Things that I should know about Genomics

Continuation to Question 1 (Q1)

Next Generation Sequencing Technologies

The next generation sequencing methods can be subdivided into three general categories:

1. Approach:  Emulsion PCR  

    Technology: Roche 454: http://454.com/products/technology.asp
 

2. Approach:  Substrate based 

    Technology:  Illumina: http://www.illumina.com/technology/sequencing_technology.ilmn
 

3. Approach:  Single molecule sequencing

    Technology:  Pacific Bio technology: http://www.pacificbiosciences.com/products/pacificbio-rs-workflow?quicktabs_2=0

 

 In general, next generation sequencing works by obtaining many small DNA fragments that need to be assembled like it was done in the shotgun method.  The short length (number of bp) of the  DNA fragments is compensated by the large number of the reads (how many copies of the DNA fragments are made), sometimes as many as 100 copies cover the same area on the chromosome. This is called coverage, and the number of overlapping sequences in the same place is denoted by X, in our example that would be 100X coverage.

However, since the human genome sequence is already known, it is not necessary to assemble DNA fragments anymore.  It is sufficient to find where the piece fits on the reference genome sequence (a standard sequence provided by the Human Genome Project).  

Another reason to use this advanced technology is that while Human genome project cost $3 billion dollars, today the sequencing cost is below $10,000.  

Thus the answer to the question is, no, I would not use the same method, or the same approach, because the progress in Genomics in the last 10 years has made it possible to sequence and assemble a genome for  much less and with a better coverage.
 

http://www.genome.gov/11006943