Abstract
The sequencing of complete human genome revolutionized the genomic medicine. However, the complex interplay of gene-environment-lifestyle and influence of non-coding genomic regions on human health remain largely unexplored. Genomic medicine has great potential for diagnoses or disease prediction, disease prevention and, targeted treatment. However, many of the promising tools of genomic medicine are still in their infancy and their application may be limited because of the limited knowledge we have that precludes its use in many clinical settings. In this review article, we have reviewed the evolution of genomic methodologies/tools, their limitations, and scope, for current and future clinical application.
Keywords: Genomic medicine, Medical genetics, Gene sequencing, DNA sequencing, RNA sequencing, Clustered regularly interspaced short palindromic repeat, Gene based therapy, Genomic tools, Genome editing
Core Tip: The field of Genomics is the future of medicine, as evidenced by the unprecedented research and clinical application which pushed the time boundaries for the coronavirus disease 2019 mRNA vaccines. However the path to unleashing the potential from genomic tools is far from perfect. A thorough research with international collaboration and cooperation is a necessity and the need of the hour.
INTRODUCTION
Understanding the human genome has come a long way since the initial discovery of DNA structure by Watson and Crick in 1953[1]. The genome study and reference used to be a very specialized area, but lately with the advent of the messenger based RNA vaccine have brought the concept of genetics even to the lay public. In the 1970s, the ability to manipulate DNA with recombinant DNA technology increased the horizon. Our understanding of medical genetics began with inheritance patterns of single-gene diseases. The database of Mendelian Inheritance in Man (MIM) was initiated in the early 1960s by McKusick[2]. As of January 5, 2021, 4368 genes were mapped to phenotype-causing mutations[3]. However, only a small portion of diseases have a monogenic cause. The majority of the common diseases are polygenic, and elucidation of their mechanism has remained elusive.
The human genome project, which was completed in 2003, revolutionized the understanding of the human genome and served as a turning point to fast forward the genomic methodologies. However, the clinical application of findings from these genomic studies is still in its infancy. This is largely because we still have not understood or made complete sense of the available information. That is, the sequence data have been difficult to correlate to functional outcomes, making it difficult to understand the genetic basis of diseases and the complex gene-lifestyle-environment influences or their interaction. Moreover, most of the initial focus of the research had been on coding regions of DNA which comprises approximately 2% of the DNA and the knowledge about specific implications of non-coding DNA regions (98% of DNA) are largely unknown[4,5].
Remarkably, the human genome and the closest related species chimpanzees differ in single nucleotide alterations by a mere 1.23% and in deletions, insertions, and copy number variations by 3%[6]. In humans, the genomes of any two individuals are about 99.9% identical. However, a mere 0.1% variation allows for changes in a massive number of nucleotides because the human genome has approximately 30 billion base pairs (3.3 × 109)[7].
In this review, we will discuss the evolution in genomic methodology, limitations, and their scope for current and future clinical application.
GENOMIC TOOLS AND THEIR EVOLUTION
DNA sequencing
After the initial DNA sequencing method by Maxam and Gilbert[8] in 1977, the chain-termination DNA sequencing method developed by Sanger et al[9] in 1977 was used for the next few decades. It relied on the template DNA strand and had limited capacity for sequencing gene panels. Subsequently, with commercial production of high throughput technologies or next-generation sequencing (NGS) revolutionized the DNA sequencing by 2007[10]. Also called as massively parallel sequencing, NGS does parallel sequencing of millions of small DNA fragments. Each DNA fragment is fixed at a unique location on the solid support. While the sample of the patient's DNA which serves as a template in NGS is amplified and fragmented, the third-generation sequencing uses single DNA molecules rather than the amplified DNA as a template thus eliminating errors from DNA amplification processes. The NGS can be used for whole-genome sequencing, exome sequencing, or targeted gene panels comprising tens to hundreds of genes.
Single nucleotide polymorphism
Single nucleotide polymorphism (SNP) is the variation in genetic sequence by a single nucleotide. It is the most common type of genetic variation in man[11]. It was detected in the 1980s using restriction enzymes[12]. With application of the microarray technology to SNPs, the scope of SNP in clinical practice has widened, especially in oncology. The first SNP array analysis was done in 1998 and the first application of SNP array analysis in cancer was done in 2000[13]. SNP array analysis is used to determine loss of heterozygosity, allelic imbalance, genomic copy number changes, frequency of homozygous chromosome regions, uniparental disomy, DNA methylation alterations and linkage analysis of DNA polymorphisms in cancer cells[13,14].
DNA amplification
Kary Banks Mullis successfully demonstrated polymerase chain reaction (PCR) in 1983[15]. PCR is a cost-effective method that can amplify a single DNA exponentially[16]. It is a rapid, highly specific, and extremely sensitive method. PCR is being used in SNP genotyping, detection of rare sequences, insertion-deletion variants, and structural variants like copy-number variants.
Linkage and association analysis
Linkage studies have been used for mapping of genes for heritable traits to their chromosomal locations. 1st genetic linkage map was done in 1911 by Sturtevant A[17]. Parametric linkage analysis is used to map the disease-causing gene for monogenic diseases. Here, the logarithm of the odds (LOD) scores and recombination fractions are used to map the gene location. Model-free linkage analysis or non-parametric linkage analysis is used for complex or polygenic diseases, or when the model of inheritance is not known[18]. Linkage analysis of the whole genome can identify large regions of the chromosome with evidence of disease containing the gene[19,20], but this large span of chromosomes can have hundreds of candidate genes.
Linkage studies have been used for mapping Mendelian traits with high penetrance in families and relatives[20]. They are especially useful to identify rare alleles that are present in a small number of families[21], for disease genes with weak effects and polygenic diseases, linkage disequilibrium association mapping has proved to be more useful. In genome-wide association studies (GWAS), genotyping of hundreds or thousands of SNPs is done in cases and control populations and their association with heritability is analyzed. A combination of linkage and association methodologies helps to identify and characterize the wider range of disease-susceptibility variants[22].
