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Computational methods to work as first-pass filter in deleterious SNP analysis of alkaptonuria.

ABSTRACT: A major challenge in the analysis of human genetic variation is to distinguish functional from nonfunctional SNPs. Discovering these functional SNPs is one of the main goals of modern genetics and genomics studies. There is a need to effectively and efficiently identify functionally important nsSNPs which may be deleterious or disease causing and to identify their molecular effects. The prediction of phenotype of nsSNPs by computational analysis may provide a good way to explore the function of nsSNPs and its relationship with susceptibility to disease. In this context, we surveyed and compared variation databases along with in silico prediction programs to assess the effects of deleterious functional variants on protein functions. In other respects, we attempted these methods to work as first-pass filter to identify the deleterious substitutions worth pursuing for further experimental research. In this analysis, we used the existing computational methods to explore the mutation-structure-function relationship in HGD gene causing alkaptonuria.

SUBMITTER: Magesh R

PROVIDER: S-EPMC3349151 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Computational methods to work as first-pass filter in deleterious SNP analysis of alkaptonuria.

Magesh R R George Priya Doss C C

TheScientificWorldJournal 20120419

A major challenge in the analysis of human genetic variation is to distinguish functional from nonfunctional SNPs. Discovering these functional SNPs is one of the main goals of modern genetics and genomics studies. There is a need to effectively and efficiently identify functionally important nsSNPs which may be deleterious or disease causing and to identify their molecular effects. The prediction of phenotype of nsSNPs by computational analysis may provide a good way to explore the function of ...[more]

PMID: 22606059

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Project description:Background: Recent trials have proved the efficacy of mechanical thrombectomy over medical treatment for patients with acute ischemic stroke, with the balance of equivalent rates of adverse events. Stent retrievers were applied predominantly in most trials; however, the role of other thrombectomy devices has not been well validated. A direct aspiration first-pass technique (ADAPT) is proposed to be a faster thrombectomy technique than the stent retriever technique. This meta-analysis investigated and compared the efficacy and adverse events of first-line ADAPT with those of first-line stent retrievers in patients with acute ischemic stroke. Methods: A structured search was conducted comprehensively. A total of 1623 papers were found, and 4 articles were included in our meta-analysis. The Critical Appraisal Skills Programme tools were applied to evaluate the quality of studies. The primary outcome was defined as the proportion of patients with the Thrombolysis in Cerebral Ischemia (TICI) scale of 2b/3 at the end of all procedures. Secondary outcomes were the proportion of patients with functional independence (modified Rankin scale of 0-2) at the third month, the proportion of patients with the Thrombolysis in Cerebral Ischemia (TICI) scale of 2b/3 by primary chosen device, and the proportion of patients who received rescue therapies. Safety outcomes were the symptomatic intracranial hemorrhage (sICH) rate and the mortality rate within 3 months. Results: One randomized controlled trial, one prospective cohort study, and two retrospective cohort studies were included. No significant difference between these 2 strategies of management were observed in the primary outcome (TICI scale at the end of all procedures, odds ratio [OR] = 0.78), two secondary outcomes (functional independence at the third month, OR = 1.16; TICI scale by primary chosen device, OR = 1.25), and all safety outcomes (sICH rate, OR = 1.56; mortality rate, OR = 0.91). The proportion of patients who received rescue therapies was higher in the first-line ADAPT group (OR = 0.64). Conclusions: Among first-line thrombectomy devices for patients with ischemic stroke, ADAPT with the latest thrombosuction system was as efficient and safe as stent retrievers.

Dataset Information

Computational methods to work as first-pass filter in deleterious SNP analysis of alkaptonuria.

Publications

Computational methods to work as first-pass filter in deleterious SNP analysis of alkaptonuria.

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