Local conservation scores without a priori assumptions on neutral substitution rates

Dingel, J.; Hanus, P.; Leonardi, Niccolò; Hagenauer, J.; Zech, J.; Mueller, Jakob C.

doi:10.1186/1471-2105-9-190

Cited by 6 publications

(4 citation statements)

References 39 publications

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“…The assumption here is that conservation of the nucleotide is related to the functional importance of it or its resultant amino acid, with higher importance leading to maintenance of the encoded feature without change over time. Some of the more commonly used algorithms are PhastCons and PhyloP (Dingel et al, 2008;Pollard et al, 2010). It is worthwhile noting that prioritization or deprioritization of a variant based on such a conservation score is only appropriate if the score has been calculated across species where the region under analysis performs the same role.…”

Section: 2411mentioning

confidence: 99%

Analysis and Annotation of Whole‐Genome or Whole‐Exome Sequencing–Derived Variants for Clinical Diagnosis

Worthey¹

2013

CP Human Genetics

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Over the last several years, next-generation sequencing (NGS) has transformed genomic research through substantial advances in technology and reduction in the cost of sequencing, and also in the systems required for analysis of these large volumes of data. This technology is now being used as a standard molecular diagnostic test under particular circumstances in some clinical settings. The advances in sequencing have come so rapidly that the major bottleneck in identification of causal variants is no longer the sequencing but rather the analysis and interpretation. Interpretation of genetic findings in a clinical setting is scarcely a new challenge, but the task is increasingly complex in clinical genome-wide sequencing given the dramatic increase in dataset size and complexity. This increase requires the development of novel or repositioned analysis tools, methodologies, and processes. This unit provides an overview of these items. Specific challenges related to implementation in a clinical setting are discussed.

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Section: 2411mentioning

confidence: 99%

Analysis and Annotation of Whole‐Genome or Whole‐Exome Sequencing–Derived Variants for Clinical Diagnosis

Worthey¹

2013

CP Human Genetics

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“…The assumption here is that conservation of the nucleotide is related to the functional importance of it or its resultant amino acid, with higher importance leading to maintenance of the encoded feature without change over time. Some of the more commonly used algorithms are PhastCons and PhyloP (Dingel et al, 2008;Pollard, Hubisz, Rosenbloom, & Siepel, 2010). It is worthwhile noting that prioritization or deprioritization of a variant based on such a conservation score is only appropriate if the score has been calculated across species where the region under analysis performs the same role.…”

Section: Class 3: Annotations Supporting Determination Of the Potenti...mentioning

confidence: 99%

Analysis and Annotation of Whole‐Genome or Whole‐Exome Sequencing Derived Variants for Clinical Diagnosis

Worthey

2017

CP Human Genetics

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Over the last 10 years, next-generation sequencing (NGS) has transformed genomic research through substantial advances in technology and reduction in the cost of sequencing, and also in the systems required for analysis of these large volumes of data. This technology is now being used as a standard molecular diagnostic test in some clinical settings. The advances in sequencing have come so rapidly that the major bottleneck in identification of causal variants is no longer the sequencing or analysis (given access to appropriate tools), but rather clinical interpretation. Interpretation of genetic findings in a complex and ever changing clinical setting is scarcely a new challenge, but the task is increasingly complex in clinical genome-wide sequencing given the dramatic increase in dataset size and complexity. This increase requires application of appropriate interpretation tools, as well as development and application of appropriate methodologies and standard procedures. This unit provides an overview of these items. Specific challenges related to implementation of genome-wide sequencing in a clinical setting are discussed. © 2017 by John Wiley & Sons, Inc.

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“…With the increased availability of genomic sequences, the evolutionary conservation information can also be yielded from the genomic sequence alignments between multiple organisms [25][26][27]. In this study, we tried to mine informative conservation-based features for improving the prediction accuracy of AS.…”

Section: Introductionmentioning

confidence: 99%

Accurate Prediction of Alternatively Spliced Cassette Exons Using Evolutionary Conservation Information and Logitlinear Model

Deng

Liu

et al. 2009

2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing

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Accurate prediction of alternative splicing (AS) is important for understanding the mechanism of gene regulation and studying the pathogenesis of diseases. By analyzing the evolutionary conservation information in alternatively spliced cassette exons (SCEs), constitutively spliced exons (CSEs) and their flanking intronic regions, we found that the average conservation score (AConScore) distributions of SCEs are significantly different from those of CSEs. We further integrated these unique features into the logitlinear model, and constructed a classifier, named AEDetector, for distinguishing SCEs from CSEs. The five-fold cross validation results show that the sensitivity and specificity of AEDetector are higher than those recently reported on the same dataset.

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Local conservation scores without a priori assumptions on neutral substitution rates

Cited by 6 publications

References 39 publications

Analysis and Annotation of Whole‐Genome or Whole‐Exome Sequencing–Derived Variants for Clinical Diagnosis

Analysis and Annotation of Whole‐Genome or Whole‐Exome Sequencing–Derived Variants for Clinical Diagnosis

Analysis and Annotation of Whole‐Genome or Whole‐Exome Sequencing Derived Variants for Clinical Diagnosis

Accurate Prediction of Alternatively Spliced Cassette Exons Using Evolutionary Conservation Information and Logitlinear Model

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