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Systems And Methods To Detect Rare Mutations And Copy Number Variation - EP2971168

EP2971168

GUARDANT HEALTH
Application Number
EP14771159A
Filing Date
Mar 15, 2014
Status
Revoked
Feb 21, 2025
Grant Date
May 5, 2021
External Links
Slate, Register, Google Patents

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The patent EP2971168B1 was granted to Guardant Health on May 5, 2021 following the initial filing on Mar 15, 2014 under the application number EP14771159A . The current legal status of the patent is Revoked.

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GRUNECKER PATENT UND RECHTSANWALTE PARTG MBBFeb 7, 2022ADMISSIBLE
MARGARET DIXONFeb 4, 2022ADMISSIBLE

Patent Citations New

Patent citations refer to prior patents cited during different phases such as opposition or international search.

Citation PhasePatent NumberPatent Link
DESCRIPTIONUS2001053519
DESCRIPTIONUS2003152490
DESCRIPTIONUS2011160078
DESCRIPTIONUS2011281736
DESCRIPTIONUS6582908
DESCRIPTIONUS7537897
DESCRIPTIONUS8209130
DESCRIPTIONWO2011155833
EXAMINATIONUS2011281736
INTERNATIONAL-SEARCH-REPORTUS2010062494
INTERNATIONAL-SEARCH-REPORTUS2012046877
INTERNATIONAL-SEARCH-REPORTUS2012059594
INTERNATIONAL-SEARCH-REPORTUS2012100548
INTERNATIONAL-SEARCH-REPORTUS2012214678
INTERNATIONAL-SEARCH-REPORTUS2013085681
INTERNATIONAL-SEARCH-REPORTUS8209130
INTERNATIONAL-SEARCH-REPORTWO2011060240
INTERNATIONAL-SEARCH-REPORTWO2012106559
OPPOSITIONUS2004185484
OPPOSITIONUS2013210643
OPPOSITIONUS8209130
OPPOSITIONWO2004081183
OPPOSITIONWO2012142213
OPPOSITIONWO2012148477
OPPOSITIONWO2013123442
OPPOSITIONWO2013142389
OPPOSITIONWO2014039556
SEARCHUS8209130
SEARCHWO2011155833

Non-Patent Literature (NPL) Citations New

NPL citations refer to non-patent references such as research papers, articles, or other publications cited during examination or opposition phases.

