111111
`
`1111111111111111111111111111111111111111111111111111111111111
`US007824889B2
`
`c12) United States Patent
`Vogelstein et al.
`
`(10) Patent No.:
`(45) Date of Patent:
`
`US 7,824,889 B2
`*Nov. 2, 2010
`
`(54) DIGITALAMPLIFICATION
`
`(75)
`
`Inventors: Bert Vogelstein, Baltimore, MD (US);
`Kenneth W. Kinzler, BelAir, MD (US)
`
`(73) Assignee: The Johns Hopkins University,
`Baltimore, MD (US)
`
`( *) Notice:
`
`Subject to any disclaimer, the term of this
`patent is extended or adjusted under 35
`U.S.C. 154(b) by 659 days.
`
`This patent is subject to a terminal dis(cid:173)
`claimer.
`
`(21) Appl. No.: 11/709,742
`
`(22) Filed:
`
`Feb.23,2007
`
`(65)
`
`Prior Publication Data
`
`US 2008/0241830Al
`
`Oct. 2, 2008
`
`Related U.S. Application Data
`
`(60) Continuation of application No. 10/828,295, filed on
`Apr. 21, 2004, now abandoned, which is a division of
`application No. 09/981,356, filed on Oct. 12, 2001,
`now Pat. No. 6,753,147, which is a continuation of
`application No. 09/613,826, filed on Jul. 11,2000, now
`Pat. No. 6,440,706.
`
`(60) Provisional application No. 60/146,792, filed on Aug.
`2, 1999.
`
`(51)
`
`Int. Cl.
`(2006.01)
`C12P 19134
`(2006.01)
`C07H 21/04
`(52) U.S. Cl. ................. 435/91.2; 536/24.31; 536/24.33
`(58) Field of Classification Search ....................... None
`See application file for complete search history.
`
`(56)
`
`References Cited
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`
`(Continued)
`
`Primary Examiner-Samuel Woolwine
`(74) Attorney, Agent, or Firm-Banner & Witcoff, Ltd.
`
`(57)
`
`ABSTRACT
`
`The identification of pre-defined mutations expected to be
`present in a minor fraction of a cell population is important for
`a variety of basic research and clinical applications. The
`exponential, analog nature of the polymerase chain reaction is
`transformed into a linear, digital signal suitable for this pur(cid:173)
`pose. Single molecules can be isolated by dilution and indi(cid:173)
`vidually amplified; each product is then separately analyzed
`for the presence of pre-defined mutations. The process pro(cid:173)
`vides a reliable and quantitative measure of the proportion of
`variant sequences within a DNA sample.
`
`22 Claims, 7 Drawing Sheets
`
`DNA
`
`STEP1 n DILUTET0~1/2COPY/
`u WELLPCR
`......
`. . . . . .
`
`. . . . . .
`. . . . . .
`STEP 2 n ADD FLUORESCENT PROBES
`D FLUOROMETRY
`......
`. . . . . .
`. . . . . .
`......
`. . . . . .
`. . . . . .
`
`···®©®®®®···
`ooo@Q@I@I@Qooo
`ooo@@@QI@IC)ooo
`
`(3l "NO PCR PRODUCT
`~ =WILD TYPE PCR PRODUCT
`I@ =MUTANT PCR PRODUCT
`
`Case 1:16-cv-01112-WO-JEP Document 1-2 Filed 09/07/16 Page 2 of 21
`
`MYR1001
`Myriad Genetics, Inc. et al. (Petitioners) v. The Johns Hopkins University (Patent Owner)
`IPR For USPN 7,824,889
`
`Page 1 of 20
`
`

