Friday, April 23, 2010

Use Genome Sequencing To Identify The Origin of A Disease

Research teams are now delving to decode the genome sequences and its hidden origins for various diseases. Previously, two independent teams began to study the genome of patient suffering from various health pathologies.

The study of genome sequences have up to now only been conducted on healthy individuals. It was extremely costly to decode the genome of an individual but costs are rapidly swinging down. The cost to examine the complete genome, according to Geneticist, is around $50,000 to decipher.

David B. Goldstein, a Duke University geneticist says that soon human genetics will provide meaningful information for clinical treatments. The key is to identify various genetic variations that are origins for some diseases.

Moreover, a team in Seattle, found out that the hereditary genes that are passed from parent to child, to produce similar DNA damages and mutations are higher than previously expected. It was found that 3 billion human genomes are self-mutated. This means that 40 percent of DNA mutations are determined by innate biological disadvantages and 60 percent is affected by random mutation.

Research Projects

There were 3 different diseases that were scrutinized in recent reports. Yet, the diseases were all caused by an uncommon mutation in a gene.

First Report

Richard A. Gibbs of the Baylor College of Medicine made a study on the “Whole-Genome Sequencing in a Patient with Charcot–Marie–Tooth Neuropathy”. The patient was Dr. James R. Lupski, an important medical geneticist who does actually suffer from nerve disease.

Second Report

“Leroy Hood and David J. Galas of the Institute for Systems Biology in Seattle decoded the genomes of two children with two rare genetic diseases, and their parents.” In a research entitled; “Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing

It has since long been thought that disease such as cancer is promulgated through mutation of various genes. An earlier human genome project which was funded with $3 billion had the goal to unravel this mystery. However, scientists have tried to alluring cheaper and easier method to find answers over the recent 8 years. .

Shortcuts envisaged turned out to be invalid. For instance, it was believed that common diseases would be generated through common mutations. The HapMap project that was worth $100 million focused on identifying common mutations in a particular population. Genomes of patients were compared to healthy genomes. Sophisticated technology and devices such as SNP (Single Nucleotide Polymorphism) chips were used to examine segment of the genome. For each genome-wide study, the cost was around $10 million.

The high cost and poor results have been inadequate. There have been around 2,000 regions in the human genome that has been correlated to particular diseases. Yet, statistics are properly quite flawed. Disease-causing mutation seems to have been left unidentified.

First Research

New research is saying that common disease is eventually found in atypical and rare mutations. It is necessary to decode the whole genome of patients to find answers. The recent study proclaims that single-gene or multi-gene diseases require a whole-genome approach to be addressed. Dr. Lupski, say that new genome-wide studies are required. Besides, whole-genome sequencing is only one way to find answers.

Dr. Gibbs, an expert in DNA sequencing, decided to ask his colleague Dr. Lupski to be a volunteer. He suffered from a genetic disease. The study involved a genome study on 10 healthy people. It was determined that 39 genes could be the root cause for the nerve disease “Charcot-Marie-Tooth”, which is known to impair various nerves that can weaken the muscle of hands and feet.

Spending $50,000 on genome sequencing showed that a rare mutation of a gene named SH3TC2 was properly the core cause. The gene was inherited from his mother and father. However, the copy found in his father caused mild symptoms whereas the copy from his mother was working effectively.

In the genetic randomness lottery of so-called human procreation, two of the eight children had inherited good copies of SH3TC2 gene. Besides, two inherited the bad copy from the mother but the good one from the father, preventing the disease. However, amidst the remaining four, including Dr. Lupski, the mutated copy of SH3TC2 was inherited from both parents. Apparently, all of these 4 individuals suffer from Charcot-Marie-Tooth disease, “according to the study”.

Second Research

The second study was conducted in Seattle by Dr. Hood and Dr. Galas who also used whole-genome sequencing to evaluate the disease. Four families of four (2 children + parents) were studied, whereby each child has two single-gene diseases, known as ciliary dyskinesia and Miller syndrome. Having four related genomes, the causative genes were spotted. The sequencing was also improved through new decoding processes.

For instance, the team believes that multi-gene diseases can be found through whole-genome sequencing. They are expected to sequence around 100 genomes from multi-generational families in the coming years to find out more.

Technology Cheaper and Better

The cost of whole genome sequencing is decreasing rapidly. The genomes reported in the Science (Second Report) was conducted by Complete Genomics of Mountain View, Calif and cost $25,000 each. However, the Chief Executive, Clifford Reid, say that they conduct around 500 genomes a month and that the price for large project will gradually decrease to $10,000 per subject. This is likely to soon fall down to $5,000 per genome.

According to Dr. Reid the genome-wide associated study, entitled HapMap was not a failure. It was only that at that time technology was not up to the capacity to give findings such as these today.

From Duck University, Dr. Goldstein says that the “rapid progress in technology” is helping research to reach the target that they have been seeking.


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