Citation PhaseReference TextLink
EXAMINATION- A. Narayan ET AL, "Ultrasensitive Measurement of Hotspot Mutations in Tumor DNA in Blood Using Error-Suppressed Multiplexed Deep Sequencing", Cancer research, US, (20120715), vol. 72, no. 14, doi:10.1158/0008-5472.CAN-11-4037, ISSN 0008-5472, pages 3492 - 3498, XP055407873
OPPOSITION- Anonymous, "Interview Professor Dennis Lo", Quiagen News, (20020000), vol. 2002, no. 5, pages 2 - 3, XP055646625-
OPPOSITION- Anonymous, "KAPA HTP Library Preparation Kit Illumina platforms", KAPA BIOSYSTEMS - Kapa - Technical Data Sheet, (20130700), pages 1 - 20, XP055894139-
OPPOSITION- Anonymous, "KAPA HTP Library Preparation Kit Illumina® platforms KR0426 - V3.13", Kapa - Technical Data Sheet, (20130701), pages 1 - 20, Kapa - Technical Data Sheet, URL: https://www.utsouthwestern.edu/labs/next-generation-sequencing-core/assets/KAPA_HTP_Library_Preparation_Kit_TDS.pdf, (20220222), XP055894139-
OPPOSITION- Anonymous, "KAPA HYPER PREP: A NEXT-GENERATION KIT FOR FAST AND EFFICIENT LIBRARY CONSTRUCTION FROM CHALLENGING DNA SAMPLES", Hyper Prep Poster - Sopachem Life Sciences at AGBT, (20140000), page 1, URL: https://www.sopachem.com/lifesciences/ag bt- 2014-hyper-prep-poster, XP055894944-
OPPOSITION- Anonymous, "Next generation sequencing experts - 2014 AGBT Agenda Highlights", Genohub Blog, (20140206), pages 1 - 3, URL: https://blog.genohub.com/ 2014/02/06 /2014-agbt- agenda, XP055895025-
OPPOSITION- Anonymous, "QuickLinkTM DNA Ligation Kit", SIGMA ALDRICH, (20090101), SIGMA ALDRICH, URL: https://www.sigmaaldrich.com/DE/, (20220222), XP055894152-
OPPOSITION- FORSHEW et al., "Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA", Sci Transl Med., (20120530), vol. 4, no. 136, pages 136 - 138, XP055894926-
OPPOSITION- RUSK, N., "Ãœber-accurate sequencing", Nat Methods Commentary on D2, vol. 9, (20120000), page 943, URL: https://doi.org/10.1038/nmeth.2189, XP055894916-
OPPOSITION- XIE et al., "High-throughput sequence-based epigenomic analysis of Alu repeats in human cerebellum", Nucleic Acids Research, vol. 37, no. 13, (20090701), pages 4331 - 4340, URL: https://doi.org/1 0.1 093/nar/gkp393, XP055894939-
OPPOSITION- FLEISCHHACKER M, SCHMIDT B, "Circulating nucleic acids (CNAs) and cancer-A survey", BBA - REVIEWS ON CANCER., ELSEVIER SCIENCE BV, AMSTERDAM., NL, NL , (20070101), vol. 1775, no. 1, doi:10.1016/j.bbcan.2006.10.001, ISSN 0304-419X, pages 181 - 232, XP002490780
OPPOSITION- Sarah-Jane Dawson, Dana W.Y. Tsui, Muhammed Murtaza, Heather Biggs, Oscar M. Rueda, Suet-Feung Chin, Mark J. Dunning, Davina Gale, Tim Forshew, Betania Mahler-Araujo, Sabrina Rajan, Sean Humphray, Jennifer Becq, David Halsall, Matthew Wallis, David Bentley, Carlos Caldas, Nitzan Rosenfeld, "Analysis of Circulating Tumor DNA to Monitor Metastatic Breast Cancer", The New England journal of medicine, Massachusetts Medical Society, US, US , (20130328), vol. 368, no. 13, doi:10.1056/NEJMoa1213261, ISSN 0028-4793, pages 1199 - 1209, XP055494258
OPPOSITION- Fan H.C., et al, "Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood.", Proceedings of the National Academy of Sciences, National Academy of Sciences, (20081021), vol. 105, no. 42, doi:10.1073/pnas.0808319105, ISSN 0027-8424, pages 16266 - 16271, XP002613056
OPPOSITION- FU et al., "Counting individual DNA molecules by the stochastic attachment of diverse labels", Proceedings of the National Academy of Sciences, (20110500), vol. 108, no. 22, doi:10.1073/pnas.1017621108, pages 9026 - 9031, XP055647656
