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Extract from the Register of European Patents

EP About this file: EP3022320

EP3022320 - WHOLE-GENOME AND TARGETED HAPLOTYPE RECONSTRUCTION [Right-click to bookmark this link]
StatusPatent maintained as amended
Status updated on  22.08.2024
Database last updated on 07.03.2026
FormerThe patent has been granted
Status updated on  11.06.2021
FormerGrant of patent is intended
Status updated on  28.01.2021
FormerExamination is in progress
Status updated on  16.12.2020
FormerGrant of patent is intended
Status updated on  19.10.2020
FormerExamination is in progress
Status updated on  11.09.2020
FormerGrant of patent is intended
Status updated on  20.07.2020
FormerExamination is in progress
Status updated on  17.05.2019
Most recent event   Tooltip06.09.2024Lapse of the patent in a contracting state
New state(s): MT		published on 09.10.2024  [2024/41]
Applicant(s)For all designated states
Ludwig Institute for Cancer Research Ltd
666 Third Avenue
28th Floor
New York, NY 10017 / US
[2021/27]
Former [2016/30]For all designated states
Ludwig Institute For Cancer Research Ltd.
666 Third Avenue
28th Floor
New York, NY 10017 / US
Former [2016/21]For all designated states
LUDWIG INSTITUTE FOR CANCER RESEARCH
666 Third Avenue 28th Floor
New York NY 10017 / US
Inventor(s)01 / REN, Bing
c/o Ludwig Institute For Cancer Research
9500 Gilman Drive
La Jolla, CA 92093 / US
02 / SELVARAJ, Siddarth
c/o Ludwig Institute For Cancer Research
9500 Gilman Drive
La Jolla, CA 92093 / US
03 / DIXON, Jesse
c/o Ludwig Institute For Cancer Research
9500 Gilman Drive
La Jolla, CA 92093 / US
04 / SCHMITT, Anthony
7755 Saranac Place, Unit 45
La Mesa, CA 91942 / US
 [2016/40]
Former [2016/21]01 / REN, Bing
c/o Ludwig Institute For Cancer Research
9500 Gilman Drive
La Jolla, CA 92093 / US
02 / SELVARAJ, Siddarth
c/o Ludwig Institute For Cancer Research
9500 Gilman Drive
La Jolla, CA 92093 / US
03 / DIXON, Jesse
c/o Ludwig Institute For Cancer Research
9500 Gilman Drive
La Jolla, CA 92093 / US
Representative(s)Dehns
10 Old Bailey
London EC4M 7NG / GB
[N/P]
Former [2021/28]Dehns
St. Bride's House
10 Salisbury Square
London EC4Y 8JD / GB
Former [2016/21]Gardner, Rebecca Katherine
Dehns
St Bride's House
10 Salisbury Square
London EC4Y 8JD / GB
Application number, filing date14826457.518.07.2014
[2016/21]
WO2014US47243
Priority number, dateUS201361856486P19.07.2013         Original published format: US 201361856486 P
US201361873671P04.09.2013         Original published format: US 201361873671 P
[2016/21]
Filing languageEN
Procedural languageEN
PublicationType: A1 Application with search report
No.:WO2015010051
Date:22.01.2015
Language:EN
[2015/03]
Type: A1 Application with search report 
No.:EP3022320
Date:25.05.2016
Language:EN
The application published by WIPO in one of the EPO official languages on 22.01.2015 takes the place of the publication of the European patent application.
[2016/21]
Type: B1 Patent specification 
No.:EP3022320
Date:14.07.2021
Language:EN
[2021/28]
Type: B2 New European patent specification 
