Copyright ©The Author(s) 2021.
World J Methodol. Sep 20, 2021; 11(5): 231-242
Published online Sep 20, 2021. doi: 10.5662/wjm.v11.i5.231
Table 1 Characteristics of commonly used genomic tools
Tools for genomics
Principle of use
Pros and application
Genome-wide association studies (GWAS)Gene mapping study using DNA microarray to identify the association between SNP and specific risk alleles that are more prevalent in cases than in controls, via linkage disequilibriumHas potential for population-based application. Example — The Severe COVID-19 GWAS Group[34] studied patients with respiratory failure from severe COVID-19 and narrowed down the genetic susceptibility locus to a gene cluster on chromosome locus 3p21.31. They also verified the potential involvement of the ABO blood group systemDoes not establish causality but only an association with SNP; Missing heritability- cannot explain variance in complex traits or genes with a small effect size; Does not account for epigenetic changes and epistasis (gene-gene interaction); GWAS data catalog mostly from individuals of European descent which may limit application in minority population[35]
Expression quantitative trait loci (eQTL) analysisLinks SNPs to changes in gene expression by measuring the expression of many genes simultaneously in microarrays. Helps to narrow down to SNPs more likely to impact the disease conditionProvides better insight into specific causal mechanisms[36]; Liver eQTL — useful in pharmacogenomic studies by analyzing Epistatic eQTL Interactions[37]Limited tissue interrogation will give misleading biological interpretations about the gene mediating the regulatory effect to increase disease risk[38]
Deep sequencing or Next-generation sequencingExome sequencing: 85% of known disease-causing mutations in Mendelian disorders are found in exons. Exome sequencing is a useful tool to find the causal genes for Mendelian disordersReduced cost and limited data to interpret; Linkage study design is unsuitable for extremely rare and sporadic Mendelian disorders for which exome sequencing would be more practical[39]Exome sequencing: It can miss pathogenic variants in a non-coding region. Repetitive regions (e.g., pseudogenes) can confound results in whole-exome sequencing[41]; Potentiate technical biases regarding exon capture limiting its use in detecting copy-number variants as well as in genomic regions where capture is less efficient[42]
Whole-genome sequencing: Can sequence every nucleotide base in the human genome (approximately 3.3 × 109 base pairs)Whole-genome sequencing: Avoids inherent biases of exome captureWhole-genome sequencing: Too much data but little clinical knowledge available to interpret; Higher cost compared to clinical utility
Targeted gene panel: Provides information on prespecified disease-associated genesExamples: Rapid whole-genome sequencing to investigate extensively drug-resistant (XDR) tuberculosis[40]
RNA-seqUses NGS to analyze RNA expression patterns or transcriptome profiling by reverse transcription of RNA sample to complementary DNAs (cDNA) and PCR amplificationCan be used: to analyze RNA expression profile at single cell level or quantify gene expression[43]; to obtain data on novel transcripts and is not limited by availability of reference genome data[44]; to identify alternatively spliced genes; to detect allele-specific gene expression[44]cDNA synthesis and PCR amplification steps can introduce bias and errors[44]
EpigenomicsEpigenomics involves methods used to identify DNA methylation and histone modifications. Sodium bisulfite can identify unmethylated cytosines due to its ability to convert unmethylated cytosines to uracil. However the methylated cytosine is resistant to this conversion. Methylation-dependent restriction enzymes are used for DNA methylation analysis[45]. Chromatin immunoprecipitation (ChIP) is used for the investigation of histone modificationsChIP allows precise mapping of the DNA-protein interaction in living cells. Cross-linked protein-DNA complex can be treated with exonucleases to remove cross-linked DNA sequences that are not avidly bound to protein of interest. This is called ChIP-Exo. This allows mapping of in vivo protein occupancy at single nucleotide-level resolution[47]Needs design of antibodies specific to DNA-bound protein of interest which could be modified histone or transcription factors
Immunoprecipitation techniques: ChIP on Chip; ChIP-Seq. Chromatin is isolated from the sample and the DNA involved in DNA protein cross-linked complex is isolated using antibodies specific to the DNA-bound protein. The isolated DNA is amplified using PCR and analyzed using gel electrophoresis imaging, microarray hybridization (ChIP-chip), or direct sequencing with NGS (ChIP-Seq)[46]
TranscriptomicsNorthern blot: RNA molecules separated by gel electrophoresis by size and subsequently hybridized with labeled complementary ssDNA and detected using chemic luminescence or autoradiographyNorthern blot can both quantify the amount of RNA and also determine the size of mRNA transcript. Can detect transcript variant of genes[49]Northern blot-need radioactive probes and has lower sensitivity
