Assays for Detection of Structural Variation

1. Assays for Detection of Structural Variation Lampros Mavrogiannis (Newcastle 13/12/2007)

2. Few Definitions Operational classification of genomic variation Positional (sequence level <~1kb) Epigenetic (methylation status) Structural (>~1kb) microscopic (>~3Mb) submiscroscopic (~1kb-3Mb) Structural variation Arrangement variation (balanced) Copy-number variation

3. The Landscape Copy-number variation Ploidy status Numerical chromosome abnormalities Large segmental duplications Gene/exon deletions and duplications Gene conversion events Re-arrangements Balanced translocations 'Clean' inversions and insertions

4. The Tools Karyotyping Array-based scans Genome re-sequencing Semi-quantitative PCR (QMPSF) MAPH and MLPA Real time quantitative PCR FISH Segregation of STR markers Genotyping of positional variants for dosage purposes Bespoke Southern blotting and PCR recipes

5. Points to Consider in Clinical Testing Applications Resolution is critical FISH STR segregation Genome re-sequencing Clone array CGH Oligo array CGH SNP array real time PCR dosage SNP typing MAPH MLPA QMPSF Karyotyping Sequence level Genome level

6. Points to Consider in Clinical Testing Applications Scope and limitations Dosage or arrangement information – and what kind of dosage exactly Variants that cannot be detected by design Use in scanning or typing capacity Analytical parameters Performance aspects Sensitivity and specificity Multiplexing potential Automation, parallel processing Cost Speed Lab integration

7. Recent Reviews Feuk L, Carson AR, Scherer SW. Structural variation in the human genome. Nat Rev Genet 2006;7:85-97