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`US 20130029852Al
`c19) United States
`
`
`c12) Patent Application Publication
`c10) Pub. No.: US 2013/0029852 Al
`(43) Pub. Date: Jan. 31, 2013
`Rava et al.
`
`(54)DETECTING AND CLASSIFYING COPY
`NUMBER VARIATION
`
`61/296,358, filed on Jan. 19, 2010, provisional appli­
`
`
`
`
`
`
`cation No. 61/360,837, filed on Jul. 1, 2010, provi­
`
`
`
`
`sional application No. 61/407,017, filed on Oct. 26,
`(75)Inventors: Richard P. Rava, Redwood City, CA
`
`
`
`
`
`
`
`2010, provisional application No. 61/455,849, filed on
`(US); B rian K. Rhees, Gilbert, AZ (US)
`Oct. 26, 2010.
`
`(73)Assignee: VERINATA HEALTH, INC., Redwood
`
`City, CA (US)
`
`
`
`Publication Classification
`
`
`
`(21) Appl. No.: 13/555,037
`
`(22)Filed:Jul. 20, 2012
`
`Related U.S. Application Data
`
`(51)Int. Cl.
`GOIN 33/50 (2006.01)
`C40B 60/10 (2006.01)
`G06F 19100 (2011.01)
`C40B 20100 (2006.01)
`
`
`
`(52) U.S. Cl. ................................. 506/2; 506/38; 702/20
`(63) Continuation-in-part of application No. 13/191,366,
`
`
`(57)
`ABST R ACT
`
`
`filed on Jul. 26, 2011, which is a continuation-in-part
`
`
`of application No. 12/958,352, filed on Dec. 1, 2010,
`The invention provides a method for determining copy num­
`
`
`
`
`
`Continuation-in-part of application No. 13/009,708,
`
`
`ber variations (CNV) ofa sequence ofinterest in a test sample
`
`filed on Jan. 19, 2011, Continuation-in-part of appli­
`
`
`
`that comprises a mixture of nucleic acids that are known or are
`
`cation No. 13/445,778, filed on Apr. 12, 2012, Con­
`
`
`
`suspected to differ in the amount of one or more sequence of
`
`
`tinuation-in-part of application No. 12/958,347, filed
`
`
`
`
`interest. The method comprises a statistical approach that
`
`
`on Dec. 1, 2010, Continuation-in-part of application
`
`
`
`
`accounts for accrued variability stemming from process-re­
`
`No. 12/958,356, filed on Dec. 1, 2010.
`
`
`
`lated, interchromosomal and inter-sequencing variability.
`(60) Provisional application No. 61/407,017, filed on Oct.
`
`
`
`
`
`The method is applicable to determining CNV of any fetal
`
`
`26, 2010, provisional application No. 61/296,464,
`
`
`
`aneuploidy, and CNVs known or suspected to be associated
`
`
`
`filed on Jan. 19, 2010, provisional application No.
`
`
`with a variety of medical conditions. CNV that can be deter­
`
`
`61/474,362, filed on Apr. 12, 2011, provisional appli­
`
`
`
`mined according to the method include trisomies and mono­
`
`
`
`cation No. 61/296,358, filed on Jan. 19, 2010, provi­
`
`somies of any one or more of chromosomes 1-22, X and Y,
`
`
`
`sional application No. 61/360,837, filed on Jul. 1,
`
`
`
`
`other chromosomal polysomies, and deletions and/or dupli­
`
`
`
`2010, provisional application No. 61/407,017, filed on
`
`
`
`cations of segments of any one or more of the chromosomes,
`
`
`
`Oct. 26, 2010, provisional application No. 61/455,849,
`
`
`which can be detected by sequencing only once the nucleic
`
`
`
`filed on Oct. 26, 2010, provisional application No.
`acids of a test sample.
`
`110 Obtain qualified samples
`
`115 Obtain test sample
`
`
`comprising nucleic acids
`
`corprising nucleic acids
`
`!
`
`125 Sequence at least a portion
`
`120 Sequence at least a portion
`
`of test nucleic acids
`
`
`of qualified nucleic acids
`!
`! 135 Determine
`test sequence
`
`
`130 Determine qualified sequence
`tag densities
`tag derities
`
`140 Determine qualified sequence
`!
`doses!
`
`
`
`145 Identify qualified normalizing sequence
`!
`
`
`150 Determine test sequence dose
`based on test normalizing
`sequence
`
`corresponding to identified
`qualified 1�
`
`normalizing sequence
`
`155 Determine thresholds
`�
`160 Compare test sequence dose
`
`
`to threshold value
`!
`
`
`165 Determine presence or absence
`of copy number variation
`
`�
`100
`
`