OPPOSITION- G. K. Fu, J. Hu, P.-H. Wang, S. P. A. Fodor, "Counting individual DNA molecules by the stochastic attachment of diverse labels", Proceedings of the National Academy of Sciences, National Academy of Sciences, (20110531), vol. 108, no. 22, doi:10.1073/pnas.1017621108, ISSN 00278424, pages 9026 - 9031, XP055164127
OPPOSITION- I. Kinde, J. Wu, N. Papadopoulos, K. W. Kinzler, B. Vogelstein, "Detection and quantification of rare mutations with massively parallel sequencing", Proceedings of the National Academy of Sciences, National Academy of Sciences, (20110607), vol. 108, no. 23, doi:10.1073/pnas.1105422108, ISSN 00278424, pages 9530 - 9535, XP055164202
OPPOSITION- M. W. Schmitt, S. R. Kennedy, J. J. Salk, E. J. Fox, J. B. Hiatt, L. A. Loeb, "Detection of ultra-rare mutations by next-generation sequencing", Proceedings of the National Academy of Sciences, National Academy of Sciences, (20120904), vol. 109, no. 36, doi:10.1073/pnas.1208715109, ISSN 00278424, pages 14508 - 14513, XP055161683
OPPOSITION- Schmitt M W; Kennedy S R; Salk J J; Fox E J; Hiatt J B; Loeb L A, "Detection of ultra-rare mutations by next-generation sequencing", PNAS, vol. 109, no. 36, (20120904), pages 14508 - 14513, URL: https://doi.ora/10.1073/pnas.1208715109, XP055825591
OPPOSITION- Krimmel Jeffrey D., Schmitt Michael W., Harrell Maria I., Agnew Kathy J., Kennedy Scott R., Emond Mary J., Loeb Lawrence A., Swisher Elizabeth M., Risques Rosa Ana, "Ultra-deep sequencing detects ovarian cancer cells in peritoneal fluid and reveals somatic TP53 mutations in noncancerous tissues", Proceedings of the National Academy of Sciences, National Academy of Sciences, (20160524), vol. 113, no. 21, doi:10.1073/pnas.1601311113, ISSN 0027-8424, pages 6005 - 6010, XP055894156
OPPOSITION- James A. Casbon, Robert J. Osborne, Sydney Brenner, and Conrad P. Lichtenstein, "A method for counting PCR template molecules with application to next-generation sequencing", Nucleic Acids Research, Oxford University Press, GB, GB , (20110701), vol. 39, no. 12, doi:10.1093/nar/gkr217, ISSN 0305-1048, pages 1 - 8, XP002666160
OPPOSITION- A. P. So, "Increasing the efficiency of SAGE adaptor ligation bydirected ligation chemistry", Nucleic Acids Research, Information Retrieval Ltd., (20040707), vol. 32, no. 12, doi:10.1093/nar/gnh082, ISSN 03051048, pages e96 - e96, XP055197519
OPPOSITION- Meyer Matthias; Kircher Martin, "Illumina sequencing library preparation for highly multiplexed target capture and sequencing.", Cold Spring Harbor Protocols, Cold Spring Harbor Laboratory Press, US, US , (20100601), no. 6, doi:10.1101/pdb.prot5448, ISSN 1559-6095, page pdb.prot5448, XP009182568
OPPOSITION- T. Forshew, M. Murtaza, C. Parkinson, D. Gale, D. W. Y. Tsui, F. Kaper, S.-J. Dawson, A. M. Piskorz, M. Jimenez-Linan, D. Bentley, J. Hadfield, A. P. May, C. Caldas, J. D. Brenton, N. Rosenfeld, "Noninvasive Identification and Monitoring of Cancer Mutations by Targeted Deep Sequencing of Plasma DNA", SCIENCE TRANSLATIONAL MEDICINE, (20120530), vol. 4, no. 136, doi:10.1126/scitranslmed.3003726, ISSN 1946-6234, pages 136ra68 - 136ra68, XP055450222
OPPOSITION- LEARY et al., "Detection of chromosomal alterations in the circulation of cancer patients with whole- genome sequencing", Sci Transl Med., (20121128), vol. 4, no. 162, doi:10.1126/scitranslmed.3004742, pages 162 - 154, XP055565752
