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Large Scale Variation Among Human and Great Ape Genomes Determined by Array Comparative Genomic Hybridization
Devin P. Locke, Richard Segraves, Lucia Carbone, Nicoletta Archidiacono, Donna G.
Albertson, Daniel Pinkel, and Evan E. Eichler (2003) Genome Research.
Presented by Nicholas Dubé
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•B.Sc. University of Saskatchewan, MB
•PhD Baylor College, Houston, TX
•Currently, Assistant Prof. & Director of the Bioinformatics Core Facility at Case Western Reserve School of Medicine, Ohio
•Research Interest: To understand the evolution, pathology and mechanisms of gene duplication and DNA transposition within the human genome
The Authors
Dr. Evan Eichler
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The Authors
Dr. Donna Albertson
Associate Professor, Cancer Research Institute at UCSF
Dr. Dan Pinkel
Professor, Lab Medicine at UCSF
Dr. N. Archidiacono
Staff Member, Dept. of anatomy and genetics, University of Bari, Italy
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The Authors
Lucia Carbone
Student, Dept. of anatomy and genetics, Bari, Italy
Richard Segraves
Student, Pinkel lab, UCSF
Devin Locke
Student, Eichler lab, Case Western
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Previous Findings
• Evolutionary change of human & nonhuman primates studied at 2 levels:
1. Karyotypically (i.e FISH)
2. At the single base-pair level (i.e. SNPs)
• Array CGH used to detect within-species DNA copy-number variation associated with tumor progression
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Previous Findings• Previous studies implicated gene-
deficient heterochomatic regions as the location of greatest variation between genomes of the great apes & humans
But this would all change…
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Aim of the Paper
1. To further the understanding of our genetic history and evolution
2. To identify sites of large-scale rearrangement, gain or loss of DNA sequence, among humans and great apes
3. To pioneer the use of array CGH for interspecies genomic comparison
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Major Findings of The Paper Identified 63 sites of DNA copy-number
variation between Humans and apes Confirmed rearrangements ranging
from 40-175 kb Localized the majority of variant sites to
interstitial euchromatin Presented the first genome-wide
comparison of the great apes
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Array CGH
To measure DNA sequence copy number gains and losses
Allows for mapping of gains & losses
Fig.1 Array CGH. To determine DNA copy number. Lung tumor (Cy3)/Reference (Cy5)
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Array CGH: How it works Genomic DNA isolated from blood Label DNAs with fluorochromes Hybridize human & primate DNA
probes to Arrays that contain 2460 different Human BACs
Primate-human intensity ratio at each locus assessed for variation
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Methods: Array CGH Compared relative hybridization
intensities among 4 great apes (chimp, bonobo, gorilla, and orangutan) pairwise with humans
Array loci designated as “variant” IFF a consistent increase/decrease in intensity ratio was observed in each species in all trials
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Results
63 variant sites detected (38 reductions & 25 increases)
Quantity of variant sites in each species consistent with amount of evolutionary time diverged
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Results
Fig. 1. Graphs depicting 2460 loci. Variant sites circled in red.
PPA=bonoboPTR=chimpanzeePPY=orangutanGGO=Gorilla
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Results: Validation Examined a subset of 63 variant sites (7
putative gains and 7 potential losses) using FISH
7 gains: Observed both intra/inter-chromosomal duplication (gains)
7 losses: Found 1 instance of complete loss of signal (loss of ~175kb or 1 BAC)
Partial signal detected for other 6 sites- FISH not suitable
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Results: Validation Developed BAC end Sequence-
based approach to tackle deletion validation problem
Compared insert size of primate BAC to estimated human BAC size
Discrepancy in sizes indicates a partial deletion
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Verified Variant Sites
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Rearrangements occur at euchromatic regions
86% of variant sites mapped to euchromatic regions
Suggests large-scale rearrangements not confined to pericentromeric or subtelomeric regions
Question: Does rearrangement occur exclusively in heterochromatic regions as previously reported?
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Chromosomal Bias Appears to be a chromosomal bias for
the number of variant sites (Table 2) Correlation between enrichment for
variant sites and segment duplications
Found 5/9 experimentally validated rearrangements were proximate to a segmental duplication
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Sites of ape/human variation
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Summary Results illustrate the power &
feasibility of CGH for comparing large-scale differences between species
Large-scale rearrangements do occur in gene-rich regions as well as gene-poor regions
Large-scale changes are not randomly distributed across the genome
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Discussion Questions What other applications might
Array CGH have? Can the authors conclude there is
a chromosomal bias for variant site location given that they examined only 12% of the genome?
Is this paper significant for the greater research community?