1. GenomeVIP: A Genomics Analysis Pipeline for Cloud Computing with Germline and Somatic Calling on Amazon’s Cloud R. Jay Mashl October 20, 2014

2. Turnkey Variant Analysis
Project
Provides a collection of analysis tools and computational frameworks for streamlined discovery and interpretation of genetic variants
Pindel
BreakDancer
VarScan
Genome
STRiP
Multi-tool Variant discovery
Cloud computing
Scalability
Extensibility
Genome Variant Investigation Portal
Cloud
(AWS)
local
Poster #1678M (Monday)
tvap.genome.wustl.edu

3. Genome Variant Investigation Portal
Web server and interface for germline and somatic variant-discovery tools
Concurrent pipelines (SNV, indel, SV) with parallelization
Launchable on local machines or on the cloud through Amazon Web Services (AWS)
Download results from AWS via web browser
Pindel
VarScan
BreakDancer
GenomeSTRiP
(Harvard U.)
Heuristic/statistical calling of single nucleotide variants (SNVs)
Indel detection for paired reads based on local realignment
Structural variant (SV) detection for paired reads
Structural variant detection and genotyping

4. Biological Discoveries (selected)
Comprehensive molecular portraits of human breast tumours
Identified four main types by combining data from five platforms
Nature 490, (2012)
Clonal evolution in relapsed acute myeloid leukaemia
“Cancer” consists of multiple variants; founding clone may give rise to relapse clone; subclones may survive therapy and mutate further
Nature 481, (2012)
Genomic Landscape of Non-Small Cell Lung Cancer in Smokers and Never-Smokers
Of patients with lung cancer, smokers found to have10x more mutations than non-smokers
Cell 150, (2012)
Discovery & genotyping for structural variants in populations
~14,000 deletion polymorphisms with allelic states (1000G pilot)
Nature Genetics 43, (2011)

5. Application to APOL1: Demo
Representative samples from PUR population from 1000 Genomes
Analyze within the range chr22 : Mbp for known variants:
Sample
Region
Variant
Isoforms
HG01242
22:36,661,906
A / G G1
(non-silent)
HG01101
22:36,662,041
AATAATT / A
G2 (D6)
HG01049
22:36,133,448
D 767bp

6. Login
Select AWS
Click Next

7. Sample & Reference Selection
Specify path & retrieve
Entering path: Copy the given URI. Click Retrieve.
Click on all the PUR low_coverage items to transfer them to the Selected bams textbox.
Select reference hs37d5.chr22.fa.
Click Next.
Select samples
Select reference (hs37d5.chr22.fa)

8. SNV Detection: VarScan
All
22:
CheckVarScan
Select Germline
Select SNVs only
Select All (pooled) samples
Select User-defined region and enter “22: ”
Keep p-value: 0.99
Set Output vcf: True
Click Next.

9. Indel Detection: Pindel
Check Run Pindel
Select All (pooled) samples
Select User-defined region and enter “22: ”
Click Next.
Select All
22:

10. SV Detection: BreakDancer
Check BreakDancer
In Step 1, select All (pooled) samples
In Step 3, select Intra (ITX) only, user-defined region and enter “22: ”
Click Next.
22:

11. SV Detection & Genotyping: GenomeSTRiP
Check Run GenomeSTRiP
Verify reference is hs37d5.chr22.fa
Select mask human_g1k_v37.mask.36.fasta
GC normalization: True, with cn2_mask_g1k_v37.fasta
Chromosome: User-defined with “22: ”
Variant size: 100bp – 100 kbp.
Hs37d5.chr22
100bp-100kbp

12. Amazon AWS Submission
Jobs have been tested to finish within a few minutes
Select machine type
Where to send results
Validate & submit

13. Results 22 36133341 DEL_1 T <DEL> …SVLEN=-762;SVTYPE=DEL
AATAATT A . PASS END= ;HOMLEN=4;HOMSEQ=ATAA;SVLEN=-6;SVTYPE=DEL;
A G . PASS ADP=7;WT=1;HET=0;HOM=0;NC=2
AATAATT A . PASS ADP=4;WT=0;HET=1;HOM=0;NC=2;

14. Poster #1678 / M (this afternoon) Jay Mashl
genome.wustl.edu)
Kai Ye
genome.wustl.edu)
Li Ding
genome.wustl.edu)
...and with thanks to the Ding Lab members
Poster #1678 / M
(this afternoon)
National Human
Genome Research
Institute

15. Alternate slides

16. Amazon AWS S3 Data Retrieval
Links to actual files to be generated, along with merged VCF
Participants will identify variants in the output
(Left) Prepared results available, in case of technology problems
Click links to download