Personalis, Inc.
`
`CEO Overview
`Board of Directors Meeting
`May 8, 2012
`
`Personalis Confidential May 8, 2012
`
`1
`
`Personalis EX2112
`
`
`
`CEO Overview
`Board of Directors Meeting
`May 8, 2012
`
`Personalis Confidential May 8, 2012
`
`1
`
`Personalis EX2112
`
`
`
`CEO Overview
`
`• Company retains focus on product for 1st revenue in 2012
`– Rich to present R&D planning & progress
`4/30 ending cash above budget (Carol to review financials)
`•
`• Progress on move to new office (Carol to review – proposal to approve)
`• Continued development of ethical infrastructure (Carol to review)
`• Progress in recruiting (>60% have commercial experience)
`• Publications & public presentations
`• Four patent applications submitted based on earlier Stanford provisionals
`• Market developments – Personalis perspective
`• Accuracy development (Gold standard genome devt budget to approve)
`• Personalis laboratory strategy (outsource & insource)
`
`Personalis Confidential May 8, 2012
`
`2
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`Personalis EX2112
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`
`
`Publications & Upcoming Presentations
`• Seminal paper by Mike Snyder & team published in Cell :
`– Ongoing clinical use of genome-scale sequencing
`– Not just a genome once in your life
`
`• Multiple publications by Rong Chen
`
`•
`
`•
`
`JW invited to speak at CHI “The Clinical Genome” meeting
`– June 13, San Francisco
`
`JW invited to speak at Institute of Medicine meeting
`– Washington, DC, July
`
`Personalis Confidential May 8, 2012
`
`3
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`Personalis EX2112
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`
`
`Market Developments
`
`•
`
`Illumina / Roche
`– Financial pressure on Illumina may drive more aggressive approach to clinical potential
`– Illumina will be asked whether it is developing that opportunity as fast as Roche might
`– MiSeq moving to 510k; Cancer-gene pullout panel released
`– 2 x 250 reads now “summer” and only MiSeq
`
`• Complete Genomics
`– Delivery times being quoted as 12-16 weeks
`
`• Oxford Nanopore
`– No data seen yet, but tentative meeting in UK in July
`
`•
`
`Life Ion Proton
`– Expect HapMap genome for analysis in the next month
`
`Personalis Confidential May 8, 2012
`
`4
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`Personalis EX2112
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`
`
`Overview of Personalis Accuracy Program
`
`Characterize errors
`
`Informatic Solutions
`
`Lab, Content Solutions
`
`Analysis
`Rates by variant type & Q-score
`Underlying mechanisms
`Medical interpretation impact
`Regulatory impact
`
`Methods
`Comparison with literature
`Studies on limited regions
`Whole genome analysis:
`Single genome metrics
`Same person twice
`Family inheritance (MIE)
`Platform comparison
`Arrays
`ILMN / CGI / Ion T…
`Sanger capillary
`
`Prioritize solutions
`Bio-informatic approaches
`Laboratory approaches
`Content approaches
`
`Advances in 3rd party alg’s
`Aligner for > 200bp reads
`New versions, current alg’s
`Other alg’s (e.g. lobSTR)
`
`Advances in our alg’s:
`SV’s : Zygocity, accuracy
`Combine SV’s & SNP’s
`Broader use of Breakseq
`
`New Personalis alg’s
`Alignment degeneracy
`Genome-aware alignment
`VNTR-specific
`
`Advances in reference
`Ethnic major-allele ref’s
`Iterative
`Admixed
`InDel’s / SV’s
`
`Flag or Filter Out
`For problems not yet solved
`
`Combine technologies
`WGS + exome
`Longer reads and/or inserts
`Multi-vendor
`Arrays (genotypes & SV’s)
`Electrophoretic sizing
`Sanger validation
`
`Content-based semi-custom
`Array (genotypes & SV’s)
`Pullout
`
`Custom sample preps
`Problematic motifs
`Degenerate regions
`Phasing
`
`Content
`Gold standard genomes
`Known healthy genomes
`
`Personalis Confidential May 8, 2012
`
`5
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`Personalis EX2112
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`
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`Example of process variation in genome sequencing
`Four individuals had blood drawn together at the same hospital, sent to the same
`CLIA / CAP accredited lab, and sequenced on the same set of instruments.