`

`US 7,824,889 B2
`Page 2
`
`U.S. PATENT DOCUMENTS
`
`5,925,517 A
`5,928,870 A
`6,020,137 A
`6,037,130 A
`6,143,496 A
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`wo
`wo
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`in Mycobacterium Tuberculosis", Nature
`Drug Resistance
`Biotechnology, Apr. 1998, pp. 359-363, vol. 16, No.4.
`S. Tyagi eta!., "Multicolor Molecular Beacons for allele discrimina(cid:173)
`tion", Nature Biotechnology, pp. 303-308, Jan. 1998, vol. 16, No. 1.
`J. A.M. Vet et a!., "Multilex Detection of Four Pathogenic
`Retroviruses Using Molecular Beacons", Proceedings of the
`National Academy of Sciences of the United States, May 25, 1999,
`pp. 6394-6399, vol. 96, No. 11.
`S. Tyagi et a!., "Molecular Beacons: probes that Fluoresce Upon
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`W. P. Halford et al., "The Inherent Quantitative Capacity of the
`Reverse Transcription-Polymerase Chain Reaction", Analytical Bio(cid:173)
`chemistry, Jan. 15, 1999, pp. 181-191, vol. 266, No.2.
`B. Vogelstein et a!., "Digital PCR", Proceedings of the National
`Academy of Sciences of the United States, Aug. 3, 1999, pp. 9236-
`9241, vol. 96, No. 16.
`K. D.E. Everett et al, "Identification of nine species of the
`Chlamydiaceae Uisng PCR-RFLP", Apr. 1999, pp. 803-813, vol. 49,
`No.2.
`Darren G. Monckton, eta!., "Minisatellite "Isoallele" Discrimination
`in Pseudohomozygotes by Single Molecule PCR and Variant Repeat
`Mapping", Genomics 11, pp. 465-467, 1991.
`Gualberto Ruano, et a!., "Haplotype of Multiple Polymorphisms
`Resolved by Enzymatic Amplification of Single DNA Molecules",
`Proc. National Science USA, 1990, vol 87, pp. 6296-6300.
`W. Navidi, eta!., "Using PCR in Preimplantation Genetic Disease
`Diagnosis", Human Reproduction, vol. 6, No.6, pp. 836-849, 1991.
`
`Hongua Li, eta!., "Amplification and Analysis of DNA Sequences in
`Single Human Sperm and Diploid Cells", Nature, vol. 335, Sep. 29,
`1988, pp. 414-417.
`Lin Zhang, eta!., "Whole Genome Amplification from a Single Cell:
`Implications for Genetic Analysis", Proc. National Science USA,
`vol. 89, pp. 5847-5851, Jul. 1992.
`David Sidransky, et a!., "Clonal Expansion of p53 Mutant Cells is
`Associated with Brain Tumour Progression", Nature, Feb. 27, 1992,
`vol. 355, pp. 846-847.
`Alec J. Jeffreys, eta!., "Mutation Processes at Human Mini satellites",
`Electophoresis, pp. 1577-1585, 1995.
`C. Schmitt, et a!., "High Sensitive DNA Typing Approaches for the
`Analysis of Forensic Evidence: Comparison of Nested Variable
`Number of Tandem Repeats (VNTR) Amplification and a Short Tan(cid:173)
`dem Repeats (STR) Polymorphism", Forensic Science International,
`vol. 66, pp. 129-141, 1994.
`Paul M. Lizardi, et a!., "Mutation Detection and Single-Molecule
`Counting Using Isothermal Rolling-Circle Amplification", Nature
`Genetics, vol. 19, Jul. 1998, pp. 225-232.
`R. Parsons, et a!., "Mismatch Repair Deficiency in Phenotypically
`Normal Human Cells", Science, vol. 268, May 5 1995, pp. 738-740.
`Marras et al., "Multiplex Detection of Single-Nucleotide Variations
`Using Molecular Beacons," Genetic Analysis: Biomolecular Engi(cid:173)
`neering, Feb. 1999, 14; 151-156.
`Whitcomb et al., "Detection of PCR Products Using Self-Probing
`Amplicons and Fluorescence," Nature Biotechnology, Aug. 1999,
`vol. 17, 804-807.
`P. J. Sykes, "Quantitation of Targets for PCR by Use of Limiting
`Dilution," BioTechniques, (1992), vol. 13, No.3, pp. 444-449.
`M.J. Brisco eta!., "Detection and Quantitation of Neoplastic Cells in
`Acute Lymphoblastic Leukaemia, by Use of the Polymerase Chain
`Reaction," British Journal ofHaematology, 1991,79, 211-217.
`M. J. Brisco et al., "Outcome Prediction in Childhood Acute
`Lymphoblastic Leukaemia by Molecular Quantification of Residual
`Disease at the End oflnduction," The Lancet, Jan. 22, 1994, vol. 343,
`pp. 196-200.
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`Notice ofReasons for Rejection dispatched Apr. 28, 2010 in Japanese
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`Single-Molecular-Dilution (SMD) Method of Direct Haplotype
`Resolution," Am. J. Hum. Gen., vol. 46, pp. 1149-1155 (1990).
`* cited by examiner
`
`Case 1:16-cv-01112-WO-JEP Document 1-2 Filed 09/07/16 Page 3 of 21
`
`Page 2 of 20
`
`

