Mapping translocation breakpoints by next- generation sequencing Chen, Wei, Vera Kalscheuer, Andreas Tzschach, Corinna Menzel, Reinhard Ullmann, Marcel Holger Schulz, Fikret Erdogan et al. Presented by: Tan Mei Hui A J

Recall: Structural Variations based on location and orientation of breakpoints 1. interchromosomal translocation 2. intrachromosomal translocation 3. inversion 4. deletion 5. insertion

Interchromosomal translocation unbalanced

Interchromosomal translocation balanced

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

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

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

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

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