throbber
Declaration of Cynthia Casson Morton
`In re: Chuu, et al., USPN 8,318,430
` 
`
`
`
`IN THE UNITED STATES PATENT AND TRADEMARK OFFICE
`
`In re Patent of: Chuu, et al.
`U.S. Patent No.: 8,318,430, claims 1-18
`Issue Date: 27 November 2012
`U.S. Serial No.: 13/368,035
`Filing Date: 7 February 2012
`
`Title: METHODS OF FETAL ABNORMALITY DETECTION
`
`
`I, Cynthia Casson Morton, declare as follows:
`Credentials
`
`1) Currently I hold the position of William Lambert Richardson Professor in the Department
`
`of Obstetrics, Gynecology and Reproductive Biology at Harvard Medical School. I am
`
`also a Professor in the Department of Pathology at Harvard Medical School and the
`
`Director of Cytogenetics at Brigham and Women's Hospital.
`
`
`
`2) I received my B.S. in Biology from The College of William and Mary and my Ph.D. in
`
`Human Genetics from the Medical College of Virginia.
`
`
`
`3) I am board-certified by the American Board of Medical Genetics in PhD Medical
`
`Genetics, Clinical Cytogenetics and Clinical Molecular Genetics. I have received
`
`numerous awards including the Warner-Lambert/Parke-Davis Award of the American
`
`Society of Investigative Pathology. I am the recent past Editor of The American Journal
`
`of Human Genetics and serve/have served on the Editorial Boards of the American
`
` 
`
`1
`
`Ariosa Exhibit 1002, pg. 1
`IPR2013-00276
`
`

`
`Declaration of Cynthia Casson Morton
`In re: Chuu, et al., USPN 8,318,430
` 
`
`Journal of Medical Genetics, Genomics, Journal of Experimental Zoology, Genes,
`
`Chromosomes and Cancer, American Journal of Human Genetics, Human Genetics,
`
`International Journal of Clinical and Experimental Pathology, The Application of
`
`Clinical Genetics, Audiology and Neurotology, International Journal of Women’s Health,
`
`and Cancer Management and Research. I also serve on various scientific/medical
`
`committees, including the Board of Directors of the American Society of Human
`
`Genetics, the Council of Scientific Trustees of the Hearing Health Foundation and the
`
`Genomic Medicine Program Advisory Committee for the Veteran's Administration.
`
`
`
`4) I have published over 260 peer-reviewed manuscripts in the field of obstetrics,
`
`reproductive biology, auditory science and human medical genetics, serve as an editor of
`
`the book Current Protocols in Human Genetics and have contributed fourteen book
`
`chapters. In addition, I am an author of over 280 abstracts presented at various scientific
`
`meetings worldwide.
`
`
`
`5) I consider myself to be well-versed in the field of medical genetics, including prenatal
`
`diagnostics. My research interests include the biology of uterine leiomyomata, the
`
`biology of hearing and deafness, gene mapping and clinical and molecular cytogenetics.
`
`I have been the Director of a clinical cytogenetics laboratory since 1987, and have had
`
`long-term involvement in prenatal diagnostics. I am knowledgeable with all major
`
`developments in the field. I am the senior author on a recent publication of the first use
`
`of whole genome sequencing in the prenatal setting for diagnosis of a genetic syndrome
`
` 
`
`2
`
`Ariosa Exhibit 1002, pg. 2
`IPR2013-00276
`
`

`
`Declaration of Cynthia C asson Morton
`In re: Chuu, et al., USPN 8,318,430
`
`(N. Engl. J. Med., 367:2226-32 (2012)). My curriculum vitae is attached hereto as
`Exhibit 1014
`Morton Exhibit A.
`
`6)
`
`I have reviewed and am familiar with the following documents: U.S. Patent No.
`
`8,318,430 to Chuu et al.
`
`(“the ‘430 patent”, Petition Exhibit 1001); U.S. Pat No.
`
`l-l0B2L);k(U.S. Patent Publication
`7,332,277 to Dhallan (“Dhallan”, Petition Exhibit
`2007/0202525 to Quake and Fan (“Quake”, Petition Exhibit ~l-€I)(;i)3'L)’);koU.S. Patent
`Publication 2008/0090239 to Shoemaker, et al., (“Shoemaker”, Petition Exhibit
`Craig et al. Nat Methods. 2008 October; 5(10): 887-893 (“Craig”, Petition Exhibit
`
`:/;.
`
`Binladen et al., PLoS ONE. 2007 Feb 14;2(2):e197 (“Binladen”, Petition Exhibit 1006);
`
`Complaint filed in Verinata Health, Inc. et al. v. Ariosa Diagnostics, Inc. et al., Civil
`
`Action No. 12--05501-SI (N .D. Cal) ( ); Patent Owner’s opposition to
`
`motion to dismiss in Verinata v. Ariosa
`
`'_l‘__echnical Background: Selective Enrichment and Seguencing Technigues
`
`7) Deoxyribonucleic acid, or “DNA” is the material that transfers genetic characteristics in
`
`all higher organisms. DNA is constructed of two nucleotide strands coiled around each
`
`other in a ladder—like arrangement called a double helix, with the internal rungs of the
`
`helix being formed by pairs of nucleotides, or “bases”. DNA is further organized into
`
`larger structures called chromosomes, and the full set of chromosomes in an organism is
`
`referred to as that organism’s genome. The genome represents the basis for all the
`
`inheritable traits of an organism, and the order of bases in the DNA of the genome forms
`
`Ariosa Exhibit 1002, pg. 3
`|PR2013—OO276
`
`Ariosa Exhibit 1002, pg. 3
`IPR2013-00276
`
`

