Spinocerebellar ataxia type 8 and methods of detection
The present invention provides an isolated nucleic acid molecule containing a repeat region of an isolated spinocerebellar ataxia type 8 (SCA8) coding sequence, the coding sequence located within the long arm of chromosome 13, and the complement of the nucleic acid molecule. Diagnostic methods based on identification of this repeat region are also provided.
1. A method for detecting the presence of a repeat region comprising a CTG repeat within an at-risk allele of an SCA8 coding sequence comprising:
(a) treating separate complementary DNA molecules containing a repeat region of the SCA8 coding sequence with a molar excess of two oligonucleotide primers, which each hybridize to a portion of the SCA8 coding region selected from nucleotides 1-448 and nucleotides 726-1159 of SEQ ID NO:1, nucleotides 1-1070 and nucleotides 1350-1472 of SEQ ID NO:2, and nucleotides 1-636 and nucleotides 915-1037 of SEQ ID NO:3;
(b) extending the primers to foam complementary primer extension products which act as templates for synthesizing a desired DNA fragment containing the repeat region;
(c) detecting the fragment so amplified; and
(d) analyzing the amplified DNA fragment for a repeat region comprising a CTG repeat.
2. The method of claim 1 wherein a first oligonucleotide primer of the two oligonucleotide primers is chosen from nucleotides 1-448 of SEQ ID NO:1, and a second oligonucleotide primer of the two oligonucleotide primers is chosen from nucleotides complementary to nucleotides 726-1,159 of SEQ ID NO:1, wherein each primer has at least 11 nucleotides.
3. The method of claim 2 wherein the first oligonucleotide primer is selected from the group consisting of SEQ ID NO:5, SEQ ID NO:8, and SEQ ID NO:4 and wherein the second oligonucleotide primer is selected from the group consisting of SEQ ID NO:6, SEQ ID NO:9, and SEQ ID NO:12.
4. The method of claim 1 wherein the step of analyzing comprises analyzing for a region comprising a combined (CTG) n repeat wherein n is at least about 80.
5. The method of claim 1 wherein the step of analyzing comprises analyzing for a repeat region comprising a combined ((CTG)/(CTA)) n repeat wherein n is at least about 92.
6. A method for detecting the presence of at least one DNA molecule containing a repeat region of an SCA8 coding sequence comprising:
(a) digesting genomic DNA with a restriction endonuclease to obtain DNA fragments;
(b) denaturating the DNA fragments to yield DNA molecules and probing the DNA molecules under hybridizing conditions with a detectably labeled probe, which hybridizes to a repeat region of an isolated SCA8 coding sequence comprising nucleotides 1-448 and nucleotides 726-1159 of SEQ ID NO:1, nucleotides 1-1070 and nucleotides 1350-1472 of SEQ ID NO:2, or nucleotides 1-636 and nucleotides 915-1037 of SEQ ID NO:3;
(c) detecting the probe which has hybridized to the DNA molecule; and
(d) analyzing the DNA molecule for a repeat region characteristic of a normal or at-risk form of the SCA8 coding sequence.
7. The method of claim 6 wherein the probe is chosen from nucleotides 1-448 of SEQ ID NO:1 or from nucleotides 726-1,159 of SEQ ID NO:1, or complements thereto, wherein the probe has at least 20 nucleotides.
8. The method of claim 6 wherein the probe comprises nucleotides 19-449 of SEQ ID NO:1, or a complement thereto.
9. The method of claim 6 wherein the step of analyzing comprises analyzing for a repeat region comprising a (CTG) n repeat wherein n is at least about 80.
10. The method of claim 6 wherein the step of analyzing comprises analyzing for a repeat region comprising a combined ((CTG/(CTA)) n repeat wherein n is at least about 92.
11. A method for detecting the presence of an expanded repeat region located within an at-risk allele of an SCA8 coding sequence comprising:
(a) treating separate complementary DNA molecules containing a repeat region of the SCA8 coding sequence with a molar excess of a first oligonucleotide primer pair, which hybridize to a portion of the SCA8 coding region selected from nucleotides 1-448 and nucleotides 726-1159 of SEQ ID NO:1, nucleotides 1-1070 and nucleotides 1350-1472 of SEQ ID NO:2, and nucleotides 1-636 and nucleotides 915-1037 of SEQ ID NO:3;
(b) extending the first primer pair to form complementary primer extension products which act as templates for synthesizing a first desired DNA fragment containing the repeat region;
(c) removing the first desired DNA fragment containing the repeat region;
(d) treating separate complementary strands of the first desired DNA fragment containing the repeat region with a molar excess of a second oligonucleotide primer pair;
(e) extending the second primer pair to form complementary primer extension products which act as templates for synthesizing a second desired DNA fragment containing the repeat region;
detecting the second desired DNA fragment so amplified; and
(g) analyzing the amplified DNA fragment for an expanded repeat region.
12. The method of claim 11 wherein the first oligonucleotide primer pair comprises a first oligonucleotide primer chosen from nucleotides 1-448 of SEQ ID NO:1, and a second oligonucleotide primer chosen from nucleotides complementary to nucleotides 726-1,159 of SEQ ID NO:1, wherein each primer has at least 11 nucleotides.
13. The method of claim 12 wherein the first oligonucleotide primer is selected from the group consisting of SEQ ID NO:5, SEQ ID NO:8, and SEQ ID NO:4 and wherein the second oligonucleotide primer is selected from the group consisting of SEQ ID NO:6, SEQ ID NO:9, and SEQ ID NO:12.
14. The method of claim 11 wherein the second oligonucleotide primer pair comprises a first oligonucleotide primer chosen from nucleotides 449-725 of SEQ ID NO:1, and a second oligonucleotide primer chosen from nucleotides complementary to nucleotides 726- 1,159 of SEQ ID NO:1, wherein each primer has at least 11 nucleotides.
15. The method of claim 11 wherein the second oligonucleotide primer pair comprises a first oligonucleotide primer that has three CTA repeats followed by three CTG repeats and a second oligonucleotide primer chosen from nucleotides complementary to nucleotides 726-1,159 of SEQ ID NO:1.
16. The method of claim 11 wherein the step of analyzing comprises analyzing for a repeat region comprising a (CTG) n repeat wherein n is at least about 80.
17. The method of claim 10 wherein the step of analyzing comprises analyzing for a repeat region comprising a combined ((CTG)/(CTA)) n repeat wherein n is at least about 92.