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1. WO2016154579 - CRISPR/CAS-MEDIATED GENE CONVERSION


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INTERNATIONAL SEARCH REPORT (ISR)
Part 1:  1  2  3  4  5  6          Part 2:  A  B  C  D  E 
International application No. Applicant's or agent's file reference
PCT/US2016/024307 126454-00420
International filing date (day/month/year) (Earliest) Priority Date (day/month/year)
25 March 2016 26 March 2015
Applicant
EDITAS MEDICINE, INC.
FOR FURTHER ACTION: See Form PCT/ISA/220 as well as, where applicable, item 5 below.
This international search report has been prepared by this International Searching Authority and is transmitted to the applicant according to Article 18. A copy is being transmitted to the International Bureau.
It is also accompanied by a copy of each prior art document cited in this report.
1. Basis of the report
a. With regard to the language, the international search was carried out on the basis of:
the international application in the language in which it was filed.
a translation of the international application into                                          which is the language of a translation furnished for the purposes of international search (Rules 12.3(a) and 23.1(b)).
b.
This international search report has been established taking into account the rectification of an obvious mistake authorized by or notified to this Authority under Rule 91 (Rule 43.6bis(a)).
c.
1. With regard to any nucleotide and/or amino acid sequence disclosed in the international application, the international search was carried out on the basis of a sequence listing:
a. forming part of the international application as filed:
in the form of an Annex C/ST.25 text file.
on paper or in the form of an image file.
b. furnished together with the international application under PCT Rule 13ter.1(a) for the purposes of international search only in the form of an Annex C/ST.25 text file.
c. furnished subsequent to the international filing date for the purposes of international search only:
in the form of an Annex C/ST.25 text file (Rule 13ter.1(a)).
on paper or in the form of an image file (Rule 13ter.1(b) and Administrative Instructions, Section 713).
2.
In addition, in the case that more than one version or copy of a sequence listing has been filed or furnished, the required statements that the information in the subsequent or additional copies is identical to that forming part of the application as filed or does not go beyond the application as filed, as appropriate, were furnished.
3.
Additional comments:
2. Certain claims were found unsearchable
3. Unity of invention is lacking
This International Searching Authority found multiple inventions in this international application, as follows:
1. claims: 19-23, 39-58(completely); 1-18, 30-38(partially)
A method of modifying an endogenous target gene in a cell, the method comprising: contacting the cell with a first gRNA molecule, a first enzymatically active Cas9 (eaCas9) molecule, a second gRNA molecule, and a second eaCas9 molecule; wherein the first gRNA molecule and the first eaCas9 molecule associate with the target gene and generate a first single strand cleavage event on a first strand of the target gene; wherein the second gRNA molecule and the second eaCas9 molecule associate with the target gene and generate a second single strand cleavage event on a second strand of the target gene, thereby forming a double strand break having a first overhang and a second overhang; and wherein the first overhang and the second overhang in the target gene are repaired using an endogenous homologous region, thereby modifying the endogenous target gene in the cell; wherein the target gene is an HBBgene; wherein the first gRNA molecule is a gRNA molecule comprising SEQ ID NO:387, and wherein the second gRNA molecule is a gRNA molecule comprising SEQ ID NO: 16318; wherein the first gRNA molecule is a gRNA molecule comprising any one of SEQ ID NOs: 387-485, 6803-6871, or 16010-16256, and wherein the second gRNA molecule is a gRNA molecule comprising any one of SEQ ID NOs: 387-485, 6803-6871, or 16010-16256; wherein the cell is in, or is taken from, a patient having sickle cell disease or beta thalassemia; wherein the endogenous homologous region comprises a region of an endogenous HDB gene; A composition comprising: a first non-naturally occurring gRNA molecule; a first non-naturally occurring enzymatically active Cas9 (eaCas9) molecule a second non-naturally occurring gRNA molecule; and a second non-naturally occurring eaCas9 molecule; A method of modifying a target region of a target gene in a mammalian cell, wherein the target gene is anHBBgene, and wherein the endogenous homologous region is a region of anHBDgene; A method of increasing the percentage of cells in a population of cells that modify a target region of a target gene by gene conversion using an endogenous homologous region.
2. claims: 24-26(completely); 1-18, 30-38(partially)
Idem as invention 1 but limited to the target gene SMN1; wherein the cell is in, or taken from, a patient having spinal muscle atrophy; wherein the nedogeneous homologous region includes a region of an endogeneous SMN2 gene;
3. claims: 27-29(completely); 1-18, 30-38(partially)
Idem asinvention 1, but limited to  the target gene NCF1 (p47-PHOX); wherein the cell is in, ot is taken from, a patient having chronic granulomateous disease, wherein the endogenous homologous region includes a region of a p47-PHOX pseudogene;
1.
As all required additional search fees were timely paid by the applicant, this international search report covers all searchable claims.
2.
As all searchable claims could be searched without effort justifying additional fees, this Authority did not invite payment of additional fees.
3.
As only some of the required additional search fees were timely paid by the applicant, this international search report covers only those claims for which fees were paid, specifically claims Nos.:
4.
No required additional search fees were timely paid by the applicant. Consequently, this international search report is restricted to the invention first mentioned in the claims; it is covered by claims Nos.: 19-23, 39-58(completely); 1-18, 30-38(partially)
Remark on Protest
The additional search fees were accompanied by the applicant’s protest and, where applicable, the payment of a protest fee.
The additional search fees were accompanied by the applicant’s protest but the applicable protest fee was not paid within the time limit specified in the invitation.
No protest accompanied the payment of additional search fees.
4. Title of the invention
The text is approved as submitted by the applicant.
The text has been established by this Authority to read as follows:
5. Abstract
The text is approved as submitted by the applicant.
The text has been established, according to Rule 38.2, by this Authority as it appears in Box No. IV. The applicant may, within one month from the date of mailing of this international search report, submit comments to this Authority.
6. Drawings
a.
The figure of the drawings to be published with the abstract is Figure No.     2    
as suggested by the applicant.
as selected by this Authority, because the applicant failed to suggest a figure.
as selected by this Authority, because this figure better characterizes the invention.
b.
none of the figures is to be published with the abstract.

