Lecture-3 EXOME SEQUENCING Huseyin Tombuloglu, Phd GBE423 Genomics & Proteomics.
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Transcript of Lecture-3 EXOME SEQUENCING Huseyin Tombuloglu, Phd GBE423 Genomics & Proteomics.
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Lecture-3EXOME SEQUENCING
Huseyin Tombuloglu, Phd
GBE423 Genomics & Proteomics
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EXOME SEQUENCING
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)͠ 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
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How it works?
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How it works?
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Target-enrichment strategies
1 PCR (Multiplex)2 Molecular inversion probes (MIP)3 Hybrid capture4 In-solution capture5 Sequencing
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Target-enrichment strategies
1 PCR (Multiplex) 2 Molecular inversion probes (MIP)3 Hybrid capture4 In-solution capture5 Sequencing
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3 Hybrid capture
Roche NimbleGen
~180,000 coding exons
Agilent Capture Array
Biotiniylated gene spesific probes
Array technology
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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
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Comparative SequencingWGS & WES
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Comparative Sequencing WGS & WES
• The CaseSomatic mutation detection between normal /
cancer pairs
WGS & WES ?
14Meyerson et al, Nat Rev Genet 2010
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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
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Clinical practices of Exome Sequencing
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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.
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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)
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Strategy to mine the Causal Gene
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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
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1% of genome, limited sizeUsefull for large genomes, such as wheat, barley …etcLess complicated results, Cost effective
Advantages
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Applications in other organisms
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