`
`Declaration of Cynthia Casson Morton
`In re: Chuu, et al., USPN 8,318,430
` 
`
`the blueprint for all biological functions of the organism. (Generally, see Collins, et al.,
`
`Nature, 422:835-47 (2003), Morton Exhibit B).
`
`
`
`8) Over the past two decades, scientists working in the disciplines of genetics and genomics
`
`have determined the sequence of genes from the genomes of many organisms, as well as
`
`determined the entire sequence of an organism’s genome. (Collins 2003, supra, Morton
`
`Exhibit B) In doing so, for example, the sequences of genes from different individuals of
`
`the same species can be compared and the sequences of genes from different species can
`
`be compared. (Collins 2003, supra, Morton Exhibit B) Although it is of scientific
`
`interest to look at entire genomes, very often it is desirable to look at only selected
`
`regions in a genome. Because the genome of an organism is very large compared to
`
`selected regions of interest such as genes, in order to be able to analyze only selected
`
`regions it is usually necessary to increase the amount of the selected regions of interest in
`
`comparison to the rest of the sample, to isolate the selected regions of interest from the
`
`rest of the sample, or to do both (Erlich, et al., Science, 252(5013):1643-51 (1991),
`
`Morton Exhibit C).
`
`
`
`9) Enrichment of selected nucleic acids in a sample—that is, enrichment of selected regions
`
`of interest as compared to the rest of the genome—can be performed by any method that
`
`results in an increased copy number of the selected nucleic acids relative to the other
`
`nucleic acids in the sample. A common feature of all selective enrichment techniques is
`
`the hybridization of sequence-specific segments of DNA to the selected nucleic acids.
`
`Commonly used methods for selectively enriching nucleic acids are selective
`
` 
`
`4
`
`Ariosa Exhibit 1002, pg. 4
`IPR2013-00276
`
`

`
`Declaration of Cynthia Casson Morton
`In re: Chuu, et al., USPN 8,318,430
` 
`
`amplification techniques, including linear amplification or exponential amplification.
`
`Both of these selective amplification methods result in an increase in copy number of the
`
`selected nucleic acids originally found in the sample. This increase in copy number of
`
`the selected nucleic acid regions facilitates analysis by increasing the amount of material
`
`available for such analysis.
`
`
`10) A first example of selective amplification is polymerase chain reaction (“PCR”)
`
`amplification, which can increase the copy number of the selected nucleic acids into
`
`millions of copies. (Erlich 1991, supra, Morton Exhibit C) The PCR amplification
`
`method relies on thermal cycling—cycles of repeated heating and cooling of the sample
`
`nucleic acids to denature and enzymatically replicate the selected nucleic acids. In the
`
`amplification process, the sequence-specific segments of DNA used to hybridize to the
`
`selected nucleic acids are generally referred to as “primers.” (Erlich 1991, supra, Morton
`
`Exhibit C) Once the primers are allowed to hybridize to the selected nucleic acids, a
`
`reaction is carried out using a heat-stable DNA polymerase to extend the primer along the
`
`length of the selected nucleic acids. (Erlich 1991, supra, Morton Exhibit C) After a
`
`period of time—typically minutes—the polymerization or copying process is halted by
`
`cooling the reaction, then the reaction is initiated once more by heating. As this cycle of
`
`heating and cooling is repeated, copies of the selected nucleic acids that are generated in
`
`each cycle are themselves copied in subsequent cycles, setting in motion a cyclical
`
`reaction in which the selected nucleic acids are amplified exponentially. (Erlich 1991,
`
`supra, Morton Exhibit C)
`
`
`
` 
`
`5
`
`Ariosa Exhibit 1002, pg. 5
`IPR2013-00276
`
`