Fluorescence in Situ Hybridization (FISH) was developed in 1987. It is a cytogenetic technique which uses fluorescent DNA probes which are designed to label precise chromosomal locations. The advantage of FISH over conventional cytogenetic metaphase karyotype analysis is lack of cell culture requirement. It can rapidly evaluate interphase nuclei in the fresh or paraffin-embedded sample[23]. However, the resolution of this technique is only as good as that of karyotype bands. Cloned DNA FISH probes of about 100 kb, called bacterial artificial chromosomes, are now available. FISH is being utilized more in making clinical diagnosis among Oncology due to its simplicity and reliability to evaluate the key biomarkers in various malignancies.
Comparative genomic hybridization
Comparative genomic hybridization (CGH) was developed in 1992. CGH can detect DNA copy number changes across the entire genome of a patient sample in a single experiment. It compares the hybridization signal intensity of a test sample (for example tumor sample) against a reference sample along the chromosomes[13].
HAPMAP AND 1000 GENOME PROJECTS HAVE CREATED A CATALOG OF SNPS
The HapMap project was started in 2002 to develop a haplotype map of the human genome. It can also describe the common patterns of human genetic variation[24]. The 1000 Genomes Project comprised a total of 26 diverse population set in which whole-genome sequencing was performed. It also used deep exome sequencing and dense microarray genotyping to give a comprehensive description of common human genetic variation[25].
TARGETED GENOME EDITING OR GENOME ENGINEERING
It involves modification of the genome at a precise, prespecified locus using programmable nucleases. Examples of some of the programmable nucleases include zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeat (CRISPR)-Cas (CRISPR-associated) system. These programmable nucleases are designed to impart site-specific double-strand breaks (dsBs) in chromosomal DNA. The cell is therefore forced to use one of the endogenous DNA repair mechanisms — homologous recombination or homology-directed repair (HDR) and nonhomologous end-joining (NHEJ). This enables targeted genetic modifications during the repair process in the living cells (in vivo) (Table 1)[26]. ZFNs and TALENS recognize the target sequence through protein-DNA interaction. CRISPR-Cas nucleases recognize target sequences through RNA and DNA base pairing[26].
Table 1.
Tools for genomics
|
Principle of use
|
Pros and application
|
Limitation
|
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 disequilibrium | Has 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 system | Does 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) analysis | Links 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 condition | Provides 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 sequencing | Exome 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 disorders | Reduced 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 capture | Whole-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 genes | Examples: Rapid whole-genome sequencing to investigate extensively drug-resistant (XDR) tuberculosis[40] | ||
RNA-seq | Uses NGS to analyze RNA expression patterns or transcriptome profiling by reverse transcription of RNA sample to complementary DNAs (cDNA) and PCR amplification | Can 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] |
Epigenomics | Epigenomics 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 modifications | ChIP 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] | |||
Transcriptomics | Northern blot: RNA molecules separated by gel electrophoresis by size and subsequently hybridized with labeled complementary ssDNA and detected using chemic luminescence or autoradiography | Northern 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 riboprobes | RNase protection assay: It can simultaneously detect and quantify multiple mRNA targets in a single RNA sample .It has high sensitivity | RNase 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 cycles | Real-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 expression | Spotted 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] |
SNP: Single nucleotide polymorphism; NGS: Next-generation sequencing; PCR: Polymerase chain reaction; RT-PCR: Real-time reverse transcription polymerase chain reaction; ssDNA: Single stranded DNA.
In the year 2013, Cong et al[27] and Mali et al[28] showed successful genome editing in mammalian cells using the CRISPR system. In the last 5 years, we have seen a leap in the research interest (both animal and human) in CRISPR genomic editing.
While genome editing holds promise to correct the defective genome in vivo, therapies can also be designed to alter the gene expression without altering the genomic code. For example, anti-sense oligonucleotide can be used to alter the splice points of pre-mRNA to correct for a defective gene or suppress its expression. Examples of drugs which use splice modulation and approved by Food and Drug Administration (FDA) are Eteplirsen (exon skipping, approved for Duchenne muscular dystrophy) and nusinersen (exon inclusion, approved for spinal muscular atrophy)[29].
Table 1 summarizes the commonly used genomic tools, their working principle, advantages/applications and limitations (see Table 1). Table 2 summarizes the major genome/gene editing tools their working principle, advantages/applications and limitations. Table 3 summarizes gene-based therapies that are either FDA approved therapies or investigational therapies showing promise.
Table 2.
Gene editing
|
Principle of use
|
Advantages or application
|
Limitation
|
CRISPR-Cas9 guided gene editing: (1)NHEJ; and (2)HDR | Cas9 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-targets | The 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 system | Cas12a 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 added | CRISPR-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 13 | CRISPR-Cas 13 system can be used via SHERLOCK technique for ultra-sensitive detection of RNA or DNA from the clinical samples | SherlockTM 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 editors | It 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 sequence | Prime 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 templates | Research 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 nucleases | Zinc 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 interaction | Potential for plant genome editing for crop improvement[67] | Necessity to engineer novel proteins for each target site: Expensive; Difficult to reproduce |
TALENS | TAL proteins have TAL effector DNA-binding domain fused to a DNA cleavage domain. TALENs create dsBs that require repair by NHEJ or HDR | The 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] |
HDR: Homology-directed repair; NHEJ: Nonhomologous end-joining; SARS-CoV-2: Severe acute respiratory syndrome coronavirus 2; TALENs: Transcription activator-like effector nucleases; dsBs: Double stranded breaks; ssDNA: Single stranded DNA; TAL: Transcription activator-like; SHERLOCK: Specific High Sensitivity Enzymatic Reporter UnLOCKing.
Table 3.
