Wednesday, April 16, 2008

Watson and Alzheimer’s disease

You must have heard that the "complete" sequencing of the genome of James D. Watson - the pioneer of molecular biology. The sequencing actually was finished about one year ago in two months and cost about 1 million. Now the results are out in Nature.

Here are some numbers:
7.4 - fold redundancy -- current sequencing technique requires redundant sequencing for assembly purposes;
3.3 million - single nucleotide polymorphisms (SNP) --these are single nucleotide variations to the reference sequences;
0.61 million - of those SNPs were previously unknown;
10,654 -- 10654 of those SNPs could cause amino-acid substitution within the coding sequence, that means that the protein sequences could be changed which could affect the protein function;
222,718 - small insertion and/or deletion polymorphisms, which affects local chromosomal regions;
345 - of above overlap gene coding sequences and could alter protein function;
1.5 million -new sequences;
49 - potential genes from above 1.5 million new sequences

Will Dr. Watson develop Alzheimer's disease? That's secret. The sequence of Apoliprotein E gene and neighboring regions was not disclosed.

How about breast cancer? --come on, not him. But his genome does contain a related mutation. He is not too concerned because he doesn't have any daughter.

Are you interested in his genome? (I am not :) ) But here is the link:
http://jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/jwsequence/

Is Dr. Watson the first one to have genome completely sequenced? -- No. The founder of J. Craig Vender Institute (Rockville, Maryland), Mr. Vender was the first one. However, the technology was different and it cost $100 million. 100 times more!

How useful the sequence is? --"it will be extremely difficult to extract medically, or even biologically, reliable inference from individual sequences" - Maynard Olson.

How useful will it be? -- Some day, it will be useful.

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