Susan M. Forrest

Deletion at ITPR1 underlies ataxia in mice and spinocerebellar ataxia 15 in humans.

We observed a severe autosomal recessive movement disorder in mice used within our laboratory. We pursued a series of experiments to define the genetic lesion underlying this disorder and to identify a cognate disease in humans with mutation at the same locus. Through linkage and sequence analysis we show here that this disorder is caused by a homozygous in-frame 18-bp deletion in Itpr1 (Itpr1Δ18/Δ18), encoding inositol 1,4,5-triphosphate receptor 1. A previously reported spontaneous Itpr1 mutation in mice causes a phenotype identical to that observed here. In both models in-frame deletion within Itpr1 leads to a decrease in the normally high level of Itpr1 expression in cerebellar Purkinje cells. Spinocerebellar ataxia 15 (SCA15), a human autosomal dominant disorder, maps to the genomic region containing ITPR1; however, to date no causal mutations had been identified. Because ataxia is a prominent feature in Itpr1 mutant mice, we performed a series of experiments to test the hypothesis that mutation at ITPR1 may be the cause of SCA15. We show here that heterozygous deletion of the 5′ part of the ITPR1 gene, encompassing exons 1–10, 1–40, and 1–44 in three studied families, underlies SCA15 in humans.

A new autosomal dominant pure cerebellar ataxia

A kindred is described with a dominantly inherited “pure” cerebellar ataxia in which the currently known spinocerebellar ataxias have been excluded. In the eight subjects studied, a notable clinical feature is slow progression, with the three least affected having only a mild degree of gait ataxia after three or more decades of disease duration. Pending an actual chromosomal locus discovery, the name spinocerebellar ataxia (SCA)15 is expectantly applied.

A duplication at chromosome 11q12.2–11q12.3 is associated with spinocerebellar ataxia type 20

Spinocerebellar ataxia type 20 (SCA20) has been linked to chromosome 11q12, but the underlying genetic defect has yet to be identified. We applied single-nucleotide polymorphism genotyping to detect structural alterations in the genomic DNA of patients with SCA20. We found a 260 kb duplication within the previously linked SCA20 region, which was confirmed by quantitative polymerase chain reaction and fiber fluorescence in situ hybridization, the latter also showing its direct orientation. The duplication spans 10 known and 2 unknown genes, and is present in all affected individuals in the single reported SCA20 pedigree. While the mechanism whereby this duplication may be pathogenic remains to be established, we speculate that the critical gene within the duplicated segment may be DAGLA, the product of which is normally present at the base of Purkinje cell dendritic spines and contributes to the modulation of parallel fiber-Purkinje cell synapses.

Spinocerebellar ataxia type 15.

Spinocerebellar ataxia type 15 (SCA15) was first reported in 2001 on the basis of a single large Anglo-Celtic family from Australia, the locus mapping to chromosomal region 3p24.2–3pter. The characteristic clinical feature was of very slow progression, with two affected individuals remaining ambulant without aids after over 50 years of symptoms. Head and/or upper limb action tremor, and gaze-evoked horizontal nystagmus were seen in several persons. MRI brain scans showed predominant vermal atrophy, sparing the brainstem. In 2004, a Japanese pedigree was reported, which displayed very similar clinical features to the original SCA15 family, and which mapped to an overlapping candidate region. These two families might plausibly reflect a locus homogeneity, but for the present this remains an open question.

Association between dependent smoking and a polymorphism in the tyrosine hydroxylase gene in a prospective population-based study of adolescent health

This study reports pilot data on an association between tobacco dependence and a five-allele tetranucleotide repeat polymorphism in the first intron of the tyrosine hydroxylase (TH) gene. One hundred and twenty-six Australian adolescents who had participated in the Health in Transition Study (1993–1997), and who showed patterns of either dependent or nondependent smoking across four waves of data collection, consented to participation in the pilot study. The smoking status of those recruited was confirmed using a telephone-administered drug use questionnaire during 2000. Tobacco dependence was defined as smoking more than 6 days per week and more than 10 cigarettes per day during wave 5 (year 2000) and at lfeast one prior wave (n = 58). A second, more stringent phenotype included smoking within an hour of waking (n = 37). The control group comprised adolescents who had used tobacco but had remained low-level social smokers across each wave of data (n = 56). DNA was collected using a mouthwash procedure. Using the more strictly defined tobacco dependence phenotype, and after adjusting for sex, a significant protective association was found between the K4 allele and tobacco dependence (OR 0.27, 95% confidence interval [CI] 0.09, 0.82). No association was found using the liberal criteria of tobacco dependence (OR 0.51, 95% confidence interval [CI] 0.23, 1.2). These preliminary results replicate a previous association between tobacco use and the K4 allele of the TH gene (Lerman et al., 1997). The potential significance of including time to first cigarette in definitions of tobacco dependence and the possible role that these TH variants might play in tobacco dependence are discussed.

Parametric and nonparametric genome scan analyses for human handedness

We have performed a genome scan using 25 nuclear families consisting of right-handed parents with at least two left-handed children. Handedness was assessed as a qualitative trait using a laterality quotient. Laterality quotients indicate the direction of handedness, which is hand preference for performing unimanual tasks. Both parametric and nonparametric linkage analyses were applied. The parametric analysis using the single-locus genetic model of Klar resulted in four different regions with LOD scores higher than 1. The region on chromosome 10q26 gave a suggestive LOD score of 2.02 at a recombination fraction of 0.05. Nonparametric analysis gave an NPL score for this region of 2.16. However, further fine mapping of the region on chromosome 10q26 failed to obtain a higher LOD score. These results suggest that handedness is a human quantitative trait locus and that the proposed non-Mendelian monogenic models are incorrect.

