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

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.

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

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.

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

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

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.

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.

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.

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: https://ghr.nlm.nih.gov/art/large/coarse-face.jpeg https://upload.wikimedia.org/wikipedia/commons/thumb/8/84/PWS8.png/250px-PWS8.png

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.

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

Population Differentiation

Population Differentiation

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

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

Suggested Readings Copy number variation in human health, disease, and evolution. 2009. 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. 2012. Marshall et.al. Talks about the effect of CNVs on Autism traits. Copy number variation in human health, disease, and evolution. 2009. Zhang et. al. Detection and characterization of copy number variation in autism spectrum disorder. 2012. Marshall et.al.