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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
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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 ...