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A Method For The Isolation Of Double-Strand Breaks - EP4200443

The patent EP4200443 was granted to University College Cardiff Consultants on Apr 10, 2024. The application was originally filed on Aug 20, 2021 under application number EP21766455A. The patent is currently recorded with a legal status of "Granted And Under Opposition".

EP4200443

UNIVERSITY COLLEGE CARDIFF CONSULTANTS
Application Number
EP21766455A
Filing Date
Aug 20, 2021
Status
Granted And Under Opposition
Mar 8, 2024
Grant Date
Apr 10, 2024
External Links
Slate, Register, Google Patents

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MERCK PATENTJan 9, 2025GRAHAM WATTADMISSIBLE

Patent Citations (9) New

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

Citation PhasePublication NumberPublication Link
DESCRIPTIONUS2010111768
DESCRIPTIONUS8951781
DESCRIPTIONWO2014142841
EXAMINATIONWO2019217816
INTERNATIONAL-SEARCH-REPORTWO2015134552
INTERNATIONAL-SEARCH-REPORTWO2017083562
INTERNATIONAL-SEARCH-REPORTWO2017218979
INTERNATIONAL-SEARCH-REPORTWO2018140695
OPPOSITIONWO2019217816

Non-Patent Literature (NPL) Citations (23) 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
DESCRIPTION- KRUEGER, F., "A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQfiles", Trim Galore, (20150000), URL: http://www.bioinformatics.babraham.ac.uk/proiects/trimgalore/[Accessed:2019-
DESCRIPTION- LI, H.HANDSAKER, B.WYSOKER, A.FENNELL, T.RUAN, J.HOMER, N., "Genome Project Data, P. (2009). The Sequence Alignment/Map format and SAMtools", Bioinformatics, vol. 25, no. 16, pages 2078 - 2079-
DESCRIPTION- SHEN, W.LE, S.LI, Y.HU, F. Q., "SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation.", Plos One, (20160000), vol. 11, page 10-
DESCRIPTION- YAN, W. X.MIRZAZADEH, R.GARNERONE, S.SCOTT, D.SCHNEIDER, M. W.KALLAS, T.CROSETTO, N., "BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks.", Nature Communications, (20170000), page 8-
DESCRIPTION- PINELLO, L.CANVER, M. C.HOBAN, M. D.ORKIN, S. H.KOHN, D. B.BAUER, D. E.YUAN, G. C., "Analyzing CRISPR genome-editing experiments with CRISPResso.", Nature Biotechnology, (20160000), vol. 34, no. 7, doi:10.1038/nbt.3583, pages 695 - 697, XP055716929
DESCRIPTION- LENSING, S. V.MARSICO, G.HANSEL-HERTSCH, R.LAM, E. Y.TANNAHILL, D.BALASUBRAMANIAN, S., "DSBCapture: in situ capture and sequencing of DNA breaks.", Nature Methods, (20160000), vol. 13, no. 10, doi:10.1038/nmeth.3960, page 855, XP055789830
DESCRIPTION- LI, H.DURBIN, R., "Fast and accurate short read alignment with Burrows-Wheeler transform.", Bioinformatics, (20090000), vol. 25, no. 14, doi:10.1093/bioinformatics/btp324, pages 1754 - 1760, XP055553969
DESCRIPTION- QUINLAN, A. R.HALL, I. M., "BEDTools: a flexible suite of utilities for comparing genomic features.", Bioinformatics, (20100000), vol. 26, no. 6, doi:10.1093/bioinformatics/btq033, pages 841 - 842, XP055307411
DESCRIPTION- BAE, S.PARK, J.KIM, J. S., "Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases.", Bioinformatics, (20140000), vol. 30, no. 10, doi:10.1093/bioinformatics/btu048, pages 1473 - 1475, XP055196964
EXAMINATION- IWANKA KOZAREWA ET AL, "Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes", NATURE METHODS, (20090401), vol. 6, no. 4, doi:10.1038/nmeth.1311, ISSN 1548-7091, pages 291 - 295, XP055087323
