Monday, May 9, 2011

Ten Years of Human Genome Mapping

Ten Years of Human Genome Mapping

By Dr Nandkumar Kamat

The international science journal ‘Nature’ has come out with a special issue ‘The Human Genome at Ten’ on April 1, to celebrate the occasion of completion of a decade of publication of the first ‘rough draft’ of the human genome.
Actually only about 93 per cent of the genome can be mapped owing to difficulties of repetitive parts found at centromeres and telomeres. But the mapped region has almost all the 24000 functional genes.
Considering the complexity of the human body and the intelligence of our species this appears as a relatively small number. Only less than two per cent of human genome codes for functional proteins. The main articles from the special issue are accessible to students and teachers at
Earlier ‘Nature’ had come out with another special issue –‘The Human Genome’ on February 15, 2001 immediately after the first draft map of the human genome was published. They had mailed me a copy with a detail map of the sequenced genome. It was the biggest science news as we entered the 21st century. Slowly with the march of molecular biology and bioinformatics the initial excitement died down. What has been accomplished in the past 10 years? What would we have in the next 10 years? Personal medicine, cure for cancers and promise of long, healthy life? Would we get our smart cards based on our bar coded genome maps?
Since no two human genomes would be exactly identical –genometry would replace biometry. Scientists are analysing the human body like a complex biological machine. The design of this machine is found in the genome so they focused on mapping it. Since functions or malfunctions are related to original design, answers to many of the fundamental questions on health, diseases, genetic abnormalities, youth and ageing, longevity and death, beauty and ugliness, intelligence and creativity, onset of cancers and tumours are likely to be obtained from understanding of the structure and function of the human genome.
The human body is a fascinating piece of biological hardware created and maintained by genetic software called Genome – a 825 megabytes program written with just four alphabets-the nucleotide bases-A, T, G and C which make the DNA. Nucleotide A pairs with T and G pairs with C - thus creating three billion base pairs in the DNA bundled as human genome. This software comes up packaged in 23 pairs of chromosomes. Of these two are sex determining. Females have two of the same kind of sex chromosomes (XX), while males have two distinct sex chromosomes (XY). The sex of the child is determined by the chromosome contributed by the father and not the mother.
End-to-end the human genome would stretch for almost 260 cms. How massive is the data in our genome? If the information coming out of the human genome sequencing were to be typed and be stored in books and if each page contains 1000 letters and each book contains 1000 pages, then 3300 such books would be needed to store it. A rough draft of human genome was finished in 2000. The full sequencing was completed in April 2003. In May 2006 the atlas of the last chromosome was published. The original project started in 1990 was supposed to take 15 years.
The international effort was sponsored by the United States Department of Energy and the National Institutes of Health, and had participation from the United Kingdom, France, Germany, Japan, China, and India. Over the past 10 years the sequencing costs have come down. Over 3,800 organisms (including around 200 humans) have had their entire genomes sequenced, while sequence information on more than 200,000 species has been obtained. It cost three billion dollars to sequence the human genome. But in 2009 a single company Complete Genomics Inc USA ( has sequenced and analysed 14 complete human genome sequences and would offer a sequencing package for just 5000 dollars. Another company Knome from the USA ( has come out with a package- KnomeDISCOVERY –a first fully integrated human genome and exome sequencing and analysis service for biomedical researchers.
Stephen Quake, an American engineer invented a powerful sequencing machine Heliscope Single Molecule Sequencer. His website claims- “The HeliScope Single Molecule Sequencer images billions of single molecules per run and produces over one gigabase of usable sequence data per day – a throughput performance almost 100X greater than Sanger methods, and faster than any of the “next-generation” methodologies.” Stephen sequenced his own genome using Heliscope and even published the results in the journal Nature Biotechnology.
Now human genome can be mapped in less than 10 days with such powerful machines. On June 26, 2000 declaring the rough draft of human genome open - the then US president Bill Clinton had said, “We are here to celebrate the completion of the first survey of the entire human genome … With this profound new knowledge, humankind is on the verge of gaining immense, new power to heal. Genome science will have a real impact on all our lives — and even more, on the lives of our children. It will revolutionise the diagnosis, prevention, and treatment of most, if not all, human diseases.”
The director of the genome mapping project Francis Collins feels that - The decade from 2000 to 2010 was characterised by breathtaking acceleration in genome science. Thanks to advances in DNA sequencing technology that dropped the cost approximately 14,000-fold between 1999 and 2009, finished sequences are now available for 14 mammals, and draft or complete sequences have been done for many other vertebrates, invertebrates, fungi, plants and micro-organisms. The 1000 Genomes Project, launched in January 2008, is an international research effort to establish by far the most detailed catalogue of human genetic variation. Scientists plan to sequence the genomes of at least one thousand anonymous participants from a number of different ethnic groups by 2011, using newly developed technologies which are faster and less expensive. There are attempts to get more information from the mapped genome.
Encyclopedia of DNA Elements (ENCODE) project was started in pilot form in 2003 and may be completed by 2011. The Roadmap Epigenomics Program started in 2008 would continue till 2013 to define the ‘parts list’ of the human genome. Cancer Genome Atlas, is a project aimed at carrying out the equivalent of 20,000 genome projects on matched tumour and blood DNA samples from 20 common types of cancer. The data would lead to better cures for cancers. By 2015 in India for less than Rs 50,000 you would have the full sequence of your genome.

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