trieste summer school – july 2011 cribi -...

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