Therapy or drug
|
Indication
|
Mechanism of action
|
Approval status
|
Janssen COVID-19 vaccine | Prevention of 2019 coronavirus disease (COVID-19) for individuals 18 yr of age and older | Recombinant, humanadenovirus type 26 vector which expresses the SARS-CoV-2 “S” antigen after entering human cells thus eliciting immune response against COVID-19 | Emergency 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 older | modRNA forumated in lipid particles when delivered to host cells express SARS-CoV-2 “S” antigen, thus eliciting immune response against COVID-19 | EUA on December 11, 2020 |
Moderna COVID-19 vaccine[76-78] | Prevention of COVID-19 for individuals 18 yr of age and older | modRNA forumated in lipid particles when delivered to host cells express SARS-CoV-2 “S” antigen, thus eliciting immune response against COVID-19 | EUA on December 18, 2020 |
Lumasiran[79] | Primary hyperoxaluria type 1 | HAO1-directed small interfering ribonucleic acid | Approved in Nov 2020 |
Viltolarsen[80] | Duchenne muscular dystrophy | Antisense oligonucleotide directed to exon 53 skipping | Approved in August 2020 |
Brexucabtagene autoleucel[81] | Relapsed/refractory mantle cell lymphoma | Genetically modified autologous CD19 T cells directed against CD19 expressing cancer cells | Approved in July 2020 |
Golodirsen[82] | Duchenne muscular dystrophy | Antisense oligonucleotide directed | Approved in December 2019 |
Givosiran[83] | Acute hepatic porphyria | Double-stranded small interfering RNA that degrades the ALAS1 mRNA in hepatocytes via RNA interference | Approved in November 2019 |
Onasemnogene abeparvovec-xioi[84] | Spinal muscular atrophy (SMA) | AAV9-based gene therapy which encodes the human SMN protein | Approved in May 2019 |
Inotersen[85] | Polyneuropathy of hereditary transthyretin-mediated amyloidosis | Transthyretin-directed antisense oligonucleotide | Approved in October 2018 |
Axicabtagene ciloleucel[86] | Relapsed or refractory large B-cell lymphoma after two or more lines of systemic therapy | Genetically modified autologous CD19 T cells directed against CD19 expressing cancer cells | Approved 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 cells | Approved in August 2017 |
Nusinersen[88] | SMA | Survival motor neuron-2 (SMN2)-directed antisense oligonucleotide | Approved in December 2016 |
Eteplirsen[89] | Duchenne muscular dystrophy | Antisense oligonucleotid that binds to exon 51 of dystrophin pre-mRNA | Approved in September 2016 |
Talimogene laherparepvec[90] | Genetically modified herpes simplex virus, type 1 used as oncolytic viral therapy | They utilized the local treatment of unresectable cutaneous, subcutaneous, and nodal lesions in patients with melanoma who had the recurrence after the initial surgery | Approved in October 2015 |
Giroctocogene fitelparvovec[91] | Moderately severe to severe hemophilia A | Factor VIII gene delivery using recombinant adeno-associated viruses as vectors | Investigational in phase 3 trial |
Inclisiran[92] | Heterozygous and possibly homozygous familial hypercholesterolemia | Small-interfering ribonucleic acid which decreases hepatic production of PCSK9 | Investigational phase 3 trial |
Volanesorsen[93] | Familial chylomicronemia syndrome | Antisense oligonucleotide that targets the messenger RNA for apo-CIII | Conditional approval by European Medicines Agency’s (EMA) but not by FDA |
CRISPR-Cas9 gene editing[94] | Sickle cell disease and β-thalassemia | CRISPR-Cas9based allele editing of the BCL11A erythroid-specific enhancer in autologous CD34+ cells | Investigational- FDA Fast Track Designation for CTX001 in sickle cell disease |
AAV: Adeno-associated virus; ALAS1: Aminolevulinate synthase 1; BCL11A: B cell lymphoma/leukemia 11A; HAO1: Hydroxyacid oxidase (glycolate oxidase) 1; modRNA: Nucleoside-modified messenger RNA; SMN: Survival motor neuron 1; FDA: Food and Drug Administration.
DISCUSSION
The newer genomic technology and tools have broadened the scope and pushed the time limits for development of new diagnostic kits, preventive strategies like vaccines, therapeutic strategies like gene modulation and gene therapy. A lot is yet to be studied in terms of the complex interaction of gene-environment-lifestyle-disease. Knowing the impact of genomics on disease pathophysiology and response to medications[30]. expands the scope of research and clinical application. While genome editing holds promise to correct the defective genome in vivo, therapies can also be designed to alter the gene expression without altering the genomic code (example exon skipping, or inclusion discussed above).
The newer genomic editing tools have showed great potential and promise but they need to be studied extensively before clinical application. Also, uniform international ethical guidelines and guiding principles need to be established so that these genomic technologies are not misused.
It is very important to include diverse populations and to represent minority population in the genomic studies, so that results could be generalized and more accurate diagnostic, predictive and therapeutic tools can be developed.
Genomics in medicine is indeed a new era in medicine. Even the control of coronavirus disease 2019 pandemic[31] has just begun at the time of writing of this article with gene based therapies eliciting immune response against severe acute respiratory syndrome coronavirus 2 spike proteins. A unified international collaboration[32,33] is needed to continue expanding gene therapy use in opening new frontiers for fight against novel infections and disease.
CONCLUSION
Genomic medicine holds great promise for providing insight into disease pathophysiology, provide better diagnostic or disease predictive tools, preventive therapies and finally for targeted treatment of diseases. Although some of the newer tools (like CRISPR system) have great potential, more research is needed before these tools can be unleashed to clinical use. Hence there is great need for studies to unravel the mystery of complex interaction of both coding and noncoding genomic regions with environment and lifestyle influences on disease occurrence and management.
Footnotes
Conflict-of-interest statement: None of the authors have any conflict of interest.
Manuscript source: Invited manuscript
Peer-review started: January 12, 2021
First decision: June 17, 2021
Article in press: July 19, 2021
Specialty type: Medical laboratory technology
Country/Territory of origin: United States
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P-Reviewer: Taheri S S-Editor: Gao CC L-Editor: A P-Editor: Guo X
Contributor Information
Vishwanath Pattan, Division of Endocrinology, Wyoming Medical Center, Casper, WY 82601, United States.
Rahul Kashyap, Department of Anesthesiology and Peri-operative Medicine, Mayo Clinic, Rochester, MN 55905, United States.
Vikas Bansal, Department of Anesthesiology and Peri-operative Medicine, Mayo Clinic, Rochester, MN 55905, United States.
