Dataset Information

Characterization of microsatellites identified by next-generation sequencing in the Neotropical tree Handroanthus billbergii (Bignoniaceae).

ABSTRACT: PREMISE OF THE STUDY:We developed microsatellite (simple sequence repeat [SSR]) markers in the Neotropical tree Handroanthus billbergii (Bignoniaceae), to be applied in assessment of genetic diversity in this species as a reference for inferring the impact of dry forest fragmentation in Ecuador. METHODS AND RESULTS:Using next-generation sequencing, we detected a total of 26,893 putative SSRs reported here. Using an ABI 3500xl sequencer, we identified and characterized a set of polymorphic markers in 23 individuals belonging to three populations of H. billbergii. CONCLUSIONS:We report a set of 30 useful SSR markers for H. billbergii and a large list of potential microsatellites for developing new markers for this or related species.

SUBMITTER: Morillo E

PROVIDER: S-EPMC4873270 | biostudies-literature | 2016 May

REPOSITORIES: biostudies-literature

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Characterization of microsatellites identified by next-generation sequencing in the Neotropical tree Handroanthus billbergii (Bignoniaceae).

Morillo Eduardo E Buitron Johanna J Limongi Ricardo R Vignes Helene H Argout Xavier X

Applications in plant sciences 20160509 5

<h4>Premise of the study</h4>We developed microsatellite (simple sequence repeat [SSR]) markers in the Neotropical tree Handroanthus billbergii (Bignoniaceae), to be applied in assessment of genetic diversity in this species as a reference for inferring the impact of dry forest fragmentation in Ecuador.<h4>Methods and results</h4>Using next-generation sequencing, we detected a total of 26,893 putative SSRs reported here. Using an ABI 3500xl sequencer, we identified and characterized a set of pol ...[more]

PMID: 27213123

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Project description:BackgroundWith the expanded availability of next generation sequencing (NGS)-based clinical genetic tests, clinicians seeking to test patients with Mendelian diseases must weigh the superior coverage of targeted gene panels with the greater number of genes included in whole exome sequencing (WES) when considering their first-tier testing approach. Here, we use an in silico analysis to predict the analytic sensitivity of WES using pathogenic variants identified on targeted NGS panels as a reference.MethodsCorresponding nucleotide positions for 1533 different alterations classified as pathogenic or likely pathogenic identified on targeted NGS multi-gene panel tests in our laboratory were interrogated in data from 100 randomly-selected clinical WES samples to quantify the sequence coverage at each position. Pathogenic variants represented 91 genes implicated in hereditary cancer, X-linked intellectual disability, primary ciliary dyskinesia, Marfan syndrome/aortic aneurysms, cardiomyopathies and arrhythmias.ResultsWhen assessing coverage among 100 individual WES samples for each pathogenic variant (153,300 individual assessments), 99.7% (n = 152,798) would likely have been detected on WES. All pathogenic variants had at least some coverage on exome sequencing, with a total of 97.3% (n = 1491) detectable across all 100 individuals. For the remaining 42 pathogenic variants, the number of WES samples with adequate coverage ranged from 35 to 99. Factors such as location in GC-rich, repetitive, or homologous regions likely explain why some of these alterations were not detected across all samples. To validate study findings, a similar analysis was performed against coverage data from 60,706 exomes available through the Exome Aggregation Consortium (ExAC). Results from this validation confirmed that 98.6% (91,743,296/93,062,298) of pathogenic variants demonstrated adequate depth for detection.ConclusionsResults from this in silico analysis suggest that exome sequencing may achieve a diagnostic yield similar to panel-based testing for Mendelian diseases.

Dataset Information

Characterization of microsatellites identified by next-generation sequencing in the Neotropical tree Handroanthus billbergii (Bignoniaceae).

Publications

Characterization of microsatellites identified by next-generation sequencing in the Neotropical tree Handroanthus billbergii (Bignoniaceae).

Similar Datasets

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