Track topics on Twitter Track topics that are important to you
Bioinformatic analysis is an integral and critical part of clinical next-generation sequencing. It is especially challenging for some pipelines to consistently identify insertions and deletions. We present the validation of an open source tumor amplicon pipeline (OTA-pipeline) for clinical next-generation sequencing targeting solid tumor-associated variants. Raw data generated from 557 TruSight Tumor 26 samples as well as in silico data were analyzed by the OTA-pipeline and legacy pipeline and compared. Discrepant results were confirmed by orthogonal methods. The OTA-pipeline reported 22 variants which were not detected by the previously validated pipeline, including seven synonymous or intronic single nucleotide variants, five single nucleotide variants at frequency <5%, one insertion, and nine deletions. Variant allele frequencies reported by the two pipelines were highly concordant, although a few significant discrepancies were present. Analysis of in silico FASTQ files demonstrated a higher sensitivity of detecting complex insertions and deletions with the OTA-pipeline. The higher sensitivity came at a cost, as false positive calls were increased in difficult-to-sequence regions. However, these calls were all flagged by our "strand bias" filter, distinguishing them from true variants. Our validation process provides a model for laboratories that wish to establish an in-house bioinformatics pipeline for clinical next-generation sequencing.
This article was published in the following journal.
Name: The Journal of molecular diagnostics : JMD
Advances in sequencing technologies have made it feasible to obtain massive datasets for phylogenomic inference, often consisting of large numbers of loci from multiple species and individuals. The ph...
Human Genome Variation Society (HGVS) nomenclature is a de facto clinical standard for reporting DNA sequence variants. With increasing use of high-throughput sequencing, manual generation of HGVS nom...
Next Generation Sequencing (NGS) has become a useful tool for gene mutation testing which is required for targeted therapies. The aim of this study was to validate the GeneRead QIAact Actionable Insig...
The application of next-generation sequencing in research and particularly in clinical routine requires valid variant calling results. However, evaluation of several commonly used tools has pointed ou...
To confirm the feasibility and explore the clinical applicability of amplicon sequencing by next generation sequencing (NGS) of biopsy samples from patients with advanced solid tumors, we conducted a ...
Infectious disease leads to deaths that accounted for more than 25% of all causes of human mortality. But the traditional microbiological diagnostic methods such as specimen culture are so...
To enhance the diagnosis of unclassifiable, non-CLL B-LPDs using next-generation sequencing technology.
Next Generation Sequencing in cancer: a feasibility study in France to assess sample circuit and to perform analyzes within a limited time.
The purpose of this study is to determine the proportion of patients diagnosed with Lynch syndrome in colorectal cancer patients with the loss of staining by immunohistochemistry (IHC) of ...
- discovery and validation of biomarker predicting gastric cancer chemotherapy response - Analysis for expression level of mRNA using Next generation sequencing in gastric ...
Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.
A highly customized interactive medium or program that allows individuals to learn and practice real world activities in an accurate, realistic, safe and secure environment.
A microscopic imaging technique that takes advantage of the process of harmonic generation that occurs when photons interact to generate new photons of a different wavelength. In second harmonic generation, two photons of the same wavelength and frequency, such as from a LASER, interact inside a medium and are converted to a photon of twice the frequency and half of the wavelength of the two incident photons. The light signals captured are used to produce images that are dependent on the unique optical properties of the material.
Systems of medicine based on cultural beliefs and practices handed down from generation to generation. The concept includes mystical and magical rituals (SPIRITUAL THERAPIES); PHYTOTHERAPY; and other treatments which may not be explained by modern medicine.
Validation of the SEX of an individual by inspection of the GONADS and/or by genetic tests.
DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule. During DNA sequencing, the bases of a small fragment of DNA are sequentially identified from signals emitted as each fragment is re-synthesized from a ...