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`EXHIBIT 2
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`EXHIBIT 2
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`I IIIII IIIIIIII Ill lllll lllll lllll lllll lllll lllll lllll lllll 111111111111111111
`US007727720B2
`
`c12) United States Patent
`Dhallan
`
`(IO) Patent No.:
`(45) Date of Patent:
`
`US 7,727,720 B2
`Jun. 1, 2010
`
`(54) METHODS FOR DETECTION OF GENETIC
`DISORDERS
`
`(75)
`
`Inventor: Ravinder S. Dhallan, Bethesda, MD
`(US)
`
`(73) Assignee: Ravgen, Inc., Columbia, MD (US)
`
`( *) Notice:
`
`Subject to any disclaimer, the term ofthis
`patent is extended or adjusted under 35
`U.S.C. 154(b) by 501 days.
`
`(21) Appl. No.: 11/212,812
`
`(22) Filed:
`
`Aug. 26, 2005
`
`(65)
`
`Prior Publication Data
`
`US 2006/0121452 Al
`
`Jun. 8,2006
`
`Related U.S. Application Data
`
`(63) Continuation of application No. PCT/US2004/
`006337, filed on Mar. 1, 2004, which is a continuation(cid:173)
`in-part of application No. PCT/US03/06198, filed on
`Feb. 28, 2003, application No. 11/212,812, which is a
`continuation of application No. 10/661,165, filed on
`Sep. 11, 2003, which is a continuation-in-partofappli(cid:173)
`cation No. PCT/US03/06198, filed on Feb. 28, 2003,
`and a continuation-in-part of application No. PCT/
`US03/27308, filed on Aug. 29, 2003.
`
`(60) Provisional application No. 60/378,354, filed on May
`8, 2002.
`
`(51)
`
`Int. Cl.
`C12Q 1/68
`(2006.01)
`C07H 21/00
`(2006.01)
`C07H 21/02
`(2006.01)
`C07H 21/04
`(2006.01)
`(52) U.S. Cl. ......................... 435/6; 536/22.1; 536/23.1;
`536/24.3; 536/25.4; 536/25.41
`(58) Field of Classification Search ..................... 435/6,
`435/91.2; 536/23.1, 24.3
`See application file for complete search history.
`
`(56)
`
`References Cited
`
`U.S. PATENT DOCUMENTS
`
`4,521,509 A
`6/1985 Benkovic et al.
`4,683,195 A
`7/1987 Mullis et al.
`4,683,202 A
`7/1987 Mullis
`4,800,159 A
`1/1989 Mullis et al.
`4,889,818 A
`12/1989 Gelfand et al.
`4,965,188 A
`10/1990 Mullis et al.
`4,994,372 A
`2/1991 Tabor et al.
`5,023,171 A
`6/1991 Ho et al.
`5,066,584 A
`11/1991 Gyllensten et al.
`5,075,216 A
`12/1991 Innis et al.
`5,079,352 A
`1/1992 Gelfand et al.
`5,091,310 A
`2/1992 Innis
`5,098,839 A
`3/1992 Polisson
`5,104,792 A
`4/1992 Silver et al.
`5,153,117 A
`10/1992 Simons
`5,326,857 A
`7/1994 Yamamoto et al.
`5,426,026 A * 6/1995 Jordan ........................... 435/6
`5,432,054 A
`7/1995 Saunders et al.
`
`5,501,963 A
`3/1996 Burckhardt et al.
`5,538,848 A
`7/1996 Livak et al.
`5,538,871 A
`7/1996 Nuovo et al.
`5,545,552 A
`8/1996 Mathur
`5,565,339 A
`10/1996 Bloch et al.
`5,576,176 A * 11/1996 Adams et al. .................. 435/5
`5,582,989 A
`12/1996 Caskey et al.
`5,618,664 A * 4/1997 Kiessling ....................... 435/2
`5,631,147 A
`5/1997 Lohman eta!.
`5,635,348 A * 6/1997 Leong ........................... 435/6
`5,639,611 A
`6/1997 Wallace et al.
`5,641,628 A
`6/1997 Bianchi
`5,648,222 A
`7/1997 Tse et al.
`5,693,469 A
`12/1997 Hogan
`5,714,325 A * 2/1998 Bianchi ......................... 435/6
`5,723,591 A
`3/1998 Livak et al.
`5,744,301 A
`4/1998 Birkenbach et al.
`5,759,772 A
`6/1998 Kirkpatrick et al.
`5,817,797 A
`10/1998 Mitchell et al.
`5,831,065 A
`11/1998 Brenner et al.
`5,858,671 A
`1/1999 Jones
`
`(Continued)
`
`FOREIGN PATENT DOCUMENTS
`
`EP
`
`0994963 Al
`
`4/2000
`
`(Continued)
`
`OTHER PUBLICATIONS
`
`Holodniy et al., Determination of Human Immunodeficiency virus
`RNA in plasma and cellular viral DNA genotypic zidovudine resis(cid:173)
`tance and viral load during zidovudine-didanosine combination
`therapy. Journal ofVirology 69 (6): 3510-3516 (1995).*
`
`(Continued)
`
`Primary Examiner-Ethan Whisenant
`(74) Attorney, Agent, or Firm-Whyte Hirschboeck Dudek
`S.C.
`
`(57)
`
`ABSTRACT
`
`The invention provides a method useful for detection of
`genetic disorders. The method comprises determining the
`sequence of alleles of a locus of interest, and quantitating a
`ratio for the alleles at the locus of interest, wherein the ratio
`indicates the presence or absence of a chromosomal abnor(cid:173)
`mality. The present invention also provides a non-invasive
`method for the detection of chromosomal abnormalities in a
`fetus. The invention is especially useful as a non-invasive
`method for determining the sequence of fetal DNA. The
`invention further provides methods of isolation of free DNA
`from a sample.
