Indian government has cleared an ambitious gene-mapping project that is being described by those involved as the “first scratching of the surface of the vast genetic diversity of India”.
- Every organism’s genetic code is contained in its Deoxyribose Nucleic Acid (DNA), the building blocks of life.
- A genome is all the genetic matter in an organism.
- It is defined as “an organism’s complete set of DNA, including all of its genes. Each genome contains all of the information needed to build and maintain that organism.
- In humans, a copy of the entire genome — more than 3 billion DNA base pairs — is contained in all cells that have a nucleus”.
- In humans, each cell consists of 23 pairs of chromosomes for a total of 46 chromosomes, which means that for 23 pairs of chromosomes in each cell, there are roughly 20,500 genes located on them.
- Some of the genes are lined up in a row on each chromosome, while others are lined up quite close to one another and this arrangement might affect the way they are inherited.
Genome mapping, essentially means figuring out the location of a specific gene on a particular region of the chromosome and also determining the location of and relative distances between other genes on that chromosome. Genome mapping provided a critical starting point for the Human Genome Project.
- A genome map highlights the key ‘landmarks’ in an organism’s genome.
- A genome map helps scientists to navigate their way around the genome.
- The landmarks on a genome map may include short DNA sequences, regulatory sites that turn genes on and off or the genes themselves.
- Genome mapping provided the basis for whole genome sequencing
- Sequenced DNA fragments can be aligned to the genome map to aid with the assembly of the genome.
- Over time, as scientists learn more about a particular genome, its map becomes more accurate and detailed. A genome map is not a final product, but work in progress.
Uses of Genome Mapping
- Genome mapping enables scientists to gather evidence if a disease transmitted from the parent to the child is linked to one or more genes.
- Furthermore, mapping also helps in determining the particular chromosome which contains that gene and the location of that gene in the chromosome.
- According to the National Human Genome Research Institute (NHGRI), genome maps have been used to find out genes that are responsible for relatively rare, single-gene inherited disorders such as cystic fibrosis and Duchenne muscular dystrophy.
- Genetic maps may also point out scientists to the genes that play a role in more common disorders and diseases such as asthma, cancer and heart disease among others.
- Studying and understanding genome maps would provide the bedrock of personalised healthcare for a very large group of persons on the planet.
- Genome maps will help in genotyping of specific viruses to direct appropriate treatment;
- Such maps will also be very beneficial for the design of medication and more accurate prediction of their effects
- Another advantage would be in the advancement in forensic applied sciences and thereby help in better crime investigation
- Another proposed benefit is the commercial development of genomics research related to DNA based products, a multibillion-dollar industry.
Different types of genome mapping
There are two general types of genome mapping called genetic mapping and physical mapping.
Both types of genome mapping guide scientists towards the location of a gene (or section of DNA) on a chromosome, however, they rely on very different information.
- Genetic mapping looks at how genetic information is shuffled between chromosomes or between different regions in the same chromosome during meiosis (a type of cell division). A process called recombination or ‘crossing over’.
- Physical mapping looks at the physical distance between known DNA sequences (including genes) by working out the number of base pairs? (A-T, C-G) between them.
- To produce a genetic map, researchers collect blood or tissue samples from members of a family, some of whom have a certain disease or characteristic.
- The researchers then isolate the DNA from samples taken from each individual and closely examine it to find unique patterns in the DNA of those individuals with the disease/characteristic, that aren’t present in the DNA of the individuals who don’t have the disease/characteristic.
- These are referred to as markers and are extremely valuable for tracking inheritance of characteristics or diseases through several generations of a family.
- One type of DNA marker, called a microsatellite, is found throughout the genome and consists of a specific repeated sequence of bases.
- The more DNA markers there are on a genetic map the more likely it is that one of them will be located close to the disease or trait-associated gene.
- While genetic maps are good at giving you the bigger picture, they have limited accuracy and therefore need to be supplemented with further information gained from other mapping techniques, such as physical mapping.
- Physical mapping gives an estimation of the (physical) distance between specific known DNA sequences on a chromosome.
- The distance between these known DNA sequences on a chromosome is expressed as the number of base pairs between them.
- There are a several different techniques used for physical mapping. These include:
- Restriction mapping (fingerprint mapping and optical mapping)
- Fluorescent in situ hybridisation (FISH) mapping
- Sequence tagged site (STS) mapping.
Illustration showing how FISH can be used to produce a genetic map
Human Genome project
The Human Genome Project (HGP) was an international programme that led to the decoding of the entire human genome.
- It has been described as “one of the great feats of exploration in history. Rather than an outward exploration of the planet or the cosmos, the HGP was an inward voyage of discovery led by an international team of researchers looking to sequence and map all of the genes — together known as the genome — of members of our species”.
- Beginning on October 1, 1990 and completed in April 2003, the HGP gave us the ability, for the first time, to read nature’s complete genetic blueprint for building a human being.
- The international project, which was coordinated by the National Institutes of Health and the US Department of Energy, was undertaken with the aim of sequencing the human genome and identifying the genes that contain it.
- The project was able to identify the locations of many human genes and provide information about their structure and organization.
- According to the Human Genome Project, there are estimated to be over 20,500 human genes.
Benefits of Human genome Project
‘Genome India’ Project
This is being spearheaded by the Centre for Brain Research at Bengaluru-based Indian Institute of Science as the nodal point of about 20 institutions, each doing its bit in collecting samples, doing the computations, and then the research.
- Its aim is to ultimately build a grid of the Indian “reference genome”, to understand fully the type and nature of diseases and traits that comprise the diverse Indian population.
- For example, if the Northeast sees a tendency towards a specific disease, interventions can be made in the region, assisting public health, which make it easier to battle the illness.
- The mega project hopes to form a grid after collecting 10,000 samples in the first phase from across India, to arrive at a representative Indian genome.
- This has been found necessary as over 95% of the genome samples available, which are the basis of new, cutting-edge research in medicine and pharmacology, use the white, Caucasian genome as the base.
- Most genomes have been sourced from urban middle-class persons and are not really seen as representative.
- The Indian project will aim to vastly add to the available information on the human species and advance the cause, both because of the scale of the Indian population and the diversity here.
- In a project that aims only to create a database of genetic information, gene modification is not among the stated objectives.
- The lure to “intervene” may be much more if this kind of knowledge is available, without one being fully aware of the attendant risks.
- The risk of doctors privately running away with the idea of fixing genetic issues came to light most recently after a Shenzen-based scientist, who helped create the world’s first gene-edited babies, was sentenced to three years in prison.
- He Jiankui stunned the world when he announced in 2018 that twin girls had been born with modified DNA to make them HIV-resistant. He claimed he had managed that using the gene-editing tool CRISPR-Cas9 before their birth.
DATA & STORAGE:
- After collection of the sample, anonymity of the data and questions of its possible use and misuse would need to be addressed.
- Keeping the data on a cloud is fraught with problems and would raise questions of ownership of the data. India is yet to pass a Data Privacy Bill with adequate safeguards.
- Launching a Genome India Project before the privacy question is settled could give rise to another set of problems.
- The question of heredity and racial purity has obsessed civilisations, and more scientific studies of genes and classifying them could reinforce stereotypes and allow for politics and history to acquire a racial twist.
- In India a lot of politics is now on the lines of who are “indigenous” people and who are not. A Genome India Project could add a genetic dimension to the cauldron.