Narsimha Candula, Hospital Medicine, University Florida Health, Jacksonville, FL 32209, United States.
Thoyaja Koritala, Hospital Medicine, Mayo Clinic Health System, Mankato, MN 56001, United States.
Salim Surani, Department of Internal Medicine, Texas A&M University, Corpus Christi, TX 78405, United States. srsurani@gmail.com.
References
- 1.Watson JD, Crick FH. The structure of DNA. Cold Spring Harb Symp Quant Biol. 1953;18:123–131. doi: 10.1101/sqb.1953.018.01.020. [DOI] [PubMed] [Google Scholar]
- 2.McKusick VA. Mendelian Inheritance in Man and its online version, OMIM. Am J Hum Genet. 2007;80:588–604. doi: 10.1086/514346. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Johns Hopkins University. OMIM Gene Map Statistics. [cited 20 December 2020]. In: Johns Hopkins University [Internet]. Available from: https://www.omim.org/statistics/geneMap .
- 4.Ling H, Vincent K, Pichler M, Fodde R, Berindan-Neagoe I, Slack FJ, Calin GA. Junk DNA and the long non-coding RNA twist in cancer genetics. Oncogene. 2015;34:5003–5011. doi: 10.1038/onc.2014.456. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Gloss BS, Dinger ME. Realizing the significance of noncoding functionality in clinical genomics. Exp Mol Med. 2018;50:1–8. doi: 10.1038/s12276-018-0087-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Suntsova MV, Buzdin AA. Differences between human and chimpanzee genomes and their implications in gene expression, protein functions and biochemical properties of the two species. BMC Genomics. 2020;21:535. doi: 10.1186/s12864-020-06962-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Gyles C. The DNA revolution. Can Vet J. 2008;49:745–746. [PMC free article] [PubMed] [Google Scholar]
- 8.Maxam AM, Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977;74:560–564. doi: 10.1073/pnas.74.2.560. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977;74:5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Reuter JA, Spacek DV, Snyder MP. High-throughput sequencing technologies. Mol Cell. 2015;58:586–597. doi: 10.1016/j.molcel.2015.05.004. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Shen LX, Basilion JP, Stanton VP Jr. Single-nucleotide polymorphisms can cause different structural folds of mRNA. Proc Natl Acad Sci U S A. 1999;96:7871–7876. doi: 10.1073/pnas.96.14.7871. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12.Gray IC, Campbell DA, Spurr NK. Single nucleotide polymorphisms as tools in human genetics. Hum Mol Genet. 2000;9:2403–2408. doi: 10.1093/hmg/9.16.2403. [DOI] [PubMed] [Google Scholar]
- 13.Mao X, Young BD, Lu YJ. The application of single nucleotide polymorphism microarrays in cancer research. Curr Genomics. 2007;8:219–228. doi: 10.2174/138920207781386924. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14.Sato-Otsubo A, Sanada M, Ogawa S. Single-nucleotide polymorphism array karyotyping in clinical practice: where, when, and how? Semin Oncol. 2012;39:13–25. doi: 10.1053/j.seminoncol.2011.11.010. [DOI] [PubMed] [Google Scholar]
- 15.Fairfax MR, Salimnia H. Diagnostic molecular microbiology: a 2013 snapshot. Clin Lab Med. 2013;33:787–803. doi: 10.1016/j.cll.2013.08.003. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 16.Wages JM. Polymerase Chain Reaction. In: Worsfold P, Townshend A, Poole C. Encyclopedia of Analytical Science. Oxford: Elsevier, 2005: 243-250. [Google Scholar]
- 17.Griffiths AJ, Miller JH, Suzuki DT, Lewontin RC, Gelbart WM. An Introduction to Genetic Analysis - NCBI Bookshelf. 7th ed. New York: W. H. Freeman, 2000. [Google Scholar]
- 18.Dawn Teare M, Barrett JH. Genetic linkage studies. Lancet. 2005;366:1036–1044. doi: 10.1016/S0140-6736(05)67382-5. [DOI] [PubMed] [Google Scholar]
- 19.Ott J, Wang J, Leal SM. Genetic linkage analysis in the age of whole-genome sequencing. Nat Rev Genet. 2015;16:275–284. doi: 10.1038/nrg3908. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 20.Pulst SM. Genetic linkage analysis. Arch Neurol. 1999;56:667–672. doi: 10.1001/archneur.56.6.667. [DOI] [PubMed] [Google Scholar]
- 21.Hinrichs AL, Suarez BK. Incorporating linkage information into a common disease/rare variant framework. Genet Epidemiol. 2011;35 Suppl 1:S74–S79. doi: 10.1002/gepi.20654. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 22.Ott J, Kamatani Y, Lathrop M. Family-based designs for genome-wide association studies. Nat Rev Genet. 2011;12:465–474. doi: 10.1038/nrg2989. [DOI] [PubMed] [Google Scholar]
- 23.Hu L, Ru K, Zhang L, Huang Y, Zhu X, Liu H, Zetterberg A, Cheng T, Miao W. Fluorescence in situ hybridization (FISH): an increasingly demanded tool for biomarker research and personalized medicine. Biomark Res. 2014;2:3. doi: 10.1186/2050-7771-2-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 24.National Human Genome Research Institute. The International HapMap Project. Updated 06/04/2012. [cited 10 December 2020]. In: National Human Genome Research Institute [Internet]. Available from: https://www.genome.gov/11511175/about-the-international-hapmap-project-fact-sheet .