`
`Declaration of Cynthia Casson Morton
`In re: Chuu, et al., USPN 8,318,430
` 
`
`11) Another example of selective amplification is rolling circle amplification (“RCA”). In
`
`RCA, the sequence-specific primer hybridizes to a selected nucleic acid, and the free end
`
`of the primer anneals to a small circular DNA template. (Generally, see Lizardi, et al.,
`
`Nature Genetics, 19 July 1998:225-32, Morton Exhibit D) A DNA polymerase is added
`
`to extend the primer to copy the selected nucleic acid. The DNA polymerase extends the
`
`primer continuously around the circular DNA template generating a long DNA product
`
`that consists of many repeated copies of the selected nucleic acid. By the end of the
`
`reaction, the polymerase generates many thousands of copies of the selected nucleic acid,
`
`with the chain of copies tethered to the original target DNA. (Lizardi 1998, supra,
`
`Morton Exhibit D) RCA allows for spatial resolution of the selected nucleic acid and
`
`rapid amplification of signal. RCA can result in a linear amplification process, or the use
`
`of forward and reverse primers can change a linear RCA reaction into an exponential
`
`process. (Lizardi 1998, supra, Morton Exhibit D)
`
`
`
`12) The selective amplification methods described in ¶¶ 10 and 11, above, are but two
`
`examples of selective enrichment of nucleic acids through amplification. Since the
`
`advent of PCR in the late 1980s, many variations of selective amplification have been
`
`developed, most of which rely on sequence-specific primers and on thermal cycling.
`
`Such additional selective amplification methods
`
`include strand displacement
`
`amplification (SDA) (see U.S. Pat. Nos. 5,270,184; and 5,422,252, Morton Exhibits E
`
`and F), transcription-mediated amplification (TMA) (see U.S. Pat. No. 5,399,491, Morton
`
`Exhibit G), linked linear amplification (LLA) (see U.S. Pat. No. 6,027,923, Morton
`
`Exhibit H), self-sustained sequence replication (see Guatelli et al., Proc. Nat. Acad. Sci.
`
` 
`
`6
`
`Ariosa Exhibit 1002, pg. 6
`IPR2013-00276
`
`

`
`Declaration of Cynthia Casson Morton
`In re: Chuu, et al., USPN 8,318,430
` 
`
`USA, 87, 1874 (1990), Morton Exhibit I), consensus sequence primed polymerase chain
`
`reaction (CP-PCR) (see U.S. Pat. No. 5,437,975, Morton Exhibit J), and isothermal
`
`amplification methods such as SDA (see Walker et al., Nucleic Acids Res. 20(7):1691-6
`
`(1992), Morton Exhibit K).
`
`13) When performing selective amplification methods, it is generally desirable to be able to
`
`selectively amplify more than one selected nucleic acid from a sample at a time, a
`
`technique referred to as multiplexing. (For a review, see Fan, et al., Nature Reviews
`
`Genetics, 7:632-44) (2006), Morton Exhibit L) In multiplexed amplification such as
`
`multiplex PCR, multiple sequence-specific primer sets are used in a single reaction to
`
`amplify multiple selected nucleic acids from a sample. Multiplex PCR was first
`
`described in 1988 as a method to detect deletions in the DMD gene (Chamberlain, et al.,
`
`Nuc. Acids Res., 16(23):11141-56 (1988), Morton Exhibit M), and has since been used
`
`ubiquitously in genetic research for such applications as pathogen identification, forensic
`
`studies, mutation analysis, linkage analysis, single nucleotide polymorphism genotyping,
`
`and paternity analysis (Edwards and Gibbs, PCR Methods and Applications, 3:S65-S75
`
`(1994), Morton Exhibit N and Fan 2006, supra, Morton Exhibit L). Commercial
`
`multiplexing kits for PCR are widely available. Multiplexing can also refer to selective
`
`amplification and analysis of nucleic acids from multiple samples, in which the samples
`
`are combined prior to sequencing and analysis.
`
`
`
`14) A second method for selective enrichment of nucleic acids from a sample is hybridization
`
`followed by separation of the hybridized nucleic acids from non-hybridized nucleic. In
`
`such selective hybridization techniques, the sequence-specific segments of DNA used to
`
` 
`
`7
`
`Ariosa Exhibit 1002, pg. 7
`IPR2013-00276
`
`

