1.Whole Genome Sequencing
As one of the comprehensive method for analyzing the DNA of an organism, Whole genome sequencing (WGS), enables us to better understand variations both within and between species, which in turn helps us to differentiate between organisms with a precision that other technologies do not allow. Along with human genomes, the scalable, flexible nature of next-generation sequencing (NGS) technology has been helped in the sequencing of other organisms such as agriculturally important livestock, plants, or disease-related microbes.
2.Exome and Targeted sequencing
One of the most widely used targeted sequencing methods is exome sequencing that selectively sequences the coding regions of the genome. It is a cost-effective alternative to whole-genome sequencing, as the exomes carry ~85% of known disease-related variants. Exome sequencing is very much useful in identifying the functional variation that is responsible for both Mendelian and common diseases.
Metagenomics helps in accessing the genetic content of entire communities of micro-organisms by direct extraction and cloning of DNA from an assemblage of microorganisms. The method enables microbiologists to evaluate bacterial diversity and detect the abundance of microbes in various environments. NGS-based metagenomic sequencing can detect microbial community with less abundance, which may be missed or are too expensive to identify using other methods.
4.Transcriptome sequencing/ RNA Seq
RNA expression studies or RNA-Seq, provide researchers the opportunity to discover, profile and quantify RNA transcripts in the whole transcriptome. Gene expression and transcriptome analysis data for a broad range of sample types (Cancer Transcriptome, Microbial Transcriptome, Complex disease research, Plant transcriptomes etc) can be easily done with Illumina's comprehensive next-generation sequencing technology. Due to its unbiased detection of novel transcripts, broader dynamic range, species compatibility, and easier detection of rare and low-abundance transcripts, it provides researchers with applications that are not possible by traditional microarray based methods.
A recently developed approach, termed ribosome profiling, based on deep sequencing of ribosome-protected mRNA fragments, enables us to monitor translation directly. Investigate translational control and measure gene expression, identify translation start sites, determine rate of protein synthesis, predict protein abundance etc. are some of the highlights of ribosome profiling.
6.DNA methylation sequencing
DNA methylation plays an important role in gene expression, embryonic development, cellular proliferation, differentiation and chromosome stability. Bisulfite genomic sequencing is regarded as a gold-standard technology for detection of DNA methylation. With the help of the NGS technology methylation patterns even at a single nucleotide level can be easily identified.
7.ChIP – Sequencing
ChIP sequencing combines the technology of Chromatin immunoprecipitation with high-throughput sequencing (NGS), which in turn reveals the DNA sequence involved in these interactions. It gives unbiased identification of binding sites of a given transcription factor that helps in overcoming several limitations inherent to microarray analysis of ChIP (ChIP-chip). This novel technology has revealed insights into gene regulation events that play a role in various diseases and biological pathways, such as development and cancer progression.