`
`30 Claims, 33 Drawing Sheets
`
`
`
`Case 1:20-cv-01644-RGA Document 1-2 Filed 12/03/20 Page 3 of 311 PageID #: 339
`
`US 7,727,720 B2
`Page 2
`
`U.S. PATENT DOCUMENTS
`
`3/1999 Western et al.
`5,882,857 A
`10/1999 Monforte et al.
`5,965,363 A
`11/1999 Shanbrom
`5,985,260 A
`12/1999 Acton
`5,998,141 A
`12/1999 Goelet et al.
`6,004,744 A
`1/2000 Jordan
`6,017,699 A
`3/2000 Schafer et al.
`6,033,861 A
`7/2000 Matson
`6,090,553 A
`8/2000 Lapidus et al.
`6,100,029 A
`8/2000 Ausubel et al.
`6,110,709 A
`9/2000 Stemmer
`6,117,679 A
`9/2000 Lizardi
`6,124,120 A
`10/2000 Stemmer
`6,132,970 A
`6,140,054 A * 10/2000 Wittwer et al. ................. 435/6
`6,153,410 A
`11/2000 Arnold et al.
`6,156,504 A
`12/2000 Gocke et al.
`6,156,886 A
`12/2000 Sone
`6,165,793 A
`12/2000 Stemmer
`6,174,681 Bl
`1/2001 Halling et al.
`6,177,263 Bl
`1/2001 Arnold et al.
`6,180,372 Bl
`1/2001 Franzen et al.
`6,180,406 Bl
`1/2001 Stemmer
`6,183,958 Bl
`2/2001 Stanton, Jr.
`6,197,563 Bl
`3/2001 Erlich et al.
`6,203,989 Bl
`3/2001 Goldberg et al.
`6,214,558 Bl
`4/2001 Shuber et al.
`6,221,600 Bl
`4/2001 MacLeod et al.
`6,225,061 Bl
`5/2001 Becker et al.
`6,251,639 Bl
`6/2001 Kum
`6,258,540 Bl
`7/2001 Lo et al.
`6,268,146 Bl
`7/2001 Shultz et al.
`6,269,957 Bl
`8/2001 Bowers et al.
`6,277,382 Bl*
`8/2001 Stoj iljkovic et al. ...... 424/249.1
`6,277,638 Bl
`8/2001 Stemmer
`6,280,949 Bl
`8/2001 Lizardi
`6,287,861 Bl
`9/2001 Stemmer et al.
`6,291,242 Bl
`9/2001 Stemmer
`6,297,053 Bl
`10/2001 Stemmer
`6,323,009 Bl
`11/2001 Lasken et al.
`6,323,030 Bl
`11/2001 Stemmer
`6,329,179 Bl* 12/2001 Kopreski ................... 435/91.2
`2/2002 Stemmer
`6,344,356 Bl
`6,357,601 Bl
`3/2002 Bowers et al.
`6,365,375 Bl
`4/2002 Dietmaier et al.
`6,372,497 Bl
`4/2002 Stemmer
`6,379,896 Bl
`4/2002 Stanton, Jr.
`6,387,621 Bl
`5/2002 Wittwer
`6,395,547 Bl
`5/2002 Stemmer
`6,413,774 Bl
`7/2002 Stemmer et al.
`6,440,706 Bl
`8/2002 Vogelstein et al.
`6,444,468 Bl
`9/2002 Stemmer et al.
`6,475,736 Bl
`11/2002 Stanton, Jr.
`6,506,561 Bl
`1/2003 Cheval et al.
`6,506,602 Bl
`1/2003 Stemmer
`6,518,065 Bl
`2/2003 Stemmer
`6,537,746 B2
`3/2003 Arnold et al.
`6,573,098 Bl
`6/2003 Stemmer
`6,573,300 B2
`6/2003 Chang et al.
`6,582,906 Bl
`6/2003 Cao et al.
`6,602,986 Bl
`8/2003 Stemmer et al.
`6,613,517 B2
`9/2003 Michelotti
`6,617,137 B2
`9/2003 Dean et al.
`6,630,301 Bl* 10/2003 Gocke et al. ................... 435/6
`6,638,722 B2
`10/2003 Ji et al.
`6,642,034 B2
`11/2003 Lizardi
`6,673,541 Bl
`1/2004 Klein et al.
`6,673,551 B2
`1/2004 Stanton, Jr.
`6,703,228 Bl
`3/2004 Landers et al.
`6,730,517 Bl
`5/2004 Koster et al.
`6,780,593 Bl
`8/2004 Galibert et al.
`6,977,162 B2
`12/2005 Dhallan
`
`7,169,555 B2 *
`7,208,274 B2
`7,332,277 B2 *
`2001/0051341 Al
`2002/0045176 Al
`2002/0119478 Al
`2003/0044388 Al
`2003/0044791 Al
`2003/0054386 Al
`2003/0082576 Al
`2003/0099964 Al
`2003/0180746 Al
`2003/0186239 Al
`2003/0232348 Al
`2003/0235834 Al
`2004/0106102 Al
`2004/0137470 Al
`2004/0185495 Al
`2005/0037388 Al
`2005/0095621 Al
`2005/0260656 Al
`2006/0160105 Al
`2007/0122835 Al
`2007/0178478 Al
`2007/0196842 Al
`2009/0203002 Al *
`
`1/2007 Stuber et al. ... ... ... .. ... ... .. 435/6
`4/2007 Dhallan
`2/2008 Dhallan ......................... 435/6
`12/2001 Lo et al.