`
`Declaration of Cynthia Casson Morton
`In re: Chuu, et al., USPN 8,318,430
` 
`
`hybridize to the selected nucleic acids are generally referred to as “probes”, and in many
`
`methods the probes are immobilized on a planar surface (often referred to as an array) or
`
`to a bead or other solid support. (See, e.g., Chetverin and Kramer, BioTechnology,
`
`12:1093-99 (1994), Morton Exhibit O.) The sequences of the probes are chosen to
`
`hybridize specifically with selected nucleic acids from the sample, while other nucleic
`
`acids in the sample do not hybridize to the probes. (Chetverin and Kramer 1994, supra,
`
`Morton Exhibit O) Because the probes are immobilized, the selected nucleic acids that
`
`hybridize to them will be immobilized as well, and can be separated from the
`
`unhybridized nucleic acids that are in solution. (Chetverin and Kramer 1994, supra,
`
`Morton Exhibit O)
`
`
`
`15) An additional method for selective enrichment combines the techniques of selective
`
`amplification and selective hybridization, in which selected nucleic acids from a sample
`
`are first amplified using sequence-specific primers, and where the sequence-specific
`
`primers also serve as probes to immobilize the amplification products for separation from
`
`the remaining nucleic acids in a sample. (Fan 2006, supra, Morton Exhibit L) The
`
`combination of selective amplification and hybridization allows isolation of highly-
`
`enriched selected nucleic acids from a nucleic acid sample containing, e.g., the DNA
`
`from an entire genome. The combination of selective amplification and hybridization are
`
`described, for example, in Fan 2006, supra (Morton Exhibit L).
`
`
`16) Once selected nucleic acids have been enriched, they typically are analyzed by, e.g.,
`
`DNA sequencing. The goal of sequencing DNA is to determine the order of bases of the
`
`selected nucleic acids. Within the past 6-7 years, “massively parallel sequencing” (also
`
` 
`
`8
`
`Ariosa Exhibit 1002, pg. 8
`IPR2013-00276
`
`

`
`Declaration of Cynthia Casson Morton
`In re: Chuu, et al., USPN 8,318,430
` 
`
`known as “next generation sequencing” or “NGS”), has been developed and become
`
`commercially available (see reviews of next generation sequencing technologies in
`
`Metzker, Nature Reviews, 11:31-46 (2010), Morton Exhibit P, and Kircher and Kelso,
`
`Bioessays, 32:524-36 (2010), Morton Exhibit Q). Massively parallel sequencing enables
`
`extremely accurate single molecule counting of literally millions of molecules in parallel,
`
`which allows one to both determine the sequence of selected nucleic acids and quantify
`
`the number of copies of the selected nucleic acids in the amplified mixture. (Metzker
`
`2010, and Kircher and Kelso 2010, supra, Morton Exhibits P and Q) Massively parallel
`
`sequencing methods and systems include pyrosequencing methods, as commercialized by
`
`454 Life Sciences; sequencing-by-ligation methods, as commercialized in the SOLiD™
`
`technology from Life Technologies, Inc. and by Complete Genomics, Inc., Mountain
`
`View, CA; sequencing-by-synthesis methods, as commercialized in the HiSeqTM
`
`technologies by Illumina, Inc., San Diego, CA; the PacBio RS system by Pacific
`
`Biosciences of California, Inc., Menlo Park, CA; and sequencing by ion detection
`
`technologies, as commercialized by Life Technologies, Inc., Carlsbad, CA (Metzker
`
`2010, and Kircher and Kelso 2010, supra, Morton Exhibits P and Q).
`
`
`
`17) With the techniques described above, therefore, it is possible to perform multiplexed
`
`amplification to amplify multiple selected nucleic acids from a sample, isolate the
`
`amplified nucleic acids, sequence millions of the amplified nucleic acids in parallel, and
`
`quantify the copies of the amplified nucleic acids. In fact, the power of massively
`
`parallel sequencing in theory allows for many samples to be pooled together and
`
`analyzed simultaneously. However, if one were to pool amplification reactions from
`
` 
`
`9
`
`Ariosa Exhibit 1002, pg. 9
`IPR2013-00276
`
`