`

`U.S. Patent
`
`Nov. 2, 2010
`
`Sheet 1 of7
`
`US 7,824,889 B2
`
`FIG. 1 A
`DNA
`STEP 1 ~ DILUTE TO,., 1/2 COPY/
`WELL PCR
`
`• • • • • •
`• • • • • •
`• • • • • •
`···®®®@®®···
`···®®®®®®···
`···®®®®®®···
`• • • • • •
`• • • • • •
`• • • • • •
`
`STEP2 ~ ADD FLUORESCENT PROBES
`FLUOROMETRY
`
`• • • • • •
`• • • • • •
`• • • • • •
`
`• • • • • •
`• • • • • •
`• • • • • •
`@) = NO PCR PRODUCT
`@ = WILD TYPE PCR PRODUCT
`@=MUTANT PCR PRODUCT
`
`Case 1:16-cv-01112-WO-JEP Document 1-2 Filed 09/07/16 Page 4 of 21
`
`Page 3 of 20
`
`

`

`U.S. Patent
`
`Nov. 2, 2010
`
`Sheet 2 of7
`
`US 7,824,889 B2
`
`1-z
`w
`(.)
`U) w
`a:
`0
`::::>
`_J u..
`
`1-z
`w
`(.)
`U) w
`a:
`0
`::::>
`_J u..
`I z
`0 z
`
`m
`
`..---(!) -u..
`
`+
`
`a:
`w
`:r:
`(.) z
`/~ a
`J(cid:173)z
`w
`"'""' ~ w
`\w>-
`a:o
`0
`=:J
`_J
`LL
`
`Case 1:16-cv-01112-WO-JEP Document 1-2 Filed 09/07/16 Page 5 of 21
`
`Page 4 of 20
`
`

`

`U.S. Patent
`
`Nov. 2, 2010
`
`Sheet 3 of7
`
`US 7,824,889 B2
`
`l ~
`
`u
`
`-CJ -u..
`
`z
`w
`w
`a:
`CJ I
`CD
`~
`
`0 w
`a: I
`CD
`~
`
`~I
`
`Case 1:16-cv-01112-WO-JEP Document 1-2 Filed 09/07/16 Page 6 of 21
`
`Page 5 of 20
`
`

`

`~
`00
`•
`~
`~
`~
`
`~ = ~
`
`z 0
`
`~
`N
`
`~
`
`N
`0 .....
`0
`
`rFJ =(cid:173)
`('D a
`0 .....
`-....l
`
`.j;o.
`
`d
`rJl
`-....l
`Oo
`N
`~
`Oo
`00
`
`\C = N
`
`::~ I
`
`FIG. 2
`
`~r-.-.l\1~.,.,.=------
`
`3 .2 - r - - - - - - - - - - - - - - - - - - - . r?a i
`
`G')
`:n 2.8-r------------------~
`m
`-::0
`S2 2.4 I
`m
`~1'1-ll·h-RIA
`m 2.0 i
`V/&'\"E!Iil<'•:z-
`0
`~''t~~Lr ··:1.'-l-'
`1.6 1
`:=m. :r:::t--::::l=m~
`1.2 1
`~::a:·: ..
`0.8 \ Vhf''A"'·'I"'.!.".V,N::)'!l I @':S' \):'.y;.l%'\:t=i'll I pm;ell')-:'f.':VN::ll/l I
`WILD TYPE
`Gly12Cys
`Gly12Ser
`j
`
`fWSl')o;.)•,Y.:N=J11 I
`
`V~'Sn\•.t•.II.!:.)!;VA I
`
`Gly12Arg
`
`Gly12Asp
`
`f:i®B:•J.··h'=U>Fl/A I
`
`Gly13Asp
`
`GCTGGTGGCGTA
`
`GCTGGTGGCGTA
`A
`
`:\I\
`I 'I I
`.. I r.
`G C T G G T G G CCG T A
`T
`
`f'./\
`. ,,
`.. l•, I
`G c T G G TGGG c G TA I WT
`
`\
`
`Hut
`
`A
`
`,
`:q'
`i\11
`,\_,.,
`GCTGGTGGCGTAIWT
`Mut
`~
`
`Case 1:16-cv-01112-WO-JEP Document 1-2 Filed 09/07/16 Page 7 of 21
`
`Page 6 of 20
`
`

