Editor's note
Editor’s Note
$1000 Genome is within reach
The quest is on to map every known function of every organism in the universe to the protein signals. Protein signals are linked then to genes in eukoryotes. According to M. Schena who along with his professor Davis pioneered the microarray analysis method in order to obtain sequencing information from gene expression studies, “human disease is going to be eradicated as we know it by the year 2050”. The HGP, human genome project was completed ahead of time. The genomes of 27 different mammals from giant panda, African elephant, gorilla, rat, mouse, to dolphin have been completed. Genome sequencing will be used to identify drugs that can stop the spread of cancerous cells within the patient.It cost Steve Jobs $100,000 for his genetic sequencing. Whole-genome sequencing can be obtained from Knome, Cambridge, MA for $68,000 and exome sequence for $25,000. $48,000 is the charge levied by Ilumina, San Diego, CA for whole genome sequencing. More universities are offering bioinformatics, nanotechnology, and bioengineering as separate branches of study. An advance in polymer blends and biomaterials has lead to the development of artificial organs.
The HGP, Human Genome Project has been completed ahead of time in 2003 - in 10 years against 15 years targeted. This involved sequencing 3 billion base pairs. The biologic databases double in size every 10 months, and the computing speed of microprocessors doubles in speed every 18 months. So a database search that cost $2 today, two years from now would quadruple in cost to $8 on account of the explosive growth of databases and would be cut back in half to $4 on account of the increase in computing power. There is scope for the development of data search and data storage algorithms and methods. It can be viewed as a marriage between information technology and computational biology (K. R. Sharma, Bioinformatics: Sequence Alignment and Markov Models, McGraw Hill, New York, 2009).
The cost of completion of the first HGP, was $ 2 billion. Advances in DNA sequencing technology have come about those males a genome completion within a month time frame possible. Reagents needed to sequence billion base pairs can run as little as $5000. Other costs such as microarray instrumentation, lab technicians need be added. As costs sink the whole genome sequencing may be ordered for not just research purposes, but also for personal treatment. One example of personal genome is Stephen R. Quake. A number of his family members responded poorly to anesthetics. The day will arrive in not-so-distant future when every Tom, Dick and Harry will know details about their personal genomes. Companies are mushrooming that sell whole-genome sequencing services. One of the advantages of whole genome sequencingis that one does not have to 'do it again'. When a new-disease causing mutation is discovered one looks at one's genome and one can tell if one has that mutation.
There are some ethical, privacy, regulatory and universal access issues that remain. Research studies are underway to link gene to protein to protein signal to function and hence disease. Exome that forms the protein coding portion of the genome is 1%. Sequence data on coding portion can be obtained with 20 times less than needed for whole-genome sequencing. Costs of sequencing are currently higher than costs of isolation of the exome portion of the genome. Hence there can be cost savings in exome sequencing. Jay Shendure of University of Washington (Nature 2009, 461, 272) has identified the mutation responsible for the Freeman Sheldon syndrome and Miller syndrome. Specialists of gastrointestinal disorders are able to diagnose the disorders rather than making educated guesses before. SSP, shot gun sequencing can be used to project the whole genome from the information in the exome. SSP is a NP complete problem. It is computationally difficult. Approximate solutions are available. RK Wilson at the genome sequencing center at Washington university, St. Louis, is participating in the TCGA, the cancer genome atlas. This is a joint effort between the National Human Genome Research Institute and the National Cancer Institute. They aim to improve the understanding of the molecular basis of cancer through whole genome sequencing. Current projects are on brain and ovarian cancer. Future projects on breast, kidney and lung cancer are underway. The PGP, personal genome project at Harvard University is ambitous in making the sequencing studies more clinically relevant. GM Church noted that if the cost of DNA sequencing per base pair continued to follow Moore's law like progression scientists would need to start connecting genes and traits. PGP has 15,000 volunteers currently. They have a goal of 100,000 participants. Participants are expected to obtain perfect score on an entrance exam that demonstrates their knowledge of human genetics and the implications for them and their families of the data being collected. All data from PGP would be made publicly available.
Sanger method of DNA sequencing was used in HGP. This involves transcription of DNA template in the presence of dye-labeled modified nucleotides that terminate DNA-strand elongation when they are incorporated. As the modified nucleotides are at random in the strands, the sequencing reaction results in a mixture of DNA strands of varied length each with its end base labeled with a fluorescent dye. Separation based on length of strand can be achieved using capillary electrophoresis. Sanger method is the gold standard for DNA sequencing. Other methods, less laborious may be used instead of the laborious Sanger method. Calibration is used in deduction of sequences from the imaged. Generalized Fick's law of diffusion based models can be used to better capture the finite speed of diffusion of the fragments. Mathematical models with improved capability (K. R. Sharma, Damped Wave Transport and Relaxation, Elesvier, 2005) can be used to decrease sequencing errors and improve the efficiency of sequence deduction. Recent lab methods developed require less extensive sample preparation, amplification of a library of fragments from genomic DNA. Parallelism is infused in these methods. A genome sequence is put together by alignment of millions of fragments against the reference sequence from HGP. In order to minimize errors each base pair is identified several times. This is referred to as 'fold coverage'.
A $1000 genome is within reach. BioNanomatrix, Philadelphia, PA works with long strands of DNA. More genetic diversity is available this way. Organization of genome varies from person to person, all with the same base layout. A nanofabricated device is used to separate double strands with 1 lakh to 2 lakh base pairs into individual lanes. Blocks of DNA with 7 bases are labeled. Location of these blocks forms a bar code for individual genome. DNA sagamis that appear to be like smiley faces can be used to design nanorobots and be used in drug delivery an dhelp the surgeon with hard to reach locations. Oxford Nanopore uses a method of reading DNA sequences using nanopores. Bases are identified by the induced charge in the amplitude of the current carried by aqueous ions passing through the pore. Intact DNA strand is threaded through the pore and the bases are identified as they pass through a reading head. This method is slow. Read length depends on the speed or throughput. Further advances in genome sequencing and proteome sequencing can be expected by utilization of single layer graphenes. As is, the capability to study more genes per biochip is increasing at a rate much like Moore’s law in electronics. Scientists in Netherlands claim they have found a method of rapidly sequencing DNA, deoxyribo nucleic acid and RNA, ribonucleic acid strands. They pass these strands through the nanometer sized sieves in graphene sheets. A voltage is applied across the sheet. Each of the nucleotide bases: Adenine, Guanine, Cytosine and Thymine for DNA and; Uracil in place of Thymine in RNA, have a unique effect on the conductance of graphene as they pass one at a instant of time. Sequence distribution of DNA and RNA are deduced from changes in voltage. Computerization of the procedure and use of sensors with shorter response times can lead to more rapid sequencing of DNA and/or RNA. As each aminoacid passes through the hexagonal sieve the change in electrical characteristics can be used to deduct the aminoacid sequence distribution by calibration. Discovery of single layer graphene was noted by the award of the Nobel Prize in Physics in 2010 to Prof. A. K. Geim and K. Nosolev.
Dr. Kal Renganathan Sharma PE
Editor
Journal of Pharmaceutical and Biomedical Sciences.
Adjunct Faculty, Energy and Manufacturing
Lone Star College - University Park
20515 State Hwy 249, Houston, TX 77070.
Adjunct Professor, Department of Physics
College of Science and Technology
Texas Southern University, Houston, TX 77004.