No.:EP3022320
Date:25.09.2024
Language:EN
[2024/39]
Search report(s)International search report - published on:US22.01.2015
(Supplementary) European search report - dispatched on:EP23.05.2017
ClassificationIPC:C12Q1/6869
[2020/32]
CPC:
C12Q1/6869 (EP,US); C12Q1/6874 (US)
C-Set:
C12Q1/6869, C12Q2523/101, C12Q2535/122 (EP,US)
Former IPC [2016/21]C12Q1/68
Designated contracting statesAL,   AT,   BE,   BG,   CH,   CY,   CZ,   DE,   DK,   EE,   ES,   FI,   FR,   GB,   GR,   HR,   HU,   IE,   IS,   IT,   LI,   LT,   LU,   LV,   MC,   MK,   MT,   NL,   NO,   PL,   PT,   RO,   RS,   SE,   SI,   SK,   SM,   TR [2016/21]
TitleGerman:GESAMTGENOM UND GEZIELTE HAPLOTYPREKONSTRUKTION[2016/21]
English:WHOLE-GENOME AND TARGETED HAPLOTYPE RECONSTRUCTION[2016/21]
French:RECONSTRUCTION D'HAPLOTYPE CIBLÉE ET AU NIVEAU DU GÉNOME INTÉGRAL[2016/21]
Entry into regional phase18.02.2016National basic fee paid 
18.02.2016Search fee paid 
18.02.2016Designation fee(s) paid 
18.02.2016Examination fee paid 
Examination procedure18.02.2016Examination requested  [2016/21]
21.12.2017Amendment by applicant (claims and/or description)
21.05.2019Despatch of a communication from the examining division (Time limit: M06)
09.01.2020Despatch of communication that the application is deemed to be withdrawn, reason: reply to the communication from the examining division not received in time
13.03.2020Reply to a communication from the examining division
21.07.2020Communication of intention to grant the patent
11.09.2020Disapproval of the communication of intention to grant the patent by the applicant or resumption of examination proceedings by the EPO
20.10.2020Communication of intention to grant the patent
16.12.2020Disapproval of the communication of intention to grant the patent by the applicant or resumption of examination proceedings by the EPO
29.01.2021Communication of intention to grant the patent
01.06.2021Fee for grant paid
01.06.2021Fee for publishing/printing paid
01.06.2021Receipt of the translation of the claim(s)
Opposition(s)Opponent(s)01  13.04.2022  19.04.2022  ADMISSIBLE
V.O.
P.O. Box 87930
Carnegieplein 5
2508 DH Den Haag / NL
Opponent's representative
V.O.
P.O. Box 87930
Carnegieplein 5
2508 DH Den Haag / NL
 [2022/24]
Former [2022/19]
Opponent(s)01  13.04.2022   
V.O.
P.O. Box 87930
Carnegieplein 5
2508 DH Den Haag / NL
Opponent's representative
V.O.
P.O. Box 106850
Carnegieplein 5
2508 DH Den Haag / NL
04.05.2022Invitation to proprietor to file observations on the notice of opposition
14.09.2022Reply of patent proprietor to notice(s) of opposition
23.01.2024Legal effect of interlocutory decision in opposition
23.01.2024Date of oral proceedings
13.02.2024Despatch of interlocutory decision in opposition
13.02.2024Despatch of minutes of oral proceedings
21.05.2024Despatch of communication that the patent will be maintained as amended
Request for further processing for:The application is deemed to be withdrawn due to failure to reply to the examination report
13.03.2020Request for further processing filed
13.03.2020Full payment received (date of receipt of payment)