`

`FIG. 3
`
`~
`00
`•
`~
`~
`~
`
`~ = ~
`
`z 0
`
`~
`N
`
`~
`
`N
`
`0 ....
`
`0
`
`140-
`100-
`
`60-
`
`20-
`
`- c-Ki-Ras
`
`PCR PRODUCT
`
`NON-SPECIFIC
`PRODUCTS
`
`('D
`('D
`
`rFJ =(cid:173)
`.....
`Ul
`0 .....
`-....l
`
`d
`rJl
`-....l
`Oo
`N
`~
`Oo
`00
`
`\C = N
`
`Case 1:16-cv-01112-WO-JEP Document 1-2 Filed 09/07/16 Page 8 of 21
`
`Page 7 of 20
`
`

`

`~
`00
`•
`~
`~
`~
`
`~ = ~
`
`z 0
`
`~
`
`~
`N
`N
`
`0 ....
`
`0
`
`rFJ =(cid:173)
`('D a
`0\
`0 .....
`-....l
`
`d
`rJl
`-....l
`Oo
`N
`~
`Oo
`00
`
`\C = N
`
`FIG. 4
`
`GCTGGTGGCGTA
`
`GCTGATGGCGTA
`
`Gly13Asp
`
`/\ ,,
`! ·,1 \
`! '-1
`AJ..
`G c T G T G G c G T A I WT
`Mux
`A
`
`GCTGGTGACGTA
`
`GCTGGTGGCGTA
`
`G c T G G T G c G T A I WT
`
`A
`
`Mux
`
`Case 1:16-cv-01112-WO-JEP Document 1-2 Filed 09/07/16 Page 9 of 21
`
`Page 8 of 20
`
`

`

`U.S. Patent
`
`Nov.2,2010
`
`Sheet 7 of7
`
`US 7,824,889 B2
`
`FIG. 5
`
`We 11 Ell
`
`WT
`.._ ___ ~_.IMux
`
`Wel I ll2
`
`Case 1:16-cv-01112-WO-JEP Document 1-2 Filed 09/07/16 Page 10 of 21
`
`Page 9 of 20
`
`

