Mapping translocation breakpoints by next-generation sequencing

1. Mapping translocation breakpoints by next-generation sequencing Chen, Wei, Vera Kalscheuer, Andreas Tzschach, CorinnaMenzel, ReinhardUllmann, Marcel Holger Schulz, FikretErdogan et al. Presented by: Tan Mei Hui A0039711J

2. Recall: Structural Variations • based on location and orientation of breakpoints • interchromosomal translocation • intrachromosomal translocation • inversion • deletion • insertion

3. Interchromosomal translocation • unbalanced

4. Interchromosomal translocation • balanced

5. Translocation breakpoints • Balanced chromosome rearrangement (BCRs) • Disease-associated Balanced Translocations (DBCRs)

6. Importance of research • Balanced chromosome rearrangement cause genetic disease by disrupting/inactivating specific gene • Characterization of breakpoints for hereditary diseases • 50% of patients with DBCR are mentally retarded • Complex and late-onset diseases

7. Issues with old methods • Traditional methods • In situ hybridization with fluorescent dye-labeled bacteria artificial chromosome clones (BAC-FISH) • Slow and laborious • Poor resolution, usually unable to identify the disrupted gene

8. Proposed method • Illumina/Sanger sequencing • Multiplex sequencing-by-synthesis technology • Bridge breakpoints in PCR amplification • Coverage sufficient to identify the exact nucleotide position in a shorter time • Low error (<1000bp) • Precise enough to define single primer pair for PCR amplification • Cost reduced • Parallel sequencing

9. Future work • Potential for breakpoint mapping on large scale • Limited number of balanced translocations studied in detail • Gene finding in patients with disease-associated balanced translocation • Method not robust for breakpoints in large duplicated segments

10. Q&A

11. Thank you!