Request granted
20.03.2020Decision despatched
Fees paidRenewal fee
28.07.2016Renewal fee patent year 03
27.07.2017Renewal fee patent year 04
30.07.2018Renewal fee patent year 05
22.07.2019Renewal fee patent year 06
22.07.2020Renewal fee patent year 07
Opt-out from the exclusive  Tooltip
competence of the Unified
Patent Court		 See the Register of the Unified Patent Court for opt-out data
Responsibility for the accuracy, completeness or quality of the data displayed under the link provided lies entirely with the Unified Patent Court.
Lapses during opposition  TooltipHU18.07.2014
AL14.07.2021
AT14.07.2021
CY14.07.2021
CZ14.07.2021
DK14.07.2021
EE14.07.2021
ES14.07.2021
FI14.07.2021
HR14.07.2021
IT14.07.2021
LT14.07.2021
LV14.07.2021
MC14.07.2021
MK14.07.2021
MT14.07.2021
PL14.07.2021
RO14.07.2021
RS14.07.2021
SI14.07.2021
SK14.07.2021
SM14.07.2021
TR14.07.2021
IE18.07.2021
LU18.07.2021
BE31.07.2021
BG14.10.2021
NO14.10.2021
GR15.10.2021
IS14.11.2021
PT15.11.2021
[2024/41]
Former [2024/29]HU18.07.2014
AL14.07.2021
AT14.07.2021
CY14.07.2021
CZ14.07.2021
DK14.07.2021
EE14.07.2021
ES14.07.2021
FI14.07.2021
HR14.07.2021
IT14.07.2021
LT14.07.2021
LV14.07.2021
MC14.07.2021
MK14.07.2021
PL14.07.2021
RO14.07.2021
RS14.07.2021
SI14.07.2021
SK14.07.2021
SM14.07.2021
TR14.07.2021
IE18.07.2021
LU18.07.2021
BE31.07.2021
BG14.10.2021
NO14.10.2021
GR15.10.2021
IS14.11.2021
PT15.11.2021
Former [2024/22]HU18.07.2014
AL14.07.2021
AT14.07.2021
CY14.07.2021
CZ14.07.2021
DK14.07.2021
EE14.07.2021
ES14.07.2021
FI14.07.2021
HR14.07.2021
IT14.07.2021
LT14.07.2021
LV14.07.2021
MC14.07.2021
MK14.07.2021
PL14.07.2021
RO14.07.2021
RS14.07.2021
SI14.07.2021
SK14.07.2021
SM14.07.2021
IE18.07.2021
LU18.07.2021
BE31.07.2021
BG14.10.2021
NO14.10.2021
GR15.10.2021
IS14.11.2021
PT15.11.2021
Former [2023/30]HU18.07.2014
AL14.07.2021
AT14.07.2021
CY14.07.2021
CZ14.07.2021
DK14.07.2021
EE14.07.2021
ES14.07.2021
FI14.07.2021
HR14.07.2021
IT14.07.2021
LT14.07.2021
LV14.07.2021
MC14.07.2021
PL14.07.2021
RO14.07.2021
RS14.07.2021
SI14.07.2021
SK14.07.2021
SM14.07.2021
IE18.07.2021
LU18.07.2021
BE31.07.2021
BG14.10.2021
NO14.10.2021
GR15.10.2021
IS14.11.2021
PT15.11.2021
Former [2023/29]HU18.07.2014
AL14.07.2021
AT14.07.2021
CZ14.07.2021
DK14.07.2021
EE14.07.2021
ES14.07.2021
FI14.07.2021
HR14.07.2021
IT14.07.2021
LT14.07.2021
LV14.07.2021
MC14.07.2021
PL14.07.2021
RO14.07.2021
RS14.07.2021
SI14.07.2021
SK14.07.2021
SM14.07.2021
IE18.07.2021
LU18.07.2021
BE31.07.2021
BG14.10.2021
NO14.10.2021
GR15.10.2021
IS14.11.2021
PT15.11.2021
Former [2022/36]AL14.07.2021
AT14.07.2021
CZ14.07.2021
DK14.07.2021
EE14.07.2021
ES14.07.2021
FI14.07.2021
HR14.07.2021
IT14.07.2021
LT14.07.2021
LV14.07.2021
MC14.07.2021
PL14.07.2021
RO14.07.2021
RS14.07.2021
SI14.07.2021
SK14.07.2021
SM14.07.2021
IE18.07.2021
LU18.07.2021
BE31.07.2021
BG14.10.2021
NO14.10.2021
GR15.10.2021
IS14.11.2021
PT15.11.2021
Former [2022/35]AL14.07.2021
AT14.07.2021
CZ14.07.2021
DK14.07.2021
EE14.07.2021
ES14.07.2021
FI14.07.2021
HR14.07.2021
LT14.07.2021
LV14.07.2021
MC14.07.2021
PL14.07.2021