`

`1
`DIGITAL AMPLIFICATION
`
`2
`SUMMARY OF THE INVENTION
`
`US 7,824,889 B2
`
`This application is a continuation of U.S. application Ser.
`No. 10/828,295 filed Apr. 21,2004, which is a divisional of
`U.S. application Ser. No. 09/981,356 filed Oct. 12,2001, now
`U.S. Pat. No. 6,753,147, which is a continuation of U.S.
`application Ser. No. 09/613,826 filed Jul. 11, 2000, now U.S.
`Pat. No. 6,440,706, which claims the benefit of provisional
`U.S. Application Ser. No. 60/146,792, filedAug. 2, 1999. The
`disclosure of all priority applications is expressly incorpo- 10
`rated herein.
`The U.S. government retains certain rights in this invention
`by virtue of its support of the underlying research, supported
`by grants CA 43460, CA 57345, and CA 62924 from the
`National Institutes of Health.
`
`TECHNICAL FIELD OF THE INVENTION
`
`This invention is related to diagnostic genetic analyses. In
`particular it relates to detection of genetic changes and gene
`expression.
`
`BACKGROUND OF THE INVENTION
`
`20
`
`It is an object of the present invention to provide methods
`for determining the presence of a selected genetic sequence in
`a population of genetic sequences.
`It is another object of the present invention to provide
`molecular beacon probes useful in the method of the inven(cid:173)
`tion.
`These and other objects of the invention are achieved by
`providing a method for determining the presence of a selected
`genetic sequence in a population of genetic sequences. A
`biological sample comprising nucleic acid template mol(cid:173)
`ecules is diluted to form a set of assay samples. The template
`molecules within the assay samples are amplified to form a
`15 population of amplified molecules in the assay samples of the
`set. The amplified molecules in the assay samples of the set
`are then analyzed to determine a first number of assay
`samples which contain the selected genetic sequence and a
`second number of assay samples which contain a reference
`genetic sequence. The first number is then compared to the
`second nnmber to ascertain a ratio which reflects the compo-
`sition of the biological sample.
`Another embodiment of the invention is a method for deter(cid:173)
`mining the ratio of a selected genetic sequence in a population
`25 of genetic sequences. Template molecules within a set com(cid:173)
`prising a plurality of assay samples are amplified to form a
`population of amplified molecules in each of the assay
`samples of the set. The amplified molecules in the assay
`samples of the set are analyzed to determine a first number of
`30 assay samples which contain the selected genetic sequence
`and a second number of assay samples which contain a ref(cid:173)
`erence genetic sequence. At least one-fiftieth of the assay
`samples in the set comprise a number (N) of molecules such
`that 1/N is larger than the ratio of selected genetic sequences
`35 to total genetic sequences required to determine the presence
`of the selected genetic sequence. The first number is com(cid:173)
`pared to the second nnmber to ascertain a ratio which reflects
`the composition of the biological sample.
`According to another embodiment of the invention, a
`40 molecular beacon probe is provided. It comprises an oligo(cid:173)
`nucleotide with a stem-loop structure having a photolnmines(cid:173)
`centdye at one of the 5' or3' ends and a quenching agent at the
`opposite 5' or 3' end. The loop consists of 16 base pairs which
`has aT m of 50-51 DC. The stem consists of 4 base pairs having
`45 a sequence 5'-CACG-3'.
`A second type of molecular beacon probe is provided in
`another embodiment. It comprises an oligonucleotide with a
`stem-loop structure having a photolnminescent dye at one of
`the 5' or 3' ends and a quenching agent at the opposite 5' or 3'
`50 end. The loop consists of 19-20 base pairs and has a T m of
`54-56DC. The stem consists of 4 base pairs having a
`sequence 5'-CACG-3'.
`Another embodiment provides the two types of molecular
`beacon probes, either mixed together or provided in a divided
`55 container as a kit.
`The invention thus provides the art with the means to obtain
`quantitative assessments of particular DNA or RNA
`sequences in mixed populations of sequences using digital
`(binary) signals.
`
`In classical genetics, only mutations of the germ-line were
`considered important for understanding disease. With the
`realization that somatic mutations are the primary cause of
`cancer, and may also play a role in aging, new genetic prin(cid:173)
`ciples have arisen. These discoveries have provided a wealth
`of new opportunities for patient management as well as for
`basic research into the pathogenesis of neoplasia. However,
`many of these opportunities hinge upon detection of a small
`number of mutant-containing cells among a large excess of
`normal cells. Examples include the detection of neoplastic
`cells in urine, stool, and sputum of patients with cancers of the
`bladder, colorectnm, and lung, respectively. Such detection
`has been shown in some cases to be possible at a stage when
`the primary tumors are still curable and the patients asymp(cid:173)
`tomatic. Mutant sequences from the DNA of neoplastic cells
`have also been found in the blood of cancer patients. The
`detection of residual disease in lymph nodes or surgical mar(cid:173)
`gins may be useful in predicting which patients might benefit
`most from further therapy. From a basic research standpoint,
`analysis of the early effects of carcinogens is often dependent
`on the ability to detect small populations of mutant cells.
`Because of the importance of this issue in so many settings,
`many useful techniques have been developed for the detection
`of mutations. DNA sequencing is the gold standard for the
`detection of germ line mutations, but is useful only when the
`fraction of mutated alleles is greater than -20%. Mutant(cid:173)
`specific oligonucleotides can sometimes be used to detect
`mutations present in a minor proportion of the cells analyzed,
`but the signal to noise ratio distinguishing mutant and wild(cid:173)
`type (WT) templates is variable. The use of mutant-specific
`primers or the digestion of polymerase chain reaction (PCR)
`products with specific
`restriction endonucleases are
`extremely sensitive methods for detecting such mutations, but
`it is difficult to quantitate the fraction of mutant molecules in
`the starting population with these techniques. Other innova- 60
`tive approaches for the detection of somatic mutations have
`been reviewed. A general problem with these methods is that
`it is difficult or impossible to independently confirm the exist(cid:173)
`ence of any mutations that are identified.
`Thus there is a need in the art for methods for accurately 65
`and quantitatively detecting genetic sequences in mixed
`populations of sequences.
`
`BRIEF DESCRIPTION OF THE DRAWINGS
`
`FIGS. lA, lB, lC. Schematic of experimental design.
`(FIG.lA) The basic two steps involved: PCR on diluted DNA
`samples is followed by addition of fluorescent probes which
`discriminate between WT and mutant alleles and subsequent
`fluorometry. (FIG. lB) Principle of molecular beacon analy-
`
`Case 1:16-cv-01112-WO-JEP Document 1-2 Filed 09/07/16 Page 11 of 21
`
`Page 10 of 20
`
`