`
`Personalis Confidential May 8, 2012
`
`6
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`Personalis EX2112
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`
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`Occurrence of bases with very low raw quality scores
`deviates markedly from a random (binomial) model
`
`# Reads below quality threshold (Loci with 30-40x coverage)
`
`Profile of systematic errors is remarkably similar between these two genomes
`
`Personalis Confidential May 8, 2012
`
`7
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`Personalis EX2112
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`
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`Region with “normal”
`sequence
`
`Region with “problematic”
`Sequence motif
`
`Tools to search for systematic errors across the genome, with their underlying
`mechanisms of action, will be followed by bio-informatic flags and (more
`importantly) bio-informatic and laboratory solutions.
`
`Personalis Confidential May 8, 2012
`
`8
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`Personalis EX2112
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`
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`Progression of Genome Data Sets for Accuracy Studies
`
`Founder Genomes
`
`Downloading
`
`Custom Sequenced
`
`West quartet (2009)
`MIE analysis:
`SNP (Dewey)
`SV’s (Manual, WG)
`InDel (TBD)
`Anecdotal error studies on
`portions of the genome:
`Phenomena
`Error rates
`Underlying mechanisms
`GA IIx vs HiSeq (early 2011)
`
`Snyder son/mother
`Data behind publications:
`Illumina vs CGI
`Snyderome paper
`Some inheritance validation
`
`HapMap NA12878
`Broad data set (late 2010):
`Hi-Seq 2x100
`10 PE insert lengths
`Total coverage > 500
`Same person “twice”:
`Same library
`Different library
`High coverage
`SV validation (Snyder)
`Fluor. Array data
`HapMap genotypes
`Some relatives’ data
`available
`
`Korean PGP
`40 HiSeq 2x100 genomes
`
`CEPH1463
`3 generations, 17 people
`Mother is HapMap NA12878
`To be “gold std”
`All 17 sequenced by CGI
`Test-bed for Personalis max
`accuracy combination of
`technologies
`Use to assess other tech’s:
`Ion Proton
`Oxford Nanopore
`MiSeq 2x250
`Anonymous samples
`(ethics)
`No Personalis relationship
`
`Venter Genome
`Only individual whole
`genome on Sanger
`technology
`
`Personalis Confidential May 8, 2012
`
`9
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`Personalis EX2112
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`
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`Segmentation of the 17-member pedigree by priority for sequencing
`
`Personalis Confidential May 8, 2012
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`10
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`Personalis EX2112
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`
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`All 11
`children
`
`Several
`optimal
`subsets
`with 5 of
`the 11
`children
`
`Mendelian Inheritance Error analysis can be confounded by genomic variation
`induced by the cell culture process. Being able to see each parental allele in two
`separate children should let us separate most of these errors from sequencing
`artifacts, letting us better identify them.
`
`Personalis Confidential May 8, 2012
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`11
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`Personalis EX2112
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`Personalis Confidential May 8, 2012
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`12
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`Personalis EX2112
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`
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`Personalis Laboratory Strategy
`
`•
`
`Laboratory goals:
`– Direct relationship with the customer
`– Quality control, sample to results (important for research and later clinical)
`– Position as “Value-Added Genome”, not “a bio-informatics company”
`– Offer a superior genome, by combining technologies from multiple companies
`– Develop superior sample preps, esp based on Personalis content
`• Outsourcing:
`– Whole genome sequencing service pricing now < reagents to do it yourself
`– Avoid infrastructure costs (instruments, initial computation, staffing)
`– Turn-around time is a disadvantage (quotes at 12-16 weeks)
`– Other assays we can outsource:
`• Arrays (standard & semi-custom)
`• Karyotyping
`• Exomes, RNAseq
`• Personalis lab
`– Receive, de-identify samples
`– QC, sample tracking
`– Ship aliquots to multiple vendors
`– Validations following primary analysis
`– Develop custom sample preps
`
`Personalis Confidential May 8, 2012
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`13
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`Personalis EX2112
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`
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`Next : VP Finance report
`
`Personalis Confidential May 8, 2012
`
`14
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`Personalis EX2112
`
`
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