Table 1.

Common data types for drug discovery

Data type	Description	Common techniques	Public availabilitya
SNP	A single nucleotide variation in a genetic sequence	SNP array: most widely used	****
		Whole genome sequencing
CNV	Variation of the number of copies of a particular gene in the genetic sequence	SNP array: most widely used; less sample DNA required; high probe density and coverage	****
		Comparative genome hybridization: high sensitivity and specificity; low spatial resolution
		Whole genome sequencing: can detect smaller CNVs and novel types (e.g., inversions)
Mutation	A permanent change of the nucleotide sequence of the DNA; mostly somatic mutation that occurs in any of the cells except the germ cells	Whole exome sequencing: most widely used	****
		Whole genome sequencing: more expensive and more coverage
Gene expression	Mostly expression of mRNA but also includes expression of other transcripts	Microarray: most widely used	*****
		RNA‐Seq: can detect novel transcripts, low abundant transcripts and isoforms
		Fluorescent in situ hybridization: can detect transcript abundance and spatial location in cells for a small number of genes
		RT‐PCR: frequently used to confirm expression for a small number of genes
Protein expression	Can be expression of multiple isoforms or variations due to posttranslational modifications	Western blot: widely used to quantify protein expression for a small number of proteins	***
		ELISA: widely used to detect and quantitatively measure a protein in samples
		Immunohistochemistry: can detect intracellular localization for a small number of proteins
		Reverse phase protein array: can detect expression for a few hundred proteins
		Mass spectrometry: can detect expression for a wide range of proteins
Protein‐protein interaction	Physical interactions between two or more proteins	Two‐hybrid screening: low‐tech; high false‐positive rate	****
		Mass spectrometry
Protein‐DNA interaction	Binding of a protein to a molecule of DNA	ChIP‐seq: combines chromatin immunoprecipitation with massively parallel DNA sequencing to identify the binding sites of DNA‐associated proteins	***
Gene silencing	Effect of loss of gene function	RNAi: established method; knocks gene down at mRNA or non‐coding RNA level; can have transient effect (siRNA) or long‐term effect (shRNA)	**
		CRISPR‐Cas9: new method; modifies gene (via knockout/knockin) at the DNA level; causes permanent and heritable changes in the genome
Gene overexpression	Effect of gain of gene function	cDNAs/ORFs: provide clones of sequence	*
Drug efficacy	Effect of drug treatment; primarily represented as IC50/EC50/GI50 in vitro	HTS: rapidly assess the activity of a large number of compounds in biochemical assays or cell‐based assays	***
		MTT assay: often used to confirm activity for a small number of compounds
Drug‐target interaction	Physical interaction between a drug and a protein target	Affinity chromatography with mass spectrometry: most sensitive and unbiased method	***
		SPR
EMR/EHR	Patient response upon interventions	Digitalization	*

CNV, copy number variation; CRISPR, clustered regularly interspaced short palindromic repeats; ELISA, enzyme‐linked immunosorbent assay; EMR/HER, electronic medical/health records; HTS, high throughput screening; MTT, methylthiazol tetrazolium; RT‐PCR, real‐time polymerase chain reaction; SNP, single‐nucleotide polymorphism; SPR, surface plasmon resonance.

^aIndicates the degree of public availability. For example, ***** shows researchers could easily access this type of data via public portals.