`

`US 7,824,889 B2
`
`4
`sequence ofWT c-Ki-Ras in well Kl (SEQ ID NO: 7), and
`mutant c-Ki-Ras in wells ClO, Ell, MlO, and L12 (SEQ ID
`NO: 14), and well F21 (SEQ ID NO: 15) were analyzed.
`
`DETAILED DESCRIPTION OF THE INVENTION
`
`5
`
`3
`sis. In the stem -loop configuration, fluorescence from a dye at
`the 5' end of the oligonucleotide probe is quenched by a
`Dabcyl group at the 3' end. Upon hybridization to a template,
`the dye is separated from the quencher, resulting in increased
`fluorescence. Modified from Marras et a!. (FIG. lC) Oligo-
`nucleotide design. Primers F 1 and Rl are used to amplifY the
`genomic region of interest. Primer INT is used to produce
`single stranded DNA from the original PCR products during
`a subsequent asymmetric PCR step (see Materials and Meth(cid:173)
`ods). MB-RED is a Molecular Beacon which detects any 10
`appropriate PCR product, whether it is WT or mutant at the
`queried codons. MB-GREEN is a Molecular Beacon which
`preferentially detects the WT PCR product.
`FIG. 2. Discrimination between WT and mutant PCR prod(cid:173)
`ucts by Molecular Beacons. Ten separate PCR products, each 15
`generated from -25 genome equivalents of genomic DNA of
`cells containing the indicated mutations of c-Ki-Ras, were
`analyzed with the Molecular Beacon probes described in the
`text. Representative examples of the PCR products used for
`Molecular Beacon analysis were purified and directly 20
`sequenced. In the cases with Glyl2Cys (SEQ ID NO: 11) and
`Glyl2Arg (SEQ ID NO: 10) mutations, contaminating non(cid:173)
`neoplastic cells within the tumor presumably accounted for
`the relatively low ratios. In the cases with Glyl2Ser (SEQ ID
`NO: 8) and Glyl2Asp (SEQ ID NO: 12), there were appar- 25
`ently two or more alleles of mutant c-Ki-Ras for every WT
`allele (SEQ ID NO: 7); both these tumors were aneuploid.
`Analysis of the Glyl3Asp mutation is also shown (SEQ ID
`NO: 9).
`FIG. 3. Detecting Dig-PCR products with MB-RED. Spe- 30
`cific Fluorescence Units of representative wells from an
`experiment employing colorectal cancer cells with Glyl2Asp
`or Glyl3Asp mutations of the c-Ki-Ras gene. Wells with
`values > 10,000 are shaded yellow. Polyacrylamide gel elec(cid:173)
`trophoretic analyses of the PCR products from selected wells 35
`are shown. Wells with fluorescence values <3 500 had no PCR
`product of the correct size while wells with fluorescence
`values > 10,000 SFU always contained PCR products of 129
`bp. Non-specific products generated during the large number
`of cycles required for Dig-PCR did not affect the fluorescence
`analysis. Ml and M2 are molecular weight markers used to
`determine the size of fragments indicated on the left (in base
`pairs).
`FIG. 4. Discriminating WT from mutant PCR products
`obtained in Dig-PCR. RED/GREEN ratios were determined 45
`from the fluorescence of MB-RED and MB-GREEN as
`described in Materials and Methods. The wells shown are the
`same as those illustrated in FIG. 3. The sequences of PCR
`products from the indicated wells were determined as
`described in Materials and Methods. The wells with RED/ 50
`GREEN ratios >3.0 each contained mutant sequences while
`those with RED/GREEN ratios of -1.0 contained WT
`sequences. WT c-Ki-Ras (SEQ ID NO: 7), Glyl2Asp (SEQ
`ID NO: 13), and Glyl3Asp (SEQ ID NO: 9) were analyzed.
`FIG. 5. Dig-PCR of DNA from a stool sample. The 384
`wells used in the experiment are displayed. Those colored
`blue contained 25 genome equivalents of DNA from normal
`cells. Each of these registered positive with MB-RED and the
`RED/GREEN ratios were 1.0+/-0.1 (mean +1-1 standard
`deviation). The wells colored yellow contained no template
`DNA and each was negative with MB-RED (i.e., fluorescence
`<3 500 fluorescence units.). The other wells contained diluted
`DNA from the stool sample. Those registering as positive
`with MB-RED were colored either red or green, depending on
