Wissenschaftliche Highlights der GSF 2007

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1 H Forschungszentrum für Umwelt und Gesundheit GmbH in der Helmholtzgemeinschaft Wissenschaftlich-Technische Abteilung Wissenschaftliche Highlights der GSF 2007 Abfrage Oktober 2007 Institut / Selbst. Abteilung / KKG / Nachwuchsgruppe: Institute of Human Genetics FE-Nr.: Kontaktperson für Rückfragen: Strom Tim M, 3296 Titel des Highlights: Copy number variations measured by SNP oligonucleotide arrays in patients with mental retardation Keywords: Copy number variations, Mental retardation, Oligonucleotide SNP arrays. Kernaussage des Highlights in einem Satz: SNP oligonucleotide arrays allow the detection of small deletions or duplications (copy number variations) and provide a tool for the identification of single gene defects causative for clinical conditions such as mental retardation. Darstellung des Highlights: By G-banded chromosome analyses, aberrations can only be detected in a small percentage of children with syndromic and non-syndromic mental retardation (MR) and other severe diseases. G-banded chromosome analysis has a resolution of 5-10 Mb. Genome-wide arraybased hybridization of genomic DNA allows the detection of copy number variations (CNV) with much higher resolution. With these techniques, causal CNVs have been detected in 10 20% of children with severe MR having normal karyotypes. These CNVs included unique de novo aberrations ( Mb), new microdeletions syndroms, but also CNVs confined to small regions or single genes. This whole-genome technique - will transform the diagnostic discipline of cytogenetics. - will not only be used to detect genomic aberrations with strong effects in rare diseases, but also with weak effects in common disorders. - will undergo fast methodological improvements during the coming years. This will concern both hardware (arrays) and analysis programs. We studied 67 children with unexplained mental retardation with normal karyotypes as assessed by G-banded chromosome analyses. Their DNAs were analyzed with Affymetrix 100K arrays. We detected 11 copy number variations that are most likely causative for mental retardation because they either arose de novo (9 cases) and/or overlapped with known microdeletions (2 cases). The 8 deletions and 3 duplications varied in size from 200 kb to 7.5 Mb. Five of the 11 copy number variations were flanked by low-copy repeats. Two 1

2 of those on chromosome 15q25.2 and Xp22.31 have not been described before and have a high probability of being causative for new deletion/duplication syndromes. In one patient we found a deletion affecting only a single gene, MBD5, which codes for the methyl-cpgbinding domain protein 5. In addition to the 67 cases, we investigated 4 mentally retarded children with apparent balanced translocations and detected 4 deletions at breakpoint regions ranging from 1.1 to 14 Mb. Wagenstaller J, Spranger S, Lorenz-Depiereux B, Kazmierczak B, Nathrath M, Wahl D, Heye B, Glaser D, Liebscher V, Meitinger T, Strom TM. Copy-number variations measured by single-nucleotide-polymorphism oligonucleotide arrays in patients with mental retardation. Am J Hum Genet. 2007,81: Epub 2007 Aug 28. Asmus F, Hjermind LE, Dupont E, Wagenstaller J, Haberlandt E, Munz M, Strom TM, Gasser T. Genomic deletion size at the epsilon-sarcoglycan locus determines the clinical phenotype. Brain 2007,130: Bezug zur GSF-Strategie: As the technology evolves, driven mainly by the need for dense SNP arrays in genome-wide association studies, the resolution to detect small CNVs will improve thus offering not only new opportunities for research but also for clinical diagnostics and possibly for treatment. GSF-interne Kooperationspartner, mit denen das Highlight ggf. erarbeitet wurde: 2

3 Copy number variations in the normal population Number of CNVs: Median length: kb Total length: 400 Mb (12% of the genome) App. 60% of the CNVs contain genes The minor allele frequency of most CNVs is low Genome 12% CNVs per person: Total CNVs per person: 24 Mb (0.8% des Genoms) Redon et al. Nature (2006)

4 G-banded chromosome analysis versus oligonucleotide arrays G-banded chromosome analysis Resolution 5-10 Mb Detection rate in mental retardation 5-10% (aside from trisomy 21) Oligonucleotide arrays Resolution depending on the probe density Current whole-genome arrays 300 k to 2 M probes Resolution several 1000 bp. Detection rate in mental retardation 10-20% (normal karyotype)

5 De novo CNVs in patients with mental retardation Wagenstaller et al. AJHG 2007

6 550k whole-genome array showing several CNVs

7 550k whole-genome array showing several CNVs

Wissenschaftliche Highlights der GSF 2007

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