`
`Declaration of Cynthia Casson Morton
`In re: Chuu, et al., USPN 8,318,430
`
`different samples into one sequencing reaction, it would be difficult to determine which
`
`selected nucleic acids came from which sample (see Binladen, et al.,
`2(2):el97.doi:l0.l371/journal.pone.0000197 (2007), Petition Exhibit
`
`lC’LoS ONE,
`To solve
`
`this problem, researchers use coded bits of DNA called “sample tags” or “sample
`
`indices” to identify the origin of the sample. That is, each copy of each selected DNA
`
`fragment in a sample is tagged so that it is possible to identify from which sample a
`
`selected nucleic acid originated.
`
`“Sample tags” or “sample indexing” of multiplexed
`
`DNA samples is described, e.g., in the following references: Binladen, et al;_PLoS ONE,
`2(2):e197.doi:l0.1371/journal.pone.0000197 (2007), Petition Exhibit 1i000C6);%raig, et al.,
`
`loo‘;
`Nat. Methods, 5(10):887—93 (2008), Petition Exhibit ‘l-005; Lizardi, et al., U.S. Pat. No.
`Exhibit 10_3_1
`Exhibit 103.2
`6,329,150, Morton Exhibit R; Strathmann, U.S. Pub. No. 2007/0224613, Morton Exhibit
`
`18) For example, Binladen, et al., PLoS ONE, 2(2):e197.doi:10.1371/joumal.pone.0000l97
`(2007)
`(“Binladen”)
`(Petition Exhibit
`l00%(£5<generally describes performing PCR
`
`amplification of selected nucleic acids from over a dozen different species of animals
`
`using primers that in addition to being complementary to selected nucleic acids, also
`
`contain indices indicative of the sample used as a template for the amplification.
`
`Including the sample indices on the primers assured that copies of selected nucleic acids
`
`could be identified as products from a particular sample (i.e., a single species), as each
`
`amplification product from the sample contained the same sample index. Copies of
`
`selected nucleic acids from different samples (i.e., from different species) contained
`
`different, uniquely identifiable sample indices. Once the copies of the selected nucleic
`
`l0
`
`Ariosa Exhibit 1002, pg. 10
`|PR2013—OO276
`
`Ariosa Exhibit 1002, pg. 10
`IPR2013-00276
`
`

`
`Declaration of Cynthia Casson Morton
`In re: Chuu, et al., USPN 8,318,430
`
`acids were sequenced, the sequences of selected nucleic acids from each sample were
`
`grouped by virtue of their sample index for analysis.
`
`19) In another example, Craig, et al., Nat. Methods, 5(10):887-93 (2008) (“Craig”) (Petition
`Exhibit l-iegfg-describes multiplexed sequencing of selected nucleic acids from different
`
`human individuals using “barcodes” (aka “sample tags” and “sample indices”). Where
`
`Binladen included the sample indices in the primers used to amplify the selected nucleic
`
`acids, Craig attached the sample indices to the copies of the selected nucleic acids by a
`
`process called ligation. Thus, the amplified selected nucleic acids of Craig also contained
`
`sample indices, where copies of selected nucleic acids from the same sample contained
`
`the same sample index, and copies of selected nucleic acids from different samples
`
`contained different, uniquely identifiable sample indices. As in Binladen, once the copies
`
`of the selected nucleic acids were sequenced, the sequences of selected nucleic acids
`
`from each sample could be grouped by virtue of the sample index for further analysis.
`
`Igachnical Background: Prenatal Diagnosis
`
`20)Prenatal diagnosis is an established and widely-used clinical practice in modern
`
`obstetrics. Until
`
`recently, however,
`
`the direct analysis of fetal nucleic acids or
`
`chromosomes required invasive sampling of fetal
`
`tissues, e.g., via amniocentesis or
`
`chorionic villus sampling, both of which run the risk of damage to or termination of a
`
`genetically normal fetus.
`Exhibit 1033
`attached as Morton Exhibit T.)
`
`(See, e.g., Chiu, et al., PNAS, 105(5l):20458-63 (2008),
`
`11
`
`Ariosa Exhibit 1002, pg. 11
`|PR2013—OO276
`
`Ariosa Exhibit 1002, pg. 11
`IPR2013-00276
`
`

