USOO8795959B2 (12) United States Patent (10) Patent No.: US 8,795,959 B2 Ryan (45) Date of Patent: * Aug. 5, 2014 (54) ISOLATED GLUCOKINASE GENOMIC FOREIGN PATENT DOCUMENTS POLYNUCLEOTDE FRAGMENTS FROM WO 952O678 8, 1995 CHROMOSOME 7 WO OO58467 10, 2000 (71) Applicant: Ryogen LLC, Suffern, NY (US) OTHER PUBLICATIONS (72) Inventor: James Ryan, Augusta, GA (US) Sulston et al., Genome Research, vol. 8, pp. 1097-1108 (1998).* Stoffel et alProc. Natl. Acad. Sci., vol. 89, pp. 2698-2702 (1992).* (73) Assignee: Ryogen LLC, Suffern, NY (US) logy et al., Molecular Endocrinol. vol. 6, pp. 1070-1081 1992). (*) Notice: Subject to any disclaimer, the term of this Table 24 of U.S. Appl. No. 60/231.498. patent is extended or adjusted under 35 ablemed, ES Froc. Nall. r Acad. N.SEs Sc1. : 14800. 1999 U.S.C. 154(b) by 0 days. Altschul, Nucleic Acids Res. 25: 3389-3402. 1997. This patent is Subject to a terminal dis- Burge, J. Mol. Biol. 268: 78-94. 1997. claimer. EMBL database Accession No. Q9UES0 May 1, 2000 SNARE pro tein Ykt6 (Fragment) Homo sapiens. (21) Appl. No.: 13/680,178 International Search Report for PCT/2001/29454, filed Mar. 27. 2003. (22) Filed: Nov. 19, 2012 Layne, J. Biol. Chem. 273:15654-15660. 1998. 9 Maestrini, Hum. Mol. Gen. 2:761-766. 1993. O O McNew, J. Biol. Chem. 272: 17776-17783. 1997. (65) Prior Publication Data Muise, Biochem J. 343: 341-345. 1999. US 2013/O13O250 A1 May 23, 2013 Nuttal, Bone 27: 177-184. 2000. Ohno, Biochem Biophys Res Comm 228: 411-414, 1996. Perez. “Characterization of the 5'-flanking region of the gene encod O O ing the 50 kDa subunit of human DNA polymerase O' Biochem Related U.S. Application Data Biophys Acta 1493: 231-236. 2000. (60) 31,Division 2009, ofnow application Pat. No. 8,313,899,No. 12/533,105, which filedis a division on Jul. SEE.E." solos 7702 of application No. 10642,946, filed on Aug. 18, 2003, Tanizawa, Mo1. Endocrinol 6: 1070-1081. 1992. now Pat. No. 7.588.915, which is a continuation of Waterston, R.H. GenBank Accession No. AC0006454.4 (gi: application No. 09/957.956, filed on Sep. 21, 2001, 28261662) Submitted Jan. 28, 1999, bases 1-153203. now abandoned. Waterston, R.H. GenBank Accession No. AC0006456.3 (gi: 21322189) Submitted Jan. 28, 1999, bases 1-75609. (60) Provisional application No. 60/234,422, filed on Sep. Waterston, R.H. GenBank Accession No. AC0006454.2 21, 2000. (gi:4337283) Submitted Jan. 28, 1999, bases 1-151965. Zhang, Genomics 29: 179-186. 1995. (51) Int. Cl. U.S. Appl. No. 13/680.203, Non-Final Office Action May 30, 2013. CI2O I/68 (2006.01) U.S. Appl.pp No. 13,680,223 Non-Final Office Action Mayy 30,5U, 2013. U.S. Appl. No. 09/957,956 Non-Final Office Action Dec. 4, 2002. Ea 3.08: U.S. Appl. No. 09/957,956 Non-Final Office Action May 21, 2003. U.S. Appl. No. 10/642,946 Non-Final Office Action Oct. 17, 2006. C7H 2L/02 (2006.01) U.S. Appl. No. 10/642,946 Non-Final Office Action Oct. 26, 2007. C7H 2L/04 (2006.01) U.S. Appl. No. 10/642,946 Non-Final Office Action Mar. 25, 2008. (52) U.S. Cl. U.S. Appl. No. 10/642,946 Non-Final Office Action Oct. 16, 2008. USPC .......... 435/6; 435/69.1:435/91. 1; 435/91.31; 435/455; 536/23.1536/23.2:536/23.5:536/24.31 (Continued) (58) Field of Classification Search Primary Examiner — Jane Zara USPC ........ 435/6, 91.1, 91.31, 69.1, 455; 536/23.1, (74) Attorney, Agent, or Firm — Cheryl H. Agris; Agris & 536/24.3, 24.31, 23.2, 23.5 von Natzmer, LLP See application file for complete search history. s (56) Refeerees Citede (57) ABSTRACT Provided are isolated genomic polynucleotide fragments that U.S. PATENT DOCUMENTS encode human SNARE YKT6, human glucokinase, human adipocyte enhancer binding protein (AEBP1) and DNA 5,541,060 A 7, 1996 Bell 5,624,803 A 4/1997 Noonberg directed 50 kD regulatory subunit (POLD2), vectors and 5,972,334 A 10/1999 Denney hosts containing these fragments and fragments hybridizing 6,783,961 B1 8, 2004 Edwards to noncoding regions as well as antisense oligonucleotides to 6,812,339 B1 1 1/2004 Venter these fragments. The invention is further directed to methods 8,313,899 B2 * 1 1/2012 Ryan ............................. 