`Richard Chen
`Draft of what we might offer as Laboratory Assays
`Friday, January 13, 2012 1:26:33 PM
`Laboratory assays JW 13Jan2012.ppt
`
`From:
`To:
`Subject:
`Date:
`Attachments:
`
`Hi Rich,
`
`I have put together an outline of the Laboratory Assays we might offer. I don't think we need
`this level of detail at the Board meeting, but we should discuss this internally, starting with
`your thoughts. In addition, some of this should be the subject of patent filings, so we should
`not circulate it outside the company until we do that.
`
`John West
`
`Personalis EX2109
`
`
`
`Laboratory Assays - Overview
`
`• Generic genome-scale assays which can be applied to any
`sample without prior knowledge of the sample
`– Whole genome Plus
`– Exome Plus
`– Genotyping Plus
`
`• Custom validation of key results from specific genomes
`
`•
`
`“Virtual genomes” directly inferred from sequence data of
`others (e.g. children from parents)
`
`Personalis Confidential Jan 13, 2012
`
`1
`
`Personalis EX2109
`
`
`
`Laboratory assays – Whole genome Plus
`
`•
`
`•
`
`Illumina or CGI whole genome sequence with short-insert paired-end reads
`(may be provided by customer). Coverage & read length recommendations
`TBD
`Targeted re-sequencing using array or oligo-based pullout:
`– Additional coverage to fill in systematic gaps due to bias of biochemistry /
`molecular biology used for whole genome
`– Long-fragment pullout to resolve repeats, particularly in approx 3,000
`genes with alignment problems due to gene-family homologies
`• Whole genome and/or exome-focused genotyping to provide:
`– Technologically orthogonal validation of numerous specific medically
`interpretable alleles
`– Calibration of the sequencing error model
`– Independent assessment of Copy Number Variation
`• Electrophoretic assay of certain VNTR’s which are difficult to assess with NGS
`•
`FISH assay of chromosomal translocations, difficult to assess with NGS
`• RNA-seq from same sample, for expression, allelic bias, genetic variant-driven
`splice variation, partial phasing of individual genomes
`
`Personalis Confidential Jan 13, 2012
`
`2
`
`Personalis EX2109
`
`
`
`Laboratory assays – “Exome plus”
`
`• Exon re-sequencing by pullout from customer sample (may be
`provided by customer)
`• Additional re-sequencing by pullout, to capture regions outside the
`exons which are in VariMed, Regulome, lincRNA catalog & possibly
`others
`• Other elements from the list of assays which supplement the Whole
`Genome product. Selection likely to be based on customer’s specific
`goals and pricing
`
`Personalis Confidential Jan 13, 2012
`
`3
`
`Personalis EX2109
`
`
`
`Laboratory assays – Genotyping Plus
`
`• Ability to run Personalis’ interpretive content against a
`large set of genome-wide genotyping data sets a customer
`may already have, potentially to select samples for more
`in-depth (sequencing based) assessment
`• Depending on the costs and the interest in this, we could
`also have a custom array made to capture more of the
`Personalis content
`
`Personalis Confidential Jan 13, 2012
`
`4
`
`Personalis EX2109
`
`
`
`Laboratory assays – Validation of key
`results from specific genomes
`
`• Sanger re-sequencing of variants which underlie key conclusions of a genome
`interpretation project.
`– Targeting of regions to re-sequence can be by PCR, or may require more
`complex methods in homologous regions.
`– For highest confidence, combine forward & reverse Sanger reads of each
`amplicon.
`Targeted Sanger re-sequencing of full-length cDNA to confirm phasing of
`compound heterozygous variant-pairs which underlie key conclusions of a
`genome interpretation project
`– Depending on spacing of the variant pair on a cDNA, this may need to be
`paired-end Sanger sequencing
`• Other assays to confirm key variations not amenable to Sanger sequencing
`(e.g. VNTR’s, certain CNV’s, certain balanced translocations)
`
`•
`
`Personalis Confidential Jan 13, 2012
`
`5
`
`Personalis EX2109
`
`
`
`Virtual Genomes
`
`•
`
`• Genomes directly inferred from the data of others who have been
`sequenced (e.g. children from parents or vice versa)
`Inference based on recombination, mapped by genotyping or from the
`sequence data itself
`• Can capture de novo mutation events
`• Can provide genomes of individuals already deceased
`• Whole genome data sets at a cost approaching exomes
`
`Personalis Confidential Jan 13, 2012
`
`6
`
`Personalis EX2109
`
`
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