EXAMINATION- CAMERON PETER ET AL, "Mapping the genomic landscape of CRISPR-Cas9 cleavage", New York, vol. 14, no. 6, doi:10.1038/nmeth.4284, ISSN 1548-7091, (20170601), pages 600 - 606, NATURE METHODS, URL: https://www.nature.com/articles/nmeth.4284.pdf, XP055852913
EXAMINATION- KUZIN ALEXANDER ET AL, "RGEN-seq for highly sensitive amplification-free screen of off-target sites of gene editors", vol. 11, no. 1, doi:10.1038/s41598-021-03160-8, (20211208), SCIENTIFIC REPORTS, URL: https://www.nature.com/articles/s41598-021-03160-8.pdf, XP093053289
INTERNATIONAL-SEARCH-REPORT- SRIRAMACHANDRAN ANNIE M ET AL, "Genome-wide Nucleotide-Resolution Mapping of DNA Replication Patterns, Single-Strand Breaks, and Lesions by GLOE-Seq", MOLECULAR CELL, ELSEVIER, AMSTERDAM , NL, vol. 78, no. 5, doi:10.1016/J.MOLCEL.2020.03.027, ISSN 1097-2765, (20200421), page 975, (20200421), XP086170050 [X] 70-84 * page 975, column 2; figure 1 *
OPPOSITION- D1- Exhibit AS01 of Declaration of Dr Alexei Slesarev dated 8th January 2025-
OPPOSITION- D2- Exhibit AS02 of Declaration of Dr Alexei Slesarev dated 8th January 2025-
OPPOSITION- D3- Exhibit AS03 of Declaration of Dr Alexei Slesarev dated 8th January 2025-
OPPOSITION- D4- Exhibit AS04 of Declaration of Dr Alexei Slesarev dated 8th January 2025-
OPPOSITION- D5 - Exhibit AS05 of Declaration of Dr Alexei Slesarev dated 8th January 2025-
OPPOSITION- Iwanka Kozarewa, Zemin Ning, Michael A Quail, Mandy J Sanders, Matthew Berriman, Daniel J Turner, "Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes", Nature Methods, (20090401), vol. 6, no. 4, doi:10.1038/nmeth.1311, ISSN 15487091, pages 291 - 295, XP055087323
OPPOSITION- Cameron Peter, Fuller Chris K, Donohoue Paul D, Jones Brittnee N, Thompson Matthew S, Carter Matthew M, Gradia Scott, Vidal Bastien, Garner Elizabeth, Slorach Euan M, Lau Elaine, Banh Lynda M, Lied Alexandra M, Edwards Leslie S, Settle Alexander H, Capurso Daniel, Llaca Victor, Deschamps Stéphane, Cigan Mark, Young Joshua K, May Andrew P, "Mapping the genomic landscape of CRISPR-Cas9 cleavage", Nature Methods, New York, (20170601), vol. 14, no. 6, doi:10.1038/nmeth.4284, ISSN 1548-7091, pages 600 - 606, XP055852913
OTHER- Iwanka Kozarewa, Zemin Ning, Michael A Quail, Mandy J Sanders, Matthew Berriman, Daniel J Turner, "Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes", Nature Methods, (20090401), vol. 6, no. 4, doi:10.1038/nmeth.1311, ISSN 15487091, pages 291 - 295, XP055087323
OTHER- Cameron Peter, Fuller Chris K, Donohoue Paul D, Jones Brittnee N, Thompson Matthew S, Carter Matthew M, Gradia Scott, Vidal Bastien, Garner Elizabeth, Slorach Euan M, Lau Elaine, Banh Lynda M, Lied Alexandra M, Edwards Leslie S, Settle Alexander H, Capurso Daniel, Llaca Victor, Deschamps Stéphane, Cigan Mark, Young Joshua K, May Andrew P, "Mapping the genomic landscape of CRISPR-Cas9 cleavage", Nature Methods, New York, (20170601), vol. 14, no. 6, doi:10.1038/nmeth.4284, ISSN 1548-7091, pages 600 - 606, XP055852913
OTHER- Kuzin Alexander, Redler Brendan, Onuska Jaya, Slesarev Alexei, "RGEN-seq for highly sensitive amplification-free screen of off-target sites of gene editors", Scientific Reports, (20211208), vol. 11, no. 1, doi:10.1038/s41598-021-03160-8, XP093053289

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