RO14.07.2021
RS14.07.2021
SI14.07.2021
SK14.07.2021
SM14.07.2021
IE18.07.2021
LU18.07.2021
BE31.07.2021
BG14.10.2021
NO14.10.2021
GR15.10.2021
IS14.11.2021
PT15.11.2021
Former [2022/34]AL14.07.2021
AT14.07.2021
CZ14.07.2021
DK14.07.2021
EE14.07.2021
ES14.07.2021
FI14.07.2021
HR14.07.2021
LT14.07.2021
LV14.07.2021
MC14.07.2021
PL14.07.2021
RO14.07.2021
RS14.07.2021
SI14.07.2021
SK14.07.2021
SM14.07.2021
LU18.07.2021
BE31.07.2021
BG14.10.2021
NO14.10.2021
GR15.10.2021
IS14.11.2021
PT15.11.2021
Former [2022/29]AL14.07.2021
AT14.07.2021
CZ14.07.2021
DK14.07.2021
EE14.07.2021
ES14.07.2021
FI14.07.2021
HR14.07.2021
LT14.07.2021
LV14.07.2021
MC14.07.2021
PL14.07.2021
RO14.07.2021
RS14.07.2021
SI14.07.2021
SK14.07.2021
SM14.07.2021
LU18.07.2021
BG14.10.2021
NO14.10.2021
GR15.10.2021
IS14.11.2021
PT15.11.2021
Former [2022/25]AT14.07.2021
CZ14.07.2021
DK14.07.2021
EE14.07.2021
ES14.07.2021
FI14.07.2021
HR14.07.2021
LT14.07.2021
LV14.07.2021
MC14.07.2021
PL14.07.2021
RO14.07.2021
RS14.07.2021
SK14.07.2021
SM14.07.2021
LU18.07.2021
BG14.10.2021
NO14.10.2021
GR15.10.2021
IS14.11.2021
PT15.11.2021
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CZ14.07.2021
DK14.07.2021
EE14.07.2021
ES14.07.2021
FI14.07.2021
HR14.07.2021
LT14.07.2021
LV14.07.2021
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PL14.07.2021
RO14.07.2021
RS14.07.2021
SK14.07.2021
LU18.07.2021
BG14.10.2021
NO14.10.2021
GR15.10.2021
IS14.11.2021
PT15.11.2021
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DK14.07.2021
ES14.07.2021
FI14.07.2021
HR14.07.2021
LT14.07.2021
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PL14.07.2021
RS14.07.2021
BG14.10.2021
NO14.10.2021
GR15.10.2021
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ES14.07.2021
FI14.07.2021
HR14.07.2021
LT14.07.2021
LV14.07.2021
PL14.07.2021
RS14.07.2021
BG14.10.2021
NO14.10.2021
GR15.10.2021
IS14.11.2021
PT15.11.2021
Former [2022/09]AT14.07.2021
ES14.07.2021
FI14.07.2021
LT14.07.2021
RS14.07.2021
BG14.10.2021
NO14.10.2021
PT15.11.2021
Former [2022/08]AT14.07.2021
ES14.07.2021
FI14.07.2021
LT14.07.2021
BG14.10.2021
NO14.10.2021
Former [2022/07]AT14.07.2021
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NO14.10.2021
Documents cited:Search[XI] WO2012106546  (UNIV WASHINGTON CT COMMERCIALI et al.) [X] 1-6,9-15 * abstract * * paragraphs [0007] , [0009] , [0019] , [0024] , [0065] , [0067] , [0068] , [0073] , [0091] , [0092] , [0125] , [0127] , [0128] , [0130] , [0141] * * paragraphs [0144] , [0157] , [0198] , [0206] , [0227] , [0233] , [0234] * * figures 17,31a *[I] 7,8
 [A]   LIEBERMAN-AIDEN EREZ ET AL: "Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome", SCIENCE, AMERICAN ASSOCIATION FOR THE ADVANCEMENT OF SCIENCE, vol. 326, no. 5950, 1 October 2009 (2009-10-01), pages 289 - 293, XP002591649, ISSN: 0036-8075 [A] 1-15 * the whole document *
 [A]   JAY SHENDURE ET AL: "The expanding scope of DNA sequencing", NATURE BIOTECHNOLOGY, vol. 30, no. 11, 1 November 2012 (2012-11-01), US, pages 1084 - 1094, XP055313781, ISSN: 1087-0156, DOI: 10.1038/2421 [A] 1-15 * the whole document *

