Symbiose Project Team - INRIA/Irisa © 2007 - 2008


Jeudi 22 mars 2012 - Zamin Iqbal (Wellcome Trust Centre - Oxford)
Written by Pierre PETERLONGO   

Accessing the full mutation spectrum by de novo assembly

10h30, salle Aurigny
High-throughput sequencing is becoming ubiquitous in the study of cell biology, but as our ambitions grow,
so does the requirement for accurate and sensitive determination of progressively more complex genetic variants.
Methods for discovering variants which are based on a reference genome suffer from reference-bias ("if we assume
we are looking for something the same as the reference, we are more likely to force the data to fit that model"),
and in fact are completely blind to a range of variants. We have developed a polymorphism-aware de novo assembly variant caller,
called Cortex, capable of simultaneously assembling multiple samples and directly comparing them without a reference genome.
I will describe what this new technique can do, demonstrating the range of mutations that it unveils by comparison
with the results of the 1000 Genomes project.  I will also show how, by assembling 164 samples from the 1000 Genomes
Project, we have found over 3Mb of "novel" sequence that is highly
diverged from the reference, and which therefore are invisible to standard techniques. These include a substantial amount of gene sequence,
some of which is highly differentiated between populations, and therefore a strong candidate for being of functional significance.
 


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