Ribonuclease (RNase) protection assay: Differs from northern blot by use of antisense RNA probes called riboprobesRNase protection assay: It can simultaneously detect and quantify multiple mRNA targets in a single RNA sample .It has high sensitivityRNase protection assay: Does not provide information on transcript size[52]
Real-time RT-PCR: cDNA are synthesized by reverse transcription from the sample RNA identified. The resulting cDNA is amplified by using fluorescently labeled oligonucleotide primers. Fluorescence intensity is monitored and correlated with several PCR cyclesReal-time RT-PCR: Allows quantitative genotyping, detection of SNPs and allelic variants or genetic variations even when mutation is found in very small fraction of cells in the sample. Has become clinical standard for diagnoses in Infectious diseases and it’s role is evolving rapidly in cancer diagnostics[50]Real-time RT-PCR: The process is complex and any errors in choice of reagents, primers or probes will affect accuracy. There could be risk for errors during data analysis and reporting. The process is expensive[53]
In situ hybridization: Tissue specimen is fixed to preserve morphology and then treated with proteases. A labeled probe is hybridized to the sample and detected using chemiluminescence or autoradiography[48]In situ hybridization: Very useful in diagnostic application when there is limited tissue sample (in embryos and biopsy specimen). Several specific hybridizations can be done on the same sample. Tissue samples can be freeze for future use[48]In situ hybridization: Low diagnostic yield when the sample has low DNA and RNA copies[48]
Spotted DNA arrays: Measures relative expression levels between 2 samples. cDNA probes amplified by PCR are spotted on a glass slide and then mRNAs are isolated from the samples. The mRNA from each sample is labeled with different fluorescent dyes. The samples are mixed, co-hybridized with cDNA probes on glass slides to measure relative gene expressionSpotted DNA arrays: The major application of DNA array is measurement of gene expression levels[51]Spotted DNA arrays: DNA array can only detect known sequences, that were used to construct the array. It only gives relative estimate of gene expression and not reliable for absolute quantification. When the genome has multiple related sequences then design of array that distinguishes these sequences is challenging. Difficult to reproduce the array[51]
Table 2 Characteristics of genome-editing technologies using programmable nucleases
Gene editing
Principle of use
Advantages or application
CRISPR-Cas9 guided gene editing: (1)NHEJ; and (2)HDRCas9 enzyme (an endonuclease) cleaves ds- DNA at a specific site as determined by the specific sequence of the guide RNA. Genome editing is done when the cell tries to repair the dsB (either via NHEJ or HDR)Has the potential to edit genes in almost any cell type in vivo; Has potential in every field, notably infections[54], genetic disease[55], cancer[56] etc.; CRISPR-Cas9 can also be used for large scale loss-of-function gene screen: Catalytically inactive Cas9 (dCas9) can be directed by guide RNA, bind to specific genes to reversibly suppress or activate gene transcription (by fusion of transcription activators or suppressors with dCas9)[57]; Epigenetic modulators (e.g., DNA methylase) can also be fused with dCas9 to achieve controlled epigenetic modulations. Cas-9 NHEJ is simpler and efficient; Cas-9 HDR is more precise but lower efficiency than NHEJ. The mutant version of the Cas9 called Cas9 nickase can be used to minimize the risk of off-targetsThe off-target activity of RNA-guided endonuclease-induced mutations[58]. Off-target mutations with a frequency below 0.5% cannot be detected by current off-target detection techniques[59]
Augmented CRISPR-Cas12a systemCas12a cuts target ds- DNA. However, unlike Cas9, Cas12a subsequently becomes activated and causes indiscriminate cleavage of ssDNA causing collateral damage. SARS-CoV-2 RNA DETECTR Assay: samples from upper airway swabs are processed using simultaneous reverse transcription and isothermal amplification with loop-mediated amplification (RT-LAMP). Subsequently the Cas12 enzyme is addedCRISPR-Cas12a system can be used to create new drug or cell delivery systems and bio-sensing (e.g., to detect methicillin-resistant Staphylococcus aureus, Ebola virus[60]. Emergency Use Authorization (EUA) Only for qualitative detection of nucleic acid from the SARS-CoV-2 in upper respiratory specimens[61,62]Limited research data and application. The technology is still in its infancy
CRISPR-Cas 13CRISPR-Cas 13 system can be used via SHERLOCK technique for ultra-sensitive detection of RNA or DNA from the clinical samplesSherlockTM CRISPR SARS-CoV-2 kit: Emergency Use Authorization (EUA) qualitative for detection of nucleic acid fromSARS-CoV-2 in upper respiratory specimens[63,64]
