Upgrading molecular diagnostics of myotonic dystrophies: multiplexing for simultaneous characterization of the DMPK and ZNF9 repeat motifs.

Myotonic dystrophy (DM) is a common neuromuscular disorder comprising at least two genetically different forms. DM1 is caused by expansion of a (CTG)(n) repeat in the DMPK gene, while DM2 is caused by expansion of a (CCTG)(n) part of a complex repetitive motif (TG)(n)(TCTG)(n)(CCTG)(n) in the ZNF9 gene. Detection of the responsible expansions is complicated in both cases because of the extremely variable length of the expanded alleles, which can contain even several thousands of repeats in both disorders. One of the commonly used detection approaches utilizes the combination of conventional PCR and "triplet" or "tetraplet" repeat-primed PCR (TP-PCR). TP-PCR can be performed simultaneously or successively in both DM1 and DM2 testing. We have designed two multiplex reactions which include bi-directionally labelled conventional PCRs and TP-PCRs for both DM1 and DM2 loci. These two reactions can be used under the same amplification and electrophoretic conditions thus allowing their parallelisation into a one step method. Simultaneous analysis of the samples using these two multiplex reactions allows characterization of both the DM1 and DM2 repeat regions in the time usually required for the first screening step in conventional DM1 or DM2 testing.

Development of high-resolution melting (HRM) analysis for population studies of Fascioloides magna (Trematoda: Fasciolidae), the giant liver fluke of ruminants.

The high-resolution melting (HRM) technique was successfully optimized as fast and effective method for population study of digenetic fluke, Fascioloides magna (Trematoda: Fasciolidae), originally North American liver parasite of free-living and domestic ruminants. Previously selected variable region (439 bp) of mitochondrial cytochrome c oxidase subunit I (cox1) of 249 fluke individuals from enzootic European and North American regions were sequenced and mutually compared. The sequence analysis of partial cox1 revealed presence of seven structurally different haplotypes. Based on the sequence structure and alignments of six of them (Ha1-Ha6), three internal probes were designed and applied in HRM-based haplotype determination of all F. magna specimens. HRM analysis, performed with three designed probes, resulted in classification of samples into the seven haplogroups, equally with their assortment according to the sequence analysis. The representative of the haplotype, which was not involved in probe design (Ha7), was characterized by a unique melting curve shape as well. This provided an evidence of optimally settled conditions in HRM assay and indicated a probability of successful discrimination of novel haplotypes in future population studies on F. magna. The successful optimization of HRM method stands for an opportunity of detection of genetically unknown North American variants of F. magna and promises its application as fast and cheap screening technique for phylogeography studies of the giant liver fluke on its original continent.

Mutation analysis of PMP22 in Slovak patients with Charcot-Marie-Tooth disease and hereditary neuropathy with liability to pressure palsies.

Charcot-Marie-Tooth disease (CMT) and related peripheral neuropathies are the most commonly inherited neurological disorders in humans, characterized by clinical and genetic heterogeneity. The most prevalent clinical entities belonging to this group of disorders are CMT type 1A (CMT1A) and hereditary neuropathy with liability to pressure palsies (HNPP). CMT1A and HNPP are predominantly caused by a 1.5 Mb duplication and deletion in the chromosomal region 17p11.2, respectively, and less frequently by other mutations in the peripheral myelin protein 22 (PMP22) gene. Despite being relatively common diseases, they haven't been previously studied in the Slovak population. Therefore, the aim of this study was to identify the spectrum and frequency of PMP22 mutations in the Slovak population by screening 119 families with CMT and 2 families with HNPP for causative mutations in this gene. The copy number determination of PMP22 resulted in the detection of CMT1A duplication in 40 families and the detection of HNPP deletion in 7 families, 6 of which were originally diagnosed as CMT. Consequent mutation screening of families without duplication or deletion using dHPLC and sequencing identified 6 single base changes (3 unpublished to date), from which only c.327C>A (Cys109X) present in one family was provably causative. These results confirm the leading role of PMP22 mutation analysis in the differential diagnosis of CMT and show that the spectrum and frequency of PMP22 mutations in the Slovak population is comparable to that seen in the global population.

High-resolution melting analysis for genotyping of the myotonic dystrophy type 1 associated Alu insertion/deletion polymorphism.

Since its introduction, high-resolution melting (HRM) analysis has been used for genotyping of various types of sequence alterations. In this study, we report the use of HRM for genotyping of the 1-kb insertion/deletion polymorphism, involving a problematic region of five consecutive Alu elements, that is associated with myotonic dystrophy type 1. We combined a three-primer polymerase chain reaction (PCR) amplification approach with HRM using two primer sets. Analyses based on curve shapes are sensitive enough to differentiate between genotypes with both primer sets. In addition, the newly designed insertion-specific primer from the second primer set equalizes the allele-specific amplicon lengths, thereby reducing the possibility of preferential amplification of shorter fragments.

Identification of 11 Novel Homogentisate 1,2 Dioxygenase Variants in Alkaptonuria Patients and Establishment of a Novel LOVD-Based HGD Mutation Database.

