SV Update Since the last meeting Improvements made

SV Update Since the last meeting. . Improvements made to duplication calls (Kim) A subset are being checked annotated manually (Binnaz) Lab work and manual annotation (Binnaz) Inversions Duplications Query deletion annotation To do for finalization: Deletions – remove 'query' deletions that are likely false positives Insertions – 12 PCR done; need more? Inversions Analyze PCR results (Binnaz), further improvements of computational calls if necessary (Kim) Duplications – FISH? (Binnaz), further improvements of computational calls if necessary/possible (Kim) Re-run local assemblies/coordinate refinements for all SVs (Kim)

Lab Timeline • Deletions: 120 query regions PCRed on chr 19. Data needs summarising and list needs further improvement. Binnaz to send final chr 19 list to Kim by Friday. For accuracy check, we also have N-level breakpoint data for 250 regions in 8 strains (send the latest list to Kim). • Insertions: 24 PCRed and SEQed. Binnaz to send final list to Kim by Friday. • Inversions: 79 PCRed – high failure rate. Sequence analysis (Amarjit) Investigation: 2 -3 weeks • CNG: Classification in progress (Helen/James/Binnaz). 24 PCRed (strategy only works for tandem CNG). We need FISH to interrogate queries. We have a partial array list of CNG (Avi) if we only want tandem CNG, then ~1 week, if we want to look at queries then 2 -3 weeks at least