This document discusses InVitae's development of a clinical genome interpretation pipeline on Amazon Web Services (AWS). It provides an overview of InVitae's mission to provide comprehensive genetic testing for over 264 conditions from a single sample through online requisitioning, CLIA-certified sequencing, and a HIPAA-compliant system. It also describes InVitae's curation of genetic variants, custom sequencing assay design, analysis pipeline on AWS, and goals to expand its testing and reduce costs over time.

1. 1/21Copyright 2013 InVitae, Inc
Reece Hart, Ph.D.
reece@invitae.com
InVitae, Inc.
invitae.com
Developing a Clinical GenomeDeveloping a Clinical Genome
Interpretation Pipeline at AWSInterpretation Pipeline at AWS

2. 2/21Copyright 2013 InVitae, Inc
The MissionThe Mission
To provide comprehensive,
clinically-relevant information from
genomic variation data in a single test.

3. 3/21Copyright 2013 InVitae, Inc
one sample
one requisition
one report
up to 264 conditions
two weeks
one lab, one price
InVitae's process features online requisitioning and reporting, CLIA-certified
sequencing, and a HIPAA-compliant information management.
intake
Requisitioning and Laboratory Information Management System
interpretationsequencing review

4. 4/21Copyright 2013 InVitae, Inc
Where does InVitae fit?Where does InVitae fit?
photos:
Baylor College of Medicine, Univ. Utah, learningradiology.com, sciencephotos.com
Patient presents with symptoms
If genomic interpretation might influence
diagnosis or treatment, doctor refers
patient to genetic counselor
GC takes history; sample is sent
to internal or one of hundreds of
labs that provide specific
genomic tests
Sequencing and other lab
data are processed into
preliminary iterpretation
Report is returned to GC
and/or physician who
verify interpretation and
consult with patient

5. 5/21Copyright 2013 InVitae, Inc
http://www.ncbi.nlm.nih.gov/sites/GeneTests/

6. 6/21Copyright 2013 InVitae, Inc
Examples of published clinical variantsExamples of published clinical variants
➢ Inherited conditions
● NM_000136.2:c.355_360delATGAGAinsT
‒ at risk for Fanconi Anemia
➢ Carrier conditions
● NM_000520.4:c.1277_1278insGATA
‒ carrier for Tay-Sachs
➢ Pharmacogenetic conditions
● HLAB*1502 & HLAB*5701 haplotypes (23 snps)
‒ Abacavir drug-induced hypersensitivity
‒ Flucloxacillin drug-induced liver injury
‒ Carbamazepine drug-induced cutaneous adverse events

7. 7/21Copyright 2013 InVitae, Inc
Reported VariantsReported Variants

8. 8/21Copyright 2013 InVitae, Inc
Our ReportOur Report

9. 9/21Copyright 2013 InVitae, Inc

10. 10/21Copyright 2013 InVitae, Inc
NOW
Early Access
Commercial Program
(CLIA Certified)
264
GENETIC TESTS
$1,500
2014
Goal to update offering
every six months
>1000
GENETIC TESTS
<$1,000
50x minimum, ~425x average
100% coverage of curated variants
>90% of targeted regions
SNVs, indels (<100nt), VUS

11. 11/21Copyright 2013 InVitae, Inc
How?How?
By deeply integrating custom genetic
curation, sequencing assay design, and
analytical pipelines.

12. 12/21Copyright 2013 InVitae, Inc
Curation + Assay Design + PipelineCuration + Assay Design + Pipeline
curation
analysis pipeline
A>T
sequence assay
curation

13. 13/21Copyright 2013 InVitae, Inc
Protected Health Information
on-site, encrypted, restricted access
Architectural OverviewArchitectural Overview
IPSec
Tunnel
4.5GB up
4 MB down

14. 14/21Copyright 2013 InVitae, Inc
Pipeline OverviewPipeline Overview
aligned readsreads
variantsaligned reads
reportvariants
bwa
samtools
gatk
picard
+ assay regions
+ GRCh37 ref
+ 1kg known indels
gatk
freebayes
custom variant calling
+ qualities
+ metrics
+ quality metrics
call haplotypes
match variants
VUS pipeline
render

15. 15/21Copyright 2013 InVitae, Inc
AWS TopologyAWS Topology
1 VPC
3 subnets
NFS
interactive hosts
web services
scaled dynamically
build/test

16. 16/21Copyright 2013 InVitae, Inc
What's worked well at AWS?What's worked well at AWS?
➢ Performance and Capacity Scaling
● on-demand
➢ Security and VPG
● Simple, comprehensive rules for VPCs
➢ Service ecosystem: EC2, EBS, S3, R53, IAM, VPC
● boto!
➢ Future:
● Archive: S3 and Glacier?
● Investigate workflows
● Reanalysis

17. 17/21Copyright 2013 InVitae, Inc
What challenges have we experienced?What challenges have we experienced?
➢ Large shared fileystems
● poor and variable performance (better now)
● familiarity, flexibility, transparency
● existing software expectations
➢ Node failures
● Once upon a time... 0-3 times per day, no warning
● moved zones no longer an issue
➢ Devops
● Built our own, but moving to puppet

18. 18/21Copyright 2013 InVitae, Inc

19. 19/21Copyright 2013 InVitae, Inc
One source of variation...One source of variation...
attribution unknown

20. 21/21Copyright 2013 InVitae, Inc