`4/2002 Lo et al.
`8/2002 Umansky et al.
`3/2003 Dennis et al.
`3/2003 Flemington
`3/2003 Antonarakis et al.
`5/2003 Jones et al.
`5/2003 Patil et al.
`9/2003 Kmiec eta!.
`10/2003 Dhallan
`12/2003 Jones et al.
`12/2003 Dunlop eta!.
`6/2004 Dhallan
`7/2004 Dhallan
`9/2004 Schueler et al.
`2/2005 Antonarakis et al.
`5/2005 Sidransky
`11/2005 Dhallan
`7/2006 Dhallan
`5/2007 Dhallan
`8/2007 Dhallan et al.
`8/2007 Dhallan
`8/2009 Brown ........................... 435/6
`
`FOREIGN PATENT DOCUMENTS
`
`EP
`GB
`GB
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`
`4/2000
`0994963 Bl
`9/1996
`2299166 A
`9/1996
`2299166 B
`6/1991
`W0-91/08304 Al
`3/1995
`W0-95/06137 Al
`3/1998
`W0-98/12355 Al
`9/1998
`W0-98/39474 Al
`10/1999
`W0-99/54498 Al
`6/2001
`W0-01/42504 A2
`6/2001
`W0-01/42504 A3
`WOOl/48237 A2 * 7/2001
`W0-02/04672 A2
`1/2002
`W0-02/04672 A3
`1/2002
`W0-02/055985 A2
`7/2002
`W0-02/055985 A3
`7/2002
`WO 02/083839 A2
`10/2002
`W0-02/083839 A3
`10/2002
`W0-03/001181 A2
`1/2003
`W0-03/001181 A3
`1/2003
`W0-03/074723 A2
`9/2003
`W0-03/074723 A3
`9/2003
`W0-03/074740 Al
`9/2003
`W0-03/106642 A2
`12/2003
`W0-03/106642 A3
`12/2003
`W0-2004/058987 A2
`7/2004
`W0-2004/058987 A3
`7/2004
`W0-2004/078994 A2
`9/2004
`W0-2004/078994 A3
`9/2004
`W0-2004/079011 Al
`9/2004
`W0-2007/075836 A2
`7/2007
`
`OTHER PUBLICATIONS
`
`Yamakami et al., PCR detection of DNA specific for Aspergillus
`species in serum of patients with invasive Aspergillosis. Journal of
`Clinical Microbiology 34 (10): 2464-2468 (1996).*
`Ahlquist, D. A. et al. (2000). "Colorectal Cancer Screening by Detec-
`tion of Altered Human DNA in Stool: Feasibility of a Multitarget
`Assay Panel," Gastroenterology 119:1219-1227.
`Amicucci, P. et al. (2000). "Prenatal Diagnosis ofMyotonic Dystro-
`phy Using Fetal DNA Obtained from Maternal Plasma," Clinical
`Chemistry 46(2):301-302.
`
`
`
`Case 1:20-cv-01644-RGA Document 1-2 Filed 12/03/20 Page 4 of 311 PageID #: 340
`
`US 7,727,720 B2
`Page 3
`
`Angert, R.M. et al. (Jan. 2003). "Fetal Cell-Free Plasma DNA Con(cid:173)
`centrations in Maternal Blood Are Stable 24 Hours after Collection:
`Analysis of First- and Third-Trimester Samples," Clinical Chemistry
`49(1):195-198.
`Anker, P. et al. (Apr. 1997). "K-ras Mutations are Found in DNA
`Extracted from the Plasma of Patients with Colo rectal Cancer," Gas(cid:173)
`troenterology 112(4):1114-1120.
`Anker, P. et al. eds. (Apr. 2000). "Circulating Nucleic Acids in Plasma
`or Serum," Table of Contents from the First International Symposium
`on Circulating Nucleic Acids in Plasma/Serum: Implication in Can(cid:173)
`cer Diagnosis, Prognosis, or Follow-up and in Prenatal Diagnosis,
`Apr. 18-20, 1999 in Menthon Saint-Bernard, France, located at
`<http://www.unige.c.h/LABPV/symposiurn/cnaps/cnaps_book.
`html> last visited on Mar. 27, 2001, four pages.
`Anonymous. (Dec. 16, 1996). "Birth Defects: Maternal Blood Gets
`Put to the Test," Physician's Weekly Clinical Updates located at:
`<http://www.physweekly.com/archive/96/12_16_l9/cu4.html>
`last visited on Mar. 27, 2001, one page.
`Anonymous. (Dec. 17, 1998). "Strategies for the Rapid Prenatal
`Detection ofDown's Syndrome," CMGS located at <http://www.ich.
`ucl/ac/uk/cmgs/downs98.html> last visited on Mar. 27, 2001, four
`pages.
`Anonymous. (2001). "Molecular Indexing (MI) Home Page," Helix
`Research Institute located at <http://www.hri.co.jp/MI> last visited
`Apr. 16, 2001, four pages.
`Anonymous. (Feb. 5, 2001 ). "Methods ofUltrasensitive Bioanalysis:
`DNA Sequencing and Indexing" Union Bay Ultrasensitive
`Bioanalysis Team located at <http://faculty.washington.edu/dovichi/
`research/application/DNA/DNASequencing.htrnl> last visited Apr.
`16, 2001, four pages.
`"AmplitTaq DNA
`(Date Unknown).
`Applied Biosystems.
`Polymerase," located at <http://www.appliedbiosystems.com> last
`visited on Jan. 7, 2007, two pages.
