Table 2.

Applications of NGS technologies

ExperimentSource DNA (input)DescriptionReferences
WGSgDNAIdentifies an individual's complete genome sequence (coding and noncoding regions); including copy number variation (e.g., repeats, indels) and structural rearragements (e.g., translocations)(1, 16)
Targeted “exome” sequencingProtein-encoding gDNA (i.e., exons)Identifies the sequence for all coding regions (exons), including copy number variation (e.g., repeats, indels) and structural rearrangements (e.g. translocations)(16, 45)
RNA-seqcDNA made from various sources of RNACan identify all transcribed sequences (transcriptome) or just coding RNA sequences; can also provide information on sequence content (e.g., splicing variants) and copy number/abundance (e.g., gene expression profiling)(28)
Bisulfite-seqBisulfite-treated DNAIdentifies sites of DNA methylation (e.g., genetic imprinting)(71, 72)
ChIP-seqImmunoprecipitated DNAIdentifies sites of protein–DNA interactions such as transcription factor–binding sites(29)
RIP-seqcDNA made from immunoprecipitated RNAIdentifies sites of protein–RNA interactions; a ChIP-seq for RNA-binding proteins(91)
DNase-seqDNase-digested chromatin DNAIdentifies genomic regions susceptible to enzymatic cleavage by DNase, i.e., hypersensitive sites and potential regulatory regions(75, 76)
FAIRE-seqOpen/accessible chromatin DNAIdentifies open/accessible chromatin regions, i.e., hypersensitive sites and potential regulatory regions(74, 75)
MNase-seqNucleosome-associated DNAIdentifies nucleosome positions on genomic DNA (i.e., primary chromatin structure); also provides information on histone/nucleosome density at each location(77, 92)
Hi-C/5C-seqCaptured chromosome conformationsIdentifies intra- and interchromosomal interactions; determines the spatial organization of chromosomes at high resolution(93, 94)
MetagenomicsMicrobial DNA populationsGenomic analysis of microbial communities; identifies bacterial/viral populations present in specific environments (e.g., human gut and tumor samples)(32, 79, 80)

NOTE: Immunoprecipitated (IP) DNA and RNA can be collected for any protein that has an antibody or using an epitope-tagged protein. IP DNA sources can include histone proteins (e.g., histone H3 or H4), as a paired or alternative approach to MNase-seq experiments (77). IP DNA sources can also include covalently modified histone proteins (i.e., specific histone acetylations/methylations; e.g., H3K36Me3)–to map “histone code.”

Abbreviations: cDNA, reverse-transcribed RNA or “complementary DNA” (i.e., introns removed during RNA splicing); Chromatin, the collection of DNA and proteins in the nucleus; openness/accessibility of chromatin, regions of looser DNA packaging, susceptible to enzymatic cleavage and protein binding/gene regulation (see Fig. 1: “Hypersensitive Sites”); indels, insertions/deletions; transcriptome, all transcribed DNA sequences, includes small noncoding RNAs, miRNAs, and coding RNAs (i.e. genes).