter region were determined in 407 lung cancer patients and 402 normal participants. The result showed that the À904 G4A genotype affected susceptibility to lung cancer risk (odd ratios (OR)¼1.53, 95% confidence interval (CI)¼1.02-2.32). Furthermore, subsequent haplotype analysis of three single-nucleotide polymorphism (SNP) regions suggested that the A-G-C haplotype was associated with a higher overall risk of lung cancer (OR¼1.59, 95% CI¼1.16-2.18). These results suggest that CDK5 promoter polymorphisms contribute to the genetic susceptibility to lung cancer in the Korean population.

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Section: Discussionmentioning

confidence: 99%

Single-nucleotide polymorphisms in the promoter of the CDK5 gene and lung cancer risk in a Korean population

et al. 2009

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“…None of the studies reviewed here reported haplotype associations, although several studies analyzed multiple polymorphisms within a gene, sometimes with inconsistent results. The analysis of haplotypes can increase power to detect disease associations because of higher heterozygosity and tighter linkage disequilibrium with disease-causing mutations [190][191][192]. In addition, analysis of haplotypes offers the advantage of not assuming that any of the genotyped polymorphisms is functional; rather, it allows for the possibility of an ungenotyped functional variant to be in linkage disequilibrium with the genotyped polymorphisms [193].…”

Section: Discussionmentioning

confidence: 99%

Molecular epidemiology of major depressive disorder

Kiyohara

Yoshimasu

2009

Environ Health Prev Med

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Major depressive disorder causes significant morbidity, affecting people's ability to work, function in relationships, and engage in social activities. Moreover, major depressive disorder increases the risk of suicidal ideation, attempted suicide and death by completed suicide. There is evidence that chronic stress can cause major depressive disorder. As for genetic factors, only minor susceptibility genes have been reliably identified. The serotonin system provides a logical source of susceptibility genes for depression, because this system is the target of selective serotonin reuptake-inhibitor drugs that are effective in treating depression. The 5-hydroxytryptamine (serotonin) transporter (5-HTT) has received particular attention because it is involved in the reuptake of serotonin at brain synapses. One common polymorphic variant of the 5-HTT-linked polymorphic region (5-HTTLPR), which affects the promoter of the 5-HTT gene, causes reduced uptake of the neurotransmitter serotonin into the presynaptic cells in the brain. The authors discussed the relationship between genetic polymorphisms and major depressive disorder, with special emphasis on the 5-HTTTLPR polymorphism. As the 5-HTTLPR polymorphism was significantly associated with an increased risk of major depressive disorder, the 5-HTT gene may be a candidate for a major depressive disorder susceptibility gene. As major depressive disorder is a multifactorial disease, an improved understanding of the interplay of environmental and genetic polymorphisms at multiple loci may help identify individuals who are at increased risk for major depressive disorder. Hopefully, in the future we will be able to screen for major depressive disorder susceptibility by using specific biomarkers.

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“…The analysis of haplotypes can increase power to detect disease associations because of higher heterozygosity and stronger linkage disequilibrium with diseasecausing mutations. [69][70][71] The ability to include haplotype information will provide more powerful and more comprehensive assessments of XRCC1 gene.…”

Section: Discussionmentioning

confidence: 99%

XRCC1 gene polymorphisms and esophageal squamous cell carcinoma risk in Chinese population: A meta‐analysis of case–control studies

Dai

Wang

Zhang

et al. 2009

Intl Journal of Cancer

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Two non-synonymous polymorphisms Arg194Trp and Arg399Gln in the DNA-base excision repair gene X-ray repair cross-complementing group 1 (XRCC1) have been implicated in risk for esophageal cancer. However, the results from different studies remain controversial. The present meta-analysis of literatures was performed to clarify these associations in Chinese population. A comprehensive literature search was conducted to identify all case-control studies of XRCC1 polymorphisms Arg194Trp and Arg399Gln and risk for esophageal squamous cell carcinoma (ESCC). A total of 9 eligible studies, including 1,538 ESCC cases and 2,472 controls, were identified to the meta-analysis. The odds ratio (OR) for the variant homozygous genotype Trp/Trp of the Arg194Trp polymorphism, compared with the wild-type homozygote Arg/Arg, was 1.59 (p 5 0.0007), with 95% confidence interval (95% CI) 1.22-2.09, for ESCC risk without between-study heterogeneity. However, there was no statistically significant associations of ESCC risk in the dominant model Arg/Trp1Trp/Trp (OR 0.97; 95% CI 0.84-1.12; p 5 0.69) and heterozygous genotype Arg/Trp (OR 0.90; 95% CI 0.77-1.04; p 5 0.16) when comparing with wild-type genotype Arg/Arg. For Arg399Gln, there was no effect in dominant modeling (Arg/Gln1Gln/Gln vs. Arg/Arg: OR 0.92; 95% CI 0.80-1.06; p 5 0.25), and the variant Gln/Gln homozygote was not associated with ESCC risk (OR 1.29; 95% CI 0.79-2.10; p 5 0.31), either. In conclusion, Arg194Trp genetic polymorphism may be associated with an increased risk for developing ESCC and a study with the larger sample size is needed to further evaluate gene-environment interaction on XRCC1 polymorphisms and ESCC risk. ' 2009 UICC

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Genotyping:The predictive power of haplotypes in clinical response

Cited by 121 publications

References 29 publications

Single-nucleotide polymorphisms in the promoter of the CDK5 gene and lung cancer risk in a Korean population

Single-nucleotide polymorphisms in the promoter of the CDK5 gene and lung cancer risk in a Korean population

Molecular epidemiology of major depressive disorder

XRCC1 gene polymorphisms and esophageal squamous cell carcinoma risk in Chinese population: A meta‐analysis of case–control studies

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