Mutation Calling IGV Exercises

Run IGV – Web search IGV (Integrative Genomics Viewer) – Go to Download page – may need to provide – 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

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?

#1 BRCA2 No Variant Poor Coverage Lack of supporting Reads

#1 BRCA2 Variant But No Coding Impact

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

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

#2 Chr Gene: BTBD16 ctT_>ctG Hetrozygous Protein L to L Synonymous

Zygosity call in cancer is complicated K562

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

#3 Chr Negative Strand Gene

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

Exercise #4 Go to the genomic position: chr 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?

#4 chr T to G Multiple Effects on different transcripts: Gene: ACP1 NM_ NM_ gTg->gGg Tga->Gga V to G Stop to G

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

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

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

#6 Chr Low Complexity Region Makes Mutation Calling Less Reliable