`their RED/GREEN ratios. Those registering negative with
`MB-RED were colored white. PCR products from the indi(cid:173)
`cated wells were used for automated sequence analysis. The
`
`The method devised by the present inventors involves sepa-
`rately amplifYing small numbers of template molecules so
`that the resultant products have a proportion of the analyte
`sequence which is detectable by the detection means chosen.
`At its limit, single template molecules can be amplified so that
`the products are completely mutant or completely wild-type
`(WT). The homogeneity of these amplification products
`makes them trivial to distinguish through existing techniques.
`The method requires analyzing a large number of amplified
`products simply and reliably. Techniques for such assess(cid:173)
`ments were developed, with the output providing a digital
`readout of the fraction of mutant alleles in the analyzed popu(cid:173)
`lation.
`The biological sample is diluted to a point at which a
`practically usable number of the diluted samples contain a
`proportion of the selected genetic sequence ( analyte) relative
`to total template molecules such that the analyzing technique
`being used can detect the analyte. A practically usable num(cid:173)
`ber of diluted samples will depend on cost of the analysis
`method. Typically it would be desirable that at least 1/so of the
`diluted samples have a detectable proportion of analyte. At
`least 1/Jo, 1/s, 3/Jo, 2/s, lf2, 3/s, 7/w, 'Vs, or 9/Jo of the diluted
`samples may have a detectable proportion of analyte. The
`higher the fraction of samples which will provide useful
`information, the more economical will be the overall assay.
`Over-dilution will also lead to a loss of economy, as many
`samples will be analyzed and provide no signal. A particu(cid:173)
`larly preferred degree of dilution is to a point where each of
`the assay samples has on average one-half of a template. The
`dilution can be performed from more concentrated samples.
`Alternatively, dilute sources of template nucleic acids can be
`used. All of the samples may contain amplifiable template
`molecules. Desirably each assay sample prior to amplifica-
`40 tion will contain less than a hundred or less than ten template
`molecules.
`Digital amplification can be used to detect mutations
`present at relatively low levels in the samples to be analyzed.
`The limit of detection is defined by the number of wells that
`can be analyzed and the intrinsic mutation rate of the poly(cid:173)
`merase used for amplification. 384 well PCR plates are com-
`mercially available and 1536 well plates are on the horizon,
`theoretically allowing sensitivities for mutation detection at
`the -0.1% level. It is also possible that Digital Amplification
`can be performed in microarray format, potentially increas(cid:173)
`ing the sensitivity by another order of magnitude. This sen-
`sitivity may ultimately be limited by polymerase errors. The
`effective error rate in PCR as performed under our conditions
`was 1.1%, i.e., four out of351 PCR products derived from
`55 WT DNA sequence appeared to contain a mutation by RED/
`GREEN ratio criteria. However, any individual mutation
`(such as a G toT transversion at the second position of codon
`12 of c-Ki-Ras), are expected to occur in <1 in 50 of these
`polymerase-generated mutants (there are at least 50 base
`60 substitutions within or surrounding codons 12 and 13 that
`should yield high RED/GREEN ratios). Determining the
`sequence of the putative mutants in the positive wells, by
`direct sequencing as performed here or by any of the other
`techniques, provides unequivocal validation of a prospective
`65 mutation: a significant fraction of the mutations found in
`individual wells should be identical if the mutation occurred
`in vivo. Significance can be established through rigorous
`
`Case 1:16-cv-01112-WO-JEP Document 1-2 Filed 09/07/16 Page 12 of 21
`
`Page 11 of 20
`
`

