Week 5 Blog 1: Speeding Genome Sequencing by Using Sudoku Method

Scientists at the Cold Spring Harbor Laboratory have discovered a new method of pooling a multitude of DNA samples for sequencing. DNA sequencing is the process of deterring the exact order of the billions of chemical building blocks called bases that make up DNA. The new method, scientists come up with, called DNA Sudoku. This method named like this because of the math game; also, it is using the same algorithm to speed up sequencing DNA. The DNA Sudoku method allows short combinations of polynucleotide with bases, T, C, A, G, to be combined and sequenced simultaneously. The sequencing is done by comparing the letter order to the correct order of known human genome. The last methods, algorithms, were not able to analyze genome sequences in a short amount of time and actually they were only able to do one sequence of DNA at a time. The Sudoku method is a big improvement on current techniques and algorithms that can ideally only combine hundreds of samples. Hannon, a genomic expert and leader of the team for Sudoku approach, said that “the technique can be used to analyze specific regions of genomes form a large population to identify those who carry genetic mutations that may cause genetic disease.” These days, the new methods that are coming out are concerning two approaches for genome sequencing speed and the cost. This method as the team leader, Hannon mentioned is cost effective. He exampled a project for other researchers that cost $10 million, for his researcher group the same size of project will cost between $50,000 to $80,000. One of the reasons that are getting done faster and cheaper is that each pool of samples needs to be tagged with barcode versus the traditional method for sequencing high number of DNA samples, each sample had to be first tagged with a barcode. “The Sudoku method is currently ideally used on genotype analyses that need only short segments of an individual's genome. Clinical applications for the new method could be for HLA typing, which is a diagnostic tool for predicting the risk of organ transplant, cancer, and autoimmune disease.” As the other article mentioned, researcher’s competition are based on how to analyze human genomes faster and cheaper. Therefore, this group of researcher made a lot of competitions for themselves. If the researchers use this method, Sudoku, to sequence genomes, I believe the number of gene sequences, that has been discovered till now, will be increased much faster.

Source:
http://www.dailytech.com/Scientists+Use+Sudoku+to+Speed+Genome+Sequencing/article15526.htm

Other Source:
http://venturebeat.com/2008/02/10/pacific-bio-lifts-the-veil-on-its-high-speed-genome-sequencing-effort/
http://www.ornl.gov/sci/techresources/Human_Genome/faq/seqfacts.shtml