`Barnett, E.V. (Jun. 1968). "Detection of Nuclear Antigens (DNA) in
`Normal and Pathologic Human Fluids by Quantitative Complement
`Fixation," Arthritis and Rheumatism 11(3):407-417.
`Bauer, M.
`et al.
`(Jan. 2002).
`"Detection of Maternal
`Deoxyribonucleic Acid in Umbilical Cord Plasma by Using Fluores(cid:173)
`cent Polymerase Chain Reaction Amplification of Short Tandem
`Repeat Sequences," Am. J Obstet. Gynecol. 186:117-120.
`Beer, A.E. et al. (Sep. 7, 1994). "The Biological Basis of Passage of
`Fetal Cellular Material into the Maternal Circulation," Annals New
`York Academy of Sciences 731:21-35.
`Bennett, P.R. et al. (Aug. 26, 1993). "Prenatal Determination of Fetal
`RhD Type by DNA Amplification," The New England Journal of
`Medicine 329(9):607-610.
`Bianchi, D.W. (1998). "Current Knowledge About Fetal Blood Cells
`in the Maternal Circulation," J Perinat. Med. 26:175-185.
`Bianchi, D.W. (1998). "Fetal DNA in Maternal Plasma: The Plot
`Thickens and the Placental Barrier Thins," Am. J Hum. Genet.
`62:763-764.
`Bianchi, D.W. (2000). "A Guest Editorial: State of Fetal Cells in
`Maternal Blood: Diagnosis or Dilemma," Obstetrical and Gyneco(cid:173)
`logical Survey 55(11):665-667.
`Bianchi, D.W. (Dec. 1995). "Prenatal Diagnosis by Analysis of Fetal
`Cells in Maternal Blood," The Journal of Pediatrics 127(6):847-856.
`Bianchi, D.W. (May 2002). "Prenatal Exclusion of Recessively
`Inherited Disorders: Should Maternal Plasma Analysis Precede
`Invasive Techniques?" Clinical Chemistry 48(5):689-670.
`Bianchi, D.W. (Sep. 2000). "Fetal Cells in the Mother: From Genetic
`Diagnosis to Diseases Associated with Fetal Cell Microchimerism,"
`European Journal of Obstetrics & Gynecology and Reproductive
`Biology 92:103-108.
`Bianchi, D.W. et al. (1990). "Isolation of Fetal DNA From Nucleated
`Erythrocytes in Maternal Blood," Proc. Natl. Acad. Sci USA 87:3279-
`3283.
`Bianchi, D.W. et al. (1997). "PCR Quantitation of Fetal Cells in
`Maternal Blood in Normal andAneuploid Pregnancies," Am. J Hum.
`Genet. 61: 822-829.
`Bianchi, D.W. et al. (2001). "Longitudinal Fetal DNA Quantitation
`Studies in Maternal Cells and Plasma over a 24 Hour Period," Pro(cid:173)
`gram Nr: 2377 located at <http://www.faseb.org/genetics/ashgOO/
`f2377 .html> last visited on Mar. 27, 2001, one page.
`
`Bianchi, D.W. et al. (Jul. 2002). "Fetal Gender and Aneuploidy
`Detection Using Fetal Cells in Maternal Blood: Analysis ofNIFTY I
`Data," Prenatal Diagnosis 22:609-615.
`Bianchi, D.W. et al. (May 12-13, 2001). "Thoughts on the Origin of
`Fetal DNA in the Pregnant Woman," Abstract 3.4 In Chapter 3 "Clini(cid:173)
`cal Applications of Fetal DNA in Maternal Plasma," In Abstracts,
`12th Fetal Cell Workshop, Fetal Diagn. Ther. 16:450.
`Bianchi, D.W. et. al. (1996). "Male Fetal Progenitor Cells Persist in
`Maternal Blood for as Long as 27 Years Postpartum," Proc. Natl.
`Acad. Sci. USA 93:705-708.
`Blanchard, A.P. andL. Hood ( 1996). "Sequence to Array: Probing the
`Genome's Secrets," Nature Biotechnology 149:1649.
`Bradley, A.F. et al. ( 1996). "Recent Developments in Automatic DNA
`Sequencing," Pure &Applied Chemistry 68(10): 1907-1912.
`Brambati, B. (Sep. 7, 1994). "Prenatal Diagnosis by Isolating and
`Analyzing Fetal Nucleated Red Cells: Dream or Reality?" Annals
`New York Academy of Sciences 731:248-252.
`Brenner, S. et al. (2000). "Gene Expression Analysis by Massively
`Parallel Signature Sequencing (MPSS) on Microbead Arrays,"
`Nature Biotechnology 18:630-634.
`Broude, N. et al. (2001). "High-Level Multiplex DNA Amplifica(cid:173)
`tion," Antisense & Nucleic Acid Drug Development 11:327-332.
`Brown, E. L. et al. (1979). "Chemical Synthesis and Cloning of a
`Tyrosine tRNA Gene," Methods in Enzymology 68: 109-151.
`Bruch, J. F. et al. (1991). "Trophoblast-Like Cells Sorted From
`Peripheral Maternal Blood Using Flow Cytometry: A
`Multiparametric Study Involving Transmission Electron Microsopy
`and Fetal DNA Amplification," Prenatal Diagnosis 11 :787-798.
`Byrne, B.M. et al. (Jul. 1, 2003). "Fetal DNA Quantitation in Periph(cid:173)
`eral Blood Is Not Useful as a Marker of Disease Severity in Women
`with Preeclampsia," Hypertens Pregnancy 22(2):157-164.