`
`Declaration of Cynthia Casson Morton
`In re: Chuu, et al., USPN 8,318,430
` 
`
`21) In the mid-1990s, it was discovered that cell-free fetal nucleic acids are naturally present
`
`in relatively high concentrations in maternal plasma and serum in normal pregnancies.
`
`(Kazakov, et al., Tsitologiia, 37(3):232-36 (1995), attached as Morton Exhibit U; and Lo,
`
`et al., Lancet, 350:485-87 (1997), attached as Morton Exhibit V). The relatively high
`
`concentrations made it commercially practical to conduct prenatal diagnosis in a
`
`noninvasive manner. Id. However, the percentage of cell-free fetal nucleic acids in
`
`maternal plasma or serum can be relatively low in comparison to maternal cell-free fetal
`
`nucleic acids —typically 10% or less—therefore, such fetal nucleic acid sequences are
`
`usually evaluated within a large background of maternal nucleic acids. (See, e.g., Chiu
`
`2008, supra, Morton Exhibit T).
`
`
`
`22) The easiest types of fetal nucleic acid sequences to detect in the background of maternal
`
`DNA are those where the sequences are known a priori to be physically absent in the
`
`mother. (Chiu, et al., Trends in Genetics, 25(7):324-31 (2009), attached as Morton
`
`Exhibit W) Examples include Y chromosome sequences such as SRY for fetal male sex
`
`determination and the RHD gene for blood group genotyping when the mother is known
`
`to have an RhD-negative phenotype. (Lo 1997, supra, Morton Exhibit V and Lo, et al.,
`
`N. Engl. J. Med., 339(4):1734-38 (1998), Morton Exhibit X) The mother is known not to
`
`possess a Y chromosome with SRY, and in mothers who are RhD-negative the RHD gene
`
`is generally absent or grossly deleted. (Lo 1998, supra, Morton Exhibit X) Such fetal-
`
`specific sequences are therefore easily detectable, e.g., with standard PCR methods that
`
`utilize primers specific for those sequences. (Lo 1997, supra, Morton Exhibit V and Lo
`
`1998, supra, Morton Exhibit X) In these cases, if a Y chromosome sequence is present in
`
` 
`
`12
`
`Ariosa Exhibit 1002, pg. 12
`IPR2013-00276
`
`

`
`Declaration of Cynthia Casson Morton
`In re: Chuu, et al., USPN 8,318,430
`
`the maternal serum or plasma sample, the fetus is typically male; and if the RHD gene is
`
`detected in a sample from an RhD-negative mother with a deletion of RHD, the fetus is
`
`RhD-positive.
`
`23) Detection of cell-free fetal nucleic acid sequences that are present in both the fetus and
`
`the pregnant mother presents different technical challenges, as does the detection of fetal
`Exhibit 1037
`(See Chiu 2009, supra, Morton Exhibit W)
`
`aneuploidies or other copy number variants.
`
`Detection of fetal sequences that are present in both the fetus and the pregnant mother is
`
`currently possible only through the use of highly precise methods for quantification by,
`
`e. g., amplification of the fetal and maternal nucleic acids in the sample followed by
`
`single molecule sequencing (e.g., NGS) as described in W10-16 herein.
`
`24)] am aware of four different, commercially-available noninvasive prenatal diagnostic
`
`tests that detect fetal aneuploidies.
`
`25)A person of skill in the art of prenatal diagnostics would be familiar with the information
`
`provided in 1111 7-24, above.
`
`final Aneuploidy Detection Prior Art
`
`26)A first reference which describes elements of the claimed invention in the ‘430 patent is
`
`Dhallan, et a1., U.S. Pat. No. 7,332,277, issued 19 February 2008, and published in 2004
`I 0 0 Ur
`(“Dha1lan”), Petition Exhibit -l-02: Dhallan describes methods for quantitating ratios of
`
`alleles at
`
`loci of interest and further
`
`that a difference in ratios may indicate a
`
`13
`
`Ariosa Exhibit 1002, pg. 13
`|PR2013—OO276
`
`Ariosa Exhibit 1002, pg. 13
`IPR2013-00276
`
`

`
`Declaration of Cynthia Casson Morton
`In re: Chuu, et al., USPN 8,318,430
`
`chromosomal abnormality. Dhallan teaches that
`
`in some embodiments,
`
`the ratio of
`
`alleles at a locus of interest on one chromosome can be compared to the ratio of alleles at
`
`a locus of interest on another chromosome. Dhallan further teaches determining the
`
`sequence of alleles of a locus of interest in a sample using various methods. Dhallan
`
`teaches that, in certain embodiments, determining the sequence of alleles of a locus of
`
`interest comprises amplifying alleles of a locus of interest on a template DNA using
`
`primers. Dhallan further teaches that the methods may be used for determination of the
`
`presence or absence of chromosomal abnormalities in a fetus. The correlation between
`
`Dhallan and each element of claims 1-18 of the ‘43O patent are detailed below.
`
`27) Quake, U.S. Pub. No. 2007/0202525, published 30 August 2007 (“Quake ‘525”), Petition
`Exhibit 1~|0(€lg);ia0lso describes elements of the claimed invention in the ‘430 patent. Quake
`
`‘525 provides non-invasive methods for determination of fetal aneuploidies by digital
`
`analysis. Quake ‘525 demonstrates that when a maternal mixed sample is diluted to a
`
`nominal value of 0.5 genome equivalents per reaction sample, massively parallel
`
`amplification via digital PCR may be performed and the relative number of fetal
`
`chromosomal sequences may be determined, which allows for determination of the
`
`presence or absence of a fetal aneuploidy. Quake ‘525, in addition to describing digital
`
`PCR, describes the use of next generation sequencing to enumerate fetal sequences in a
`
`maternal sample. The correlation between Quake ‘525 and each element of claims 1-18
`
`of the ‘430 patent are detailed below.
`
`14
`
`Ariosa Exhibit 1002, pg. 14
`|PR2013—OO276
`
`Ariosa Exhibit 1002, pg. 14
`IPR2013-00276
`
`

