Methods for detecting a genetic variation in subjects with parkinsonism
This document provides methods and materials related to genetic variations of neurological disorders. For example, this document provides methods for using such genetic variations to assess susceptibility of developing Parkinson's disease.
1. A method of hybridizing a nucleic acid probe comprising:
(a) hybridizing a nucleic acid probe to a polynucleic acid from a human subject by nucleic acid hybridization or microarray analysis, wherein the human subject has parkinsonism; and
(b) detecting a genetic variation by the nucleic acid hybridization or microarray analysis, wherein the genetic variation is selected from the group consisting of a single nucleotide variant (SNV) of G to A at position 31212342 in chromosome 14, a copy number variation that is a loss of the 2557 base pair sequence from position 31189082 to 31191639 in chromosome 14, and the complements thereof; wherein the chromosome positions are defined with respect to NCBI build 36/hg18.
2. A method of synthesizing a nucleic acid product comprising:
(a) synthesizing a nucleic acid product from a polynucleic acid from a human subject by PCR or sequencing, wherein the human subject has parkinsonism; and
(b) detecting a genetic variation by the PCR or sequencing, wherein the genetic variation is selected from the group consisting of a single nucleotide variant (SNV) of G to A at position 31212342 in chromosome 14, a copy number variation that is a loss of the 2557 base pair sequence from position 31189082 to 31191639 in chromosome 14, and the complements thereof; wherein the chromosome positions are defined with respect to NCBI build 36/hg18.
3. The method of claim 1 or 2 , wherein the genetic variation is the copy number variation that is a loss of the 2557 base pair sequence from position 31189082 to 31191639 in chromosome 14, or the complement thereof.
4. The method of claim 1 or 2 , wherein the genetic variation is the single nucleotide variant (SNV) of G to A at position 31212342 in chromosome 14, or the complement thereof.
5. The method of claim 2 , wherein the nucleic acid product synthesized from the polynucleic acid is cDNA.
6. The method of claim 1 or 2 , wherein the polynucleic acid comprises a nucleic acid from blood, saliva, urine, serum, tears, skin, tissue, or hair from the subject.
7. The method of claim 1 , wherein the detecting comprises purifying the polynucleic acid; and performing a microarray analysis of the purified polynucleic acid.
8. The method of claim 1 , wherein the microarray analysis is selected from the group consisting of a Comparative Genomic Hybridization (CGH) array analysis and an SNP array analysis.
9. The method of claim 2 , wherein the sequencing is a high-throughput sequencing method.
10. The method of claim 1 or 2 , wherein the detecting comprises detecting a first genetic variation selected from the group consisting of the single nucleotide variant (SNV) of G to A at position 31212342 in chromosome 14, the copy number variation that is a loss of the 2557 base pair sequence from position 31189082 to 31191639 in chromosome 14, and the complements thereof, wherein the first genetic variation and a second genetic variation are in a panel comprising two or more genetic variations.
11. The method of claim 1 or 2 , wherein the whole genome or the exome of the subject is analyzed.
12. The method of claim 10 , wherein the second genetic variation is selected from the group consisting of CNVs comprising a sequence that is SEQ ID NOs: 2 and 16-298 and the complements thereof.
13. The method of claim 10 , wherein the second genetic variation is a SNV in the NUBPL gene.
14. The method of claim 12 , wherein the second genetic variation is selected from the group consisting of CNVs comprising a sequence that is SEQ ID NOs: 2, 16 and 17, and the complements thereof.
15. The method of claim 10 , wherein the detecting comprises detecting the first genetic variation and the second genetic variation.
16. The method of claim 10 , wherein the panel comprises 10 or more genetic variations.
17. The method of claim 10 , wherein the second genetic variation is intergenic.
18. The method of claim 10 , wherein the second genetic variation is a low frequency genetic variation that occurs at a frequency of 1% or less in a population of human subjects with parkinsonism.
19. The method of claim 10 , wherein the second genetic variation has an odds ratio (OR) of 6 or more, and wherein the odds ratio is calculated based on percentages of human subjects with the genetic variation in a population of human subjects with and without parkinsonism.