United States Patent
`US 9,834,822 B2
`(10) Patent No.:
`(12)
`Talasaz
`(45) Date of Patent:
`*Dec. 5, 2017
`
`
`US009834822B2
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`
`(54) SYSTEMS AND METHODS TO DETECT
`RARE MUTATIONS AND COPY NUMBER
`VARIATION
`.
`.
`(71) Applicant: Guardant Health, Inc., Redwood City,
`CA (US)
`
`(72)
`
`Inventor: AmirAli Talasaz, Menlo Park, CA (US)
`:
`:
`(73) Assignee: Guardant Health, Inc., Redwood City,
`CA (US)
`
`21)
`(21)
`(22)
`65
`(65)
`
`Appl. No.: 15/492,659
`Appl.
`No
`,
`Filed:
`Apr. 20, 2017
`Prior
`Publication
`Data
`rior Publication
`US 2017/0218460 Al
`Aug. 3, 2017
`
`D
`
`CN
`EP
`
`OTHER PUBLICATIONS
`
`Related U.S. Application Data
`Alkan, et al. Personalized copy number and segmental duplication
`.
`.
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`using
`next-generation
`sequencing. Nat Genet. Oct.
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`(Continued)
`
`Primary Examiner — Kenneth Horlick
`(74) Attorney, Agent, or Firm — Wilson Sonsini Goodrich
`& Rosati
`
`(57)
`
`ABSTRACT
`.
`.
`The presentdisclosure provides a system and methodfor the
`detection of rare mutations and copy numbervariations in
`cell free polynucleotides. Generally, the systems and meth-
`ods comprise sample preparation, or the extraction and
`isolation of cell free polynucleotide sequences from a bodily
`fluid; subsequent sequencing ofcell free polynucleotides by
`techniques known in the art; and application of bioinfor-
`matics tools to detect rare mutations and copy number
`variations as compared to a reference. The systems and
`methods also may contain a database or collection of dif-
`ferent rare mutations or copy numbervariation profiles of
`different diseases, to be used as additional references in
`aiding detection of rare mutations, copy number variation
`profiling or general genetic profiling of a disease.
`
`20 Claims, 16 Drawing Sheets
`
`PGDX EX. 1008
`Page 1 of 56
`
`(51)
`
`(2006.01)
`(2006.01)
`(2011.01)
`
`Int. Cl.
`C12P 1934
`C12Q 1/68
`GO6F 19/22
`(52) U.S. Cl.
`CPC ou... C12Q 1/6886 (2013.01); C12Q 1/6869
`(2013.01); C12Q 1/6874 (2013.01); GO6F
`19/22 (2013.01); CI2Q 2600/156 (2013.01);
`C12Q 2600/158 (2013.01)
`(58) Field of Classification Search
`USPC cieccceccssessececsecsecseeneeseeeeneeneese 435/6.12, 91.2
`See application file for complete search history.
`
`(56)
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