`
`Declaration of Cynthia Casson Morton
`In re: Chuu, et al., USPN 8,318,430
`
`28) Another reference which describes elements of the claimed invention in the ‘430 patent is
`
`Shoemaker, et al., U.S. Pub. No. 2008/0090239, published 17 April 2008 (“Shoemaker”),
`
`Petition Exhibit +i9(S4?.§vith a priority date of 14 June 2006.
`
`Shoemaker describes
`
`methods for labeling selected nucleic acid regions—including regions comprising one or
`
`more polymorphisms—of genomic DNA in individual cells with different unique tags
`
`(i.e., “labels” where each label is specific to a cell). Shoemaker describes methods for
`
`quantifying the labeled selected regions of genomic DNA from each cell. Shoemaker
`
`teaches that the methods may be used for determining the presence or absence of fetal
`
`abnormalities. Shoemaker teaches that,
`
`in some embodiments,
`
`the selected genomic
`
`regions are amplified prior to being quantified, and that “ultra deep” sequencing can be
`
`used to provide an accurate and quantitative measurement of allele abundance.
`
`Quantitative genotyping using the sequence information obtained can be used to declare
`
`the presence of fetal cells and to determine copy numbers of fetal chromosomes. The
`
`correlations between Shoemaker and each element of claims 1-18 of the ‘430 patent are
`
`detailed below.
`
`The ‘430 Patent
`
`29) Application No. 13/368,035 (“the ‘035 application”) that issued as the ‘430 patent was
`
`filed on February 7, 2012, as a continuation of and claiming priority to, Application No.
`
`13/012,222, filed on January 24, 2011. Both the ‘035 application and Application No.
`
`13/012,222 claim priority to U.S. provisional application No. 61/297,755, filed on
`
`January 23, 2010.
`
`15
`
`Ariosa Exhibit 1002, pg. 15
`|PR2013—OO276
`
`Ariosa Exhibit 1002, pg. 15
`IPR2013-00276
`
`

`
`Declaration of Cynthia Casson Morton
`In re: Chuu, et al., USPN 8,318,430
` 
`
`30) The independent claims of the ‘430 patent recite the following claim elements: use of a
`
`plurality of maternal and fetal cell free DNA samples for detecting aneuploidies;
`
`enriching and indexing at least 100 non-random genomic DNA sequences of 10-1000
`
`nucleotides in length from each of two different chromosomes from each of the samples;
`
`pooling the enriched and indexed non-random genomic DNA sequences from the
`
`samples; sequencing the pooled, enriched and indexed non-random genomic DNA
`
`sequences from the samples; and comparing the number of non-random genomic DNA
`
`sequences from each of the two different chromosomes from each sample to determine
`
`the presence or absence of an aneuploidy.
`
`
`31) I have been instructed that the claim elements, unless a special and particular definition is
`
`provided, should be afforded their ordinary and accustomed meaning. I have also been
`
`instructed that the plain and ordinary meaning must be supported by the description of the
`
`term as found in the patent and discussion of the terms by the Inventors during
`
`prosecution of the patent. I have thus interpreted the elements of the ‘430 patent claims
`
`following these guidelines. For example, the only forms of selective enrichment taught
`
`or described in the ‘430 patent are selective amplification techniques that increase the
`
`concentration of a selected molecule relative to other molecules; thus, the analysis I have
`
`performed has focused on selective amplification as exemplary of selective enrichment.
`
`
`32) In another example, the phrase “sequence reads corresponding to enriched and indexed
`
`fetal and maternal non-random polynucleotide sequences” is used in step d of claim 1.
`
`“Sequence reads” as taught in the ‘430 refers to the order of nucleotides determined from
`
`sequencing selectively enriched and indexed polynucleotides; that is, “sequence reads”
`
` 
`
`16
`
`Ariosa Exhibit 1002, pg. 16
`IPR2013-00276
`
`

