Monday, January 26, 2009

Basic knowledge of bioinformatics needed

Wired is running a story of a father whose daughter has an unknown genetic disease. With clinical genetics professional background, the father started sequencing candidate genes to identify the cause.

I read the story with increasing disbelief. Read on:

The sequencing results came back organized into charts resembling seismographs of a minor earthquake, with each sharp spike indicating an individual nucleotide. Rienhoff printed out everything and stored the sheets in white three-ring binders. He combed through these pages while logged on to Ensembl, a public database jointly funded by the UK's Wellcome Trust Sanger Institute and the European Bioinformatics Institute.
...
The job was daunting: The printouts contained data for approximately 20,000 base pairs, and there was no feasible way to automate the hunt for variants.
...
Progress was slow, but after a decade in the boardroom, Rienhoff enjoyed doing pure science again.
...
Two months later, in March 2007, he completed his study. He had identified about 20 places where the DNA for Beatrice's activin receptors didn't match the reference genome.


He should have known better than print the DNA traces out and do everything by hand! That work could have been in an afternoon instead of a two months had he bothered to learn a bit of bioinformatics!

He has started a website discussing rare genetic diseases, http://mydaughtersdna.org/, and is planning to continue to check all the transcribed genes. I really hope he will learn to use bioinformatics tools before doing that or he will not have enough days left in his life!

3 comments:

Tamara Kulikova said...

maybe you could enlighten him, Heikki :)

Anonymous said...

One thing I have always wanted is to have my daughters chromosome 8 fully sequenced to know exactly which genes are missing. No way I'd check it all out by hand though! You would think someone who went to all the trouble of buying a PCR machine and doing all these experiments in their own home would have the knowledge to use publically accessible databases.....

Anonymous said...

You hope that he learns bioinformatics to help him in this task? I'm inclined to send him a colour cartridge for his printer... :-)