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 determining the presence of a repeat region comprising a CTG repeat within an at-risk allele of an SCA8 coding sequencing, comprising:
(a) treating separate complementary DNA molecules containing a repeat region of an SCA8 coding sequence in a biological specimen from a human subject with a molar excess of an oligonucleotide primer pair, wherein the primers in the primer pair hybridize to a portion of the SCA8 coding sequence selected from the group consisting of nucleotides 1-448 and nucleotides 726-1159 of SEQ ID NO:1 or complements thereof, nucleotides 1-1070 and nucleotides 1350-1472 of SEQ ID NO:2 or complements thereof, and nucleotides 1-636 and nucleotides 915-1037 of SEQ ID NO:3 or complements thereof;
(b) amplifying the SCA8 sequence flanked by the primers to produce a DNA fragment;
(c) sequencing the amplified DNA fragment; and
(d) determining the presence of the repeat region comprising the CTG repeat in the amplified DNA fragment.
2. The method of claim 1 , wherein a first oligonucleotide primer of the primer pair is chosen from nucleotides 1-448 of SEQ ID NO:1, and a second oligonucleotide primer of the primer pair 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 NO:6, SEQ ID NO:9, and SEQ ID NO:12.
4. The method of claim 1 , wherein the repeat region comprises at least about 80 CTG repeats.
5. The method of claim 1 , wherein the repeat region comprises at least about 92 CTG/CTA repeats.
6. The method of claim 1 , wherein the sequencing is dideoxy sequencing.
7. A method for determining the presence of a repeat region comprising a CTG repeat within an at-risk allele of an SCA8 coding sequencing, comprising:
(a) treating separate complementary DNA molecules containing a repeat region of an SCA8 coding sequence in a biological specimen from a human subject with a molar excess of a first oligonucleotide primer pair, wherein the primers in the first oligonucleotide primer pair hybridize to a portion of the SCA8 coding sequence selected from the group consisting of nucleotides 1-448 and nucleotides 726-1159 of SEQ ID NO:1 or complements thereof, nucleotides 1-1070 and nucleotides 1350-1472 of SEQ ID NO:2 or complements thereof, and nucleotides 1-636 and nucleotides 915-1037 of SEQ ID NO:3 or complements thereof;
(b) amplifying the SCA8 sequence flanked by the primers in the first oligonucleotide primer pair to produce a first DNA fragment;
(c) treating separate complementary DNA molecules of the first fragment with a molar excess of a second oligonucleotide primer pair;
(d) amplifying the SCA8 sequence flanked by the primers in the second oligonucleotide primer pair to produce a second DNA fragment;
(e) sequencing the amplified second DNA fragment; and
(d) determining the presence of the repeat region comprising the CTG repeat in the amplified second DNA fragment.
8. The method of claim 7 , 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.
9. The method of claim 8 , 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.
10. The method of claim 7 , 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 726-1,159 of SEQ ID NO:1, wherein each primer has at least 11 nucleotides.
11. The method of claim 7 , wherein the second oligonucleotide primer pair comprises a first oligonucleotide primer comprising three CTA repeats followed by three CTG repeats and a second oligonucleotide primer chosen from nucleotides 726-1,159 of SEQ ID NaI, wherein each primer has at least 11 nucleotides.
12. The method of claim 7 , wherein the repeat region comprises at least about 80 CTG repeats.
13. The method of claim 7 , wherein the repeat region comprises at least about 92 CTG/CTA repeats.
14. The method of claim 7 , wherein he sequencing is dideoxy sequencing.
15. A method of diagnosing whether an individual has, or is at-risk for developing, spinocerebellar ataxia type 8, comprising:
(a) treating separate complementary DNA molecules containing a repeat region of an SCA8 coding sequence in a biological specimen from a human subject with a molar excess of an oligonucleotide primer pair, wherein the primers in the primer pair hybridize to a portion of the SCA8 coding sequence selected from the group consisting of nucleotides 1-448 and nucleotides 726-1159 of SEQ ID NO:1 or complements thereof, nucleotides 1-1070 and nucleotides 1350-1472 of SEQ ID NO:2 or complements thereof, and nucleotides 1-636 and nucleotides 915-1037 of SEQ ID NO:3 or complements thereof;
(b) amplifying the SCA8 sequence flanked by the primers to produce a DNA fragment;
(c) sequencing the amplified DNA fragment;
(d) determining the presence of a repeat region comprising a CTG repeat in the amplified DNA fragment; and
(e) diagnosing the individual as having, or is at-risk for developing, spinocerebellar ataxia type 8 if the repeat region comprises at least about 80 CTG repeats, or if the repeat region comprises at least about 92 CTG/CTA repeats.
16. The method of claim 15 , wherein a first oligonucleotide primer of primer pair is chosen from nucleotides 1-448 of SEQ NO:1, and a second oligonucleotide primer of the primer pair is chosen from nucleotides complementary to nucleotides 726-1,159 of SEQ ID NO:1, wherein each primer has at least 11 nucleotides.
17. The method of claim 15 , 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.
18. The method of claim 15 , wherein the sequencing is dideoxy sequencing.