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Structural variation and Pacific Biosciences

August 9, 2011

This is an interesting paper on human genetic variation ( – a topic out of my expertise.  The authors have come up with a much better method to detect structural variations using de-novo genome assembly of data from the 1000 Genomes Project.  With most of the focus of genome wide association studies (GWAS) on single nucleotide polymorphisms (SNPs), we’ve probably been missing a lot of the picture.  This leads to the following thoughts:

1. People will be doing a lot more de-novo assembly than previously thought.

2. The Pacific Biosciences technology may be more important than previously thought for GWAS and genotyping in general.

3. It’s sort of funny how it has gone from Eric Lander and the Human Genome Project saying you couldn’t shotgun assemble a human genome from Sanger reads to the Craig Venter’s shotgun assembly to we can do it from Illumina short reads to everybody was wrong and right in some ways. Usually the way it goes I guess.


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