1. Mutation Calling IGV Exercises

2. Run IGV – Web search IGV (Integrative Genomics Viewer) – Go to Download page – may need to provide email – Launch with JavaWebStart – 1.2 GB will work Set genome (top left) to Human hg19 Copy Exome.bam Exome.bam.bai and Exome.bam.tdf to your computer. Use File / Load from File to open the.bam file Setup

3. Exercise #1 Find BRCA2 gene. Double click to zoom in and see the reads Can you find a mutation in BRCA2 that will affect the protein sequence of the gene? If so, what is the codon change and protein impact?

4. #1 BRCA2 No Variant Poor Coverage Lack of supporting Reads

5. #1 BRCA2 Variant But No Coding Impact

6. #1 BRCA2 Gene: BRCA2 gTa->gCa Protein: Val(V) to Ala(A) Missense

7. Exercise #2 Go to the genomic position: chr 10 124066731 How would you characterize this mutation? What is its protein impact?

8. #2 Chr 10 124066731 Gene: BTBD16 ctT_>ctG Hetrozygous Protein L to L Synonymous

9. Zygosity call in cancer is complicated K562

10. Exercise #3 Go to the genomic position: chr 2 136575534 What would the impact of this mutation be?

11. #3 Chr 2 136575534 Negative Strand Gene

12. #3 Chr 2 136575534 Negative Strand Gene Gene: LCT Missense Mutation Atc->Gtc Protein I to V

13. Exercise #4 Go to the genomic position: chr 2 272256 If T was mutated to G what would the impact be? If a G was inserted at the position what would the impact be? If TGA was deleted at the position what would the impact be?

14. #4 chr2 272256 T to G Multiple Effects on different transcripts: Gene: ACP1 NM_070099 NM_001040649 gTg->gGg Tga->Gga V to G Stop to G

15. Exercise #5 Go to the genomic position: chr 13 32953452 If the 'G' that shows up on one read represented a real mutation, what would the impact on the protein be?

16. #5 Chr 13 32953452 Negative Strand Gene If the G represented a real Variant, impact: SpliceSite mutation with potential to cause exon skip.

17. Exercise #6 Go to the genomic position: chr 2 11094125 Is there any reason to have reduced confidence in a mutation call here?

18. #6 Chr 2 11094125 Low Complexity Region Makes Mutation Calling Less Reliable