DOI:   http://dx.doi.org/10.1038/nbt.2421
International search[X] WO2012106546  (UNIV WASHINGTON CT COMMERCIALI et al.) [X]
 [Y] US2012220494  (SAMUELS MICHAEL et al.) [Y]
 [Y] US2007172853  (MCCARROLL STEVEN A et al.) [Y]
 [Y]   SHENDURE ET AL.: "The expanding scope of DNA sequencing", NAT BIOTECHNOL., vol. 30, no. 11, 8 November 2012 (2012-11-08), pages 1084 - 1094, XP055313781 [Y]

DOI:   http://dx.doi.org/10.1038/nbt.2421
 [A]   LEBEOEMAN-AIDEN ET AL.: "Comprehensive mapping of long range interactions reveals folding principles of the human genome", SCIENCE, vol. 326, 9 October 2009 (2009-10-09), pages 289 - 293, XP002591649 [A]
 [XP]   SELVARAJ ET AL.: "Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing", NAT BIOTECHNOL., vol. 31, 3 November 2013 (2013-11-03), pages 1111 - 1118, XP055313784 [XP]

DOI:   http://dx.doi.org/10.1038/nbt.2728
by applicantUS2013096009
   WHEELER ET AL., NATURE, vol. 452, 2008, pages 872 - 876
   PUSHKAREV ET AL., NATURE BIOTECHNOLOGY, vol. 27, 2009, pages 847 - 850
   KITZMAN ET AL., SCIENCE TRANSLATIONAL MEDICINE, vol. 4, 2012, pages 137ra176 [Y]
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   PETERSDORF ET AL., PLOS MEDICINE, vol. 4, 2007, pages e8
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   CIRULLI ET AL., NATURE REVIEWS. GENETICS, vol. 11, 2010, pages 415 - 425
   NG ET AL., NATURE GENETICS, vol. 42, 2010, pages 30 - 35
   ERYTHEMATOSUS ET AL., NATURE GENETICS, vol. 40, 2008, pages 1062 - 1064
   ZSCHOCKE, JOURNAL OF INHERITED METABOLIC DISEASE, vol. 31, 2008, pages 599 - 618
   SANYAL ET AL., NATURE, vol. 489, 2012, pages 109 - 113
   KIRKNESS ET AL., GENOME RESEARCH, vol. 23, 2013, pages 826 - 832
   TEWHEY ET AL., NATURE REVIEWS. GENETICS, vol. 12, 2011, pages 215 - 223
   LEE ET AL., THE PLANT CELL, vol. 19, 2007, pages 731 - 749
   LIEBERMAN-AIDEN ET AL., SCIENCE, vol. 326, 2009, pages 289 - 293
   KAPER ET AL., PROC NATL ACAD SCI USA, vol. 110, 2013, pages 5552 - 57
OppositionWO2012005595
 WO2012005595
   SIDDARTH SELVARAJ, JESSE R DIXON, VIKAS BANSAL, BING REN: "Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing", NATURE BIOTECHNOLOGY, NATURE PUBLISHING GROUP US, NEW YORK, vol. 31, no. 12, New York, pages 1111 - 1118, XP055313784, ISSN: 1087-0156, DOI: 10.1038/nbt.2728 [A] 1-15 * the whole document *