Spinocerebellar ataxia type 20.

Spinocerebellar ataxia type 20 (SCA20) was reported in 2004 in a single Australian Anglo-Celtic pedigree. The phenotype is distinctive, with palatal tremor, and hypermetric saccades, and early dentate (but not pallidal) calcification in the absence of abnormalities of calcium metabolism. Dysarthria, rather than gait ataxia, was the initial symptom in most, and was typically conjoined with dysphonia, clinically resembling adductor spasmodic dysphonia. The onset of these speech abnormalities was abrupt in some cases. MRI scanning showed mild to moderate pancerebellar atrophy with dentate calcification, with olivary pseudohypertrophy in some cases, in the absence of other brainstem or cerebral changes. Nerve conduction studies were normal. Progression appeared to be slow. SCA20 is probably rare, as despite the distinctive phenotype, only this one pedigree has been described. The locus mapped to the pericentromeric region of chromosome 11 with a LOD score of 4.47, and its candidate region overlaps that of SCA5. It seems probable that these two SCAs may be separate genetic entities, on the basis of their divergent clinical features, but formal proof awaits discovery of one or both responsible genes.

Early-onset Alzheimer's disease caused by a novel mutation at codon 219 of the presenilin-1 gene.

Mutations in the presenilin 1 (PS1) gene are responsible for approximately 50% of early onset autosomal-dominant Alzheimers disease cases. A PCR based mutation detection method, chemical cleavage of mismatch, was used to detect a novel PS1 mutation in the coding sequence of the PS1 gene. Sequencing confirmed a T to C transition altering a leucine to proline at codon 219 of the PS1 gene. This is a novel mutation in exon 7 of the PS1 gene occurring outside the transmembrane regions of IV and V.

Genes for left-handedness: How to search for the needle in the haystack?

Although several genes that determine left-right asymmetry for structural syndromes such as situs inversus have been characterised in recent years (Supp, Witte, Potter, & Brueckner, 1997), there has been little progress in determining which genes or loci predispose to left-right handedness in humans. Linkage analysis has been used widely for the localisation of genes followed by their positional cloning. The complex genetics of handedness is one of the greatest problems for standard linkage analysis. Several genetic models have been proposed for the inheritance of handedness in humans. On the basis of these models, lefthandedness can be considered a common single gene trait with a high gene frequency and a non-mendelian inheritance pattern. We report here a possible strategy, using these genetic models, that can be applied for the identification for genes determining handedness in humans.

Universal fluorescent labeling of PCR products for DHPLC analysis: reducing cost and increasing sample throughput

Discovery and analysis of DNA sequence variations is an important part of genetic research (1). Denaturing high-performance liquid chromatog-raphy (DHPLC) fits the requirements in this area, addressing throughput issues by being compatible with automation while being robust, sensitive, and cost-effective. Multiplexing with fluores-cently labeled PCR products offers great hope for further improvements in sample throughput with compatible hydrophobic dye selection (2-5). However, purchasing fluorescently tagged primers for each PCR product may make its use cost-inhibitive. An added complexity is that maximum throughput involves the design of pools of four different PCR products that need to share a common melting temperature, which is not always possible.In an effort to utilize this option, we have investigated a universal fluorescent labeling (UFL) technique for its compatibility with DHPLC. This method involves a single PCR using three primers: a template-specific forward primer with a 20-bp extension at its 5′ end matching M13(-21), a template-specific reverse primer, and a fluorescently labeled M13(-21) primer (the universal primer). This technique, shown in Figure 1, involves the forward and reverse primer generating a PCR product and, when the forward primer is exhausted, the temperature is then lowered to allow the universal labeled primer to be used and to incorporate fluorescence into the accumulating PCR fragment (5). The significant advantage of this method is that the costs of project design for multiple genes or large genes are reduced considerably. Indeed, a set of only four fluorescent universal primers is required regardless of the number of PCR products to be analyzed. In addition, the same PCR product obtained from four different DNA samples that are labeled with different fluorophores can be easily pooled and run under the PCR product’s optimal conditions. This improves the flexibility in the design of the study and makes the interpretation of the results substantially easier. The first test of this technique utilized a plasmid library known as the Universal Mismatch System™ (UMS™; Genera Biosystems Pty, Ltd., Bundoora, VIC, Australia). By concen-trating on a set four plasmids that differ only in the central base with a C, G, T, or A, we were able to mix two of these plasmids at an equimolar ratio, allowing us to analyze all possible forms of single base mismatches. In this way, we can mimic naturally occurring single nucleotide polymorphisms (SNPs) in diploid genomes, making it ideal for testing the robustness of the UFL technique. This study was undertaken on the plasmid combinations that yielded the eight possible forms of mismatched bases. Illustrated in Figure 2 is one representative of the four combinations where the plasmid selection creates a CC and GG physical base mismatch. The product was analyzed by UV detection (Figure 2A). This produced four distinct peaks that represented the four species of DNA present in the sample: the two heteroduplex forms (CC and GG) followed by the two homoduplex forms (CG and GC). These same mismatches were reana-lyzed using the UFL procedure, as detailed below.Four separate PCR amplifications using one of each of the four fluores-cently labeled universal primers were performed on one UMS plasmid