Compositions and methods for detecting polymorphisms associated with pigmentation

) The method of claim 1, further comprising identifying in the nucleic acid sample at least a second pigmentation-related haplotype allele of the following:

• a) nucleotides of the dopachrome tautomerase (DCT) gene corresponding to a DCT-A haplotype, which comprises:
• nucleotide 609 of SEQ ID NO:
• 1,
• nucleotide 501 of SEQ ID NO:2, and
• nucleotide 256 of SEQ ID NO:3;
• b) nucleotides of the melanocortin-1 receptor (MC1R) gene corresponding to a MC1R-A haplotype, which comprises:
• nucleotide 442 of SEQ ID NO:4,
• nucleotide 619 of SEQ ID NO:5, and
• nucleotide 646 of SEQ ID NO:6;
• c) nucleotides of the oculocutaneous albinism II (OCA2) gene, corresponding to an OCA2-A haplotype, which comprises:
• nucleotide 135 of SEQ ID NO:7,
• nucleotide 193 of SEQ ID NO:8,
• nucleotide 228 of SEQ ID NO:9, and
• nucleotide 245 of SEQ ID NO:10;
• d) nucleotides of the OCA2 gene, corresponding to an OCA2-B haplotype, which comprises:
• nucleotide 189 of SEQ ID NO:
• 11,
• nucleotide 573 of SEQ ID NO:12, and
• nucleotide 245 of SEQ ID NO:
• 13;
• e) nucleotides of the OCA2 gene, corresponding to an OCA2-C haplotype, which comprises:
• nucleotide 643 of SEQ ID NO:
• 14,
• nucleotide 539 of SEQ ID NO:15,
• nucleotide 418 of SEQ ID NO:16, and
• nucleotide 795 of SEQ ID NO:
• 17,
• f) nucleotides of the OCA2 gene, corresponding to an OCA2-D haplotype, which comprises:
• nucleotide 535 of SEQ ID NO:18,
• nucleotide 554 of SEQ ID NO:
• 19, and
• nucleotide 210 of SEQ ID NO:20;
• g) nucleotides of the OCA2 gene, corresponding to an OCA2-E haplotype, which comprises:
• nucleotide 225 of SEQ ID NO:21,
• nucleotide 170 of SEQ ID NO:22, and
• nucleotide 210 of SEQ ID NO:20;
• or
• h) nucleotides of the tyrosinase-related protein 1 (TYRP1) gene corresponding to a TYRP1-B haplotype which comprises:
• nucleotide 172 of SEQ ID NO:23, and
• nucleotide 216 of SEQ ID NO:24;
• or any combination of a) through h).

) The method of claim 1, further comprising identifying in the nucleic acid sample at least one latent pigmentation-related haplotype allele of a pigmentation gene, wherein the latent pigmentation-related haplotype allele is:

• i) nucleotides of the agouti signaling protein (ASIP) gene corresponding to an ASIP-A haplotype, which comprises:
• nucleotide 201 of SEQ ID NO:26, and
• nucleotide 201 of SEQ ID NO:28;
• j) nucleotides of the DCT gene corresponding to a DCT-B haplotype, which comprises:
• nucleotide 451 of SEQ ID NO:33, and
• nucleotide 657 of SEQ ID NO:29;
• k) nucleotides of the silver homolog (SILV) gene corresponding to a SILV-A haplotype, which comprises:
• nucleotide 61 of SEQ ID NO:35, and
• nucleotide 61 of SEQ ID NO:36;
• l) nucleotides of the tyrosinase (TYR) gene corresponding to a TYR-A haplotype, which comprises:
• nucleotide 93 of SEQ ID NO:38, and
• nucleotide 114 of SEQ ID NO:39;
• or
• m) nucleotides of the TYRP1 gene corresponding to a TYRP1-A haplotype, which comprises:
• nucleotide 364 of SEQ ID NO:44,
• nucleotide 169 of SEQ ID NO:48, and
• nucleotide 214 of SEQ ID NO:49,
• or any combination of i) through m).

) The method of claim 10, wherein the subject is a Caucasian, the genetic pigmentation trait is eye shade or eye color, and the penetrant pigmentation-related haplotype allele is:

• a) the MC1R-A haplotype allele CCC;
• b) the OCA2-A haplotype allele TTAA, CCAG, or TTAG;
• c) the OCA2-B haplotype allele CAA, CGA, CAC, or CGC;
• d) the OCA2-C haplotype allele GGAA, TGAA, or TAAA,
• e) the OCA2-D haplotype allele AGG or GGG;
• f) the OCA2-E haplotype allele GCA;
• g) the TYRP1-B haplotype allele TC;
• and
• h) the DCT-B haplotype allele CTG, or GTG.

