Caution Regarding the Interpretation of Homoallelism in Polyglutamine Multiplex Assays

False-negative tests in Huntington's disease: A new variant within primer hybridization site

BACKGROUND

Establishing the diagnosis of Huntington's disease (HD) involves molecular genetic testing and estimation of the number of CAG repeats.

MATERIAL AND METHODS

We report a 42-year-old patient with clinical phenotype suggestive of HD, who was repeatedly negative on genetic testing for HD at a reference laboratory. He had positive history of similar symptoms in his father, but not in other family members. During a 2-year follow-up his symptoms slowly deteriorated (videos attached). The family history was misleading, as we discovered that patient's father was adopted as infant. Having excluded HD-like disorders and other causes of the symptoms we hypothesized that the primer could not bind to the mutated allele.

RESULTS

The PCR reaction with primers HD1 and Hu3 revealed homozygosity of the other adjacent microsatellite tract consisting of the CCG repeats. The newly designed set of primers, located outside of the CAG tract (HD6extF, HD7extR) was used and enabled amplification of the mutant allele and detection of the abnormal range of CAG repeats.

CONCLUSIONS

As application of the novel primers led to the diagnosis of HD in other 5 patients previously tested negative, we propose their incorporation into routine genetic testing in patients suspected of HD displaying homoallelism in the standard protocol.

A Pipeline to Assess Disease-Associated Haplotypes in Repeat Expansion Disorders: The Example of MJD/SCA3 Locus

At least 40 human diseases are associated with repeat expansions; yet, the mutational origin and instability mechanisms remain unknown for most of them. Previously, genetic epidemiology and predisposing backgrounds for the instability of some expanding loci have been studied in different populations through the analysis of diversity flanking the respective pathogenic repeats. Here, we aimed at developing a pipeline to assess disease-associated haplotypes at oligonucleotide repeat loci, combining analysis of single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs). Machado-Joseph disease (MJD/SCA3), the most frequent dominant ataxia worldwide, was used as an example of a detailed procedure. Thus, to identify genetic backgrounds that segregate with expanded/mutated alleles in MJD, we selected a set of 26 SNPs and 7 STRs flanking the causative CAG repeat. Key criteria and steps for this selection are described, and included (1) haplotype blocks minimizing the occurrence of recombination (for SNPs); and (2) match scores to increase potential for polymorphic information content of repetitive sequences found in Tandem Repeats Finder (for STRs). To directly assess SNP haplotypes in phase with MJD expansions, we optimized a strategy with preferential amplification of normal over expanded alleles, in addition to SNP allele-specific amplifications; this allowed the identification of disease-associated SNP haplotypes, even when only the proband is available in a given family. To infer STR haplotypes, we optimized a multiplex PCR, including 7 STRs plus the MJD_CAG repeat, followed by analysis of segregation or the use of the PHASE software. This protocol is a ready-to-use tool to assess MJD haplotypes in different populations. The pipeline designed can be used to assess disease-associated haplotypes in other repeat-expansion diseases. This should be of great utility to study (1) genetic epidemiology (population-of-origin, age and spreading routes of mutations) and (2) mechanisms responsible for de novo expansions, in these neurological diseases; (3) to detect predisposing haplotypes and (4) phenotype modifiers; (5) to help solving cases of apparent homoallelism (two same-size normal alleles) in diagnosis; and (6) to identify the best targets for the development of allele-specific therapies in ethnically diverse patient populations.

Clinical and genetic analysis of spinocerebellar ataxia type 7 (SCA7) in Zambian families

BACKGROUND

To date, 43 types of Spinocerebellar Ataxias (SCAs) have been identified. A subset of the SCAs are caused by the pathogenic expansion of a CAG repeat tract within the corresponding gene. Ethnic and geographic differences are evident in the prevalence of the autosomal dominant SCAs. Few descriptions of the clinical phenotype and molecular genetics of the SCAs are available from the African continent. Established studies mostly concern the South African populations, where there is a high frequency of SCA1, SCA2 and SCA7. The SCA7 mutation in South Africa (SA) has been found almost exclusively in families of indigenous Black African ethnic origin.

OBJECTIVE

To present the results of the first clinical description of seven Zambian families presenting with autosomal dominant SCA, as well as the downstream molecular genetic analysis of a subset of these families.

METHODS

The study was undertaken at the University Teaching Hospital in Lusaka, Zambia. Ataxia was quantified with the Brief Ataxia Rating Scale derived from the modified international ataxia rating scale. Molecular genetic testing for 5 types of SCA (SCA1, SCA2, SCA3, SCA6 and SCA7) was performed at the National Health Laboratory Service at Groote Schuur Hospital and the Division of Human Genetics, University of Cape Town, SA. The clinical and radiological features were evaluated in seven families with autosomal dominant cerebellar ataxia. Molecular genetic analysis was completed on individuals representing three of the seven families.

RESULTS

All affected families were ethnic Zambians from various tribes, originating from three different regions of the country (Eastern, Western and Central province). Thirty-four individuals from four families had phenotypic features of SCA7. SCA7 was confirmed by molecular testing in 10 individuals from 3 of these families. The age of onset of the disease varied from 12 to 59 years. The most prominent phenotypic features in these families were gait and limb ataxia, dysarthria, visual loss, ptosis, ophthalmoparesis/ophthalmoplegia, pyramidal tract signs, and dementia. Affected members of the SCA7 families had progressive macular degeneration and cerebellar atrophy. All families displayed marked anticipation of age at onset and rate of symptom progression. The pathogenic SCA7 CAG repeat ranges varied from 47 to 56 repeats. Three additional families were found to have clinical phenotypes associated with autosomal dominant SCA, however, DNA was not available for molecular confirmation. The age of onset of the disease in these families varied from 19 to 53 years. The most common clinical picture in these families included a combination of cerebellar symptoms with slow saccadic eye movements, peripheral neuropathy, dementia and tremor.

CONCLUSION

SCA is prevalent in ethnic Zambian families. The SCA7 families in this report had similar clinical presentations to families described in other African countries. In all families, the disease had an autosomal dominant pattern of inheritance across multiple generations. All families displayed anticipation of both age of onset and the rate of disease progression. Further clinical and molecular investigations of the inherited ataxias in a larger cohort of patients is important to understand the natural history and origin of SCAs in the Zambian population.

Evidence for a common founder effect amongst South African and Zambian individuals with Spinocerebellar ataxia type 7

Spinocerebellar ataxia type 7 (SCA7) is an inherited neurodegenerative disease caused by the expansion of a CAG repeat within the ataxin 7 gene, leading to a pathogenic polyglutamine tract within the ataxin 7 protein. SCA7 patients suffer from progressive cerebellar ataxia and macular degeneration. SCA7 is considered to be rare, although founder effects have been reported in South Africa, Scandinavia and Mexico. The South African SCA7-associated haplotype has not been investigated in any other populations, and there have been limited reports of SCA7 patients from other African countries. Here, we describe the first two ethnic Zambian families with confirmed SCA7. Haplotype analysis showed that the South African SCA7 haplotype alleles were significantly associated with the pathogenic expansion in affected Zambian individuals, providing strong evidence for a shared founder effect between South African and Zambian SCA7 patients.