WO2001077129A2

WO2001077129A2 - Haplotypes of the apoc1 gene

Info

Publication number: WO2001077129A2
Application number: PCT/US2001/011808
Authority: WO
Inventors: Steven C. Bentivegna; Anne Chew; Julie Y. Choi; Beena Koshy; J. Claiborne Stephens
Original assignee: Genaissance Pharmaceuticals Inc
Current assignee: Cogenics Inc
Priority date: 2000-04-11
Filing date: 2001-04-10
Publication date: 2001-10-18
Anticipated expiration: 2002-10-11
Also published as: AU2001253367A1; WO2001077129A3

Abstract

Novel single nucleotide polymorphisms in the human apolipoprotein C1 (APOC1) gene are described. In addition, various genotypes, haplotypes and haplotype pairs for the APOC1 gene that exist in the population are described. Compositions and methods for haplotyping and/or genotyping the APOC1 gene in an individual are also disclosed. Polynucleotides containing one or more of the APOC1 polymorphisms disclosed herein are also described.

Claims

(a) isolating from the individual a nucleic acid sample containing only one of the two copies of the APOCl gene, or a fragment thereof, that is present in the individual;

(b) amplifying from the nucleic acid molecule a target region containing the selected polymoφhic site;

(c) hybridizing a primer extension oligonucleotide to one allele of the amplified target region;

(d) performing a nucleic acid template-dependent, primer extension reaction on the hybridized genotyping oligonucleotide in the presence of at least two different - terminators of the reaction, wherein said terminators are complementary to the alternative nucleotides present at the selected polymoφhic site; and

(e) detecting the presence and identity of the terminator in the extended genotyping oligonucleotide.

10. A method for predicting a haplotype pair for the apolipoprotein C 1 (APOC 1 ) gene of an individual comprising:

(a) identifying an APOCl genotype for the individual, wherein the genotype comprises the nucleotide pair at two or more polymoφhic sites selected from the group consisting of PSl, PS3, PS4, PS5 and PS6;

(b) enumerating all possible haplotype pairs which are consistent with the genotype; (c) comparing the possible haplotype pairs to the data in Table 3; and

(d) assigning a haplotype pair to the individual that is consistent with the data..

11. The method of claim 10, wherein the identified genotype of the individual comprises the nucleotide pair at each of PS1-PS6.

12. A method for identifying an association between a trait and at least one haplotype or haplotype pair of the apolipoprotein CI (APOCl) gene which comprises comparing the frequency of the haplotype or haplotype pair in a population exhibiting the trait with the frequency of the haplotype or haplotype pair in a reference population, wherein the haplotype is selected from haplotypes 1-9 shown in Table 4 and the haplotype pair is selected from the haplotype pairs shown in Table 3, wherein a higher frequency of the haplotype or haplotype pair in the trait population than in the reference population indicates the trait is associated with the haplotype or haplotype pair.

13. The method of claim 12, wherein the trait is a clinical response to a. drag targeting APOC 1.

14. A composition comprising at least one genotyping oligonucleotide for detecting a polymoφhism in the apohpoprotein CI (APOCl) gene at a polymoφhic site selected from the group consisting of PSl, PS3, PS4, PS5 and PS6.

15. The composition of claim 14, wherein the genotyping oligonucleotide is an allele-specific oligonucleotide that specifically hybridizes to an allele of the APOCl gene at a region containing the polymoφhic site.

33

16. The composition of claim 15, wherein the allele-specific oligonucleotide comprises a nucleotide sequence selected from the group consisting of SEQ ID NOS:4-8, the complements of SEQ ID NOS4-8, and SEQ ID NOS:9-18.

17. The composition of claim 14, wherein the genotyping oligonucleotide is a primer-extension oligonucleotide.

18. The composition of claim 17, wherein the primer extension oligonucleotide comprises a nucleotide sequence selected from the group consisting of SEQ ID NOS: 19-28.

19. A kit for genotyping the APOC 1 gene of an individual, which comprises a set of oligonucleotides designed to genotype each of PSl, PS3, PS4, PS5 and PS6.

20. The kit of claim 19, which further comprises oligonucleotides designed to genotype PS2.

21. An isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of:

(a) a first nucleotide sequence which is a polymoφhic variant of a reference sequence for the apolipoprotein CI (APOCl) gene or a fragment thereof, wherein the reference sequence comprises SEQ ID NO:l and the polymoφhic variant comprises an APOCl isogene defined by a haplotype selected from the group consisting of haplotypes 1-9 in Table 4; and a second nucleotide sequence which is complementary to the first nucleotide sequence.

22. The isolated polynucleotide of claim 21, which is a DNA molecule and comprises both the first and second nucleotide sequences and further comprises expression regulatory elements operably linked to the first nucleotide sequence.

23. A recombinant nonhuman organism transformed or transfected with the isolated polynucleotide of claim 21, wherein the organism expresses an APOCl protein encoded by the first nucleotide sequence.

24. The recombinant organism of claim 23, which is a nonhuman transgenic animal.

25. The isolated polynucleotide of claim 21 , wherein the first nucleotide sequence is a polymoφhic variant of a fragment of the APOCl gene, the fragment comprising one or more polymoφhisms selected from the group consisting of cytosine at PSl, adenine at PS3, guanine at PS4, guanine at PS5 and guanine at PS6.

26. A computer system for storing and analyzing polymoφhism data for the apohpoprotein C 1 gene, comprising:

(a) a central processing unit (CPU);

(b) a communication interface;

(c) a display device;

(d) an input device; and

(e) a database containing the polymoφhism data; wherein the polymoφhism data comprises the genotypes and haplotype pairs shown in Table

34 3 and the haplotypes shown in Table 4. 27. A genome anthology for the apolipoprotein CI (APOCl) gene which comprises APOCl isogenes defined by any one of haplotypes 1-9 shown in Table 4.