- 25.1000 Genomes Project Consortium. Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR. A global reference for human genetic variation. Nature. 2015;526:68–74. doi: 10.1038/nature15393. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 26.Kim H, Kim JS. A guide to genome engineering with programmable nucleases. Nat Rev Genet. 2014;15:321–334. doi: 10.1038/nrg3686. [DOI] [PubMed] [Google Scholar]
- 27.Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F. Multiplex genome engineering using CRISPR/Cas systems. Science. 2013;339:819–823. doi: 10.1126/science.1231143. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 28.Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM. RNA-guided human genome engineering via Cas9. Science. 2013;339:823–826. doi: 10.1126/science.1232033. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 29.Lim KRQ, Yokota T. Invention and Early History of Exon Skipping and Splice Modulation. Methods Mol Biol. 2018;1828:3–30. doi: 10.1007/978-1-4939-8651-4_1. [DOI] [PubMed] [Google Scholar]
- 30.Pattan V, Seth S, Jehangir W, Bhargava B, Maulik SK. Effect of Atorvastatin and Pioglitazone on Plasma Levels of Adhesion Molecules in Non-Diabetic Patients With Hypertension or Stable Angina or Both. J Clin Med Res. 2015;7:613–619. doi: 10.14740/jocmr2178e. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 31.Shah A, Kashyap R, Tosh P, Sampathkumar P, O'Horo JC. Guide to Understanding the 2019 Novel Coronavirus. Mayo Clin Proc. 2020;95:646–652. doi: 10.1016/j.mayocp.2020.02.003. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 32.Walkey AJ, Kumar VK, Harhay MO, Bolesta S, Bansal V, Gajic O, Kashyap R. The Viral Infection and Respiratory Illness Universal Study (VIRUS): An International Registry of Coronavirus 2019-Related Critical Illness. Crit Care Explor. 2020;2:e0113. doi: 10.1097/CCE.0000000000000113. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 33.Walkey AJ, Sheldrick RC, Kashyap R, Kumar VK, Boman K, Bolesta S, Zampieri FG, Bansal V, Harhay MO, Gajic O. Guiding Principles for the Conduct of Observational Critical Care Research for Coronavirus Disease 2019 Pandemics and Beyond: The Society of Critical Care Medicine Discovery Viral Infection and Respiratory Illness Universal Study Registry. Crit Care Med. 2020;48:e1038–e1044. doi: 10.1097/CCM.0000000000004572. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 34.Severe Covid-19 GWAS Group. Ellinghaus D, Degenhardt F, Bujanda L, Buti M, Albillos A, Invernizzi P, Fernández J, Prati D, Baselli G, Asselta R, Grimsrud MM, Milani C, Aziz F, Kässens J, May S, Wendorff M, Wienbrandt L, Uellendahl-Werth F, Zheng T, Yi X, de Pablo R, Chercoles AG, Palom A, Garcia-Fernandez AE, Rodriguez-Frias F, Zanella A, Bandera A, Protti A, Aghemo A, Lleo A, Biondi A, Caballero-Garralda A, Gori A, Tanck A, Carreras Nolla A, Latiano A, Fracanzani AL, Peschuck A, Julià A, Pesenti A, Voza A, Jiménez D, Mateos B, Nafria Jimenez B, Quereda C, Paccapelo C, Gassner C, Angelini C, Cea C, Solier A, Pestaña D, Muñiz-Diaz E, Sandoval E, Paraboschi EM, Navas E, García Sánchez F, Ceriotti F, Martinelli-Boneschi F, Peyvandi F, Blasi F, Téllez L, Blanco-Grau A, Hemmrich-Stanisak G, Grasselli G, Costantino G, Cardamone G, Foti G, Aneli S, Kurihara H, ElAbd H, My I, Galván-Femenia I, Martín J, Erdmann J, Ferrusquía-Acosta J, Garcia-Etxebarria K, Izquierdo-Sanchez L, Bettini LR, Sumoy L, Terranova L, Moreira L, Santoro L, Scudeller L, Mesonero F, Roade L, Rühlemann MC, Schaefer M, Carrabba M, Riveiro-Barciela M, Figuera Basso ME, Valsecchi MG, Hernandez-Tejero M, Acosta-Herrera M, D'Angiò M, Baldini M, Cazzaniga M, Schulzky M, Cecconi M, Wittig M, Ciccarelli M, Rodríguez-Gandía M, Bocciolone M, Miozzo M, Montano N, Braun N, Sacchi N, Martínez N, Özer O, Palmieri O, Faverio P, Preatoni P, Bonfanti P, Omodei P, Tentorio P, Castro P, Rodrigues PM, Blandino Ortiz A, de Cid R, Ferrer R, Gualtierotti R, Nieto R, Goerg S, Badalamenti S, Marsal S, Matullo G, Pelusi S, Juzenas S, Aliberti S, Monzani V, Moreno V, Wesse T, Lenz TL, Pumarola T, Rimoldi V, Bosari S, Albrecht W, Peter W, Romero-Gómez M, D'Amato M, Duga S, Banales JM, Hov JR, Folseraas T, Valenti L, Franke A, Karlsen TH. Genomewide Association Study of Severe Covid-19 with Respiratory Failure. N Engl J Med. 2020;383:1522–1534. doi: 10.1056/NEJMoa2020283. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 35.Mills MC, Rahal C. A scientometric review of genome-wide association studies. Commun Biol. 2019;2:9. doi: 10.1038/s42003-018-0261-x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 36.Battle A, Montgomery SB. Determining causality and consequence of expression quantitative trait loci. Hum Genet. 2014;133:727–735. doi: 10.1007/s00439-014-1446-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 37.Glubb DM, Dholakia N, Innocenti F. Liver expression quantitative trait loci: a foundation for pharmacogenomic research. Front Genet. 2012;3:153. doi: 10.3389/fgene.2012.00153. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 38.Nica AC, Dermitzakis ET. Expression quantitative trait loci: present and future. Philos Trans R Soc Lond B Biol Sci. 2013;368:20120362. doi: 10.1098/rstb.2012.0362. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 39.Ku CS, Naidoo N, Pawitan Y. Revisiting Mendelian disorders through exome sequencing. Hum Genet. 2011;129:351–370. doi: 10.1007/s00439-011-0964-2. [DOI] [PubMed] [Google Scholar]
