“The human genome project was initiated in 1990 in order to sequence the whole genetic content of the human genome and other species to know genes and their functions.”
The human genome is the collection of all the genetic information of a cell including coding, non-coding and regulatory elements.
The genome of us is a mysterious thing! It’s a collection of all DNA, some are protein-coding, some are not, some help in the regulation of gene expression and some are just sequences.
The molecular structure of DNA was just postulated in 1953 by Watson and Crick earlier, scientists were aware that something is inherited from parents to their offspring but didn’t know that exactly it is.
Even Though the inheritance of traits was conceptualized by Mendel in the 18s, genes were known to us in the early 19s. After the postulation of the molecular structure of DNA, researchers know that change in DNA sequence, as well as content, influences one’s health adversely.
To understand genes, their structure, function and role in disease, the concept of the human genome project came to light. Further, the outline of the human genome project was designed to unfold the mystery of the human genome and see inside it.
The funds for the project were raised by the US Department of Energy and National Institute of Health, collectively.
In the early 90s, the human genome project was developed to determine the sequence of the entire human genome and completed in 2003. The human genome project has an extraordinary trove of information about DNA sequences, genes, non-coding elements and gene expression.
The information helps to understand human development, physiology, medicine and evolution.
It is a larger genome that has been sequenced so far with a lot of information tailored in three billion chemical base pairs. This article includes the ethical, legal and social implications that might arise from coding the entire human genome.
The talk of the present topic is one of the most fascinating and anticipated projects of mankind, that is the “human genome project”.
A short history:
The idea of sequencing the human genome was first proposed in the USA committee appointed by the US national research council. It refers to the international 13-year effort, formally begun in October 1990 and completed in 2003, to discover all estimated 20,000 to 25000 human genes.
Another goal of projects is to determine the complete sequence of the 3 billion DNA subunits. The first genetic map was completed in September 1994 while the physical map with 30,000 or more STSs was completed in October 1998.
The sequencing of 99% of portions of gene-rich regions was completed in April 2003. Meanwhile, identification and characterization of disease-causing genes, sequencing of other model organisms and other uncompleted tasks that were done in the same year.
Related article: DNA: Definition, Structure and Function.
Aims and objectives of HGP:
The Human genome project was started in the 90s and completed after almost 13 years of hard work by scientists.
The project was designed not only to sequence the whole genome but also to make it readily accessible for scientists across the world. To fulfill the present aim, initially, more than 200 different genetic laboratories from the USA and 18 different countries had taken part to support the project.
Also, the project was a kind of open initiative in which any country can take part to support the human genome project.
The core values or objectives of the present projects are to tailor a physical or genetic map of the whole human as well as mice genome.
To sequence both the genome and other genomes like yeast and microbes in order to use it as a test run for human genome sequencing.
Overall, two broader objectives of it are:
- Creating a physical map of the human genome
- To sequence the whole genome of around 3 billion base pairs.
Other objectives are,
To make the information available for all researchers thereby developing a computational system to store, transfer, process and retrieve the data across the world.
To identify all the disease-causing genes.
To understand the function of genes
To map and tag genes on chromosomes.
To develop tools to process and analyze data.
Note that only the euchromatin region of the chromosomes which are the gene-rich regions are only sequenced during the human genome project. The non-coding heterochromatin regions were excluded from the project which is the centromeric and telomeric regions and is gene fewer regions.
Techniques used in HGP:
Initially, the shotgun sequencing technique was used to initiate the human genome project. The present technique was powerful enough to sequence the whole genome at that time.
The whole project using the SGS is divided into two phases; in the initial phase, approximately 90% of DNA (coding genes) would be sequenced while in the later phase, the remaining gaps and breaks would be filled using the data of physical mapping.
The overview of the technique is explained here;
DNA extraction is performed followed by the restriction digestion that makes chumps of larger DNA fragments. The endonucleases cleave DNA into thousands of fragments.
Later the fragments are inserted into the BAC- bacterial artificial chromosomes and a library of fragments are constructed.
Soon after, digested fragments are further divided even smaller fragments are ligated into the plasmid vector.
These smaller fragments are sequenced in amplification reactions. This is a comprehensive overview of the shotgun technique used in sequencing.
Besides the shotgun sequencing technique, secondary techniques like PCR, FISH, restriction digestion and Sanger sequencing are also practiced to achieve various milestones during the human genome project.
Restriction digestion technique is used to construct the restriction map. HindIII, EcoRI, PstI and other restriction endonucleases are employed to digest the genomic DNA in order to produce sticky end and blunt-end DNA fragments.
The restriction endonuclease cleaves DNA at its known recognition sites. These fragments are either ligated into BAC or plasmid.
The application of polymerase chain reaction here is to amplify the DNA fragments to success in DNA sequencing.
The chromosomal map by sequence-tag sites was also generated by utilizing the PCR technique.
Here the set of known primers were allowed to amplify 500 to 600 bp fragments of DNA- STSs within the vector library. STS- amplification allows mapping DNA sequences on chromosomes.