Prime editorsIt uses a catalytically impaired Cas9 which is fused to an engineered reverse transcriptase and prime editing guide RNA. The guide RNA specifies the target site and encodes the desired sequencePrime editing is associated with fewer off-target edits when compared with conventional CRISPR-Cas system[65]. Anzalone et al[66] applied prime editing in human cells to correct the primary genetic causes of sickle cell disease and Tay-Sachs disease. It does not require double-strand breaks or donor DNA templatesResearch literature on application of prime editing is limited. Unlike conventional CRISPR-Cas system prime editing may not be able to provide large DNA insertions or deletions[65]
Zinc finger nucleasesZinc finger nuclease (dimer of zinc finger hybrid bound to restriction endonuclease) is a programmable nuclease that cleaves specific sites in DNA. They recognize the target sequence through protein-DNA interactionPotential for plant genome editing for crop improvement[67]Necessity to engineer novel proteins for each target site: Expensive; Difficult to reproduce
TALENSTAL proteins have TAL effector DNA-binding domain fused to a DNA cleavage domain. TALENs create dsBs that require repair by NHEJ or HDRThe DNA-binding specificity of TALEs is easier to engineer than zinc-fingerProteins[68]Necessity to engineer novel proteins for each target site. TALENs are large and pose packaging challenge in viral delivery systems[69]
Table 3 Gene based therapies: List of Food and Drug Administration approved therapies and investigational therapies showing promise
Therapy or drug
Mechanism of action
Approval status
Janssen COVID-19 vaccinePrevention of 2019 coronavirus disease (COVID-19) for individuals 18 yr of age and olderRecombinant, humanadenovirus type 26 vector which expresses the SARS-CoV-2 “S” antigen after entering human cells thus eliciting immune response against COVID-19Emergency use authorization (EUA) on February 27, 2021[70]. Pause placed on vaccine use on April 13, 2021[71]. FDA lifted vaccination pause on April 23, 2021[72]
Pfizer-BioNTech COVID-19 Vaccine[73-75]Prevention of COVID-19 for individuals 16 yr of age and oldermodRNA forumated in lipid particles when delivered to host cells express SARS-CoV-2 “S” antigen, thus eliciting immune response against COVID-19EUA on December 11, 2020
Moderna COVID-19 vaccine[76-78]Prevention of COVID-19 for individuals 18 yr of age and oldermodRNA forumated in lipid particles when delivered to host cells express SARS-CoV-2 “S” antigen, thus eliciting immune response against COVID-19EUA on December 18, 2020
Lumasiran[79]Primary hyperoxaluria type 1HAO1-directed small interfering ribonucleic acidApproved in Nov 2020
Viltolarsen[80]Duchenne muscular dystrophyAntisense oligonucleotide directed to exon 53 skippingApproved in August 2020
Brexucabtagene autoleucel[81]Relapsed/refractory mantle cell lymphomaGenetically modified autologous CD19 T cells directed against CD19 expressing cancer cellsApproved in July 2020
Golodirsen[82]Duchenne muscular dystrophyAntisense oligonucleotide directedApproved in December 2019
Givosiran[83]Acute hepatic porphyriaDouble-stranded small interfering RNA that degrades the ALAS1 mRNA in hepatocytes via RNA interferenceApproved in November 2019
Onasemnogene abeparvovec-xioi[84]Spinal muscular atrophy (SMA)AAV9-based gene therapy which encodes the human SMN proteinApproved in May 2019
Inotersen[85]Polyneuropathy of hereditary transthyretin-mediated amyloidosisTransthyretin-directed antisense oligonucleotideApproved in October 2018
Axicabtagene ciloleucel[86]Relapsed or refractory large B-cell lymphoma after two or more lines of systemic therapyGenetically modified autologous CD19 T cells directed against CD19 expressing cancer cellsApproved in October 2017
Tisagenlecleucel[87]Refractory or relapsed B-cell precursor acute lymphoblastic leukemia (ALL)Genetically modified autologous CD19 T cells directed against CD19 expressing cancer cellsApproved in August 2017
Nusinersen[88]SMASurvival motor neuron-2 (SMN2)-directed antisense oligonucleotideApproved in December 2016
Eteplirsen[89]Duchenne muscular dystrophyAntisense oligonucleotid that binds to exon 51 of dystrophin pre-mRNAApproved in September 2016
Talimogene laherparepvec[90]Genetically modified herpes simplex virus, type 1 used as oncolytic viral therapyThey utilized the local treatment of unresectable cutaneous, subcutaneous, and nodal lesions in patients with melanoma who had the recurrence after the initial surgeryApproved in October 2015
Giroctocogene fitelparvovec[91]Moderately severe to severe hemophilia AFactor VIII gene delivery using recombinant adeno-associated viruses as vectorsInvestigational in phase 3 trial
Inclisiran[92]Heterozygous and possibly homozygous familial hypercholesterolemiaSmall-interfering ribonucleic acid which decreases hepatic production of PCSK9Investigational phase 3 trial
Volanesorsen[93]Familial chylomicronemia syndromeAntisense oligonucleotide that targets the messenger RNA for apo-CIIIConditional approval by European Medicines Agency’s (EMA) but not by FDA
CRISPR-Cas9 gene editing[94]Sickle cell disease and β-thalassemiaCRISPR-Cas9based allele editing of the BCL11A erythroid-specific enhancer in autologous CD34+ cellsInvestigational- FDA Fast Track Designation for CTX001 in sickle cell disease