NGS

What Is Next Generation Sequencing (NGS) And How Is It Used In Drug Development

By: Deepak Kumar, PhD

NGS methodologies have been used to produce high-throughput sequence data. These data with appropriate computational analyses facilitate variant identification and prove to be extremely valuable in pharmaceutical industries and clinical practice for developing drug molecules inhibiting disease progression. Thus, by providing a comprehensive profile of an individual’s variome — particularly that of clinical relevance consisting of pathogenic variants — NGS helps in determining new disease genes. The information thus obtained on genetic variations and the target disease genes can be used by the Pharma companies to develop drugs impeding these variants and their disease-causing effect. However simple this may allude…

Structural Variant Calling From NGS Data

By: Deepak Kumar, PhD

Single Nucleotide Variant (SNVs) have been considered as the main source of genetic variation, therefore precisely identifying these SNVs is a critical part of the Next Generation Sequencing (NGS) workflow. However, in this report from 2004, the authors identified another form of variants called the Structural Variants (SVs), which are genetic alterations of 50 or more base pairs, and result in duplications, deletions, insertions, inversions, and translocations in the genome. The changes in the DNA organization resulting from these SVs have been shown to be responsible for both phenotypic variation and a variety of pathological conditions. While the average variation,…

Essential Concepts in Gene Prediction and Annotation

By: Deepak Kumar, PhD

After genome assembly (covered in my previous blog) comes the vital step of gene prediction and annotation. This step entails the prediction of all the genes present in the assembled genome and to provide efficient functional annotation to these genes from the data available in diverse public repositories; such as Protein Family (PFAM), SuperFamily, Conserved Domain Database (CDD), TIGRFAM, PROSITE, CATH, SCOP, and other protein domain databases. It is imperative to understand that prediction and annotation of non-protein-coding genes, Untranslated Regions (UTR), and tRNA are as vital as protein-coding genes to determine the overall genetic constitution of the assembled genome. …

5 Essential Concepts In Genome Assembly From NGS data

By: Deepak Kumar, PhD

The main goal for researchers, clinicians, and students who perform Next Generation Sequencing (NGS) and produce sequenced data for diverse projects involving human samples is to find biomarkers or variants to make diagnoses; and deduce the genetic anomalies that could be responsible for the disease they are conducting research on. Most projects (academic or non-academic) constitute the prior ideology on deciphering the “unknown.” There are well-versed computational protocols and pipelines formulated by labs across the world in determining what the “unknown” variants are. The fact that we have the “reference” human genome available – thanks to the Human Genome Project – plays…