Human Genome project

Genetic constitution of an individual lies in the sequence of DNA nucleotides. The differences in two individuals will naturally be reflected in the differences of their nucleotide sequences. They can be known only if the entire human genome is mapped. As the young science of genetic engineering developed, the technique to isolate and clone DNA fragments evolved. A fast technique of determining DNA sequence was also found out. In 1990, an ambitious project of mapping human genome was launched.

Context

• Goals
• Salient Features Of Human Genome
• Applications and Future Challenges

Human genome project or HGP was a project of sequencing the entire human genome and find out its characteristic features. The project was estimated to be completed in thirteen years. It was coordinated by

U.S. Department of Energy and National Institutes of Health. Soon Wellcome Trust (U.K.) joined the project as a major partner.France, Japan, Germany and China also contributed. The project of human genome sequencing (first phase) was completed on June 26, 2000. HGP has been called a mega project due to

(i) Huge cost estimated to be 9 billion dollars.

(ii) Very large number of base pairs (3 x 10° bP) to be identified and sequenced.

(iii) A large number of scientists, technicians and supporting staff.

(iv) Storage of data generated which requires some 3300 books, each with 1000 pages and each page having 1000 typed letters. However, high speed computational devices for storage, retrieval and analysis of data made it easier to do the same. The science of bioinformatics also developed during this period and helped HGP.

1. Goals

1. Sequencing. To sequence the whole human genome and find out the entire range of base pairs.

2. Storage. To store the information in data bases.

3. Analysis. To develop as well as conduct computer based analysis.

4. Genes. Indentify all the genes (approximately 20000-30000). 

5. Technology. Transfer technologies developed during the project to other sectors like industry, agriculture and forestry.

6. ELSI. To solve any ethical, legal and social issues (ELSI) that may arise from the project.

Methodologies. There are two approaches for sequencing human genome. (1) Expressed Sequence Tags (ESTs). Identify all the genes that are expressed as RNAs and sequence the same. (ii) Sequence Annotation. The whole genome, including both coding and non-coding regions is first sequenced. Later, functions are assigned to different regions. In HGP, sequence annotation has been carried out.

(i) The whole DNA of a cell was isolated.

(ii) DNA was broken into random fragments of relatively smaller sizes. 

(iii) The fragments were separated. 

(iv) The fragments were attached to vectors like BAC (bacterial artificial chromosomes) and YAC (yeast artificial chromosomes). They were cloned in bacterial or yeast cells. Alternately, the fragments could be amplified through PCR (polymerase chain reaction).

(v) The fragments were sequenced by using automated DNA sequences developed on the principle of a method developed by Frederick Sanger (Nobel Prize for it, as well as the earlier Nobel Prize for sequencing insulin). 

(vi) The sequences were then arranged with the help of some overlapping fragments.

The alignment of the sequences was carried out with the help of special computers based programmes.

(vii) The sequences were later annotated and assigned to individual chromosomes (22 autosomes, X and Y chromosomes). The last annotation was for chromosome I. It was completed in May, 2006. (viii) Assignment of genetic and physical maps on the genome was carried out with the help of information on polymorphism of restriction endonuclease sites and microsatellites or repetitive DNA sequences.

  

2.  Salient Features Of Human Genome

1. Human genome contains 3.1647 billion base pairs. Fruit Fly Drosophila melanogaster has 132 millio base pairs or roughly 1/24 of total length of human genome.
2. The total number of genes is about 30,000. The number is the same as present in mouse, double th number in fruitfly and about 6 times the genes contained in Escherichia coli. Previously it was believed the human beings carry 80000-140, 000 genes.
3. The size of genome / number of genes is unconnected with the complexity of organisation of body. Lih has 18 times more DNA than human genome. Inspite of this fact, Lily produces fewer proteins than a humabeing
4. The functions of over 50% of the discovered genes is unknown.
5. Less than 2% of the genome contains coded information for protein synthesis.
6. By differential splicing, a gene may code for two or more proteins.
7. The Part of DNA which has contains repeated sequences is known as satellite DNA. Satellite DNA is of sever types. One of them is moderately repetitive sequences of 150-300 base pairs long. They include transposon and Alu elements. There are several thousand Alu repeats in human genome. Mini-satellite sequences ar 11-60 base pairs long hypervariable repeat sequences. They are VNTR used in DNA finger printing. Ove a million copies of simple sequence repeats (SSR) or microsatellites occur in the genome. They have 54 pairs. These sequences are clustered around centromere and other areas of constitutive heterochromatin These repeated sequences are called junk DNA. Repetitive sequences have no direct coding functions They, however, provide information about chromosome structure, dynamics and evolution.
8. 99 9% of DNA of human population is identical so that genomically speaking all human beings ar exactly the same. The genetic difference is shared by various ethnic groups or races found in various geographical regions and the variability that allows us to differentiate between Ram and Shyam or Si and Gita is 0-1% of the genome.
9. The length of different human genes varies widely. The average size is 3000 bp. B-globin insulin genes are less than 10 kilo base pairs long. The longest gene of human body is that of Duchenne Muscular Dystrophy on 'X' chromosome. It is 24,000 kilo base pair long. The smallest gene is that of TD (Testis Determining Factor), a holandric gene, present on 'Y' chromosome. It is only 14 base pairs lon (Page et al, 1987).
10. Chromosome Y carries the minimum number of genes (231). Chromosome I has the most gene (2968).
11. About 1-4 million single base DNA differences or single nucleotide polymorphisms (SNP pronounced as 'snips') have been identified in humans. Their number may be more than 10 million (Lewin, 2008). This will be helpful in finding chromosomal locations with disease associated sequence and Tracing human history.

3. Applications and Future Challenges

• Completion of first phase of human genome project has been compared to discovery of antibiotics because it has opened a vast data base of knowledge about various aspects of human genome.

• Soon we shall be mapping all the human genes, Alu sequences, transposons and junk DNA.

• There are more than 1200 genes that cause common cardiovascular ailments, endocrine diseases like diabetes, Alzheimer's disease and other neurological ailments, cancers, etc. After taking their snapshots, it will be possible to know the method to alter them and remove the possibility of the disorders.

• Single gene defects produce a number of hereditary diseases. Their exact location, reason for defect and method of correcting the same can be found out.

• Studying the genes that will cause reversion of cancerous cells to normal cells.

• It will be possible to study interactions between various genes, proteins, as well as mechanism of forming tissues, organs, tumors or switch over to different developmental stages.

•  It holds promise of healthier and longer living, designer drugs and genetically modified diets

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