APM1 biallelic markers and uses thereof
The invention provides novel APM1 genomic sequences, polypeptides, antibodies, and polynucleotides including biallelic markers derived from the APM1 locus. Primers hybridizing to regions flanking these biallelic markers are also provided. This invention also provides polynucleotides and methods suitable for genotyping a nucleic acid containing sample for one or more biallelic markers of the invention. Additionally, the invention provides methods to detect a statistical correlation between a biallelic marker allele and a phenotype and/or between a biallelic marker haplotype and a phenotype. Further, the invention provides diagnostic methods for early detection of obesity-related disorders.
1 . A composition of matter comprising:
a) an isolated, purified, or recombinant polynucleotide:
i) comprising SEQ ID NO: 1 or the complement thereof;
ii) comprising SEQ ID NO: 5 or the complement thereof;
iii) consisting essentially of a contiguous span of 8 to 50 nucleotides of SEQ ID NO: 1 or the complement thereof, wherein said span includes an APM1-related biallelic marker in said sequence and said APM1-related biallelic marker is selected from the group consisting of A1 (SEQ ID NO: 1, position 3787), A2 (SEQ ID NO: 1, position 11118), A4 (SEQ ID NO: 1, position 15196), A7 (SEQ ID NO: 1, position 15863) and A8 (SEQ ID NO: 1, position 17170);
iv) consisting essentially of a contiguous span of 18 to 35 nucleotides of SEQ ID NO: 1 or the complement thereof, wherein said span includes an APM1-related biallelic marker in said sequence, said biallelic marker is within 4 nucleotides of the center of said polynucleotide and said APM1-related biallelic marker is selected from the group consisting of A1 (SEQ ID NO: 1, position 3787), A2 (SEQ ID NO: 1, position 11118), A4 (SEQ ID NO: 1, position 15196), A7 (SEQ ID NO: 1, position 15863) and A8 (SEQ ID NO: 1, position 17170);
v) consisting of a contiguous span of 25 nucleotides of SEQ ID NO: 1 or the complement thereof, wherein said span includes an APM1-related biallelic marker in said sequence, said biallelic marker is at the center of said polynucleotide and said APM1-related biallelic marker is selected from the group consisting of A1 (SEQ ID NO: 1, position 3787), A2 (SEQ ID NO: 1, position 11118), A4 (SEQ ID NO: 1, position 15196), A7 (SEQ ID NO: 1, position 15863) and A8 (SEQ ID NO: 1, position 17170);
vi) consisting essentially of a contiguous span of 8 to 50 nucleotides of SEQ ID NO: 1 or the complement thereof, wherein the 3′ end of said contiguous span is located at the 3′ end of said polynucleotide, said biallelic marker is present at the 3′ end of said polynucleotide and said span includes an APM1-related biallelic marker in said sequence selected from the group consisting of A1 (SEQ ID NO: 1, position 3787), A2 (SEQ ID NO: 1, position 11118), A4 (SEQ ID NO: 1, position 15196), A7 (SEQ ID NO: 1, position 15863) and A8 (SEQ ID NO: 1, position 17170);
vii) consisting essentially of a contiguous span of 8 to 50 nucleotides of SEQ ID NO: 1 or the complement thereof, wherein the 3′ end of said contiguous span is located at the 3′ end of said polynucleotide, said biallelic marker in said sequence is located within 20 nucleotides upstream of the 3′ end of said polynucleotide and said span includes an APM1-related biallelic marker in said sequence selected from the group consisting of A1 (SEQ ID NO: 1, position 3787), A2 (SEQ ID NO: 1, position 11118), A4 (SEQ ID NO: 1, position 15196), A7 (SEQ ID NO: 1, position 15863) and A8 (SEQ ID NO: 1, position 17170);
viii) consisting essentially of a contiguous span of 8 to 50 nucleotides of SEQ ID NO: 1 or the complement thereof, wherein the 3′ end of said contiguous span is located at the 3′ end of said polynucleotide, said biallelic marker in said sequence is located 1 nucleotide upstream of the 3′ end of said polynucleotide and said span includes an APM1-related biallelic marker in said sequence selected from the group consisting of Al (SEQ ID NO: 1, position 3787), A2 (SEQ ID NO: 1, position 11118), A4 (SEQ ID NO: 1, position 15196), A7 (SEQ ID NO: 1, position 15863) and A8 (SEQ ID NO: 1, position 17170);
b) a recombinant vector comprising a polynucleotide comprising: 1) SEQ ID NO: 1 or the complement thereof; or 2) SEQ ID NO: 5 or the complement thereof; or
c) a host cell, or non-human host animal or mammal, comprising a recombinant vector comprising a polynucleotide comprising: 1) SEQ ID NO: 1 or the complement thereof; or 2) SEQ ID NO: 5 or the complement thereof.
2 . A method of genotyping comprising determining the identity of a nucleotide at an APM1-related biallelic marker of SEQ ID NO: 1 or the complement thereof in a biological sample,
wherein said APM1-related biallelic marker is selected from the group consisting of A1 (SEQ ID NO: 1, position 3787), A2 (SEQ ID NO: 1, position 11118), A4 (SEQ ID NO: 1, position 15196), A7 (SEQ ID NO: 1, position 15863) and A8 (SEQ ID NO: 1, position 17170).
3 . The method according to claim 2 , wherein said biological sample is derived from a single subject.
4 . The method according to claim 3 , wherein the identity of the nucleotides at said biallelic marker is determined for both copies of said biallelic marker present in said individual's genome.
5 . The method according to claim 2 , wherein said biological sample is derived from multiple subjects.
6 . The method according to claim 2 , further comprising amplifying a portion of said sequence comprising the biallelic marker prior to said determining step.
7 . The method according to claim 2 , wherein said determining is performed by:
(i) a hybridization assay;
(ii) a sequencing assay;
(iii) a microsequencing assay; or
(iv) an allele specific amplification assay.
8 . A method of detecting an association between a genotype and a phenotype, comprising the steps of:
a) genotyping at least one APM1-related biallelic marker in a trait positive population according to the method of claim 2;
b) genotyping said APM1-related biallelic marker in a control population according to the method of claim 2; and
c) determining whether a statistically significant association exists between said genotype and said phenotype.
9 . A method of estimating the frequency of a haplotype for a set of biallelic markers in a population, comprising:
a) genotyping at least one APM1-related biallelic marker according to claim 3 for each individual in said population;
b) genotyping a second biallelic marker by determining the identity of the nucleotides at said second biallelic marker for both copies of said second biallelic marker present in the genome of each individual in said population; and
c) applying a haplotype determination method to the identities of the nucleotides determined in steps a) and b) to obtain an estimate of said frequency.
10 . A method of detecting an association between a haplotype and a phenotype, comprising the steps of:
a) estimating the frequency of at least one haplotype in a trait positive population according to the method of claim 9;
b) estimating the frequency of said haplotype in a control population according to the method of claim 9; and
c) determining whether a statistically significant association exists between said haplotype and said phenotype.
11 . The method according to claim 8 , wherein said phenotype is a disease involving obesity or disorders related to obesity.
12 . The method according to claim 10 , wherein said phenotype is a disease involving obesity of disorders related to obesity.