`
`Declaration of Cynthia Casson Morton
`In re: Chuu, et al., USPN 8,318,430
` 
`
`are informational. However, I have interpreted the term “enriched and indexed non-
`
`random polynucleotide sequences” to mean a nucleic acid molecule that has been
`
`selectively enriched and indexed, such as a nucleic acid molecule that has been amplified
`
`using tagged primers that amplify a specific region in a genome. In contrast to the word
`
`“sequence” in “sequence reads”, the word “sequence” in the term “non-random
`
`polynucleotide sequences” refers to a physical molecule; a non-random enriched and
`
`indexed fetal or maternal nucleic acid.
`
`
`33) As described below, it is my opinion that all three of the following combinations of art
`
`teach each and every element of claims 1-18 of the ‘430 patent: Dhallan and Binladen,
`
`Quake and Craig, and Shoemaker, Dhallan and Binladen. Binladen and Craig are
`
`described briefly in relation to multiplexing and indexing at ¶¶18-19, above. Dhallan,
`
`Quake and Shoemaker are described briefly in relation to prenatal diagnostics at ¶¶26-28,
`
`above.
`
`
`
`The techniques of claims 1-18 of the ‘430 patent would have been obvious to any skilled
`
`artisan reading Dhallan U.S. Pat No. 7,332,277 in view of the general knowledge concerning
`
`indexed PCR techniques, as reflected in Binladen et al., PLoS ONE. 2007 Feb 14;2(2):e197
`
`34) I have reviewed U.S. Pat. No. 7,332,277 to Dhallan (“Dhallan”) and Binladen et al.,
`
`PLoS ONE. 2007 Feb 14;2(2):e197 (“Binladen”). It is my view that the combination of
`
`Dhallan and Binladen discloses each element of Claims 1-18 of the ‘430 patent when the
`
`teachings of Dhallan are considered in view of the general knowledge concerning
`
` 
`
`17
`
`Ariosa Exhibit 1002, pg. 17
`IPR2013-00276
`
`

`
`Declaration of Cynthia Casson Morton
`In re: Chuu, et al., USPN 8,318,430
` 
`
`indexed PCR techniques at the time of filing, as reflected in the Binladen reference. I
`
`will discuss each equivalent element of the claims in more detail below.
`
`
`
`35) The first element of Claim 1 of the ‘430 patent is disclosed in Dhallan. Claim 1 recites,
`
`“A method for determining a presence or absence of a fetal aneuploidy in a fetus…”
`
`Dhallan states at 25:63-26:6, “The present invention provides a method for detecting
`
`genetic disorders, including but not limited to mutations, insertions, deletions, and
`
`chromosomal abnormalities, and is especially useful for the detection of genetic disorders
`
`of a fetus. The method is especially useful for detection of a translocation, addition,
`
`amplification, transversion, inversion, aneuploidy, polyploidy, monosomy, trisomy,
`
`trisomy 21, trisomy 13, trisomy 14, trisomy 15, trisomy 16, trisomy 18, trisomy 22,
`
`triploidy, tetraploidy, and sex chromosome abnormalities including but not limited to
`
`XO, XXY, XYY, an

This document is available on Docket Alarm but you must sign up to view it.


Or .

Accessing this document will incur an additional charge of $.

After purchase, you can access this document again without charge.

Accept $ Charge
throbber

Still Working On It

This document is taking longer than usual to download. This can happen if we need to contact the court directly to obtain the document and their servers are running slowly.

Give it another minute or two to complete, and then try the refresh button.

throbber

A few More Minutes ... Still Working

It can take up to 5 minutes for us to download a document if the court servers are running slowly.

Thank you for your continued patience.

This document could not be displayed.

We could not find this document within its docket. Please go back to the docket page and check the link. If that does not work, go back to the docket and refresh it to pull the newest information.

Your account does not support viewing this document.

You need a Paid Account to view this document. Click here to change your account type.

Your account does not support viewing this document.

Set your membership status to view this document.

With a Docket Alarm membership, you'll get a whole lot more, including:

  • Up-to-date information for this case.
  • Email alerts whenever there is an update.
  • Full text search for other cases.
  • Get email alerts whenever a new case matches your search.

Become a Member

One Moment Please

The filing “” is large (MB) and is being downloaded.

Please refresh this page in a few minutes to see if the filing has been downloaded. The filing will also be emailed to you when the download completes.

Your document is on its way!

If you do not receive the document in five minutes, contact support at support@docketalarm.com.

Sealed Document

We are unable to display this document, it may be under a court ordered seal.

If you have proper credentials to access the file, you may proceed directly to the court's system using your government issued username and password.


Access Government Site

We are redirecting you
to a mobile optimized page.





Document Unreadable or Corrupt

Refresh this Document
Go to the Docket

We are unable to display this document.

Refresh this Document
Go to the Docket