- 40.Köser CU, Bryant JM, Becq J, Török ME, Ellington MJ, Marti-Renom MA, Carmichael AJ, Parkhill J, Smith GP, Peacock SJ. Whole-genome sequencing for rapid susceptibility testing of M. tuberculosis. N Engl J Med. 2013;369:290–292. doi: 10.1056/NEJMc1215305. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 41.Zhang Y, Li S, Abyzov A, Gerstein MB. Landscape and variation of novel retroduplications in 26 human populations. PLoS Comput Biol. 2017;13:e1005567. doi: 10.1371/journal.pcbi.1005567. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 42.Rabbani B, Tekin M, Mahdieh N. The promise of whole-exome sequencing in medical genetics. J Hum Genet. 2014;59:5–15. doi: 10.1038/jhg.2013.114. [DOI] [PubMed] [Google Scholar]
- 43.Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, Xu N, Wang X, Bodeau J, Tuch BB, Siddiqui A, Lao K, Surani MA. mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods. 2009;6:377–382. doi: 10.1038/nmeth.1315. [DOI] [PubMed] [Google Scholar]
- 44.Kukurba KR, Montgomery SB. RNA Sequencing and Analysis. Cold Spring Harb Protoc. 2015;2015:951–969. doi: 10.1101/pdb.top084970. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 45.Gasperskaja E, Kučinskas V. The most common technologies and tools for functional genome analysis. Acta Med Litu. 2017;24:1–11. doi: 10.6001/actamedica.v24i1.3457. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 46.Pillai S, Chellappan SP. ChIP on chip and ChIP-Seq assays: genome-wide analysis of transcription factor binding and histone modifications. Methods Mol Biol. 2015;1288:447–472. doi: 10.1007/978-1-4939-2474-5_26. [DOI] [PubMed] [Google Scholar]
- 47.Rhee HS, Pugh BF. ChIP-exo method for identifying genomic location of DNA-binding proteins with near-single-nucleotide accuracy. Curr Protoc Mol Biol. 2012;Chapter 21:Unit 21.24. doi: 10.1002/0471142727.mb2124s100. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 48.Jensen E. Technical review: In situ hybridization. Anat Rec (Hoboken) 2014;297:1349–1353. doi: 10.1002/ar.22944. [DOI] [PubMed] [Google Scholar]
- 49.He SL, Green R. Northern blotting. Methods Enzymol. 2013;530:75–87. doi: 10.1016/B978-0-12-420037-1.00003-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 50.Deepak S, Kottapalli K, Rakwal R, Oros G, Rangappa K, Iwahashi H, Masuo Y, Agrawal G. Real-Time PCR: Revolutionizing Detection and Expression Analysis of Genes. Curr Genomics. 2007;8:234–251. doi: 10.2174/138920207781386960. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 51.Bumgarner R. Overview of DNA microarrays: types, applications, and their future. Curr Protoc Mol Biol. 2013;Chapter 22:Unit 22.1.. doi: 10.1002/0471142727.mb2201s101. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 52.Qu Y, Boutjdir M. RNase protection assay for quantifying gene expression levels. Methods Mol Biol. 2007;366:145–158. doi: 10.1007/978-1-59745-030-0_8. [DOI] [PubMed] [Google Scholar]
- 53.Bustin SA, Nolan T. Pitfalls of quantitative real-time reverse-transcription polymerase chain reaction. J Biomol Tech. 2004;15:155–166. [PMC free article] [PubMed] [Google Scholar]
- 54.Xu L, Wang J, Liu Y, Xie L, Su B, Mou D, Wang L, Liu T, Wang X, Zhang B, Zhao L, Hu L, Ning H, Zhang Y, Deng K, Liu L, Lu X, Zhang T, Xu J, Li C, Wu H, Deng H, Chen H. CRISPR-Edited Stem Cells in a Patient with HIV and Acute Lymphocytic Leukemia. N Engl J Med. 2019;381:1240–1247. doi: 10.1056/NEJMoa1817426. [DOI] [PubMed] [Google Scholar]
- 55.Wu SS, Li QC, Yin CQ, Xue W, Song CQ. Advances in CRISPR/Cas-based Gene Therapy in Human Genetic Diseases. Theranostics. 2020;10:4374–4382. doi: 10.7150/thno.43360. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 56.Tian X, Gu T, Patel S, Bode AM, Lee MH, Dong Z. CRISPR/Cas9 - An evolving biological tool kit for cancer biology and oncology. NPJ Precis Oncol. 2019;3:8. doi: 10.1038/s41698-019-0080-7. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 57.Lu XJ, Xue HY, Ke ZP, Chen JL, Ji LJ. CRISPR-Cas9: a new and promising player in gene therapy. J Med Genet. 2015;52:289–296. doi: 10.1136/jmedgenet-2014-102968. [DOI] [PubMed] [Google Scholar]
- 58.Cho GY, Schaefer KA, Bassuk AG, Tsang SH, Mahajan VB. CRISPR GENOME SURGERY IN THE RETINA IN LIGHT OF OFF-TARGETING. Retina. 2018;38:1443–1455. doi: 10.1097/IAE.0000000000002197. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 59.Kang SH, Lee WJ, An JH, Lee JH, Kim YH, Kim H, Oh Y, Park YH, Jin YB, Jun BH, Hur JK, Kim SU, Lee SH. Prediction-based highly sensitive CRISPR off-target validation using target-specific DNA enrichment. Nat Commun. 2020;11:3596. doi: 10.1038/s41467-020-17418-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 60.English MA, Soenksen LR, Gayet RV, de Puig H, Angenent-Mari NM, Mao AS, Nguyen PQ, Collins JJ. Programmable CRISPR-responsive smart materials. Science. 2019;365:780–785. doi: 10.1126/science.aaw5122. [DOI] [PubMed] [Google Scholar]
- 61.Broughton JP, Deng X, Yu G, Fasching CL, Servellita V, Singh J, Miao X, Streithorst JA, Granados A, Sotomayor-Gonzalez A, Zorn K, Gopez A, Hsu E, Gu W, Miller S, Pan CY, Guevara H, Wadford DA, Chen JS, Chiu CY. CRISPR-Cas12-based detection of SARS-CoV-2. Nat Biotechnol. 2020;38:870–874. doi: 10.1038/s41587-020-0513-4. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 62.U. S. Food and Drug Administration. SARS-CoV-2 RNA DETECTR Assay Accelerated Emergency Use Authorization (EUA) Summary SARS-COV-2 RNA Detectr Assay (UCSF Health Clinical Laboratories, UCSF Clinical Labs at China Basin). [cited 10 December 2020] In: U.S. Food and Drug Administration [Internet]. Available from: https://www.fda.gov/media/139937/download .
