IGV Demo and Data Management

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Presentation transcript:

IGV Demo and Data Management Alona Sosinsky and Shirley Henderson

Data Management Alona Sosinsky 07.11.2018

Accessing analysed data Static data analysis Extended reporting of germline variants Somatic mutation burden Mutational signature analysis FFPE reports: somatic domain 1&2 + germline variants Interpretation portal Flags on portal (FFPE, re-issued analysis, fast-track) Case priority (high, medium, low) Tabs: ready for dispatch, to be reviewed, to be closed, archived cases Access to IGV viewer from HTML 07 April 2019

Interpretation Portal 07 April 2019

Small variants read support in IGV https://igv.genomicsengland.nhs.uk/?samples=1000000034:NormalLP;1000000038:TumourLP&region=chr7:140753335-140753335 Reported as CA>TT CA > AT in genome 07 April 2019

Structural Variants read support in IGV https://https://igv.genomicsengland.nhs.uk/?samples=1000000038:TumourLP&region=chr12:11755686-11755765 07 April 2019

IGV viewer Download batch script and open on your local IGV viewer for extended functionality cluster of mismatches after the breakpoint For BP format look at Fig.1 at https://samtools.github.io/hts-specs/VCFv4.2.pdf soft clipped reads NN]COORD] [COORD[NN ETV6 breakpoint

Quality metrics QC portal in LabKey is replaced with MI portal Five flags for marking groups of variants which are enriched with false positives Edge cases Nano library prep Tumour samples with low level of cross-sample contamination (1-5%) 07 April 2019

Nano library prep - outlier Number of somatic indels in 2Mb window Ratio of normalised depth of coverage for tumour vs normal MULTIPLE MYELOMA COSMIC content with low coverage (<30x): 15.29% Total somatic SNVs: 13,377 Total somatic indels: 55,931 (10-13K is expected)

Nano library prep: high burden of 1 bp indels in polyA runs 07 April 2019

Cross-sample contamination in tumour: 3.5% ACUTE MYELOID LEUKAEMIA FF PCR-free Total somatic SNVs: 100,553 Total somatic indels: 9,960 Number of somatic SNVs in 2Mb window