`Cairns, P. et al. (Sep.2001 ). "Molecular Detection of Prostate Cancer
`in Urine by GSTPl Hypermethylation," Clin. Can. Res. 7:2727-
`2730.
`Camaschella, C. et al. (Jun. 1, 1990). "Prenatal Diagnosis of Fetal
`Hemoglobin Lepore-Boston Disease on Maternal Peripheral Blood,"
`Blood 75(11):2102-2106.
`Center for Medical Genetics. (1998-2003). "Human Insertion/Dele(cid:173)
`tion Polymorphisms," at <http://research.marshfieldclinicorg/ genet(cid:173)
`ics/>. last visited on Apr. 14, 2003, three pages.
`Chen, J. et al. (2000). "A Microsphere-BasedAssay for Multiplexed
`Single Nucleotide Polymorphism Analysis Using Single Base Chain
`Extension," Genome Research 10:549-557.
`Chen, X.Q. et al. (Sep. 1996). "Microsatellite Alterations in Plasma
`DNA of Small Cell Lung Cancer Patients," Nature Medicine
`2(9): 1033-1035.
`Cheung, V.G. et al. (Dec. 1996). "Whole Genome Amplification
`Using a Degenerate Oligonucleotide Primer Allows Hundreds of
`Genotypes to be Performed on Less Than One Nano gram of Genomic
`DNA," PNAS93:14676-14679.
`Chicurel, M. (Aug. 9, 2001). "Faster, Better, Cheaper Genotyping,"
`Nature 412:580-582.
`Cohen, J. (Oct. 2002). "Fetal Fortunes," Technology Review 54-61.
`Collins, F. S. and Mansoura, M. K. (2001). "The Human Genome
`Project: Revealing the Shared Inheritance of All Humankind," pre(cid:173)
`sented at 7th Biennial Symposium on Minorities, the Medically
`Underserved and Cancer 91(1):221-225.
`Cooper, D. N. and Krawczak, M. eds.(1993). "Human Gene Muta(cid:173)
`tion," In Duchenne Muscular Dystrophy, Alzheimer's Disease, Cystic
`Fibrosis, and Huntington's Disease. BIOS Scientific Publishers Lim(cid:173)
`ited. (Table of Contents only).
`Cox, R.A. et al. (Feb. 1977). "DNA Concentrations in Serum and
`Plasma," Clinical Chemistry 23(2):297.
`Cunningham, J. et al. (Oct. 1999). "Non-Invasive RNA-Based Deter(cid:173)
`mination of Fetal Rhesus D Type: A Prospective Study Based on 96
`Pregnancies," British J ofOb-Gyn 106:1023-1028.
`Cutler, D. J. et al.(2001 ). "High-Throughput Variation Detection and
`Genotyping Using Microarrays," Genome Research 11: 1913-1925.
`Davis, G.L. eta!. (Jan.-Feb.1973). "DetectionofCirculatingDNAby
`Counterimmuno-electrophoresis (CIE)," Arthritis and Rheumatism
`16(1):52-58.
`
`
`
`Case 1:20-cv-01644-RGA Document 1-2 Filed 12/03/20 Page 5 of 311 PageID #: 341
`
`US 7,727,720 B2
`Page 4
`
`Dean, F. B. et al. (2001 ). "Rapid Amplification of Plasmid and Phage
`DNA Using Phi29 DNA Polymerase and Multiple-Printed Rolling
`Circle Amplification," Genomic Research 11: 1095-99.
`Dean, F.B. et al. (Apr. 16, 2002). "Comprehensive Human Genome
`Amplification Using Multiple Displacement Amplification," PNAS
`99(8):5261-5266.
`Defrancesco, L. (1998). "The Next New Wave in Genome Analysis:
`Invaderâ„¢ Assays Developed by Third Wave Technologies, Inc.," The
`Scientist 12(21):16.
`Dhallan, R. et al. (Mar. 3, 2004). "Methods to Increase the Percentage
`of Free Fetal DNA Recovered From the Maternal Circulation," JAMA
`291(9): 1114-1119.
`Ding, C. et al. (Jul. 20, 2004). "MS Analysis of Single-Nucleotide
`Differences
`in Circulating Nucleic Acids: Application
`to
`Noninvasive Prenatal Diagnosis," PNAS 101(29)10762-10767.
`Douglas, G.W. et al. (Nov. 1959). "Trophoblast in the Circulating
`Blood During Pregnancy," American Journal of Obstetrics and
`Gynecology 78(5):960-973.
`Drabek, J. (2001). "A Commented Dictionary of Techniques for
`Genotyping," Electrophoresis 22:1024-1045.
`Durant, J. et al. (Jun. 26, 1999). "Drug-Resistance Genotyping in
`HIV-1 Therapy: The VIRADAPT Randomised Controlled Trial," The
`Lancet 353:2195-2199.
`Durant, J. et al. (Sep. 25, 1999). "Drug-Resistant Genotyping in
`HIV-1 Therapy," TheLancet354:1120-1122.
`Egholm, M. et al.
`(1992). "Peptide Nucleic Acids (PNA).
`Oligonucleotide Analogues with an Achiral Peptide Backbone," J
`Am. Chem. Soc. 114(5):1895-1897.
`El-Nagger, A.K. et al. (2001). "Genetic Heterogeneity in Saliva from
`Patients with ORal Squamous Carcinomas: Implications in Molecu(cid:173)
`lar Diagnosis and Screening," J Mo!. Diag. 3(4): 164-170.
`Emanuel, S.L. et al. (1993). "Amplification of Specific Gene Prod(cid:173)
`ucts from Human Serum," GATA 10(6):144-146.