`

`
`Patent Application Publication
`
`
`Jan. 31, 2013 Sheet 1 of 75 US 2013/0029852 Al
`
`
`
`110 Obtain qualified samples
`
`115
`Obtain test sample
`
`
`comprising nucleic acids
`cor ,ising
`
`nucleic acids
`i
`125
`
`Sequence at least a portion
`
`120 Sequence at least a portion
`
`of test nucleic acids
`
`
`of qualified nucleic acids
`i
`i 135 Determine
`test sequence
`
`
`130 Determine qualified sequence
`tag densities
`1ag derties
`
`
`140 Determine qualified sequence
`l
`doses i
`
`
`
`145 Identify qualified normalizing sequence
`l 150 Determine test sequence dose
`
`
`based on test normalizing
`sequence
`qualified j
`
`corresponding to identified
`
`normalizing sequence
`
`155 Determine thresholds
`
`160
`+ Compare test sequence dose
`
`
`to threshold value
`
`
`i Determine presence or absence
`165
`of copy number variation
`
`� 100
`
`FIG.1
`
`

`

`Patent Application Publication
`
`Jan. 31, 2013 Sheet 2 0f 75
`
`US 2013/0029852 A1
`
`FULL-
`DNA REPAlRand
`ADAPTOR
`LENGTH PHOSPHORYLATION P dATA'L'NG P LlGATlNG P PCRAMPL'FY‘NG P
`
`ABB
`
`DNA REPAlR and
`PHOSPHORYLATION
`
`X dATAlLING
`
`ADAPTOR
`X UGATWG P PCRAMPLIFYING P
`
`X X- X- P—P
`
`X X— X- X—P
`
`FIG. 2
`
`Streptavidin
`
`
`
`. /;>Add DNA and
`Ligate 15t adapter
`
`
`
`Streptavidin
`
`—>
`
`
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`
`
`
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`
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`
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`
`amplify in
`
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`Library ready
`
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`
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`
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`
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`
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`
`4b
`
`Amplify on solid
`surface and
`
`detached l—step
`
`

`

`Patent Application Publication
`
`Jan. 31, 2013 Sheet 3 0f 75
`
`US 2013/0029852 A1
`
`(- 400
`
`Obtain a Biological Source Sample
`Comprising Genomic Nucleic Acids
`
`Combine Marker Nucleic Acrds wrth
`
`Biological Source Sample
`
`
`
`Prepare Sequencing Libraries of
`Sample Genomic and Marker
`Nucleic Acids
`
`Perform Massively Parallel
`Singleplex Sequencing
`
`Analyze Sequencing lnformation
`
`Verify the Integrity of Samples
`
`410
`
`420
`
`430
`
`440
`
`450
`
`460
`
`FIG. 4
`
`

`

`Patent Application Publication
`
`Jan. 31, 2013 Sheet 4 0f 75
`
`US 2013/0029852 A1
`
`/ 500
`
`510
`
`
`
`Obtain a Plurality of Biological
`Samples Comprising Genomic
`Nucleic Acids
`
`Combine Unique Marker Nucleic
`Acids with Biological Source
`
`Prepare Sequencing Libraries of
`Indexed Genomic Sample and
`
`Marker Nucleic Acids
`
`Sequencing
`
`520
`
`530
`
`540
`
`550
`
`560
`
`Verify the integrity of Each of the
`Plurality of Samples
`
`FIG. 5
`
`

`

`Patent Application Publication
`
`Jan. 31, 2013 Sheet 5 0f 75
`
`US 2013/0029852 A1
`
`610
`
`620
`
`630
`
`540
`
`Obtain test sample comprising a mixture of fetal and
`maternal nucleic acids
`
`Enrich the mixture of nucleic acids for polymorphic target
`nucleic acids
`
`presence or absence of aneuploidy in the test sample
`
`Sequence the enriched mixture of nucleic acids
`
`Determine the fraction of fetal nucleic acids and the
`
`600
`
`FIG. 6
`
`