- 63.Joung J, Ladha A, Saito M, Segel M, Bruneau R, Huang MW, Kim NG, Yu X, Li J, Walker BD, Greninger AL, Jerome KR, Gootenberg JS, Abudayyeh OO, Zhang F. Point-of-care testing for COVID-19 using SHERLOCK diagnostics. medRxiv. 2020 [Google Scholar]
- 64.U. S. Food and Drug Administration. Instructions For Use Sherlock Tm Crispr SARS-CoV-2 kit.[cited 10 December 2020] In: U.S. Food and Drug Administration [Internet]. Available from: https://www.fda.gov/media/137746/download .
- 65.Matsoukas IG. Prime Editing: Genome Editing for Rare Genetic Diseases Without Double-Strand Breaks or Donor DNA. Front Genet. 2020;11:528. doi: 10.3389/fgene.2020.00528. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 66.Anzalone AV, Randolph PB, Davis JR, Sousa AA, Koblan LW, Levy JM, Chen PJ, Wilson C, Newby GA, Raguram A, Liu DR. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature. 2019;576:149–157. doi: 10.1038/s41586-019-1711-4. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 67.Davies JP, Kumar S, Sastry-Dent L. Use of Zinc-Finger Nucleases for Crop Improvement. Prog Mol Biol Transl Sci. 2017;149:47–63. doi: 10.1016/bs.pmbts.2017.03.006. [DOI] [PubMed] [Google Scholar]
- 68.Kim MS, Kini AG. Engineering and Application of Zinc Finger Proteins and TALEs for Biomedical Research. Mol Cells. 2017;40:533–541. doi: 10.14348/molcells.2017.0139. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 69.Epstein BE, Schaffer DV. Combining Engineered Nucleases with Adeno-associated Viral Vectors for Therapeutic Gene Editing. Adv Exp Med Biol. 2017;1016:29–42. doi: 10.1007/978-3-319-63904-8_2. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 70.U. S. Food and Drug Administration. Fact Sheet for Healthcare Providers Administering Vaccine (Vaccination Providers): emergency use authorization (EUA) of the Janssen COVID-19 vaccine. [cited 10 December 2020] In: U.S. Food and Drug Administration [Internet]. Available from: https://www.cdc.gov/vaccines/covid-19/clinical-considerations/managing-anaphylaxis.html .
- 71.U. S. Food and Drug Administration. Joint CDC and FDA Statement on Johnson & Johnson COVID-19 Vaccine. [cited 11 December 2020] In: U.S. Food and Drug Administration [Internet]. Available from: https://www.fda.gov/news-events/press-announcements/joint-cdc-and-fda-statement-johnson-johnson-covid-19-vaccine .
- 72.U. S. Food and Drug Administration. FDA and CDC Lift Recommended Pause on Johnson & Johnson (Janssen) COVID-19 Vaccine Use Following Thorough Safety Review. [cited 11 December 2020] In: U.S. Food and Drug Administration [Internet]. Available from: https://www.fda.gov/news-events/press-announcements/fda-and-cdc-lift-recommended-pause-johnson-johnson-janssen-covid-19-vaccine-use-following-thorough .
- 73.Polack FP, Thomas SJ, Kitchin N, Absalon J, Gurtman A, Lockhart S, Perez JL, Pérez Marc G, Moreira ED, Zerbini C, Bailey R, Swanson KA, Roychoudhury S, Koury K, Li P, Kalina WV, Cooper D, Frenck RW Jr, Hammitt LL, Türeci Ö, Nell H, Schaefer A, Ünal S, Tresnan DB, Mather S, Dormitzer PR, Şahin U, Jansen KU, Gruber WC C4591001 Clinical Trial Group. Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine. N Engl J Med. 2020;383:2603–2615. doi: 10.1056/NEJMoa2034577. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 74.U. S. Food and Drug Administration. Fact Sheet for Healthcare Providers Administering Vaccine (Vaccination Providers): Emergency use authorization (EUA) of the Pfizer-BioNTech COVID-19 vaccine to prevent coronavirus disease 2019 (COVID-19). [cited 11 December 2020] In: U.S. Food and Drug Administration [Internet]. Available from: https://www.fda.gov/media/144413/download .
- 75.U. S. Food and Drug Administration. Pfizer-BioNTech COVID-19 Vaccine. [cited 11 December 2020] In: U.S. Food and Drug Administration [Internet]. Available from: https://www.fda.gov/emergency-preparedness-and-response/coronavirus-disease-2019-covid-19/pfizer-biontech-covid-19-vaccine .
- 76.Jackson LA, Anderson EJ, Rouphael NG, Roberts PC, Makhene M, Coler RN, McCullough MP, Chappell JD, Denison MR, Stevens LJ, Pruijssers AJ, McDermott A, Flach B, Doria-Rose NA, Corbett KS, Morabito KM, O'Dell S, Schmidt SD, Swanson PA 2nd, Padilla M, Mascola JR, Neuzil KM, Bennett H, Sun W, Peters E, Makowski M, Albert J, Cross K, Buchanan W, Pikaart-Tautges R, Ledgerwood JE, Graham BS, Beigel JH mRNA-1273 Study Group. An mRNA Vaccine against SARS-CoV-2 - Preliminary Report. N Engl J Med. 2020;383:1920–1931. doi: 10.1056/NEJMoa2022483. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 77.U. S. Food and Drug Administration. Fact Sheet for Healthcare Providers Administering Vaccine (Vaccination Providers): Emergency use authorization (EUA) of the moderna COVID-19 vaccine to prevent coronavirus disease 2019 (COVID-19). [cited 11 December 2020] In: U.S. Food and Drug Administration [Internet]. Available from: https://www.fda.gov/media/144637/download .
- 78.U. S. Food and Drug Administration. Moderna COVID-19 Vaccine. [cited 11 December 2020] In: U.S. Food and Drug Administration [Internet]. Available from: https://www.fda.gov/emergency-preparedness-and-response/coronavirus-disease-2019-covid-19/moderna-covid-19-vaccine .