`Erlich, H. A. ed. (1989). PCR Technology: Principals and Applica(cid:173)
`tions of DNA Amplification, Stockton Press. pp. ix-x. (Table of
`Contents only).
`Fan, S. et al. (Aug. 12, 1998). "Down-Regulation of BRCAl and
`BRCA2 in Human Ovarian Cancer Cells Exposed to Adriamycin and
`Ultraviolet Radiation," International Journal of Cancer 77(4):600-
`609.
`Farnia, A. et al. (1998). "Fetal Cells in Maternal Blood as a Second
`Non-Invasive Step for Fetal Down Syndrome Screening," Prenat.
`Diagn. 18:983-986.
`Field, J.K. et al. (Jun. 1, 1999). "Genetic Alterations in Bronchial
`Lavage as a Potential Marker for Individuals with a High Risk of
`Developing Lung Cancer," Cancer Research 59:2690-2695.
`Foreman, K. E. et al. (Jun. 1997). "In Situ Polymerase Chain Reac(cid:173)
`tion-Based Localization Studies Support Role of Human
`Herpesvirus-8 as the Cause of Two AIDS-related Neoplasms:
`Kaposi's Sarcoma and Body Cavity Lymphoma." J Clinical Inves.
`99(12):2971-2978.
`Fortina, P. et al. (2001). "DOP-PCR Amplification of Whole
`Genomic DNA and Microchip-Based Capillary Electrophoresis,"
`Methods Mo! Biol. 163:211-219.
`Fournie, G.J. et al. (1993). "Plasma DNA as Cell Death Marker in
`Elderly Patients," Gerontology 39:215-221.
`Fowke, K.R. et al. ( 1995). "Genetic Analysis of Human DNA Recov(cid:173)
`ered From Minute Amounts of Serum or Plasma," Journal of Immu(cid:173)
`nological Methods 180:45-51.
`Gadkar, V. et al. (Jan. 1, 2005). "Application of Phi29 DNA
`Polymerase Mediated Whole Genome Amplification on Single
`Spores of Arbuscular Mycorrhizal (AM) Fungi," FEMS Microbiol(cid:173)
`ogy Letters 242(1):65-71.
`Giinshirt-Ahlert, D. et al. (May 1992). "Magnetic Cell Sorting and the
`Transferrin Receptor as Potential Means of Prenatal Diagnosis from
`Materanl Blood," Am. J Obstet. Gynecol. 166:1350-1355.
`Gerhold, D. et al. ( 1999). "DNA Chips: Promising Toys have Become
`Powerful Tools," T/BS24:168-173.
`Green, A. et al. (1990). "Direct Single Stranded Sequencing from
`Agarose of Polymerase Chain Reaction Products," Nucleic Acids
`Res. 18(20):6163-6164.
`
`Grosch, S. et al. (2001). "A Rapid Screening Method for a Single
`Nucleotide Polymorphism (SNP) in the Human MOR Gene," Br. J
`Clin Pharmacol 52:711-714.
`Gusev, Y. et al. (Jul. 2001). "Technical Advance: Rolling Circle
`Amplification-A New Approach to Increase Sensitivity for
`Immunohistochemistry and Flow Cytometry," American Journal of
`Pathology 159( 1 ):63-69.
`Halm, S. et al. (May 12 -13, 2001). "An Examination of Fetal Cells,
`Free Fetal DNA and Fetal Cell Culture: The Basel Experience,"
`Abstract 3.2 In Chapter 3 "Clinical Applications of Fetal DNA in
`Maternal Plasma," In Abstracts, 12th Fetal Cell Workshop, Fetal
`Diagn. Ther. 16:449.
`Halm, S. et al. (Sep. 2002). "Prenatal Diagnosis Using Fetal Cells and
`Cell-Free Fetal DNA in Maternal Blood: What is Currently Fea(cid:173)
`sible?" Clinical Obstetrics and Gynecology 45(3):649-656.
`Harrington, J.J. et al. (1994). "Functional Domains within FEN-1
`RAD2 Define a Family of Structure-specific Endonucleases: Impli(cid:173)
`cations for Nucleotide Excision Repair," Gene and Development
`8:1344-1355.
`Hedenfalk, I. et al. (Feb. 22, 2001). "Gene-Expression Profiles in
`Hereditary Breast Cancer," New Engl. Jnl. Med. 344(8):539-548.
`Heinemann, J.A. et al. (Apr. 2000). "New Hypotheses on the Material
`Nature of Horizontally Mobile Genes," Annals New YorkAcademy of
`Sciences 906:169-186.
`Herzenberg, L.A. et al. (1979). "Fetal Cells in the Blood of Pregnant
`Women: Detection and Enrichment by Fluorescence-Activated Cell
`Sorting," Proc. Natl. Acad. Sci. USA 76(3):1453-1455.
`Hielm, S. et al. (Feb. 1998). "Genomic Analysis of Clostridium
`Botulinum Group II by Pulsed-Field Gel Electrophoresis," Applied
`and Environmental Microbiology 64(2):703-708.
`Hogervorst, F.B.L. et al. (1995). "Rapid Detection ofBRCAl Muta(cid:173)
`tions by the Protein Truncation Test," Nature Genetics 10:208-212.
`Holzgreve, W. et al. (2000). "Fetal Cells in Cervical Mucus and
`Maternal Blood," Bailliere's Clinical Obstetrics and Gynaecology
`14(4):709-722.
`Holzgreve, W. et al. (Jun. 2001). "Prenatal Diagnosis Using Fetal
`Cells and Free Fetal DNA in Maternal Blood," Clinical Perinatology
`28(2):353-365.