`

`Patent Application Publication
`
`Jan. 31, 2013 Sheet 6 of 75
`
`US 2013/0029852 A1
`
`710
`
`720
`
`730
`
`l Maternal Plasma Sample I
`
`
`
`
`
`chNA purification
`
`
`
`Polymorphic Nucleic Acid
`Amplification
`
`
`
`
`
`740
`
`760
`
`
`
`
`
`Massively Parallel
`Sequencing
`
`
`
`Fetal Fraction
`Determination
`
`,
`
`750
`
`Size Separation by
`Electrophoresis
`
`770
`
`Fetal Fraction
`Determination
`
`
`
`
`
`
`
`
`FIG. 7
`
`

`

`Patent Application Publication
`
`Jan. 31, 2013 Sheet 7 of 75
`
`US 2013/0029852 A1
`
`
`
`
`
`
`Obtain test sample comprising a mixture of fetal and maternal
`nucleic acids
`
`
`
`810
`
`Amplify polymorphic target nucleic acids in a portion of the
`mixture of fetal and maternal nucleic acids in the test sample
`
`820
`
`
`
`Enrich the mixture of nucleic acids by combining the
`amplified polymorphic target nucleic acids
`
`830
`
`Purify the enriched mixture
`
`Sequence the enriched mixture of nucleic acids
`
`Determine the fraction of fetal nucleic acids and the presence
`or absence of aneuploidy in the test sample
`
`850
`
`860
`
`
`
`
`800
`
`FIG. 8
`
`

`

`Patent Application Publication
`
`Jan. 31, 2013 Sheet 8 0f 75
`
`US 2013/0029852 A1
`
`
`
`
`
`
`
`Obtain test sample comprising a mixture of fetal and maternal
`nucleic acids
`
`910
`
`
`
`Purify said mixture of fetal and maternal nucleic acids
`
`
`
`
`
`Amplify polymorphic target nucleic acids in a portion of the
`mixture of fetal and maternal nucleic acids in the purified
`sample
`
`Enrich the mixture of nucleic acids by combining the amplified
`polymorphic target nucleic acids
`
`940
`
`Sequence the enriched mixture of nucleic acids
`
`Determine the fraction of fetal nucleic acids and the presence
`or absence of aneuploidy in the test sampie
`
`950
`
`960
`
`
`
`
`900
`
`FIG. 9
`
`

`

`Patent Application Publication
`
`Jan. 31, 2013 Sheet 9 of 75
`
`US 2013/0029852 A1
`
`Obtain test sample comprising a mixture of fetal and maternal
`nucleic acids
`
`1010
`
`Purify said mixture of fetal and maternal nucleic acids
`
`1020
`
`Amplify polymorphic target nucleic acids in a portion of the
`mixture of fetal and maternal nucleic acids in the purified sample
`
`1040
`
`Prepare sequencing library of amplified polymorphic target
`nucleic acids
`
`
`
`
`1030
`
`1050
`
`Prepare sequencing library of purified mixture of fetal and
`maternal nucleic acids
`
`
`
`Enrich the mixture of nucleic acids by combining the library of
`amplified polymorphic target nucleic acids
`
` Sequence the enriched mixture of nucleic acids
`
`1070
`
`Determine the fraction of fetal nucleic acids and the presence
`or absence of aneuploidy in the test sample
`
`1030
`
`1000
`
`FIG. 10
`
`

`

`Patent Application Publication
`
`Jan. 31, 2013 Sheet 10 0f 75
`
`US 2013/0029852 A1
`
`
`
`Maternal Plasma Sample
`
`
`
`Polymorphic Nucleic Acid
`Amplification -
`
`
`
`
`chNA Purification
`
`
`
`
`
`
`
`
`
`
`Polymorphic Nucleic Acid
`Amplification
`
`Sequencing Library
`Preparation
`
`
`
`l
`
`Polynworphic Nucleic Acid
`Amplification
`
`
`
`__
`,,
`Sequencing Library
`
`Preparation
`
`Massively Parallel
`Sequencing
`
`FIG. 11
`
`

