Until recently, single nucleotide polymorphisms (SNPs) were thought to represent the only source of inter-individual variation at the genome level. Subsequently, it became apparent that different individuals may harbor various copy numbers of certain genes or genomic regions.
This newly unveiled source of genetic variability, which became known as copy number variation (CNV), is believed to involve more nucleotides than all SNPs combined. Such extensive inter-individual genetic variation reveals that human genomes are more dissimilar than initially thought, and even raised the question about whether it is still meaningful to talk about a single reference human genome.
“Copy number variations, in addition to DNA mutations assayed by sequencing, are probably the most reliable data in understanding what is involved in tumor formation, and are key for evaluating potential therapeutic targets,” notes Gregory J. Riggins, M.D., Ph.D., professor of neurosurgery and oncology at the Johns Hopkins Medical Institute.
At next month’s CHI conference, “Comprehending Copy Number Variation”, Dr. Riggins will talk about a genome-wide CNV analysis that he and colleagues conducted to investigate the genomic changes in glioblastoma multiforme. This malignant brain tumor was previously shown to be frequently associated with copy number alterations, either as losses or gains of various chromosomal regions.
By using digital karyotyping and Illumina bead arrays, the scientists found that a locus on the large arm of chromosome 12, which contains the GLI1 and CDK4 oncogenes, is amplified in 33% of the patients. Learning about the genes amplified or deleted by CNVs can provide significant clues about the pathogenic mechanisms involved in tumor formation or progression.
“Since the alterations are in the DNA and easy to decipher, it is relatively easy to do genome-wide assays, and this has become a valuable means for assessing gene alterations in large numbers of tumors,” says Dr. Riggins.
In addition to confirming that different techniques used to survey CNVs lead to similar results, Dr. Riggins and colleagues also established a large collection of copy number changes for this brain disease, which will provide a framework for future studies aiming to design therapies based on molecular targets.
Studies on Schizophrenia
While many CNVs are linked to specific medical conditions, others have been described in apparently healthy individuals. Establishing whether a newly found copy number variant is pathogenic or not has emerged as a significant challenge. In a genome-wide survey examining chromosomal changes in schizophrenia, David B. Goldstein, Ph.D., professor of molecular genetics and microbiology and director of the Institute of Genome Sciences and Policy Center for Human Genome Variation at Duke University, together with Anna C. Need, Ph.D., and other collaborators, identified two new deletions (exceeding 2 Mb in size) that were present in a minority of the participants, but were not found in a healthy subject control group.
“We think that such findings can be a suggestion of pathogenicity, even when they are observed in just one or a few cases. One can identify pathogenic copy number variants because of how unusual they are in people who are healthy,” explains Dr. Goldstein.
The study, which was the first to involve an integrated survey of SNPs and CNVs in schizophrenia, demonstrated that rare copy number variants might be more important than more frequently occurring SNPs. Further investigation of the same 2 Mb region in a group of patients with epilepsy uncovered several smaller deletions, pointing toward the possible involvement of a CNV in several neuropsychiatric conditions.
A key difficulty facing future work is being able to accurately survey and characterize CNVs in the genome.
“It is very difficult to figure out, not only the exact copy number status in different parts of the genome, but also the content. These structurally variable parts of the genome are difficult to assay, and the challenge is being able to clearly describe a variation in order to relate it to disease,” continues Dr. Goldstein.