A. CLASSIFICATION OF SUBJECT MATTER

     C12N 15/10 (2006.01)i
According to International Patent Classification (IPC) or to both national classification and IPC

B. FIELDS SEARCHED

Minimum documentation searched (classification system followed by classification symbols):
     C12N
Documentation searched other than minimum documentation to the extent that such documents are included in the fields searched:
Electronic data base consulted during the international search (name of data base and, where practicable, search terms used):
EPO-Internal, BIOSIS, CAB Data, Sequence Search, WPI Data

C. DOCUMENTS CONSIDERED TO BE RELEVANT

Category* Citation of document, with indication, where appropriate, of the relevant passages Relevant to claim No.
(1)
X
Jennifer Hollywood, "Cystic fibrosis gene repair: correction of [Delta]F508 using ZFN and CRISPR/Cas9 guide RNA gene editing tools", 01 January 2013 (2013-01-01), page 1-193,
Retrieved from the Internet:
URL:https://cora.ucc.ie/bitstream/handle/10468/1407/JH thesis.pdf?sequence=3
XP055209264
[retrieved on  2015-08-24]
39-41
Y
page 133, line 1 - page 151, line 26
1-18,30-38,45-49,52-58
(2)
X
RAN F ANN ET AL, "Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity", CELL,Vol. 154, No. 6, 12 September 2013 (2013-09-12), page 1380-1389,
XP055299681
1-6,10,13-18,37-41,45-49,52-54,56-58
Y
the whole document
1-18,30-38,45-49,52-58
(3)
X
TREVINO ALEXANDRO E ET AL, "Genome editing using Cas9 nickases", METHODS IN ENZYMOLOGY, ACADEM. PRESS, USA,Vol. 546, 12 November 2014 (2014-11-12), page 161-174,
XP009187160
1-6,10,13-18,37-40,45-49,52-54,56-58
Y
the whole document
1-18,30-38,45-49,52-58
(4)
X
RAN F ANN ET AL, "Genome engineering using the CRISPR-Cas9 system", NATURE PROTOCOLS, NATURE PUBLISHING GROUP, GB,Vol. 8, No. 11, 01 November 2013 (2013-11-01), page 2281-2308,
XP009174668
1,37-40,45,54
Y
the whole document
1-18,30-38,45-49,52-58
(5)
X
WO 2014191518 A1 (CELLECTIS [FR]) 04 December 2014 (2014-12-04)
1,37-41,45-49,52-58
Y
the whole document
1-18,30-38,45-49,52-58
(6)
X,P
S. W. CHO ET AL, "Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases", GENOME RESEARCH,Vol. 24, No. 1, 05 November 2015 (2015-11-05), page 132-141,
XP055227885
39,40
the whole document
(7)
X,P
WO 2015048577 A2 (EDITAS MEDICINE INC [US]) 02 April 2015 (2015-04-02)
39,40
cited in the application
claims 1-258
(8)
A
L. CONG ET AL, "Multiplex Genome Engineering Using CRISPR/Cas Systems", SCIENCE,Vol. 339, No. 6121, 15 February 2013 (2013-02-15), page 819-823,
XP055067741
1-23,30-58
cited in the application
the whole document
A
& L. CONG ET AL, "Supplementary Material to: Multiplex Genome Engineering Using CRISPR/Cas Systems",  SCIENCE,Vol. 339, No. 6121, 03 January 2013 (2013-01-03), page 819-823,
XP055153963
1-23,30-58
the whole document
(9)
A
P. MALI ET AL, "RNA-Guided Human Genome Engineering via Cas9", SCIENCE,Vol. 339, No. 6121, 15 February 2013 (2013-02-15), page 823-826,
XP055300091
1-23,30-58
cited in the application
the whole document
(10)
A
WO 2014065596 A1 (TOOLGEN INC [KR]) 01 May 2014 (2014-05-01)
1-23,30-58
the whole document
(11)
A
PRASHANT MALI ET AL, "CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering", NATURE BIOTECHNOLOGY,Vol. 31, No. 9, 01 August 2013 (2013-08-01), page 833-838,
XP055299678
1-23,30-58
the whole document
A
& PRASHANT MALI ET AL, "Supplementary Information: CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering (Nature Biotechnology Vol. 31:833-838,2013)",  NATURE BIOTECHNOLOGY,Vol. 31, No. 9, 01 August 2013 (2013-08-01), page 1-36,
XP055294730
1-23,30-58
the whole document
(12)
A
WO 2015006498 A2 (HARVARD COLLEGE [US]; CHILDRENS MEDICAL CENTER [US]) 15 January 2015 (2015-01-15)
1-23,30-58
the whole document
(13)
X,P
WO 2015148863 A2 (EDITAS MEDICINE INC [US]) 01 October 2015 (2015-10-01)
1-23,30-58
the whole document
*
Special categories of cited documents:
"A"
document defining the general state of the art which is not considered to be of particular relevance
"D"
document cited by the applicant in the international application
"E"
earlier application or patent but published on or after the international filing date
"L"
document which may throw doubts on priority claim(s) or which is cited to establish the publication date of another citation or other special reason (as specified)
"O"
document referring to an oral disclosure, use, exhibition or other means
"P"
document published prior to the international filing date but later than the priority date claimed
"T"
later document published after the international filing date or priority date and not in conflict with the application but cited to understand the principle or theory underlying the invention
"X"
document of particular relevance; the claimed invention cannot be considered novel or cannot be considered to involve an inventive step when the document is taken alone
"Y"
document of particular relevance; the claimed invention cannot be considered to involve an inventive step when the document is combined with one or more other such documents, such combination being obvious to a person skilled in the art
"&"
document member of the same patent family

