Abstract for presentation at 11th International Congress of Human Genetics

High throughput detection of relevant copy number variation in the human genome for association studies

  • Dr Benjamin Rodríguez-Santiago, Unitat de Genčtica, Universitat Pompeu Fabra, Spain
  • Dr Ivon Cuscó, Unitat de Genčtica, Universitat Pompeu Fabra, Spain
  • Dr Lluís Armengol, Genes and Disease Program, Center for Genomic Regulation, Spain
  • Mireia Vilardell, Unitat de Genčtica, Universitat Pompeu Fabra, Spain
  • Manel Garcia, Genes and Disease Program, Center for Genomic Regulation, Spain
  • Dr Eva González, Genes and Disease Program, Center for Genomic Regulation, Spain
  • Dr Xavier Estivill, Genes and Disease Program, Center for Genomic Regulation, Spain
  • Prof Luis Pérez-Jurado, Unitat de Genčtica, Universitat Pompeu Fabra, Spain

    • Uncovering the genetic basis of human phenotypic differences requires the identification of relevant genetic variants. In addition to single-nucleotide differences, structural variants of the human genome appear to be frequent and potentially relevant. Approximately 250 large Copy Number Variants (CNVs) involving gains or losses of genomic DNA have been recently reported using different hybridization-based methodologies (Array-CGH, ROMA,...), along with 1,000 smaller deletions unmasked by SNP genotyping. Large CNVs are specially abundant in genomic regions enriched in segmental duplications (SDs) which appear to represent hotspots for microchromosomal rearrangements. The frequencies of these CNVs among phenotypically normal and disease-affected individuals and whether they represent ancient or recurrent events still remain unknown, due to the lack of high throughput and cost-efficient detection methods. We have designed a CGH array with 5222 human BAC clones that covers ~23% of the genome (~0.8Mb resolution) with higher density in putative hotspot regions. Multiple technical replicates were used for array validation. Applying this genome-wide array-CGH to 20 healthy individuals, we have detected 68 CNVs, 37% newly identified with an average of 10,7 CNVs per individual. Thereafter, we have also developed a multiplex-ligation-probe-amplification (MLPA) based method to target a set of putatively relevant CNVs. Forty regions in two MLPA assays were selected on the basis of containing at least one single copy gene of the human genome (previously reported and/or detected by us). We have established the frequency and Mendelian inheritance of all these CNVs by genotyping 150 controls and 50 trios. No de novo rearrangement was detected. This rapid and high throughput MLPA approach will be useful for association and susceptibility gene studies aimed to understand psychiatric and other complex disorders. Work supported by Genoma Espańa.

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