United States Patent
`US 9,598,731 B2
`(10) Patent No.:
`(12)
`Talasaz
`(45) Date of Patent:
`Mar. 21, 2017
`
`
`US009598731B2
`
`(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)
`Subject to any disclaimer, the term ofthis
`patent is extended or adjusted under 35
`U.S.C. 154(b) by 0 days.
`
`(*) Notice:
`
`(21) Appl. No.: 14/712,754
`
`(22)
`
`Filed:
`
`May 14, 2015
`
`5,654,413 A
`eee ‘
`5.714.330 A
`5,744,305 A
`5,759,778 A
`5,763,175 A
`5,800,992 A
`5,846,719 A
`5,854,033 A
`5,871,928 A
`5,925,525 A
`5,935,793 A
`2908740 A
`5,981,176 A
`5,981,179 A
`6,013,445 A
`6,020,124 A
`6,040,138 A
`6,046,005 A
`
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`Prior Publication Data
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`Oct. 22, 2015
`
`FOREIGN PATENT DOCUMENTS
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`10/1997
`EP
`
`Related U.S. Application Data 1647600 A2=4/2006EP
`
`(63) Continuation of application No. 14/425,189,filed as
`(Continued)
`application No. PCT/US2013/058061 on Sep. 4,
`2013.
`
`OTHER PUBLICATIONS
`
`(60) Provisional application No. 61/845,987, filed on Jul.
`13, 2013, provisional application No. 61/793,997,
`filed on Mar. 15, 2013, provisional application No.
`61/704,400,
`filed on Sep. 21, 2012, provisional
`application No. 61/696,734, filed on Sep. 4, 2012.
`
`(51)
`
`(2006.01)
`(2006.01)
`(2006.01)
`(2011.01)
`
`Int. CL
`C12P 1934
`C12Q 1/68
`CI2N 15/10
`GO6F 19/22
`(52) U.S. Cl.
`CPC wees C12Q 1/6874 (2013.01); CI2N 15/1065
`(2013.01); C12Q 1/6806 (2013.01); C12Q
`1/6869 (2013.01); C12Q 1/6886 (2013.01);
`GO06F 19/22 (2013.01); C12O 2600/118
`(2013.01); C12Q 2600/156 (2013.01); C12Q
`2600/16 (2013.01)
`
`(58) Field of Classification Search
`None
`See application file for complete search history.
`
`(56)
`
`References Cited
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`
`Primary Examiner — Kenneth Horlick
`(74) Attorney, Agent, or Firm — Wilson Sonsini Goodrich
`& Rosati
`
`(57)
`
`ABSTRACT
`
`The present disclosure 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.
`
`17 Claims, 16 Drawing Sheets
`
`PGDX EX. 1007
`Page | of 55
`
`PGDX EX. 1007
`Page 1 of 55
`
`

`

`US 9,598,731 B2
`
`Page 2
`
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