D. INFORMATION ON PATENT FAMILY MEMBERS

Patent document cited in search report Publication date
(day/month/year)
Patent family member(s) Publication date
(day/month/year)
WO 2014191518 A1
04 December 2014
AU 2014273082 A1
CA 2913865 A1
EP 3004349 A1
JP 2016520317 A
US 2016122774 A1
WO 2014191518 A1
17 December 2015
04 December 2014
13 April 2016
14 July 2016
05 May 2016
04 December 2014
WO 2015048577 A2
02 April 2015
US 2016237455 A1
WO 2015048577 A2
18 August 2016
02 April 2015
WO 2014065596 A1
01 May 2014
AU 2013335451 A1
AU 2015218519 A1
CA 2888190 A1
CN 104968784 A
CN 105441440 A
EP 2912175 A1
HK 1212732 A1
JP 2016027807 A
JP 2016500003 A
KR 20150101446 A
KR 20150101476 A
KR 20150101477 A
KR 20150101478 A
SG 11201503059X A
US 2015284727 A1
US 2015322457 A1
US 2015344912 A1
WO 2014065596 A1
07 May 2015
17 September 2015
01 May 2014
07 October 2015
30 March 2016
02 September 2015
17 June 2016
25 February 2016
07 January 2016
03 September 2015
03 September 2015
03 September 2015
03 September 2015
29 June 2015
08 October 2015
12 November 2015
03 December 2015
01 May 2014
WO 2015006498 A2
15 January 2015
EP 3019595 A2
JP 2016528890 A
US 2015152436 A1
WO 2015006498 A2
WO 2016057835 A2
18 May 2016
23 September 2016
04 June 2015
15 January 2015
14 April 2016
WO 2015148863 A2
01 October 2015
NONE
Name and mailing address of the ISA/:
European Patent Office
P.B. 5818, Patentlaan 2, 2280 HV Rijswijk,
Netherlands
Telephone No. (+31-70)340-2040
Facsimile No. (+31-70)340-3016
Date of the actual completion of the international search:
10 October 2016
Date of mailing of the international search report:
22 December 2016
Authorized officer:
Hornig, Horst
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