) The method of claim 4, wherein the combination of penetrant pigmentation-related haplotype alleles is:

• a) the MC1R-A haplotype allele CCC;
• b) the OCA2-A haplotype allele TTAA, CCAG, or TTAG;
• c) the OCA2-B haplotype allele CAA, CGA, CAC, or CGC;
• d) the OCA2-C haplotype allele GGAA, TGAA, or TAAA;
• e) the OCA2-D haplotype allele AGG or GGG;
• f) the OCA2-E haplotype allele GCA;
• g) the TYRP1-B haplotype allele TC;
• and
• h) the DCT-B haplotype allele CTG, or GTG;
• and
• wherein the combination of latent pigmentation-related haplotype alleles is:
• i) the ASIP-A haplotype allele GT or AT;
• j) the DCT-B haplotype allele TA or TG;
• k) the SILV-A haplotype allele TC, TT, or CC;
• l) the TYR-A haplotype allele GA,AA or GG;
• and
• m) the TYRP1-B haplotype allele GTG, TTG, or GTT.

) A method for inferring hair color or hair shade of a human subject from a nucleic acid sample of the subject, the method comprising identifying in the nucleic acid sample at least one penetrant pigmentation-related haplotype allele of the following:

• a) nucleotides of the agouti signaling protein (ASIP) gene corresponding to an ASIP-B haplotype, which comprises:
• nucleotide 202 of SEQ ID NO:27, and
• nucleotide 61 of SEQ ID NO:25,
• b) nucleotides of the oculocutaneous albinism II (OCA2) gene corresponding to an OCA2-G haplotype, which comprises:
• nucleotide 418 of SEQ ID NO:
• 16,
• nucleotide 210 of SEQ ID NO:20, and
• nucleotide 245 of SEQ ID NO:10;
• c) nucleotides of the OCA2 gene corresponding to a OCA2-H haplotype, which comprises:
• nucleotide 225 of SEQ ID NO:21,
• nucleotide 643 of SEQ ID NO:
• 14, and
• nucleotide 193 of SEQ ID NO:8;
• d) nucleotides of the OCA2 gene corresponding to a OCA2-I haplotype, which
• nucleotide 135 of SEQ ID NO:7, and
• nucleotide 554 of SEQ ID NO:
• 19;
• e) nucleotides of the OCA2 gene corresponding to a OCA2-J haplotype, which comprises:
• nucleotide 535 of SEQ ID NO:
• 18, and
• nucleotide 228 of SEQ ID NO:9;
• or
• f) nucleotides of the tyrosinase-related protein 1 (TYRP1) gene corresponding to a TYRP1-C haplotype, which comprises:
• nucleotide 473 of SEQ ID NO:45, and,
• nucleotide 214 of SEQ ID NO:49;
• or any combination thereof.

) The method of claim 16, further comprising identifying in the nucleic acid sample at least a second pigmentation-related haplotype allele of the following:

• a) nucleotides of the agouti signaling protein (ASIP) gene corresponding to an ASIP-B haplotype, which comprises:
• nucleotide 202 of SEQ ID NO:27, and
• nucleotide 61 of SEQ ID NO:25,
• b) nucleotides of the melanocortin-1 receptor (MC1R) gene corresponding to an MC1R-A haplotype, which comprises:
• nucleotide 442 of SEQ ID NO:4,
• nucleotide 619 of SEQ ID NO:5, and
• nucleotide 646 of SEQ ID NO:6;
• c) nucleotides of the oculocutaneous albinism II (OCA2) gene corresponding to an OCA2-G haplotype, which comprises:
• nucleotide 418 of SEQ ID NO:16,
• nucleotide 210 of SEQ ID NO:20, and
• nucleotide 245 of SEQ ID NO:10;
• d) nucleotides of the OCA2 gene corresponding to a OCA2-H haplotype, which comprises:
• nucleotide 225 of SEQ ID NO:21,
• nucleotide 643 of SEQ ID NO:
• 14, and
• nucleotide 193 of SEQ ID NO:8;
• e) nucleotides of the OCA2 gene corresponding to a OCA2-I haplotype, which
• nucleotide 135 of SEQ ID NO:7, and
• nucleotide 554 of SEQ ID NO:
• 19;
• f) nucleotides of the OCA2 gene corresponding to a OCA2-J haplotype, which comprises:
• nucleotide 535 of SEQ ID NO:
• 18, and
• nucleotide 228 of SEQ ID NO:9;
• or
• g) nucleotides of the tyrosinase-related protein 1 (TYRP1) gene corresponding to a TYRP1-C haplotype, which comprises:
• nucleotide 473 of SEQ ID NO:45, and
• nucleotide 214 of SEQ ID NO:49;
• or any combination thereof.

) The method of claim 17, wherein at least one penetrant pigmentation-related haplotype allele is:

• a) the ASIP-B haplotype allele GA or AA;
• b) the MC1R-A haplotype allele CCC, CTC, TCC or CCT;
• c) the OCA2-G haplotype allele AGG or AGA;
• d) the OCA2-H haplotype allele AGT or ATT;
• e) the OCA2-I haplotype allele TG;
• f) the OCA2-J haplotype allele GA or AA;
• and
• g) the TYRP1-C haplotype allele AA or TA.