Development of TAF1 genotyping assay for X-linked dystonia-parkinsonism-associated haplotype detection
Laboratory Genetics and Genomics
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Primary Categories:
- Laboratory Genetics
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Secondary Categories:
- Laboratory Genetics
Introduction:
X-linked dystonia-parkinsonism (XDP) is a movement disorder that primarily affects men of Filipino ancestry, with a variable clinical course characterized by parkinsonism, dystonia, and abnormal limb movements. The molecular cause of the disorder, which has been extensively studied, has been mapped to a 220 kb region within Xq13.1, which includes the TAF1 gene. On the disease haplotype, a SINE-VNTR-Alu (SVA) retrotransposon has been inserted into an intron of TAF1, promoting intron retention and decreasing TAF1 expression. A hexanucleotide repeat (CCCTCT)n within the SVA has also been shown to be inversely associated with age at onset of XDP. In addition, there are several single nucleotide variants, referred to as disease-specific single nucleotide changes (DSCs), that are in strong linkage disequilibrium with the disorder, and serve as markers of the disease-associated haplotype. We aimed to design an assay to sequence the DSCs for detection of the disease haplotype.
Methods:
Introns 18 and 32 of TAF1 (NM_004606.3) were Sanger sequenced. The following DSCs were assessed: c.2782-1374T>G, historically known as DSC12; c.4754-12681C>T, historically known as DSC10; and c.4754-3111T, historically known as DSCn8.
Results:
Targeted sequencing of three DSCs was performed on 8 positive controls (4 males and 4 females), 7 negative controls, and 3 clinical cases. The XDP-associated haplotype was detected in all 8 positive controls and 3 clinical cases. All negative controls were negative for the XDP-associated haplotype. The first clinical case is a 38-year-old male with dystonia, parkinsonism, chorea, and other neurological disorders. He had previous negative spinocerebellar ataxia gene panel, Huntington disease testing, and exome sequencing (ES) testing. The second clinical case is a 40-year-old male with dystonia, parkinsonism, and a prior negative next generation sequencing (NGS) gene panel, which included TAF1. The third clinical case, a relative of an affected individual, was heterozygous for the DSCs.
Conclusion:
Commercially available NGS gene panels and ES/GS assays do not assess for the DSCs in linkage disequilibrium with the XDP-associated haplotype, missing this diagnosis in affected individuals. Including this testing as part of the diagnostic differential may increase diagnosis rate in this population and reduce the costs associated with a diagnostic odyssey for these patients. Ordering providers need to be aware that currently only custom XDP-specific assays assess and report this disease haplotype. Therefore, this test should be ordered alongside other tests in individuals who are at high suspicion for this condition.
X-linked dystonia-parkinsonism (XDP) is a movement disorder that primarily affects men of Filipino ancestry, with a variable clinical course characterized by parkinsonism, dystonia, and abnormal limb movements. The molecular cause of the disorder, which has been extensively studied, has been mapped to a 220 kb region within Xq13.1, which includes the TAF1 gene. On the disease haplotype, a SINE-VNTR-Alu (SVA) retrotransposon has been inserted into an intron of TAF1, promoting intron retention and decreasing TAF1 expression. A hexanucleotide repeat (CCCTCT)n within the SVA has also been shown to be inversely associated with age at onset of XDP. In addition, there are several single nucleotide variants, referred to as disease-specific single nucleotide changes (DSCs), that are in strong linkage disequilibrium with the disorder, and serve as markers of the disease-associated haplotype. We aimed to design an assay to sequence the DSCs for detection of the disease haplotype.
Methods:
Introns 18 and 32 of TAF1 (NM_004606.3) were Sanger sequenced. The following DSCs were assessed: c.2782-1374T>G, historically known as DSC12; c.4754-12681C>T, historically known as DSC10; and c.4754-3111T, historically known as DSCn8.
Results:
Targeted sequencing of three DSCs was performed on 8 positive controls (4 males and 4 females), 7 negative controls, and 3 clinical cases. The XDP-associated haplotype was detected in all 8 positive controls and 3 clinical cases. All negative controls were negative for the XDP-associated haplotype. The first clinical case is a 38-year-old male with dystonia, parkinsonism, chorea, and other neurological disorders. He had previous negative spinocerebellar ataxia gene panel, Huntington disease testing, and exome sequencing (ES) testing. The second clinical case is a 40-year-old male with dystonia, parkinsonism, and a prior negative next generation sequencing (NGS) gene panel, which included TAF1. The third clinical case, a relative of an affected individual, was heterozygous for the DSCs.
Conclusion:
Commercially available NGS gene panels and ES/GS assays do not assess for the DSCs in linkage disequilibrium with the XDP-associated haplotype, missing this diagnosis in affected individuals. Including this testing as part of the diagnostic differential may increase diagnosis rate in this population and reduce the costs associated with a diagnostic odyssey for these patients. Ordering providers need to be aware that currently only custom XDP-specific assays assess and report this disease haplotype. Therefore, this test should be ordered alongside other tests in individuals who are at high suspicion for this condition.