`Hosono, S. et al. (Apr. 14, 2003). "Unbiased Whole-Genome Ampli(cid:173)
`fication Directly From Clinical Samples," Genome Research
`13(5)954-964.
`Hsu, T. M. et al.
`(2001). "Genotyping Single-Nucleotide
`Polymorphisms by the Invader Assay with Dual-Color Fluorescence
`Polarization Detection," Clinical Chemistry 47(8): 1373-1377.
`Huber, M. et al. (2001 ). "Detection of Single Base Alterations in
`Genomic DNA by Solid Phase Polymerase Chain Reaction on
`Oligonucleotide Microarrays," Analytical Biochemistry 299:24-30.
`Hughes, G.R. et al. (Mar.-Apr. 1971). "The Release of DNA into
`Serum and Synovial Fluid," Arthritis and Rheumatology 14(2):259-
`266.
`Human Gene Mutation Database (HGMD). (Date Unknown).
`Located at <http:archive.uwcm.ac.uk/uwcm/mg/hgmdO.htrnl> last
`visited on Sep. 20, 2004. 3 pages total.
`Imamura, A. et al. (1996). "Short Communication: Prenatal Diagno(cid:173)
`sis of Adrenoleukodystrophy by Means of Mutation Analysis,"
`PreNatal Diagnosis 16:259-261.
`Innis, M.A. ed., (1990). PCR Protocols: A Guide to Methods and
`Applications. Academic Press, Inc. pp. v-x. (Table of Contents only).
`International Search Report mailed on Jul. 17, 2003, for PCT Patent
`Application No. PCT/US03/06376 filed on Feb. 28, 2003, four pages.
`International Search Report mailed on Jul. 20, 2004 for PCT patent
`application No. PCT/US03/27308 filed Aug. 29, 2003, eight pages.
`International Search Report mailed on Jun. 14, 2005 for PCT patent
`application No. PCT/US04/06337 filed Mar. 1, 2004, five pages.
`International Search Report mailed on Sep. 2, 2003, for PCT patent
`application No. PCT/US03/06198 filed on Feb. 28, 2003, nine pages.
`International Searh Report mailed on Jun. 14, 2005 for PCT patent
`application No. PCT/US04/06337 filed Mar. 1, 2004, five pages.
`James, P. et al. ( 1994). "Protein Identification in DNA Databases by
`Peptide Mass Fingerprinting," Protein Science 3:1347-1350.
`Kamm, R.C. et al. (1972). "Nucleic Acid Concentrations in Normal
`Human Plasma," Clinical Chemistry 18(6):519-522.
`
`
`
`Case 1:20-cv-01644-RGA Document 1-2 Filed 12/03/20 Page 6 of 311 PageID #: 342
`
`US 7,727,720 B2
`Page 5
`
`Isolation From Maternal
`Implications," Adv. Obstet.
`
`Kamm, R.C. et al. (1975). "Plasma Deoxyribonucleic Acid Concen(cid:173)
`trations ofWomen in Labor and Umbilical Cords," American Journal
`of Obstetrics and Gynecology 121(1):29-31.
`Kandpal, R.P. et al. (1990). "Selective Enrichment of a Large Size
`Genomic DNA Fragment by Affinity Capture: An Approach for
`Genome Mapping," Nucleic Acids Res. 18(7): 1789-1795.
`Kaneoka, H. et al. (1991). "Solid-Phase Direct DNA Sequencing of
`Allele-Specific Polymerase Chain Reaction-Amplified HLA-DR
`Genes," Biotechniques 10(1):30, 32 and 34 only.
`Kang, A. et al. ( 1999). "Fetal Cells in Maternal Blood: Their Role in
`Non-Invasive Prenatal Diagnosis and in the Etiology of Certain Dis(cid:173)
`eases," ("Fetale Zellen im miitterlichen Blut-ihre Bedeutung fiir
`eine nicht-invasive priinatale Diagnostik und bei der Atiotogie
`bestimmter Erkrankungen,") Schweiz Med. Wochenschr 129: 1470-
`1743. English Translation and original language article.
`Kawasaki, E. S. (1990). "Sample Preparation From Blood, Cells and
`Other Fluids," Chapter 18 In PCR Protocol: A Guide to Methods and
`Applications. Innis, M. A. et al., eds., Academic Press, Inc., pp.
`146-152.
`Kinzler, K. W. et al. (Aug. 9, 1991). "Indentification of FAP Locus
`Genes from Chromosome 5q21," Science 253:661-665.
`Kosel, S. et al. (May 8,2001 ). "Inter-Laboratory Comparison of DNA
`Preservation in Archival Paraffin-Embedded Human Brain Tissue
`from Participating Centres on Four Continents," Neurogenetics
`3(3):164-170.
`"Fetal Cell
`Kuo, P-L.
`(1999).
`Blood-Clinical and Biological
`Perinatal. 10(1):15-24.
`Kusaka, T. et al. (Oct. 2000). "Analysis ofK-ras Codon 12 Mutations
`and P53 Overexpression
`in Colorectal Nodule-Aggregating
`Tumors," Journal of Gastroenterology and Hepatology 15( 10) 1151-
`1157.
`Kwak, J.Y.H. et al. ( Sep. 7, 1994). "Biological Basis ofFetoplacental
`Antigenic Determinants in the Induction of the Antiphospholipid
`Antibody Syndrome and Recurrent Pregnancy Loss," Annals New
`York Academy of Sciences 731 :242-245.
`Kwok, P-Y. (2001). "Methods for Genotyping Single Nucleotide
`Polymorphisms," Annual Review ofGenomics and Human. Genetics
`2:235-258.
