Trieste Summer School – July 2011 CRIBI - Università di Padova
Trieste Summer School – July 2011 CRIBI - Università di Padova
Trieste Summer School – July 2011 CRIBI - Università di Padova
Mate pair signatures
Trieste Summer School – July 2011 CRIBI - Università di Padova
Mate pair libraries
Trieste Summer School – July 2011 CRIBI - Università di Padova
CRIBI APPROACH
STEP 1Use of insert length statistics for the identification of structural variations
STEP 2Use of sequence alignment (“splice-like” alignment) for the identification of the precise points of insertion/deletion.
Trieste Summer School – July 2011 CRIBI - Università di Padova
Trieste Summer School – July 2011 CRIBI - Università di Padova
FIRST STEP
• 4 indexes are created:
– unique MP, right distance, right orientation → useful for short indels(difference between observed and expected, after filtering low coverage)
– unique MP, wrong distance, rigth orientation → useful for long deletions(physical coverage)
– unique MP, wrong orientation → useful for inversions (physical coverage)
– unique reads lacking the partner → useful for long insertions (number of reads)
Trieste Summer School – July 2011 CRIBI - Università di Padova
SECOND STEP
– The alignment of a structural variation aligns like a splicing site
– Reads that cover a breakpoint can be spliced-aligned, showing a pattern of alignment compatible with that specific structural variation
– By analysing these patterns, it is possibile to detect the correct breakpoint with a base-precision
Trieste Summer School – July 2011 CRIBI - Università di Padova
FIRST STEP: LONG-DELETIONS AND INVERSIONS
Trieste Summer School – July 2011 CRIBI - Università di Padova
Long deletions
Trieste Summer School – July 2011 CRIBI - Università di Padova
Short deletions
Trieste Summer School – July 2011 CRIBI - Università di Padova
FIRST STEP: LONG INSERTIONS
Trieste Summer School – July 2011 CRIBI - Università di Padova
Long insertions
Trieste Summer School – July 2011 CRIBI - Università di Padova
Inversions and more
Trieste Summer School – July 2011 CRIBI - Università di Padova
• random genome
• structural variations randomly added (type, position, length, hetero/homozygosity)
• SNP random added (type, position, nucleotide)
SV \ Coverage 5X 10X 20X 40X
DELETIONS 58% 59% 72% 90%
INSERTIONS 43% 76% 78% 85%
INVERSIONS 56% 58% 74% 88%
Results on random SV
Trieste Summer School – July 2011 CRIBI - Università di Padova