1. IGV Demo and Data Management
Alona Sosinsky and Shirley Henderson

2. Data Management
Alona Sosinsky

3. 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

4. Interpretation Portal
07 April 2019

5. Small variants read support in IGV
Reported as CA>TT
CA > AT in genome
07 April 2019

6. Structural Variants read support in IGV
07 April 2019

7. 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
soft clipped reads
NN]COORD]
[COORD[NN
ETV6 breakpoint

8. 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

9. 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)

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

11. 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