`

`Patent Application Publication
`
`Jan. 31, 2013 Sheet 11 0f 75
`
`US 2013/0029852 A1
`
`1e+5
`
`-----------------------------------------------------------------------------------------------
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`m Allele 1
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`Jan. 31, 2013 Sheet 12 of 75
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`US 2013/0029852 A1
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`Patent Application Publication
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`Jan. 31, 2013 Sheet 13 0f 75
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`US 2013/0029852 A1
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`Patent Application Publication
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`Jan. 31, 2013 Sheet 14 0f 75
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`US 2013/0029852 A1
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`Jan. 31, 2013 Sheet 15 of 75
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`Jan. 31, 2013 Sheet 16 of 75
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`Patent Application Publication
`
`Jan. 31, 2013 Sheet 17 0f 75
`
`US 2013/0029852 A1
`
`Calculate non-CNV
`fetal fraction (NCNFF)
`
`Calculate CNV fetal
`fraction (CNFF)
`(based on
`assumption about
`type of aneuploidy)
`
`Compare NCNFF and
`CNFF
`
`CNFF assumption
`regarding aneuploidy
`is correct
`
`1806
`
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`
`No Conclusion
`
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`
`Bin chromosome or
`
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`determine whether any
`bins have a DNA amount
`indicating aneuploidy
`
`
`
`
`Do any bins have a DNA amount
`indicating aneuploidy?
`
`Partial Aneuploidy
`located in affected
`bin(s)
`
`FIG. 18
`
`1816
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`Mosaic
`
`

`

`Patent Application Publication
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`Jan. 31, 2013 Sheet 18 0f 75
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`US 2013/0029852 A1
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`Patent Application Publication
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`Jan. 31, 2013 Sheet 19 of 75
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`US 2013/0029852 A1
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`Jan. 31, 2013 Sheet 20 0f 75
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`US 2013/0029852 A1
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`Jan. 31, 2013 Sheet 21 of 75
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`Patent Application Publication
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`Jan. 31, 2013 Sheet 22 0f 75
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`US 2013/0029852 A1
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`1.2
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`Patent Application Publication
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`Jan. 31, 2013 Sheet 23 0f 75
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`US 2013/0029852 A1
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`Patent Application Publication
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`Jan. 31, 2013 Sheet 24 0f 75
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`US 2013/0029852 A1
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`Patent Application Publication
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`Jan. 31, 2013 Sheet 25 0f 75
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`US 2013/0029852 A1
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`

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`Patent Application Publication
`
`Jan. 31, 2013 Sheet 26 0f 75
`
`US 2013/0029852 A1
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`FIG. 25C
`
`

`

`Patent Application Publication
`
`Jan. 31, 2013 Sheet 27 of 75
`
`US 2013/0029852 A1
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`
`FIG. 263
`
`
`
`
`

`

`Patent Application Publication
`
`Jan. 31, 2013 Sheet 28 0f 75
`
`US 2013/0029852 A1
`
`
`
`1—STEPLibrary
`
`(nM)
`
`10
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`Patent Application Publication
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`Jan. 31, 2013 Sheet 29 0f 75
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`US 2013/0029852 A1
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`Patent Application Publication
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`Jan. 31, 2013 Sheet 30 0f 75
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`US 2013/0029852 A1
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`Patent Application Publication
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`Jan.31,2013 Sheet310f75
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`US 2013/0029852 A1
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`Patent Application Publication
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`Jan. 31, 2013 Sheet 32 0f 75
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`US 2013/0029852 A1
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`Patent Application Publication
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`Jan. 31, 2013 Sheet 34 0f 75
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`US 2013/0029852 A1
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`Patent Application Publication
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`Jan. 31, 2013 Sheet 35 0f 75
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`US 2013/0029852 A1
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`Patent Application Publication
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`Jan. 31, 2013 Sheet 36 0f 75
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`US 2013/0029852 A1
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`Patent Application Publication
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`Jan. 31, 2013 Sheet 37 0f 75
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`Patent Application Publication
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`Jan. 31, 2013 Sheet 38 0f 75
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`US 2013/0029852 A1
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`Patent Application Publication
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`Jan. 31, 2013 Sheet 39 0f 75
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`US 2013/0029852 A1
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`Patent Application Publication
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`Jan. 31, 2013 Sheet 40 0f 75
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`US 2013/0029852 A1
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`Patent Application Publication
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`Jan. 31, 2013 Sheet 41 of 75
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`US 2013/0029852 A1
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`Patent Application Publication
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`Jan. 31, 2013 Sheet 42 0f 75
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`US 2013/0029852 A1
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`Patent Application Publication
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`Jan. 31, 2013 Sheet 43 0f 75
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`US 2013/0029852 A1
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`Patent Application Publication
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`Jan. 31, 2013 Sheet 44 0f 75
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`US 2013/0029852 A1
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`Patent Application Publication
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`Jan. 31, 2013 Sheet 45 0f 75
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`US 2013/0029852 A1
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`Patent Application Publication
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`Jan. 31, 2013 Sheet 46 0f 75
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`US 2013/0029852 A1
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`

