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Accuracy and validation of targeted sequencing analysis pipelines
Attila Berces
Posted: Friday, July 27, 2012 6:18 PM
Joined: 3/11/2012
Posts: 1

I am leading a discussion with the same title at the upcoming NGS Data Analysis meeting in Providence.

Targeted sequencing has its own challenges:
artifacts can arise from the target amplification

gene targets are of diverse level of complexity having different repetitive structures
GC content and rate of polymorphism

All these factors affect analysis accuracy. Since targeted sequencing often aims at diagnostic gene targets such as BRCA, CFTR or HLA, false variants can have extremely harmful consequences. With all these considered I have the following questions to start the discussion.

Given the diversity of protocols, should these procedures be validated one by one for each protocol (including target gene, amplification method, sequencer) or can we define some common validation benchmarks?

What false positive/negative rate would be clinically acceptable for some of the common gene targets: BRCA, CFTR?

What can we learn from simulation based testing of analysis pipelines?

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