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ATGACTGCGTGTCATG CCA G GCTAACTGCATG CTGATCGTACTCGATC ATGTGGTTAAGTACTC GTCAATCGC T TGCATA

N Chr7. Dup Chr7. Microscopically-visible abnormalities ~0.4-0.6% of population -disease risk depends on type of alteration. ATGACTGCGTGTCATG CCA G GCTAACTGCATG CTGATCGTACTCGATC ATGTGGTTAAGTACTC GTCAATCGC T TGCATA TGTCTAGTCGCTAGCT GTACTCGATCGATGCA CTGATCATTTCCCGAG CGTATACTGCGTCCAA.

evan-jimenez
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ATGACTGCGTGTCATG CCA G GCTAACTGCATG CTGATCGTACTCGATC ATGTGGTTAAGTACTC GTCAATCGC T TGCATA

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  1. N Chr7 Dup Chr7 Microscopically-visible abnormalities ~0.4-0.6% of population -disease risk depends on type of alteration ATGACTGCGTGTCATG CCAGGCTAACTGCATG CTGATCGTACTCGATC ATGTGGTTAAGTACTC GTCAATCGCTTGCATA TGTCTAGTCGCTAGCT GTACTCGATCGATGCA CTGATCATTTCCCGAG CGTATACTGCGTCCAA SNP variants -100% of population -percent associated with disease? Sub-microscopic structural variants ~1kb to 3 Mb deletions, duplications, copy number variants -100% of populations -de novo frequency? -meiotic and mitotic stability? -how do they affect gene expression? -disease risk?

  2. What is content of structural variation in the human genome? What component of that is involved in disease susceptibility?

  3. Reference DNA Test DNA 1 Test DNA 2 Test DNA • 26,973 large insert clones • 94.4% of euchromatin Technologies are good for finding >50kb changes Comparative Intensity Analysis: Affymetrix 500K Early Access SNP chip Comparative Genome Hybridisation: Whole Genome TilePath (WGTP array)

  4. Constructing a CNV map of the human genome -269 Hapmap samples examined using tiling BAC + Affy 500k -1448 CNVs -360 Mb of CNVs in 269 HapMap samples covering 12% Of genome -avg. size 254 kb -avg. of 111 CNVs per genome ~10-20 Mb CNV per genome -overlap 2,909 genes -overlap 286 OMIM genes Consortium unpublished Matt Hurles/Nigel Carter (Sanger), Charles Lee (Harvard), Keith Jones (Affymetrix), Hiro Aburatani (Univ. of Tokyo), Xavier Estivill (Spain), Steve Scherer (Toronto)

  5. The next frontier… -robust identification of variants in 1-50 kb size -optical mapping (D. Schwarz) -paired-end clone mapping (E. Eichler) -other techniques -technologies that capture all variation? -complete sequencing and comparison

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