NGS

How To Profile DNA And RNA Expression Using Next Generation Sequencing (Part-2)

By: Deepak Kumar, PhD

In the first blog of this series, we explored the power of sequencing the genome at various levels. We also dealt with how the characterization of the RNA expression levels helps us to understand the changes at the genome level. These changes impact the downstream expression of the target genes. In this blog, we will explore how NGS sequencing can help us comprehend DNA modification that affect the expression pattern of the given genes (epigenetic profiling) as well as characterizing the DNA-protein interactions that allow for the identification of genes that may be regulated by a given protein.  DNA Methylation Profiling…

How To Profile DNA And RNA Expression Using Next Generation Sequencing

By: Deepak Kumar, PhD

Why is Next Generation Sequencing so powerful to explore and answer both clinical and research questions. With the ability to sequence whole genomes, identifying novel changes between individuals, to exploring what RNA sequences are being expressed, or to examine DNA modifications and protein-DNA interactions occurring that can help researchers better understand the complex regulation of transcription. This, in turn, allows them to characterize changes during different disease states, which can suggest a way to treat said disease.  Over the next two blogs, I will highlight these different methods along with illustrating how these can help clinical diagnostics as well as…

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…