Lecture-3 EXOME SEQUENCING Huseyin Tombuloglu, Phd GBE423 Genomics & Proteomics.

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Presentation transcript:

Lecture-3 EXOME SEQUENCING Huseyin Tombuloglu, Phd GBE423 Genomics & Proteomics

EXOME SEQUENCING

͠ 1% of genome Mutations or variations in this portion of genome have severe consequences than in the remaining 99% Exome sequencing is especially effective in the study of rare Mendelian diseases EXOME SEQUENCING

How it works?

Target-enrichment strategies 1 PCR (Multiplex) 2 Molecular inversion probes (MIP) 3 Hybrid capture 4 In-solution capture 5 Sequencing

Target-enrichment strategies 1 PCR (Multiplex) 2 Molecular inversion probes (MIP) 3 Hybrid capture 4 In-solution capture 5 Sequencing

3 Hybrid capture Roche NimbleGen ~180,000 coding exons Agilent Capture Array Biotiniylated gene spesific probes Array technology

4 In Solution Capture Probes in solution can capture all exons (exome) for high throughput sequencing Biotin-streptovidin based 1-2% of whole genome seq Easily multiplex 20 samples in one lane 11

Comparative Sequencing WGS & WES

The Case Somatic mutation detection between normal / cancer pairs WGS & WES ? 14 Meyerson et al, Nat Rev Genet 2010

Figure 1 Steps in the generation of whole-genome or whole-exome sequencing data for analysis Foo, J.-N. et al. (2012) Whole-genome and whole-exome sequencing in neurological diseases Nat. Rev. Neurol. doi: /nrneurol

Clinical practices of Exome Sequencing

Rare diseases Some rare diseases affect as many as 200,000 people, but some are so rare that they affect one or two people in the world.

This was the first reported study that used exome sequencing as an approach to identify an unknown causal gene for a rare mendelian disorder (2009)

Strategy to mine the Causal Gene

Exome Sequencing Services The pilot program announced by 23andMe costs $999 and requires no physician signature, but provides only raw data without analysis. In November 2012, DNADTC, a division of Gene by Gene started offering exomes at 80X coverage and introductory price of $695. This price per DNADTC web site is currently $895. In October 2013, Beijing Genomics Institute (BGI) announced a promotion for personal whole exome sequencing at 50X coverage for $499

1% of genome, limited size Usefull for large genomes, such as wheat, barley …etc Less complicated results, Cost effective Advantages

Applications in other organisms