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 Title Page Trevor Pugh MEDG505 – Genomic Analysis University of BC

Large-scale Copy-Number Variations: 5 W’s & How W hat are Large-scale Copy Number Variations? W ho have Large-scale Copy Number Variations? W here are Large-scale Copy Number Variations? W hy are there LCVs? W hen did LCVs arise? H ow are LCVs generated?

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

Who have Large-scale Copy-Number Vars? Deletion! Five steps of of Genomic DNA from two of Genomic DNA into short of each sample with DIFFERENT detectable Hybridization of labeled probes to of amount of hybridization to each applied array CGH to 55 unrelated spots are large DNA fragments ‘tiled’ ~1MB across the genome  low resolution, captures 12% of genome

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

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

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

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

@ tandem copy-number changes > visualized using FISH Where are Large-scale Copy-Number Vars.? RELATIVE: LossesNormalGains signals only from sister chromatids > CN gains show more head-to-tail gene copies RED = 5’ head GREEN = 3’ tail & fibre-FISH 6 duplicates9 duplicates12 duplicates

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

Why do Large-scale Copy-Number Variations Unknown! When did Large-scale Copy-Number Variations Arise? “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, , March gene-rich regions susceptible to CN changes between humans and great local repatterning of hominoid chromosomes in euchromatic regions > duplication-driven mechanism of genome Unknown!

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

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

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

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