IIIT Hyderabad Publications |
|||||||||
|
Detection and Analysis of Sequence Variants in Next Generation Sequencing DataAuthor: SAMPREETH REDDY SEELAM Date: 2019-05-29 Report no: IIIT/TH/2019/48 Advisor:Nita Parekh AbstractSequence Variants are the most common variants observed in human genome, with single nucleotide variations (SNVs) occurring at a frequency of 1 in every 300bp and small insertions and deletions (INDELs) at a slightly lower frequency. When these variations occur in the coding regions, they can have a deleterious effect on the protein product and function, leading to disease situations. Reducing costs of next generation sequencing technologies has made it possible to take genetic profiling to the clinical setting. This requires not just fast and accurate algorithms for variant detection, but also a knowledge-base for variant annotation and prioritization to facilitate tailored therapeutics based on an individual’s genetic profile. With this objective, we have developed a pipeline, Sequence Variants Identification and Annotation (SeqVItA) that provides an end-to-end solution for small sequence variants detection, annotation and prioritization on a single platform. Parallelization of the variant detection step and incorporation of numerous resources to infer functional impact, clinical relevance and drug-variant associations, SeqVItA will benefit the clinical and research communities alike. Its open-source platform and modular framework allows for easy customization of the workflow depending on the data type (single, paired or pooled samples), variant type (germline and somatic), and variant annotation and prioritization. Performance comparison of SeqVItA on simulated data, real genomic data, and detection, interpretation and analysis of somatic variants on 24 liver cancer patients is carried out. In this study we demonstrate the efficacy of annotation module in facilitating personalized medicine based on patient’s mutational landscape. Full thesis: pdf Centre for Computational Natural Sciences and Bioinformatics |
||||||||
Copyright © 2009 - IIIT Hyderabad. All Rights Reserved. |