Lecture-3 EXOME SEQUENCING Huseyin Tombuloglu, Phd GBE423 Genomics & Proteomics
Jan 18, 2016
Lecture-3EXOME 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?
How it works?
Target-enrichment strategies
1 PCR (Multiplex)2 Molecular inversion probes (MIP)3 Hybrid capture4 In-solution capture5 Sequencing
Target-enrichment strategies
1 PCR (Multiplex) 2 Molecular inversion probes (MIP)3 Hybrid capture4 In-solution capture5 Sequencing
3 Hybrid capture
Roche NimbleGen
~180,000 coding exons
Agilent Capture Array
Biotiniylated gene spesific probes
Array technology
4 In Solution CaptureProbes 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 SequencingWGS & WES
Comparative Sequencing WGS & WES
• The CaseSomatic mutation detection between normal /
cancer pairs
WGS & WES ?
14Meyerson 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 diseasesNat. Rev. Neurol. doi:10.1038/nrneurol.2012.148
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 ServicesThe 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 sizeUsefull for large genomes, such as wheat, barley …etcLess complicated results, Cost effective
Advantages
Applications in other organisms