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We analyzed the performance of our approaches for mutation series and impact extraction in detail on different corpora.
Candidate gene approaches for mutation screening rely on a priori information about biological gene function and are thus limited by how much is known about the biology of the disease.
The major innovations were to: design novel impact grounding techniques and to couple this with existing approaches for mutation grounding to protein sequences; exploit the utility of the SADI framework to expose the grounding and relation detection algorithms as semantic web services.
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These categories rely on two systematic approaches: for mutations we selectively analyzed the list of SMGs identified by the algorithm MuSiC [ 28], for copy number we analyzed frequently amplified and deleted region of interest (ROI) as identified by GISTIC [ 29].
Using a sensitive approach for mutation detection, we found a 68.6% VHL mutational rate along with 74.5 and 13.7% deletion and promoter methylation rates, respectively, which is consistent with what is generally reported in the literature (Banks et al, 2006; Nickerson et al, 2008).
To establish a comprehensive approach for mutation detection of PMS2, we have designed a strategy combining targeted capture next-generation sequencing (NGS), multiplex ligation-dependent probe amplification, and long-range PCR followed by NGS to simultaneously detect point mutations and copy number changes of PMS2.
We first performed conventional dideoxy-nucleotide chain termination-based ("Sanger") sequencing on all of these specimens because, despite its limitations, this method is still the most widely used approach for mutation detection in clinical specimens.
It may be best to have a two-tiered approach for mutation detection, with an economical first step and further more elaborate techniques for identifying rare mutations [ 19].
With advances in next generation sequencing technologies and genomic capture techniques, exome sequencing has become a cost-effective approach for mutation detection in genetic diseases [ 1].
With advances in next generation sequencing technologies and genomic capture techniques, exome sequencing has become a cost-effective approach for mutation detection in genetic diseases.
The traditional approach for mutation identification involves three-factor mapping followed by several rounds of complementation testing using deficiencies and duplications.
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