The fluorescence in situ hybridization technique was also practiced to construct the physical map of chromosomes. It is a hybridization-based technique in which the known DNA probes hybridize on complementary regions of chromosomes.
Moreover, tools like Restriction enzymes, ligases, helicases, BAC, plasmids and other biological tools were also used during the human genome project.
Outcomes of HGP:
After completion of the project, scientists have gained tremendous information regarding the genome of us. A glimpse of some of them are here;
In the human genome, 25,000 – 30,000 protein-coding genes are present which is two times larger than other eukaryotes such as worm and fly. It is obvious that the human genome is more complex with more alternating splicing generating more protein products.
Genes are supposed to be derived from the transposable elements and horizontal gene transfer from bacteria.
Mutation rates are twice as high in males as females.
The cytogenetic analysis also revealed that the ‘Gene rich’ rich regions stain lighter while ‘Gene poor’ regions stain darker by G bands.
Some numbers of HGP:
- The human genome contains 97% repetitive junk DNA content.
- Only 2 to 3% portion of the genome encodes proteins
- The human genome contains 3.2 bbp, which means 6.4 bases which are approximately 3164.7mb.
- Around 25,000 to 30,000 genes are present in the human genome in which the average length of a gene is 3000 base pairs.
- The largest gene is the dystrophin having 2.4Mb in size.
- All the genetic content of a cell is located on 23 pairs of chromosomes.
- The genome of us has 1.4 million known SNPs.
Importance of HGP
The human genome project was established aiming to diagnose genetic disease and to know the predisposition of disease in order to improve the drug delivery system.
Using gene therapy more precisely to treat and cure disease. A mutant gene can be repaired or replaced through gene therapy.
To study the risk of toxic exposure to individuals and how it impacts the genetics of individuals.
To study the evolution through germline gene therapy and migration of races and species.
Identification and classification of organisms by DNA sequencing.
Read more: What is DNA sequencing?- Beginner’s guide.
Ethical, legal and social implications
HGP assists scientists with the knowledge of gene sequence and they can modify it by knocking out or knocking in, though because of gene-gene and gene-environment interactions, it is difficult to predict the effect of many such interconversions.
As the project progressed, it had created controversies and ethical issues. For instance, One biggest controversy arose when NIH applied for patenting some cDNA sequences of genes, even without knowing their functions. Genes can’t be patented.
Implementations of medical activities raise many ethical and legal controversies, such as those related to the nature of informed consent that should be guaranteed to those who have a genetic test.
Also, the issues related to privacy and confidentiality of genetic information of a person and much further lead to psychological impact and social stigmatization on an individual due to genetic differences.
People would be discriminated against because of their DNA that increases the chances of getting a certain disease.
Applications of human genome project:
Diagnosis of disease:
The prime goal to conduct the human genome sequencing is to know the location of disease-causing genes. By knowing the structure, function, or location of genes related to the disease can be understood more. Thereby inherited, non-inherited, chromosomal as well as gene-disease can be diagnosed.
Nowadays various disorders like cystic fibrosis, hemophilia, thalassemia, sickle cell anemia, Huntington’s disease and diabetes-like disorders can be diagnosed using the genetic technique.
The information gained from the HGP has already been used in the healthcare industry. Publicized successes are cloning of genes responsible for the Duchenne muscular dystrophy, retinoblastoma, cystic fibrosis and neurofibromatosis.
If other diseases related genes are isolated, scientists can begin to understand the structure and pathology of disorders like heart disease, cancer, diabetes. This would lead to better medical management of these disorders and pharmaceutical discovery.
Curing genetic disorders:
Gene therapies, gene transfer techniques and genetic engineering tools make it possible to cure genetic disorders by removing, altering or replacing the faulting gene or portion of a gene.
Gene therapies, though are still under preclinical phases, are the futuristic novel approach to treat genetic disorders. Here the gene of interest is first introduced into the vectors and transferred to the target location.
In vivo, in vitro, germ-line and somatic cell gene therapies are popular types of it.
|In vivo||Performed inside body or living cell.|
|In vitro||Performed outside body or living cell, in the lab.|
|Somatic cell||Performed on the somatic cells and thus restricted to some tissues or portion of a body.|
|Germline||Performed on the germ cells thus transfer to the fetus and next generations.|
Related article: What is gene therapy? and how does it work?
Genetic or molecular medicines:
Again the futuristic and novel approach to design medicine specific to a particular gene or to influence the function of only a gene or genetic disorder we wish to treat sounds like a fairy tale.
genetic screening will enable rapid and specific diagnostic tests making it possible to test countless maladies. Genetic medicines will enable healthcare workers to treat a disease with a specific treatment.
Conclusively, the Human genome project was one of the most challenging tasks, though, an important part of world history. Because, We had sequenced the whole genome, every single nucleotide of a genome.
The project was declared as completed in 2003, however, some portions and gaps also remained unfilled, which were later on sequenced and mapped on chromosomes.
Collins FS, Fink L. The Human Genome Project. Alcohol Health Res World. 1995;19(3):190-195.