`

`US 7,824,889 B2
`
`5
`statistical analysis, as positive signals should be distributed
`according to Poisson probabilities. Moreover, the error rate in
`particular Digital Amplification experiments can be precisely
`determined through performance of Digital Amplification on
`DNA templates from normal cells.
`Digital Amplification is as easily applied to RT-PCR prod(cid:173)
`ucts generated from RNA templates as it is to genomic DNA.
`For example, the fraction of alternatively spliced or mutant
`transcripts from a gene can be easily determined using pho(cid:173)
`toluminescent probes specific for each of the PCR products
`generated. Similarly, Digital Amplification can be used to
`quantitate relative levels of gene expression within an RNA
`population. For this amplification, each well would contain
`primers which are used to amplify a reference transcript
`expressed constitutively as well as primers specific for the
`experimental transcript. One photoluminescent probe would
`then be used to detect PCR products from the reference tran(cid:173)
`script and a second photoluminescent probe used for the test
`transcript. The number of wells in which the test transcript is
`amplified divided by the number of wells in which the refer(cid:173)
`ence transcript is amplified provides a quantitative measure of
`gene expression. Another group of examples involves the
`investigations of allelic status when two mutations are
`observed upon sequence analysis of a standard DNA sample.
`To distinguish whether one variant is present in each allele
`(vs. both occurring in one allele), cloning ofPCR products is
`generally performed. The approach described here would
`simplifY the analysis by eliminating the need for cloning.
`Other potential applications of Digital Amplification are
`listed in Table 1. When the goal is the quantitation of the
`proportion of two relatively common alleles or transcripts
`rather than the detection of rare alleles, techniques such as
`those employing TaqMan and real time PCR provide an
`excellent alternative to use of molecular beacons. Advantages
`of real time PCR methods include their simplicity and the
`ability to analyze multiple samples simultaneously. However,
`Digital Amplification may prove useful for these applications
`when the expected differences are small, (e.g., only -2-fold,
`such as occurs with allelic imbalances.)
`
`TABLE 1
`
`Potential Applications ofDig-PCR
`
`Application
`
`Example
`
`Probe 1
`Detects:
`
`Probe 2 Detects:
`
`Base
`Cancer gene mutations mutant or WT PCR products
`in stool, blood,
`substitution
`WT alleles
`lymph nodes
`mutations
`Chromosomal Residual leukemia
`translocations
`cells after therapy
`(DNA or RNA)
`Determine presence
`or extent of
`amplification
`
`Gene
`amplifi-
`cations
`
`normal or
`trans! ocated
`alleles
`sequence
`within
`arnplicon
`
`translocated allele
`
`sequence from
`another part of
`same chromosome
`arm
`common exons
`
`6
`The ultimate utility of Digital Amplification lies in its
`ability to convert the intrinsically exponential nature ofPCR
`to a linear one. It should thereby prove useful for experiments
`requiring the investigation of individual alleles, rare variants/
`mutations, or quantitative analysis of PCR products.
`In one preferred embodiment each diluted sample has on
`average one half a template molecule. This is the same as one
`half of the diluted samples having one template molecule.
`This can be empirically determined by amplification. Either
`10 the analyte (selected genetic sequence) or the reference
`genetic sequence can be used for this determination. If the
`analysis method being used can detect analyte when present
`at a level of20%, then one must dilute such that a significant
`number of diluted assay samples contain more than 20% of
`15 analyte. If the analysis method being used requires 100%
`analyte to detect, then dilution down to the single template
`molecule level will be required.
`To achieve a dilution to approximately a single template
`molecule level, one can dilute such that between 0.1 and 0.9
`20 of the assay samples yield an amplification product. More
`preferably the dilution will be to between 0.1 and 0.6, more
`preferably to between 0.3 and 0.5 of the assay samples yield(cid:173)
`ing an amplification product.
`The digital amplification method requires analysis of a
`25 large number of samples to get meaningful results. Preferably
`at least ten diluted assay samples are amplified and analyzed.
`More preferably at least 15, 20, 25, 30, 40, 50, 75, 100, 500,
`or 1000 diluted assay samples are amplified and analyzed. As
`in any method, the accuracy of the determination will
`30 improve as the number of samples increases, up to a point.
`Because a large number of samples must be analyzed, it is
`desirable to reduce the manipulative steps, especially sample
`transfer steps. Thus it is preferred that the steps of amplifying
`and analyzing are performed in the same receptacle. This
`35 makes the method an in situ, or "one-pot" method.
`The number of different situations in which the digital
`amplification method will find application is large. Some of
`these are listed in Table 1. As shown in the examples, the
`method can be used to find a tumor mutation in a population
`40 of cells which is not purely tumor cells. As described in the
`examples, a probe for a particular mutation need not be used,
`but diminution in binding to a wild-type probe can be used as
`an indicator of the presence of one or more mutations. Chro-
`mosomal translocations which are characteristic ofleukemias
`or lymphomas can be detected as a measure of the efficacy of
`therapy. Gene amplifications are characteristic of certain dis(cid:173)
`ease states. These can be measured using digital amplifica(cid:173)
`tion. Alternatively spliced forms of a transcript can be
`detected and quantitated relative to other forms of the tran(cid:173)
`script using digital amplification on eDNA made from
`mRNA. Similarly, using eDNA made from mRNA one can
`determine relative levels of transcription of two different
`genes. One can use digital amplification to distinguish
`between a situation where one allele carries two mutations
`and one mutation is carried on each of two alleles in an
`individual. Allelic imbalances often result from a disease
`state. These can be detected using digital amplification.
`Biological samples which can be used as the starting mate(cid:173)
`rial for the analyses may be from any tissue or body sample
`from which DNA or mRNA can be isolated. Preferred sources
`include stool, blood, and lymph nodes. Preferably the bio(cid:173)
`logical sample is a cell-free lysate.
`Molecular beacon probes according to the present inven(cid:173)
`tion can utilize any photoluminescent moiety as a detectable
`moiety. Typically these are dyes. Often these are fluorescent
`dyes. Photoluminescence is any process in which a