Table 1a.
Summary of Omics Omics technologies can be largely classified into four categories based on subjects to be analysed: genomic sequencing, transcriptome sequencing, proteome profiling, and interactome profiling. The principle and distinct feature of each technology are here
| Technology | Principle | Features |
|---|---|---|
| Genome sequencing | ||
| pyrosequencing (e.g. GS FLX Titanium XLR70) | SBS: detection of released PPi during DNA synthesis | •Elimination of the use of cloning vectors and library construction |
| •Maximum 500 read length | ||
| illumina sequencing (e.g. HiSeq 2500) | SBS: detection of fluorescent signal that is emitted by each base during DNA synthesis | •Short read assembly |
| •High computation needs | ||
| •Maximum 250 read length | ||
| ion semiconductor sequencing (e.g. Ion torrent) | SBS: detection of released protons (H+) during DNA synthesis | •Removal of optical measurement |
| •Maximum 400 read length | ||
| SMRT sequencing (e.g. PacBio RS II: P6‐C4) | SBS: detection of fluorescent signal that is emitted when base‐paired with immobilised DNA by zero‐mode waveguides (ZMWs) | •Long and highly accurate DNA sequences |
| •Single molecule sequencing (does not need of amplification steps) | ||
| •Provision of epigenetic information through identification of methylated base pairs | ||
| •Maximum 50 kb read length | ||
| nanopore sequencing (e.g. MiniON device from Oxford) | sequencing by translocation: detection of electrical conductivity changes as DNA bases pass through the nanopore (transmembrane protein channels) | •Removal of optical measurement |
| •Single molecule sequencing (does not need of amplification steps) | ||
| •Provision of epigenetic information through identification of methylated base pairs | ||
| •Maximum 48 kb read length | ||
| Transcriptome sequencing | ||
| RNA‐Seq | SBS: Sequencing of the cDNA reverse transcribed from RNA | •High potential for biased results depending on GC content, transcription length, position relative to RNA termini, and priming sequence bias |
| •Needs normalisation of raw data | ||
| GRO‐Seq | SBS: Capturing and SBS of RNA transcript being synthesised tagged with bromouridine enables to identify genes being transcribed at certain time. | •Useful for investigation of the genes that are transcribed at a certain time |
| •High potential for biased results depending on GC content, transcription length, position relative to RNA termini, and priming sequence bias | ||
| •Needs normalisation (through RPKM, FPKM, TPM, spike‐in controls) of raw data to deal with bias | ||
| •Requirement for incubation procedure | ||
| STARR‐Seq | identification of enhancer sequences by making each fragmented DNA self‐transcribe and measuring the amount of the resultant transcribed RNA | •99% detection rate by using pair‐end sequencing |
| •Does not depend on position effects by random genomic integration | ||
| ribosome profiling | capturing global snapshot of transcriptome at a specific time using ribosome foot print and NGS | Capacity to identify |
| •the location of translation start sites | ||
| •the complement of translated ORFs in a cell or tissue | ||
| •the distribution of ribosomes on a messenger RNA | ||
| •the speed of translating ribosomes |