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Computational methods for genomics-guided immunotherapy
Sahar Al Seesi Computer Science & Engineering Department, UCONNImmunology Department, UCONN Health
Sequencing QC and Mapping
Calling SNVs
EpitopePrediction
TCR Sequencin
g
Ion Proton
Tumor DNA
Exome AmpliSeq
Normal DNA Tumor RNA
Sequencing
Whole TranscriptomeLibrary prep
Whole GenomeLibrary prep
or
Sequencing QC and Mapping
Calling SNVs
Epitope Prediction
TCR Sequencing
Tumor DNA
Sequencing
Nextera Rapid Capture Exome
Normal DNA Tumor RNA
Whole TranscriptomeLibrary prep
Illumina HiSeq
Whole GenomeLibrary prep
or
Sequencing QC and Mapping
Calling SNVs
Epitope Prediction
TCR Sequencing
Sequencing QC and Mapping
Calling SNVs
Epitope Prediction
TCR Sequencing
C C G C G G T C A GT C T C G G A A T TT C C C G G T A A TT C C C G G T A A TT C C C G G T A A TA T C G G T T T A TC C T C T A A C A CT A A T G G A A T TC C G C G A A C A CA A C A C C C C G G
Read Quality Control
Low quality base
• Tools to analyze and preprocess fastq files– FASTX
http://hannonlab.cshl.edu/fastx_toolkit/
– PRINSEQ http://prinseq.sourceforge.net/)
Sequencing QC and Mapping
Calling SNVs
Epitope Prediction
TCR Sequencing
Sequencing QC and Mapping
Calling SNVs
Epitope Prediction
TCR Sequencing
Normal Exome Reads
Tumor Exome Reads
Tumor RNA-Seq Reads
Human reference
Human reference
Read Mapping
Normal Exome Reads
Human Reference
Tumor Exome Reads
Sequencing QC and Mapping
Calling SNVs
Epitope Prediction
TCR Sequencing
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Somatic Variant Callers• Mutect (Broad Inst.)• VarScan2 (Wash. U.)• SomaticSniper (Wash. U)• Strelka (Illumina)• SNVQ w/ subtraction (UConn)
Sequencing QC and Mapping
Calling SNVs
Epitope Prediction
TCR Sequencing
Normal Exome Reads
Human Reference
Tumor Exome Reads
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The ICGC-TCGA DREAM Somatic Mutation Calling Challenge• Initial Goal: Find the Best WGS Analysis Methods• Challenge 1 Data: 10 Real Tumor/Normal pairs
– 5 from pancreatic tumors and 5 from prostate tumors– Sequenced to ~50x/30x
• Up to 10K candidates will be validated• Re-sequencing to ~300x coverage using AmpliSeq
primers on IonTorrent
Sequencing QC and Mapping
Calling SNVs
Epitope Prediction
TCR Sequencing
• Criteria for selecting candidate epitopes1) Gene harboring the SNV must be expressed (FPKM
estimation)
Sequencing QC and Mapping
Calling SNVs
Epitope Prediction
TCR Sequencing
Tumor RNA-Seq Reads
* ***
• Criteria for selecting candidate epitopes1) Gene harboring the SNV must be expressed2) Peptide will be generated inside the cell upon protein being
cleaved by the proteasome3) Peptide will bind to an MHC molecule that will chaperon it to the
cell surface • NetChop
Predicts cleavage sites of the human proteasome http://www.cbs.dtu.dk/services/NetChop/• SYFPEITHI Predicts MHC I, MHC II binding http://www.syfpeithi.de/• NETMHC Predicts MHC I binding http://www.cbs.dtu.dk/services/NetMHC/• NetCTL
Combined cleavage and MHC biding predictions http://www.cbs.dtu.dk/services/NetCTL/
Sequencing QC and Mapping
Calling SNVs
Epitope Prediction
TCR Sequencing