OPPOSITION- Enrique Ramos;Benjamin T Levinson;Sara Chasnoff;Andrew Hughes;Andrew L Young;Katherine Thornton;Allie Li;Francesco LM Vallania;Michael Province;Todd E Druley, "Population-based rare variant detection via pooled exome or custom hybridization capture with or without individual indexing", BMC Genomics, BioMed Central Ltd, London, UK, London, UK , (20121206), vol. 13, no. 1, doi:10.1186/1471-2164-13-683, ISSN 1471-2164, page 683, XP021134772
OPPOSITION- Zhaojie Zhang;Jerome E Lee;Kent Riemondy;Emily M Anderson;Rui Yi, "High-efficiency RNA cloning enables accurate quantification of miRNA expression by deep sequencing", Genome Biology, BioMed Central Ltd., (20131007), vol. 14, no. 10, doi:10.1186/gb-2013-14-10-r109, ISSN 1465-6906, page R109, XP021165698
OPPOSITION- KENNEDY et al., "Ultra-sensitive sequencing reveals an age-related increase in somatic mitochondrial mutations that are inconsistent with oxidative damage", PLoS Genet, (20130926), vol. 9, no. 9, pages 1 - 9, XP055529664
OPPOSITION- Filip Van Nieuwerburgh, Sandra Soetaert, Katie Podshivalova, Eileen Ay-Lin Wang, Lana Schaffer, Dieter Deforce, Daniel R. Salomon, Steven R. Head, Phillip Ordoukhanian, "Quantitative Bias in Illumina TruSeq and a Novel Post Amplification Barcoding Strategy for Multiplexed DNA and Small RNA Deep Sequencing", PLoS ONE, Public Library of Science, (20110101), vol. 6, no. 10, doi:10.1371/journal.pone.0026969, ISSN 19326203, page e26969, XP055157339
OPPOSITION- Geraldine Perkins, Timothy A. Yap, Lorna Pope, Amy M. Cassidy, Juliet P. Dukes, Ruth Riisnaes, Christophe Massard, Philippe A. Cassier, Susana Miranda, Jeremy Clark, Katie A. Denholm, Khin Thway, David Gonzalez De Castro, Gerhardt Attard, L. Rhoda Molife, Stan B. Kaye, Udai Banerji, Johann S. de Bono, "Multi-purpose utility of circulating plasma DNA testing in patients with advanced cancers", PLoS ONE, Public Library of Science, US, US , (20121107), vol. 7, no. 11, doi:10.1371/journal.pone.0047020, ISSN 1932-6203, pages e47020 - e47020-10, XP002730501
OPPOSITION- K. C. A. Chan, P. Jiang, Y. W. L. Zheng, G. J. W. Liao, H. Sun, J. Wong, S. S. N. Siu, W. C. Chan, S. L. Chan, A. T. C. Chan, P. B. S. Lai, R. W. K. Chiu, Y. M. D. Lo, "Cancer Genome Scanning in Plasma: Detection of Tumor-Associated Copy Number Aberrations, Single-Nucleotide Variants, and Tumoral Heterogeneity by Massively Parallel Sequencing", Clinical Chemistry, P.B. Hoeber, (20130101), vol. 59, no. 1, doi:10.1373/clinchem.2012.196014, ISSN 00099147, pages 211 - 224, XP055181307
OPPOSITION- Park Naomi, Shirley Lesley, Gu Yong, Keane Thomas M., Swerdlow Harold, Quail Michael A., "An improved approach to mate-paired library preparation for Illumina sequencing", Methods in Next Generation Sequencing, (20130129), vol. 1, no. 1, doi:10.2478/mngs-2013-0001, pages 10 - 20, XP055894143
SEARCH- M. W. SCHMITT ET AL, "Detection of ultra-rare mutations by next-generation sequencing", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES, (20120801), vol. 109, no. 36, doi:10.1073/pnas.1208715109, ISSN 0027-8424, pages 14508 - 14513, XP055161683 [I] 1-15 * page 14509, column l, paragraph l - column r, paragraph 2 * * figure 1 *
SEARCH- M. HAFNER ET AL, "RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries", RNA, (20110901), vol. 17, no. 9, doi:10.1261/rna.2799511, ISSN 1355-8382, pages 1697 - 1712, XP055076478 [I] 1-15 * abstract * * figure 1A * * page 1698, column l, paragraph 2 * * page 1699, column r, paragraph 2 * * page 1707, column l, paragraph l - column r, paragraph 1 *

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