`

`Patent Application Publication
`
`Jan. 31, 2013 Sheet 47 0f 75
`
`US 2013/0029852 A1
`
`Chromosome 21
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`FIG. 41A
`
`

`

`Patent Application Publication
`
`Jan. 31, 2013 Sheet 48 0f 75
`
`US 2013/0029852 A1
`
`Chromosome 1 8
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`FIG. 41B
`
`

`

`Patent Application Publication
`
`Jan. 31, 2013 Sheet 49 0f 75
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`US 2013/0029852 A1
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`Chromosome 1 3
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`8 s A
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`NormalizedDose
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`FIG. 41C
`
`

`

`Patent Application Publication
`
`Jan. 31, 2013 Sheet 50 0f 75
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`Chromosome X
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`FIG. 41D
`
`

`

`Patent Application Publication
`
`Jan. 31, 2013 Sheet 51 0f 75
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`
`Chromosome Y
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`FIG. 41E
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`

`

`Patent Application Publication
`
`Jan. 31, 2013 Sheet 52 0f 75
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`US 2013/0029852 A1
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`
`
`NormalizedChromosome
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`
`
`

`

`Patent Application Publication
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`Jan. 31, 2013 Sheet 53 0f 75
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`US 2013/0029852 A1
`
`
`
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`

`Patent Application Publication
`
`Jan. 31, 2013 Sheet 54 0f 75
`
`US 2013/0029852 A1
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` md
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`OChromosome 21
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`FIG. 45
`
`

`

`Patent Application Publication
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`Jan. 31, 2013 Sheet 55 0f 75
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`
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`FIG. 463
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`

`

`Patent Application Publication
`
`Jan. 31, 2013 Sheet 56 0f 75
`
`US 2013/0029852 Al
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`O Chromosome 21
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`FIG. 47
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`

`

`Patent Application Publication
`
`Jan. 31, 2013 Sheet 57 0f 75
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`US 2013/0029852 A1
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`
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`FIG. 49
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`

`Patent Application Publication
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`Jan. 31, 2013
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`Sheet 58 of 75
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`US 2013/0029852 A1
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`

`Patent Application Publication
`
`Jan. 31, 2013 Sheet 59 0f 75
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`US 2013/0029852 A1
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`

`

`Patent Application Publication
`
`Jan. 31, 2013 Sheet 60 0f 75
`
`US 2013/0029852 A1
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`fi/
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`FIG. 51B
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`

`

`Patent Application Publication
`
`Jan. 31, 2013 Sheet 61 0f 75
`
`US 2013/0029852 A1
`
`if
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`

`

`Patent Application Publication
`
`Jan. 31, 2013 Sheet 62 0f 75
`
`US 2013/0029852 Al
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`“x
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`FIG. 51D
`
`

`

`Patent Application Publication
`
`Jan. 31, 2013 Sheet 63 0f 75
`
`US 2013/0029852 A1
`
`1"
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`n==532
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`FIG. 51E
`
`

`

`Patent Application Publication
`
`Jan. 31, 2013 Sheet 64 of 75
`
`US 2013/0029852 A1
`
`n=532
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`n=l
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`n=416
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`FIG. 51F
`
`

