AI Article Synopsis
- Next-generation amplicon sequencing allows for simultaneous genetic analysis of multiple genes across several patients, but currently lacks a reliable open-source software solution for reporting genetic variations.
- Researchers have developed a customizable software pipeline in Perl that efficiently analyzes 454/Roche GS-FLX amplicon resequencing data, validating detected variations and optimizing PCR processes.
- This open-source pipeline is database-oriented, facilitating integration with other tools for variant interpretation, and includes clear documentation for users to test the system before applying it to actual sequencing data.
Article Abstract
Background: Next-generation amplicon sequencing enables high-throughput genetic diagnostics, sequencing multiple genes in several patients together in one sequencing run. Currently, no open-source out-of-the-box software solution exists that reliably reports detected genetic variations and that can be used to improve future sequencing effectiveness by analyzing the PCR reactions.
Results: We developed an integrated database oriented software pipeline for analysis of 454/Roche GS-FLX amplicon resequencing experiments using Perl and a relational database. The pipeline enables variation detection, variation detection validation, and advanced data analysis, which provides information that can be used to optimize PCR efficiency using traditional means. The modular approach enables customization of the pipeline where needed and allows researchers to adopt their analysis pipeline to their experiments. Clear documentation and training data is available to test and validate the pipeline prior to using it on real sequencing data.
Conclusions: We designed an open-source database oriented pipeline that enables advanced analysis of 454/Roche GS-FLX amplicon resequencing experiments using SQL-statements. This modular database approach allows easy coupling with other pipeline modules such as variant interpretation or a LIMS system. There is also a set of standard reporting scripts available.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2880033 | PMC |
| http://dx.doi.org/10.1186/1471-2105-11-269 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Riverine mycobiome dynamics: From South African tributaries to laboratory bioreactors.
Mycology
January 2024
Department of Microbiology, University of Stellenbosch, Stellenbosch, South Africa.
Riverine fungi have the capacity for both pathogenicity, pertinent for countries with elevated immunosuppressed individuals, and bioremediation potential. The purpose was (i) to screen for the presence of clinically relevant riverine fungi and associations with anthropogenic influence, and (ii) the acclimatisation of environmental communities toward potential bioremediation application. Communities were harvested from polluted rivers in Stellenbosch, South Africa, and mycobiomes characterised by high-throughput amplicon sequencing.
View Article and Find Full Text PDFScreening a transposon-mutagenized soybean population led to the discovery of a recessively inherited chlorotic phenotype. This "y24" phenotype results in smaller stature, weaker stems, and a smaller root system. Genome sequencing identified 15 candidate genes with mutations likely to result in a loss of function.
View Article and Find Full Text PDFRare occurrence of cryptic 5' splice sites by downstream 3' splice site/exon boundary mutations in a heavy-ion-induced allele of .
Front Plant Sci
September 2024
Graduate School of Science and Technology, Sophia University, Chiyoda, Tokyo, Japan.
Pre-mRNA splicing is a fundamental process in eukaryotic gene expression, and the mechanism of intron definition, involving the recognition of the canonical GU (5'-splice site) and AG (3'-splice site) dinucleotides by splicing factors, has been postulated for most cases of splicing initiation in plants. Splice site mutations have played crucial roles in unraveling the mechanism of pre-mRNA splicing . Typically, splice site mutations abolish splicing events or activate one or more cryptic splice sites surrounding the mutated region.
View Article and Find Full Text PDFSensitive and modular amplicon sequencing of diversity and resistance for research and public health.
bioRxiv
August 2024
EPPIcenter Research Program, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco, California, USA.
Targeted amplicon sequencing is a powerful and efficient tool to interrogate the genome and generate actionable data from infections to complement traditional malaria epidemiology. For maximum impact, genomic tools should be multi-purpose, robust, sensitive and reproducible. We developed, characterized, and implemented MADHatTeR, an amplicon sequencing panel based on Multiplex Amplicons for Drug, Diagnostic, Diversity, and Differentiation Haplotypes using Targeted Resequencing, along with a bioinformatic pipeline for data analysis.
View Article and Find Full Text PDFIdentification of causative gene variants for patients with known monogenic diabetes using a targeted next-generation sequencing panel in a single-center study.
Diabetol Int
April 2024
Department of Neurology, Hematology, Metabolism, Endocrinology and Diabetology, Faculty of Medicine, Yamagata University, 2-2-2 Iida-nishi, Yamagata, 990-9585 Japan.
Article Synopsis
- The study aimed to assess the effectiveness of targeted next-generation sequencing (NGS) for diagnosing monogenic diabetes in patients under 50 who are not highly obese.
- Researchers designed an NGS panel to analyze 34 genes and found 16 potential causative variants in 56 patients, confirming known mutations in two cases and identifying two novel variants based on family history.
- The conclusion highlighted that the targeted NGS approach proved beneficial for diagnosing types of monogenic diabetes, though further improvements are necessary for wider clinical application.
Want AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!