435/455 2002/0048763 A1 4/2002 Penn of using these fragments to obtain SNARE YKT6, human 2003/OO778O8 A1 4/2003 Rosen glucokinase, AEBP1 protein and POLD2 and to diagnose, 2003/0204075 A9 10/2003 Wang treat, prevent and/or ameliorate a pathological disorder. 2007, OO15162 A1 1/2007 Rosen 2007/0031842 A1 2/2007 Rosen 2 Claims, No Drawings US 8,795,959 B2 Page 2 (56) References Cited U.S. Appl. No. 60/231.498, filed Sep. 8, 2000, Venter. (Priority for US Patent 68.12339). OTHER PUBLICATIONS Table 1 of U.S. Appl. No. 60/231.498, Sep. 8, 2000 Table 2 of U.S. Appl. No. 60/231.498, Sep. 8, 2000. Appl. ... 10/642,946 Notice of Allowance Apr. 28, 2009. Table 3 of U.S. Appl. No. 60/231.498, Sep. 8, 2000. Appl. 12/533,105 Non-Final Office Action May 21, 2010. Table 4 of U.S. Appl. No. 60/231.498, Sep. 8, 2000. Appl. 12/533,105 Final Office Action Nov. 29, 2010. No. Appl. 12/533,105 Non-Final Office Action Mar. 5, 2012. Table 5 of U.S. Appl. 60/231.498, Sep. 8, 2000. Appl. 12/533,105 Notice of Allowance Jul. 16, 2012. Table 6 of U.S. Appl. No. 60/231.498, Sep. 8, 2000. Appl. 12/533,130 Non-Final Office Action May 20, 2010. Table 7 of U.S. Appl. No. 60/231.498, Sep. 8, 2000. Appl. 12/533,130 Final Office Action Nov. 29, 2010. Table 8 of U.S. Appl. 60/231.498, Sep. 8, 2000. Appl. 12/533,130 Non-Final Office Action Mar. 29, 2012. Table 9 of U.S. Appl. 60/231.498, Sep. 8, 2000. Appl. 12/533,130 Notice of Allowance Jul. 24, 2012. Table 10 of U.S. Appl. 60/231.498, Sep. 8, 2000. Appl. 12/533,164 Non-Final Office Action Jun. 15, 2010. Table 11 of U.S. Appl. 60/231.498, Sep. 8, 2000. Appl. 12/533,164 Final Office Action Dec. 29, 2010. Table 12 of U.S. Appl. 60/231.498, Sep. 8, 2000. Appl. 12/533,164 Non-Final Office Action Mar. 2, 2012. Table 13 of U.S. Appl. 60/231.498, Sep. 8, 2000. Appl. 12/533,164 Notice of Allowance Jul. 11, 2012. Appl. 12/533,087 Non-Final Office Action Apr. 6, 2011. Table 14 of U.S. Appl. 60/231.498, Sep. 8, 2000. Appl. No. 12/533,087 Final Office Action Oct. 4, 2011. Table 15 of U.S. Appl. 60/231.498, Sep. 8, 2000. Appl. No. 12/533,087 Notice of Allowance Jan. 12, 2012. Table 16 of U.S. Appl. 60/231.498, Sep. 8, 2000. Sequence Alignment U.S. Appl. No. 12/533,105 Non-final Office Table 17 of U.S. Appl. 60/231.498, Sep. 8, 2000. Action May 21, 2010 SEQID No. 6 NT 20.485-33,460 Result 3 (vs Table 18 of U.S. Appl. 60/231.498, Sep. 8, 2000. AC006454.4 PRI May 30, 2003. Table 19 of U.S. Appl. 60/231.498, Sep. 8, 2000. Sequence Alignment U.S. Appl. No. 12/533,130 Non-final Office Action May 20, 2010 SEQ ID No. 5 Result 3 (vs AC006454.4 PRI Table 20 of U.S. Appl. 60/231.498, Sep. 8, 2000. May 30, 2003 GI:28261662) No SEQID. Table 21 of U.S. Appl. 60/231.498, Sep. 8, 2000. Sequence Alignment U.S. Appl. No. 12/533,164 Non-final Office Table 22 of U.S. Appl. 60/231.498, Sep. 8, 2000. Action Jun. 15, 2010 No SEQID, Result 3 (vs AC006454.4 PRI May Table 23 of U.S. Appl. 60/231.498, Sep. 8, 2000. 20, 2003 GI:2921662) Result 7 (vs AF2397 10.1 PRI Sep. 15, 2000 GI:9963917. * cited by examiner US 8,795,959 B2 1. 2 SOLATED GLUCOKNASE GENOMIC 341-345). B-like carboxypeptidases remove C-terminal argi POLYNUCLEOTIDE FRAGMENTS FROM nine and lysine residues and participate in the release of active CHROMOSOME 7 peptides, such as insulin, alter receptor specificity for polypeptides and terminate polypeptide activity (Skidgel. PRIORITY CLAIM 1988, Trends Pharmacol. Sci. 9:299-304). For example, they are thought to be involved in the onset of obesity (Naggert et This application is a divisional of application Ser. No. al., 1995, Nat. Genet. 10:1335-1342). It has been reported 12/533,105, filed Jul. 31, 2009, which is a divisional of Ser. that obese and hyperglycemic mice homozygous for the fat No. 10/642,946, filed Aug. 18, 2003, now U.S. Pat. No. 7,588, mutation contain a mutation in the CP-E gene. 915, issued Sep. 15, 2009, which is a continuation of appli 10 Full length cDNA clones encoding AEBP1 have been iso cation Ser. No. 09/957.956, filed Sep. 21, 2001, now aban lated from human osteoblast and adipose tissue (Ohno et al., doned, the contents of which all are incorporated herein by 1996, Biochem.