1. Global Variation in Copy Number in the Human Genome
Redon et. al.
Presentation By
Nguyen Dinh
Samer Metri

2. What are CNVs?
CNVs are segments of DNA that are 1kb or larger and show up at variable copy numbers.
CNVs can include both deletions and duplications
Samer
Copy Number Variation
Some context: during the time of this study, they knew about Single Nucleotide Polymorphisms (SNPS), however, nothing was known about Copy Number Variations
CNVRs can include: regions of DNA, or entire genes.
CNVRs are caused by: deletions, duplications, insertions, complex multisite variants
CNVRs size: >= 1kb
Figure:
It is important to realize that each letter represents a sequence and not a gene.
It can either be a small sequence, or a sequence large enough to encompass multiple genes.

3. What are CNVRs?
CNVRs are unions of CNV segments that partially overlap between individuals
Samer

4. Methods used to Detect CNVs
Comparative Genome Hybridization
Whole Genome TilePath Assay
More powerful in detecting CNVs in duplicated genome regions
Comparative Intensity Analysis
Affymetrix 500K Early Access SNP Chip
Powerful in detecting small sized CNVs
To detect and study CNVs, the researchers used two different platforms.
The Whole Genome TitlePath Assay works through hybridization and is powerful when it comes to large duplicated regions
The Affymetrix 500K Early Access SNP Chip works through intensity analysis and is very powerful in detecting small sequences of CNVs.
The results from the two platforms were later combined to obtain the final result.

5. Whole Genome TilePath Assay
Test and Reference DNAs are labeled
Hybridization
Detection of fluorescence signal
Log2 normalization

6. Affymetrix 500K Early Access SNP Chip
Digestion of genomic DNA.
Hybridization.
Detection.
Log2 normalization.

7. Variation Between Methods
Whole Genome TilePath Assay
Affymetrix 500K Early Access SNP Chip
Median CNV Size
228 kb
81 kb
Mean CNV Size
341 kb
206 kb
Average size of CNVs in the genome in a single experiment
24 Mb
5 Mb
Ratio of Deletions to Duplications
1:1
2:1
Samer
As you can see,Whole Genome TilePath reports larger values overall, which is a result of using hybridization. When only a part of the insert clone hybridizes, it is still counted as a whole and therefore it results in overestimation
However, when using signal intensity analysis, they were able to obtain more reasonable values.
Overlapping CNVs among individuals were then merged, leading to the total discovery of 913 CNVRs using Whole Genome TilePath Assay, and 980 CNVRs by using 500K
43% of the CNVRs were found by both platforms, resulting in a total of about 360 Mb of CNVRs in the human genome.

8. Results
Large CNVs are distributed in a heterogenous manner throughout the genome
CNVs were classified as:
Deletions
Duplications
Deletions & Duplications at the same locus
Multi-allelic Loci
Complex Loci that could not be identified
Samer
Large sized CNVs are distributed in a heterogenous manner throughout the human genome.
Based on their results, they were able to classify CNVs are one of 5:
Deletions
Duplications
Deletions & Duplications at the same locus
Multi-Allelic loci
And Complex Loci that could not be determined.
They also determined that while duplications are likely to encompass whole genes, deletions were biased towards areas without genes.

9. Genomic Impact of CNV
No significant difference between the number of deletions and duplications
The size of duplications is on average three times larger than deletions
CNVRs overlap with cell adhesion, smell and chemical stimulus sensory genes.
CNVRs do not overlap with cell signaling, proliferation, kinase and phosphorylation genes.

10. Medical Relevance
CNVs are relevant to both mendelian and complex diseases, such as:
Prader-Willi
Angelman Syndrome
Schizophrenia
CNVs were found at the ends of 36 chromosomal arms, helping to assess subtelomeric arrangements PW AS
Image Sources:

11. Imprint of CNV on SNP Genotypes
Deletion of CNVs
Null SNP genotype
Mendelian inconsistency
Duplication of CNVs
Hardy-Weinberg disequilibrium
Both deletion and duplication of CNV.
Mendelian inconsistency is more common in deletion.

12. Population Differentiation
Vst = (Vt - Vs)/Vt
Formula:
Vst = (Vt - Vs)/Vt
T = everything
S = within a population

13. Population Differentiation

14. Population Differentiation

15. Population Genetics of CNV
Samer
Based on the information from the last slide, they were able to sequence 210 individuals and analyze their DNA for CNVs. They were able to group them into 3 different ancestry groups: African, European, and Asian
While some individuals do not appear very closely related to others from their ancestry group, using CNVs works pretty well overall.
Three ancestries: African, European, Asian
210 individuals
67 biallelic CNVs.
Population Clustering from CNV Genotypes

16. Summary
CNVs can be caused by insertions, duplications, and deletions and is found everywhere in the genome
CNVs can be used to group and identify individuals
Important for the study of disease -- i’ll say this

17. Suggested Readings
Copy number variation in human health, disease, and evolution Zhang et. al.
Talks about the effect of CNVs on diseases and traits, and their effect on evolution
Detection and characterization of copy number variation in autism spectrum disorder Marshall et.al.
Talks about the effect of CNVs on Autism traits.
Copy number variation in human health, disease, and evolution Zhang et. al.
Detection and characterization of copy number variation in autism spectrum disorder Marshall et.al.