![]() In our best case scenario that involved the TMAP aligner and SAMtools, we achieved 100% sensitivity, 99.99% specificity and 29% False Discovery Rate (FDR) in indel calling from all 23 samples, which is a good performance for mutation screening using PGM. Furthermore, we identified two variant calling measures, Quality-by-Depth (QD) and VARiation of the Width of gaps and inserts (VARW), which substantially reduced false positive indels, including non-homopolymer associated errors without compromising sensitivity. However, indel calling with the same data using the open source variant callers, GATK and SAMtools showed that false negatives could be minimised with the use of appropriate bioinformatics analysis. Our analysis revealed that false negative indels could be generated by TS under both default calling parameters and parameters adjusted for maximum sensitivity. We evaluated three major upgrades of TS by calling indels in the BRCA1 and BRCA2 genes. Recently, the proprietary analytical workflow for the Ion Torrent sequencer, Torrent Suite (TS), underwent a series of upgrades. Despite the PGM's reported high accuracy in calling single nucleotide variations, it tends to generate many false positive calls in detecting insertions and deletions (indels), which may hinder its utility for clinical genetic testing. The Ion Torrent PGM is a popular benchtop sequencer that shows promise in replacing conventional Sanger sequencing as the gold standard for mutation detection. Yeo, Zhen Xuan Wong, Joshua Chee Leong Rozen, Steven G Lee, Ann Siew Gek All rights reserved.Įvaluation and optimisation of indel detection workflows for ion torrent sequencing of the BRCA1 and BRCA2 genes. It could be a good option for analysis of less complex food, saving time and cost per sample. This together with some taxonomical discrepancies between methodologies suggest that the PGM platform is still pre-mature for its use in food traceability of complex highly processed products. Significantly higher AT-content in sequences of the same species was also obtained from PGM. The majority of samples exhibited consistency between methodologies, yielding more information and species per product from the PGM platform than PCR-CS. Here, we tested the usefulness of the Ion Torrent Personal Genome Machine ( PGM) in food traceability analyzing candies as a model of high processed foods, and compared the results with those obtained by PCR-cloning-sequencing (PCR-CS). The Next Generation Sequencing methodologies are considered the next step within DNA-based methods and their applicability in different fields is being evaluated. Muñoz-Colmenero, Marta MartÃnez, Jose Luis Roca, AgustÃn Garcia-Vazquez, Eva NGS tools for traceability in candies as high processed food products: Ion Torrent PGM versus conventional PCR-cloning. ![]()
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