Enzymatic loss in alkaptonuria (AKU), an autosomal recessive disorder, is caused by mutations in the homogentisate 1,2 dioxygenase (HGD) gene, which decrease or completely inactivate the function of the HGD protein to metabolize homogentisic acid (HGA). AKU shows a very low prevalence (1:100,000-250,000) in most ethnic groups, but there are countries with much higher incidence, such as Slovakia and the Dominican Republic. In this work, we report 11 novel HGD mutations identified during analysis of 36 AKU patients and 41 family members from 27 families originating from 9 different countries, mainly from Slovakia and France. In Slovak patients, we identified two additional mutations, thus a total number of HGD mutations identified in this small country is 12. In order to record AKU-causing mutations and variants of the HGD gene, we have created a HGD mutation database that is open for future submissions and is available online ( http://hgddatabase.cvtisr.sk/ ). It is founded on the Leiden Open (source) Variation Database (LOVD) system and includes data from the original AKU database ( http://www.alkaptonuria.cib.csic.es ) and also all so far reported variants and AKU patients. Where available, HGD-haplotypes associated with the mutations are also presented. Currently, this database contains 148 unique variants, of which 115 are reported pathogenic mutations. It provides a valuable tool for information exchange in AKU research and care fields and certainly presents a useful data source for genotype-phenotype correlations and also for future clinical trials.

Repeat-primed polymerase chain reaction in myotonic dystrophy type 2 testing.

Myotonic dystrophy type 1 (DM1) and type 2 (DM2) are the most common autosomal dominant neuromuscular disorders in adults. DM1 is caused by an unstable expansion of the (CTG)(n) repeat tract in the DMPK gene, whereas DM2 is caused by an unstable expansion of the (CCTG)(n) repeat tract in the ZNF9 gene. The (CCTG)(n) repeat is a part of a complex repetitive motif (TG)(n)(TCTG)(n)(CCTG)(n), in which each of the elements is highly polymorphic. Repeat-primed polymerase chain reaction (PCR) is a commonly used technique for the determination of the presence or absence of the expanded alleles in both DM1 and DM2. Besides the expansion detection, it can be used for the determination of the repeat structure (repeat number, presence of interruptions, and their localization) in healthy-range alleles. Because the (CCTG)(n) part of the motif in DM2 is generally interrupted with other sequences, "tetraplet" repeat-primed PCR (TP-PCR) results interpretation is more complicated than for DM1. Most of the studies, published so far, used TP-PCR in a direction such that they amplified through the (TG)(n)(TCTG)(n) part of the motif. We compared the features of TP-PCR performed in the commonly used direction with the results obtained by TP-PCR performed in the opposite direction. Our results suggest that the direction that does not include the (TG)(n)(TCTG)(n) tract leads to better quality and more informative results in comparison with the direction containing the (TG)(n)(TCTG)(n) tract.

Effect of unexpected sequence interruptions to conventional PCR and repeat primed PCR in myotonic dystrophy type 1 testing.

Myotonic dystrophy type 1 (DM1) is caused by expansion of the CTG trinucleotide repeat in the DMPK gene. Our study focuses on the effect of recently described unusual sequence interruptions inside the CTG tract on conventional polymerase chain reaction (PCR) and triplet repeat primed PCR (TP-PCR) amplifications, which are the methods now widely used in molecular testing for DM1. For molecular characterization of the CTG repeat tract, we used conventional fluorescent PCR with bidirectional labeling and both forward and reverse direction TP-PCR. Though the results of the methods are still unambiguous for most alleles, mistyping and false results may occur in the typing of some unordinary alleles carrying sequence interruptions. The presence of these interruptions may lead not only to altered TP-PCR profiles, as can be expected, but also to abnormal electrophoretic mobility of complementary strands produced by conventional amplification of such alleles. Our findings suggest that the simultaneous combination of bidirectionally labeled conventional PCR with TP-PCR performed in both directions may be necessary for increasing the reliability and accuracy of the TP-PCR-based assay for DM1 testing.

The expanding world of myotonic dystrophies: how can they be detected?

Myotonic dystrophy (DM) comprises at least two genetically distinct forms, both of which are caused by expansions of microsatellite repeats. The expansion of a CTG repeat in the DMPK gene leads to the first genetic form (DM type 1), and the expansion of a CCTG repeat in the ZNF9 gene causes the second genetic form of the disease (DM type 2). In both cases, the repeat units may expand to several thousand repeats, and the number of repeats in the expanded alleles shows a high degree of meiotic and somatic instability. The unprecedented size of expansions and their dynamic nature still represents a diagnostic challenge, which has been facilitated using different methods and modifications since the identification of the underlying mutations of these disorders. Here, we present an overview of the basic methods described for the purpose of identification of the DM type 1 and DM type 2 expansions and discuss particular modifications and improvements implemented to extend the detection ranges of these methods. Our review focuses on the advantages and disadvantages of the methods based on Southern blot analysis, polymerase chain reaction amplification, and in situ hybridization techniques and also on the possibilities of preimplantation and prenatal genetic testing.