- 79.Liebow A, Li X, Racie T, Hettinger J, Bettencourt BR, Najafian N, Haslett P, Fitzgerald K, Holmes RP, Erbe D, Querbes W, Knight J. An Investigational RNAi Therapeutic Targeting Glycolate Oxidase Reduces Oxalate Production in Models of Primary Hyperoxaluria. J Am Soc Nephrol. 2017;28:494–503. doi: 10.1681/ASN.2016030338. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 80.Roshmi RR, Yokota T. Viltolarsen for the treatment of Duchenne muscular dystrophy. Drugs Today (Barc) 2019;55:627–639. doi: 10.1358/dot.2019.55.10.3045038. [DOI] [PubMed] [Google Scholar]
- 81.Beyar-Katz O, Gill S. Advances in chimeric antigen receptor T cells. Curr Opin Hematol. 2020;27:368–377. doi: 10.1097/MOH.0000000000000614. [DOI] [PubMed] [Google Scholar]
- 82.Heo YA. Golodirsen: First Approval. Drugs. 2020;80:329–333. doi: 10.1007/s40265-020-01267-2. [DOI] [PubMed] [Google Scholar]
- 83.Scott LJ. Givosiran: First Approval. Drugs. 2020;80:335–339. doi: 10.1007/s40265-020-01269-0. [DOI] [PubMed] [Google Scholar]
- 84.Hoy SM. Onasemnogene Abeparvovec: First Global Approval. Drugs. 2019;79:1255–1262. doi: 10.1007/s40265-019-01162-5. [DOI] [PubMed] [Google Scholar]
- 85.Benson MD, Waddington-Cruz M, Berk JL, Polydefkis M, Dyck PJ, Wang AK, Planté-Bordeneuve V, Barroso FA, Merlini G, Obici L, Scheinberg M, Brannagan TH 3rd, Litchy WJ, Whelan C, Drachman BM, Adams D, Heitner SB, Conceição I, Schmidt HH, Vita G, Campistol JM, Gamez J, Gorevic PD, Gane E, Shah AM, Solomon SD, Monia BP, Hughes SG, Kwoh TJ, McEvoy BW, Jung SW, Baker BF, Ackermann EJ, Gertz MA, Coelho T. Inotersen Treatment for Patients with Hereditary Transthyretin Amyloidosis. N Engl J Med. 2018;379:22–31. doi: 10.1056/NEJMoa1716793. [DOI] [PubMed] [Google Scholar]
- 86.Riedell PA, Bishop MR. Safety and efficacy of axicabtagene ciloleucel in refractory large B-cell lymphomas. Ther Adv Hematol. 2020;11:2040620720902899. doi: 10.1177/2040620720902899. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 87.Maude SL, Laetsch TW, Buechner J, Rives S, Boyer M, Bittencourt H, Bader P, Verneris MR, Stefanski HE, Myers GD, Qayed M, De Moerloose B, Hiramatsu H, Schlis K, Davis KL, Martin PL, Nemecek ER, Yanik GA, Peters C, Baruchel A, Boissel N, Mechinaud F, Balduzzi A, Krueger J, June CH, Levine BL, Wood P, Taran T, Leung M, Mueller KT, Zhang Y, Sen K, Lebwohl D, Pulsipher MA, Grupp SA. Tisagenlecleucel in Children and Young Adults with B-Cell Lymphoblastic Leukemia. N Engl J Med. 2018;378:439–448. doi: 10.1056/NEJMoa1709866. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 88.Chiriboga CA. Nusinersen for the treatment of spinal muscular atrophy. Expert Rev Neurother. 2017;17:955–962. doi: 10.1080/14737175.2017.1364159. [DOI] [PubMed] [Google Scholar]
- 89.Lim KR, Maruyama R, Yokota T. Eteplirsen in the treatment of Duchenne muscular dystrophy. Drug Des Devel Ther. 2017;11:533–545. doi: 10.2147/DDDT.S97635. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 90.Bommareddy PK, Patel A, Hossain S, Kaufman HL. Talimogene Laherparepvec (T-VEC) and Other Oncolytic Viruses for the Treatment of Melanoma. Am J Clin Dermatol. 2017;18:1–15. doi: 10.1007/s40257-016-0238-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 91.Business Wire. Pfizer and Sangamo Announce Updated Phase 1/2 Results Showing Sustained Factor VIII Activity Levels and No Bleeding Events or Factor Usage in 3e13 vg/kg Cohort Following giroctocogene fitelparvovec (SB-525) Gene Therapy. [cited 10 December 2020]. In: Business Wire: Berkshire Hathaway Company. Available from: https://www.businesswire.com/news/home/20200618005091/en/
- 92.Brandts J, Ray KK. Clinical implications and outcomes of the ORION Phase III trials. Future Cardiol. 2020 doi: 10.2217/fca-2020-0150. [DOI] [PubMed] [Google Scholar]
- 93.Witztum JL, Gaudet D, Freedman SD, Alexander VJ, Digenio A, Williams KR, Yang Q, Hughes SG, Geary RS, Arca M, Stroes ESG, Bergeron J, Soran H, Civeira F, Hemphill L, Tsimikas S, Blom DJ, O'Dea L, Bruckert E. Volanesorsen and Triglyceride Levels in Familial Chylomicronemia Syndrome. N Engl J Med. 2019;381:531–542. doi: 10.1056/NEJMoa1715944. [DOI] [PubMed] [Google Scholar]
- 94.Frangoul H, Altshuler D, Cappellini MD, Chen YS, Domm J, Eustace BK, Foell J, de la Fuente J, Grupp S, Handgretinger R, Ho TW, Kattamis A, Kernytsky A, Lekstrom-Himes J, Li AM, Locatelli F, Mapara MY, de Montalembert M, Rondelli D, Sharma A, Sheth S, Soni S, Steinberg MH, Wall D, Yen A, Corbacioglu S. CRISPR-Cas9 Gene Editing for Sickle Cell Disease and β-Thalassemia. N Engl J Med. 2021;384:252–260. doi: 10.1056/NEJMoa2031054. [DOI] [PubMed] [Google Scholar]