`Lagona, F. et al. (1998). "Multiple Testing in Fetal Gender Determi(cid:173)
`nation from Maternal Blood by Polymerase Chain Reaction," Human
`Genetics 102:687-690.
`Lagona, F. et al. (Apr. 2000). "Fetal DNA Analysis from Maternal
`Plasma and Nucleated Blood Cells," Annals New York Academy of
`Sciences 906:156-160.
`Lander, E. S. et al. (2001). "Initial Sequencing and Analysis of the
`Human Genome," Nature 409: 860-921.
`Lee, M.-S. et al. (1989). "Detection of Two Alternative bcr/abl
`mRNA Junctions and Minimal Residual Disease in Philadelphia
`Chromosome Positive Chronic Myelogenous Leukemia by
`Polymerase Chain Reaction," Blood 73(8):2165-2170.
`Lee, T. eta!. (Nov. 2002). "DownSyndromeandCell-FreeFetalDNA
`in Archived Maternal Serum," Am. J Obstet. Gynecol. 187:1217-
`1221.
`Leon, S.A. et al. (1977). "Free DNA in the Serum of Rheumatoid
`Arthritis Patients," Journal of Rheumatology 4(2): 139-143.
`Leon, S.A. et al. (Mar. 1977). "Free DNA in the Serum of Cancer
`Patients and the Effect of Therapy," Cancer Research 37:646-650.
`Li, J. et al. ( 1999). "Single Nucleotide Polymorphism Determination
`using Primer Extension and Time-of-Flight Mass Spectrometry,"
`Electrophoresis 20: 1258-1265.
`Liloglou, T. et al. (2001 ). "Cancer-Specific Genomic Instability in
`Bronchial Lavage: A Molecular Tool for Lung Cancer Detection,"
`Cancer Research 61:1624-1628.
`Lindblad-Toh, K. et al. (2000). "Loss of-Heterozygoisty Analysis of
`Small-Cell
`Lung
`Carcinomas Using
`Single-Nucleotide
`Polymorphism Arrays," Nature Biotechnology 18: 1001-1005.
`Livak, K.J. et al. (1995). "Oligonucleotides With Fluorescent Dyes at
`Opposite Ends Provide a Quenched Probe System Useful for Detect(cid:173)
`ing PCR Product and Nucleic Acid Hybridization," PCR Methods
`and Applications 4:357-362.
`
`Lo, Y.M. D. et al. (Sep. 7, 1994). "Strategies for the Detection of
`Autosomal Fetal DNA Sequence from Maternal Peripheral Blood,"
`Annals New York Academy of Sciences 731 :204-213.
`Lo, Y.M.D. (Apr. 2000). "Fetal DNA in Maternal Plasma," Annals of
`New York Academy of Sciences 906:141-147.
`Lo, Y.M.D. (Dec. 1994) "Non-Invasive Prenatal Diagnosis Using
`Fetal Cells in Maternal Blood," Journal of Clinical Pathology
`47(12): 1060-1065.
`Lo, Y.M.D. (1999). "Fetal RhD Genotyping From Maternal Plasma,"
`Annals of Medicine 31(5):308-312.
`Lo, Y.M.D. (1999). "Rapid Clearance of Fetal DNA from Maternal
`Plasma," Am. J Hum. Genet. 64:218-224.
`Lo, Y.M.D. (Dec. 2000). "Fetal DNA in Maternal Plasma: Biology
`and Diagnostic Applications," Clinical Chemistry 46(12): 1903-
`1906.
`Lo, Y.M.D. (Jan. 2003). "Fetal DNA in Maternal Plasma/Serum: The
`First 5 Years," Pediatric Research 53(1): 16-17.
`Lo, Y.M.D. (Jun.2001 ). "Fetal DNA in Maternal Plasma: Application
`to Non-Invasive Blood Group Genotyping of the Fetus," Transfus.
`Clin. Biol. 8(3):306-310.
`Lo, Y.M.D. (May 12-13, 2001). "Fetal DNA in Maternal Plasma,"
`Abstract 3.1 In Chapter 3 "Clinical Applications of Fetal DNA in
`Maternal Plasma," In Abstracts, 12th Fetal Cell Workshop, Fetal
`Diagn. Ther. 16:448-449.
`Lo, Y.M.D. (Sep. 7, 1994). "An Improved PCR-Based System for
`Prenatal Sex Determination from Maternal Peripheral Blood,"
`Annals New York Academy of Sciences 731:214-216.
`Lo, Y.M.D. (Sep. 7, 1994). "Prenatal Determination of Fetal Rhesus
`D Status by DNA Amplification of Peripheral Blood of Rhesus(cid:173)
`Negative Mothers," Annals New York Academy of Sciences 731 :229-
`236.
`Lo, Y.M.D. et al. (1994). "Detection of Fetal RhD Sequence From
`Peripheral BloodofSensitizedRhD-Negative Women," British Jour(cid:173)
`nal of Hematology 87:658-660.
`Lo, Y.M.D. et al. (1998). "Quantitative Anaylysis of Fetal DNA in
`Maternal Plasma and Serum: Implications for Noninvasive Prenatal
`Diagnosis," Am. J Hum. Genet. 62:768-775.
`Lo, Y.M.D. et al. (1999). "Increased Fetal DNA Concentrations in the
`Plasma of Pregnant Women Carrying Fetuses with Trisomy 21,"
`Clinical Chemistry 45(10): 1747-1751.
`Lo, Y.M.D. et al. (Aug. 16, 1997). "Presence of Fetal DNA in Mater(cid:173)
`nal Plasma and Serum," The Lancet 350:485-487.
`Lo, Y.M.D. et al. (Dec. 1, 1996). "Two-Way Cell Traffic Between
`Mother