`

`Patent Application Publication
`
`Jan. 31, 2013 Sheet 65 0f 75
`
`US 2013/0029852 A1
`
`23'
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`Jan. 31, 2013 Sheet 72 0f 75
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`US 2013/0029852 A1
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`MELISSA STUDY: Trisomy 13 samples
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`US 2013/0029852 A1
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`Jan. 31,2013
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`DETECTING AND CLASSIFYING COPY
`NUMBER VARIATION
`
`CROSS-REFERENCE TO RELATED
`APPLICATIONS
`
`[0001] This application is a continuation-in-part of U.S.
`application Ser. No. 13/191,366, filed on Jul. 26, 201 1, which
`is a continuation-in-part of U.S. application Ser. No. 12/958,
`352, filed on Dec. 1, 2010, which claims priority to U.S.
`ProvisionalApplication No(s). 61/296,358 filed Jan. 19, 2010
`and 61/360,837 filed Jul. 1,2010 and 61,407,017 and 61/455,
`849 both filed Oct. 26, 2010, all of which are incorporated by
`reference in their entireties. This application is also a continu-
`ation-in-part of U.S. application Ser. No. 13/009,708 filed
`Jan. 19, 201 1, which claims benefit ofU.S. Provisional Patent
`ApplicationNo. 61/296,464 filed Jan. 19, 2010, both ofwhich
`are incorporated herein by reference their entireties. This
`application is also a continuation-in-part of U.S. application
`Ser. No. 13/445,778 filedApr. 12, 2012, which claims benefit
`of U.S. Provisional Patent Application No. 61/474,362 filed
`Apr. 12, 2011, both of which are incorporated herein by
`reference in their entireties. This application is also a continu-
`ation-in-part of U.S. application Ser. No. 12/958,347 filed
`Dec. 1, 2010, which claims benefit ofU.S. Provisional Patent
`Application No(s). 61/296,358 filed Jan. 19, 2010 and
`61/360,837 filed Jul. 1,2010 and 61/407,017 and 61/455,849
`both filed Oct. 26, 2010, all of which are incorporated by
`reference in their entireties and for all purposes. This appli-
`cation is also a continuation-in-part of U.S. application Ser.
`No. 12/958,356 filed Dec. 1, 2010, which claims benefit of
`U.S. Provisional Patent Application No(s). 61/296,358 filed
`Jan. 19,2010 and 61/360,837 filed Jul. 1,2010 and 61/407,
`017 and 61/455,849 both filed Oct. 26, 2010, all ofwhich are
`incorporated by reference in their entireties and for all pur-
`poses.
`
`BACKGROUND
`
`[0002] One of the critical endeavors in human medical
`research is the discovery of genetic abnormalities that pro-
`duce adverse health consequences. In many cases, specific
`genes and/or critical diagnostic markers have been identified
`in portions of the genome that are present at abnormal copy
`numbers. For example, in prenatal diagnosis, extra or missing
`copies of whole chromosomes are frequently occurring
`genetic lesions. In cancer, deletion or multiplication of copies
`of whole chromosomes or chromosomal segments, and
`higher level amplifications of specific regions of the genome,
`are common occurrences.
`
`[0003] Most information about copy number variation has
`been provided by cytogenetic resolution that has permitted
`recognition of structural abnormalities. Conventional proce-
`dures for genetic screening and biological dosimetry have
`utilized invasive procedures e.g. amniocentesis, to obtain
`cells for the analysis ofkaryotypes. Recognizing the need for
`more rapid testing methods that do not require cell culture,
`fluorescence in situ hybridization (FISH), quantitative fluo-
`rescence PCR (QF-PCR) and array-Comparative Genomic
`Hybridization (array-CGH) have been developed as molecu-
`lar-cytogenetic methods for the analysis of copy number
`variations.
`
`[0004] The advent of technologies that allow for sequenc-
`ing entire genomes in relatively short time, and the discovery
`of circulating cell-free DNA (chNA) have provided the
`
`opportunity to compare genetic material originating from one
`chromosome to be compared to that of another without the
`risks associated with invasive sampling methods. However,
`the limitations of the existing methods, which include insuf-
`ficient sensitivity stemming from the limited levels of
`chNA, and the sequencing bias of the technology stemming
`from the inherent nature ofgenomic information, underlie the
`continuing need for noninvasive methods that would provide
`any or all of the specificity, sensitivity, and applicability, to
`reliably diagnose copy number changes in a variety ofclinical
`settings.
`[0005] Embodiments disclosed herein fulfill some of the
`above needs and inparticular offers an advantage in providing
`a reliable method that is applicable at least to the practice of
`noninvasive prenatal diagnostics, and to the diagnosis and
`monitoring of metastatic progression in cancer patients.
`
`SUMMARY
`
`[0006] Methods are provided for determining copy number
`variations (CNV) of a sequence of interest in a test sample
`that comprises a mixture ofnucleic acids that are known or are
`suspected to differ in the amount of one or more sequence of
`interest. The method comprises a statistical approach that
`accounts for accrued variability stemming from process-re-
`lated,
`interchromosomal and inter-sequencing variability.
`The method is applicable to determining CNV of any fetal
`aneuploidy, and CNVs known or suspected to be associated
`with a variety of medical conditions. CNV that can be deter-
`mined according to the present method include trisomies and
`monosomies of any one