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SV validation plate #1

Format : 384 amplicons ( two 384-well plates of primers ) Events: 4 different types of SVs: Deletions Insertions Tandem duplications ( evertions ) Insertions Methods: 4 SV calling algorithms Breakdancer DWAC-Seq Pindel 1-2-3-SV Public data

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SV validation plate #1

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  1. Format: 384 amplicons ( two 384-well plates of primers ) Events: 4 different types of SVs: Deletions Insertions Tandem duplications ( evertions ) Insertions Methods: 4 SV calling algorithms Breakdancer DWAC-Seq Pindel 1-2-3-SV Public data Deletion list published by 1000 genomes project (October 2010; trio + low coverage ) SV validation plate #1

  2. We consider that everything which was found in 1000 genome projects represents positive calls. • GoNL SV calls that are made by several tools are likely to be true • In the first verification we want to see how to improve calling for the tools used for GoNL SV analysis. • Amplicon sizes are between 200 and 500 bases • If SV allele is <= 300 bp we fully resequence it • If SV allele is > 300 bp we resequence only 5-prime breakpoint from it Selection creteria & amplicon design

  3. Deletions Breakdancer (27) DWAC-Seq (27) Pindel (27) 123SV (27) Evertions Breakdancer (28) DWAC-Seq (28) Pindel (28) 123SV (27) Insertions Breakdancer (27) Pindel (28) 123SV (28) Inversions Breakdancer (28) Pindel (27) 123SV (27) Randomly selected sets Total: 384 SV candidates

  4. Verification with Ion torrent Primer ~ 23 bp (+tail). Breakpoint should be close to the primer

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