DOI:   http://dx.doi.org/10.1038/nbt.2728
   LIEBERMAN-AIDEN EREZ, ET AL: "Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome", SCIENCE, AMERICAN ASSOCIATION FOR THE ADVANCEMENT OF SCIENCE, US, vol. 326, no. 5950, 1 October 2009 (2009-10-01), US , pages 289 - 293, XP002591649, ISSN: 0036-8075 [A] 1-15 * the whole document *
   J. LEE, K. HE, V. STOLC, H. LEE, P. FIGUEROA, Y. GAO, W. TONGPRASIT, H. ZHAO, I. LEE, X. W. DENG: "Analysis of Transcription Factor HY5 Genomic Binding Sites Revealed Its Hierarchical Role in Light Regulation of Development", THE PLANT CELL, AMERICAN SOCIETY OF PLANT BIOLOGISTS, US, vol. 19, no. 3, US , pages 731 - 749, XP055515865, ISSN: 1040-4651, DOI: 10.1105/tpc.106.047688

DOI:   http://dx.doi.org/10.1105/tpc.106.047688
   IANNONE M A, ET AL.: "MULTIPLEXED SINGLE NUCLEOTIDE POLYMORPHISM GENOTYPING BY OLIGONUCLEOTIDE LIGATION AND FLOW CYTOMETRY", CYTOMETRY, ALAN LISS, NEW YORK., US, vol. 39, no. 02, 1 January 2000 (2000-01-01), US , pages 131 - 140, XP001073442, ISSN: 0196-4763, DOI: 10.1002/(SICI)1097-0320(20000201)39:2<131::AID-CYTO6>3.0.CO;2-U

DOI:   http://dx.doi.org/10.1002/(SICI)1097-0320(20000201)39:2<131::AID-CYTO6>3.0.CO;2-U
   BROWNING BRIAN L, BROWNING SHARON R: "Improving the Accuracy and Efficiency of Identity-by-Descent Detection in Population Data", GENETICS, vol. 194, no. 2, 1 June 2013 (2013-06-01), pages 459 - 471, XP055915356, DOI: 10.1534/genetics.113.150029

DOI:   http://dx.doi.org/10.1534/genetics.113.150029
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   DAVID WHEELER NULL: "The complete genome of an individual by massively parallel DNA sequencing", NATURE, vol. 452, 17 April 2008 (2008-04-17), XP055329056, DOI: 10.1038/nature06884 [I] 7,8

DOI:   http://dx.doi.org/10.1038/nature06884
   SAMUEL LEVY, SUTTON GRANGER, NG PAULINE C, FEUK LARS, HALPERN AARON L, WALENZ BRIAN P, AXELROD NELSON, HUANG JIAQI, KIRKNESS EWEN : "The Diploid Genome Sequence of an Individual Human", vol. 5, 1 October 2007 (2007-10-01), XP055339811, Retrieved from the Internet [retrieved on 20170127], DOI: 10.1371/journal.pbio.0050254 [A] 1-15 * the whole document *

DOI:   http://dx.doi.org/10.1371/journal.pbio.0050254
   HUANG X, MADAN A: "CAP3: A DNA Sequence Assembly Program", GENOME RESEARCH, COLD SPRING HARBOR LABORATORY PRESS, US, vol. 9, 1 January 1999 (1999-01-01), US , pages 868 - 877, XP002267210, ISSN: 1088-9051, DOI: 10.1101/gr.9.9.868 [A] 1-15 * the whole document *

DOI:   http://dx.doi.org/10.1101/gr.9.9.868
   ANONYMOUS: "His-tag", WIKIPEDIA, THE FREE ENCYCLOPEDIA, 4 October 2022 (2022-10-04), XP093146299, Retrieved from the Internet [retrieved on 20240327]
The EPO accepts no responsibility for the accuracy of data originating from other authorities; in particular, it does not guarantee that it is complete, up to date or fit for specific purposes.