35

. 1/5 POLYMORPHISMS IN THE APOCl GENE (Accession No. M20902.1)

GCATGCAGCC CCCAGTCACG CATCCCCTGC TTGTTCAATC GATCACGACC CTCTCACGTG CACCCACTTA GAGTTGTGAG CCCTTAAAAG GAACAGGGAT ^• 100 TGCTCACTCG GGGAGCTCGG CTCTTGAGAC AGGAATCTTG CCCATTCCCC

^' C ^• GAACGAATAA ACCCCTTCCT TCGTTAACTC AGCGTCTGAG GAATTTTGTC 200 TGCGGCTCCT CCTGCTACAT TCTGAGTGGG GGAAAGGGAC TAAGGTGGTC TGAGGACCCC ACAGAGTCAG GAAGATTGAG AGGTGAGAGT GCTGAACGGG 300 GAGGGGCTTT GGGGCTAAGG GAAGTGCCCG GGACCCCACC TGACCCCAAC GCTCACGGGA CAGGGGCAGA GGAGAAAAAC GTGGGTGGAC AGAGGGAGGC 400 AGGCGGTCAG GGGAAGGCTC AGGAGGAGGG AGATCAACAT CAACCTGCCC CGCCCCTCCC CAGCCTGATA AAGGTCCTGC GGGCAGGACA GGACCTCCCA 500 ACCAAGCCCT CCAGCAAGGA TTCAGGTTGG TGCTGAGTGC CTGGGAGGGA CACCCGCCTA CACTCTGCAA GAAACTCAAA AAGGGAGATG AGGGGATCGT 600 GGGAGGGAGG TAGGGAGGGA GGAGGGTGCC ACTGATCCCC TGAACCCCTG CCTCTGCCTC CAGAGTGCCC CTCCGGCCTC GCCATGAGGC TCTT^'CCTGTC 700

[EXON 1: 684.. GCTCCCGGTC CTGGTGGTGG TTCTGTCGAT CGTCTTGGAA GGTAAAAGTG

G

..741] GGATGGGAGA ATTGGGGAGT TTGGAGATTT GGAAGAGTGA AGGTGGCTAC 800

A AGGCCTGGGG TCCCGGCTTA GAGGACCTCT GAGAGCTCCG GGGCCCCTTC TGGGTCGTGG TTGCCTCATC GTGGTCGGGT GGGTCTCCAG GTTCTCCCAG 900^' GCTCAGTCCC GCAGGCGCCA AATCTGCGCA GGAGAGCACT AGCAACCGAT GACGTATTGA GGCCCACACC TCTGGGATTG GCTGTCCTGC TTCGACAGCC 1000 TTGAAAGTGG GTAAGCTGGG TGGGGGGCTC T.GGGAGAGGT CAGTGCTGAG TAAGGCAATT CCCAGCAGCT TGAGCCCCAC CAGGTCACTC CAGTATTCCT 1100 CCCCATTCTT TTTTTTTTTT TTTTTTTTTC TCTTGAGACG GAGTCTCGCT CTGTCGCCGA GGCTGGAGTG CAGTGGCGCG ATCTCGGCTC ACTGCAAGCT 1200 CCGCCTCCCT GGTTCACGCC ATTCTCCTGC CTCAGCAGGA CTACAGGCGC CCGCCTCCGC GCCCGGCTAA TTTTTTGTAT TTTCAGTAGA GACAGGGTTT 1300 CACCGTGGTC TCGATCTCCT GACTTTGTGA TCCGCCTGCC TCGACCTCCC AAAGTGCTGG GATTACAGGC GTGAGCCACC GCGTCCGGCC ATTCCTCCCC . 1400 ATTCTAACCA CATGATCCCC AAGGATCTCT ATCCATCCCG GTATCCCAAC CTAAGGGGGT TCCAATAACA AATTTTTGGC CGGGCAGGGT GGCTCATGCC .1500 TGTAATCCCA GCACTTTGGG AGGCCGAGGC GGGCAGATCA CTTGAGGTCA GGAGTTCAAA CCAGCCAGGC CAACATGGTG GAAACTTCGT CTCTAGCTAA 1600 AAATACAAAA AAATTAGGCC AGGTGTGGAG GCACGCGCCT GTAGGCCCAG CTACTCGGGA GGCTGAGGCA GGAGAATCAC TTGAACCCGG GAGGCGGAGG 1700 TTGCAGTGAG CCGAGATCAT ACCACTGCAC TCCAGCCTGG CTGACACAGC AAGACTCCGT CTCAAAACAA AACAAAACAA AAATAGGCTG GGTGTGGTGG 1800 TGCACACCTG TAATCCCAGC TACTTGGGAG GCTGAGGCAG GAGAACTGCT . TGAACCCGGG AGGTGGTGGT TGCAGTAGGC CGAGATCATG CCACTGCACT 1900 CCAGCTTGGG CTACAGAGCA AGACTCCATC TCCAAAAAAA AAAAAAAAAA AACAAATTTT GAACCCCTGC CCATCTTCCT GGCAGGCCCA GCCCCAGCCC 2000

[EXON 2: 1986.. AGGGGACCCC AGACGTCTCC AGTGCCTTGG ATAAGCTGAA GGAGTTTGGA AACACACTGG AGGACAAGGC TCGGGAACTC ATCAGCCGCA TCAAACAGAG 2100 TGAACTTTCT GCCAAGATGC GGTTAGAACC CTTCCCAGGG CACGGGAGAG

..2121] CTGGGGTGTG TTTTTGGGTG GAGCCCTGGC AGATGGTCCA AGATGAACAG 2200

FIGURE 1A