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Title Page. Nature Genetics Vol.36 Sept 2004 Detection of Large-scale Variation In the Human Genome Iafrate, Feuk, Rivera, Listewnik, Donahoe, Qi, Scherer, Lee. any image here. Trevor Pugh MEDG505 – Genomic Analysis University of BC. Large-scale Copy-Number Variations: 5 W’s & How.

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  1. Title Page Nature Genetics Vol.36 Sept 2004 Detection of Large-scale Variation In the Human Genome Iafrate, Feuk, Rivera, Listewnik, Donahoe, Qi, Scherer, Lee any image here Trevor Pugh MEDG505 – Genomic Analysis University of BC

  2. Large-scale Copy-Number Variations: 5 W’s & How What are Large-scale Copy Number Variations? Who have Large-scale Copy Number Variations? Where are Large-scale Copy Number Variations? Why are there LCVs? When did LCVs arise? How are LCVs generated?

  3. What are Large-scale Copy-Number Vars.? @gains or losses of kb’s-Mb’s of genomic DNA @ seen in phenotypically normal individuals > may not be direct cause of genetic disease > may give rise to disease? chromosomal rearrangements subtle phenotypic variation (gene expression) @ NOT limited to intergenic or intronic regions

  4. Who have Large-scale Copy-Number Vars? @applied array CGH to 55 unrelated individuals Deletion! Five steps of CGH @ Isolation of Genomic DNA from two patients/sources @ Digestion of Genomic DNA into short fragments @ Labeling of each sample with DIFFERENT detectable dyes @ SIMULTANEOUS Hybridization of labeled probes to targets @ Quantification of amount of hybridization to each target 1111111 1 1 1 2 1 1 1 @spots are large DNA fragments ‘tiled’ ~1MB across the genome  low resolution, captures 12% of genome

  5. Who have Large-scale Copy-Number Vars? @applied array CGH to 55 unrelated individuals > 39 healthy phenotypes (normal karyotype) > 16 with known chromosomal abnormalities ... against a pool of (different) normal controls @detected *all* known LCVs in 16 abnormal samples > good sensitivity and specificity @on average, detected 12.4 LCVs in normal controls! > mostly single large insert clones  up to 2Mb affected!

  6. Who have Large-scale Copy-Number Vars? @on average, detected 12.4 LCVs in normal controls # of LCVs found in: 102 (False Positive rate <1 per 5,264 clones) @26 mapped to previously recognized segmental dupes @ 13 reside within 100kb gaps of current human genome sequence presentation  complicates assembly of final HGP sequence

  7. Where are Large-scale Copy-Number Vars? Everywhere! RED= copy gains BLUE= copy losses

  8. Where are Large-scale Copy-Number Vars.? @ across the genome involving as much as 2MB @not limited to intergenic or intronic regions > can include duplicate genes! @ confined to localized chromosomal regions > NOT duplication events of other chromosomes >tandem copy-number changes OR

  9. Where are Large-scale Copy-Number Vars.? @tandem copy-number changes >visualized using FISH & fibre-FISH signals only from sister chromatids RELATIVE: Losses Normal Gains RED = 5’ head GREEN = 3’ tail 6 duplicates 9 duplicates 12 duplicates >CN gains show more head-to-tail gene copies

  10. Where are Large-scale Copy-Number Vars.? @ tandem copy-number changes >verified by QT-PCR >ratios track FISH & CGH ratios almost perfectly!

  11. Why do Large-scale Copy-Number Variations Exist? When did Large-scale Copy-Number Variations Arise? @Unknown! @Unknown! “Large-Scale Variation Among Human and Great Ape Genomes Determined by Array Comparative Genomic Hybridization” Locke, Segraves, Carbone, Archidiacono, Albertson, Pinkel, Eichler Genome Research Vol 13, Issue 3, 347-357, March 2003 @ gene-rich regions susceptible to CN changes between humans and great apes @local repatterning of hominoid chromosomes in euchromatic regions > duplication-driven mechanism of genome evolution

  12. How do LCVs Impact Us? @new explanations for individual uniqueness > lineage studies? > forensics? @ increased gene copy number associated with increased susceptibility to diseases? > use as genetic markers? @ added level of complexity to the genome > comparative genomics? > phylogenetics? @simplification of the genome > less regulatory networks, more ‘dosage effects’

  13. Summary:Large-scale Copy-Number Variations (LCVs) What? @ gains or losses of kb’s-Mb’s of tandem genomic sequences Who? @ varies from person to person, 12.4 LCVs on average Where? @ throughout the genome, localized to chromosomal regions @not limited to intergenic or intronic regions When? @ Unknown! Conjecture: Complex organisms? Plant/Animal? Why? @ Unknown! Conjecture: Gene evolution? Regulatory? How? @ new basis for human uniqueness & treatment @ new ways of interpreting the genome and its interactions

  14. Questions? Questions @ Why do LCVs exist? When did they arise? @Are these LCVs random? If not, what types of genes would have copy number variation? @ What possible mechanisms could create LCVs? @ Is this a genomic simplification or an added level of complexity? @ What are the implications of LCVs for current technologies, databases, and assemblies? > PCR, gene expression, genetics? > GenBank, OMIM? > Human Genome Project?

  15. Extra Figures

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