Detecting exon deletions and duplications of the DMD gene using Multiplex Ligation-dependent Probe Amplification (MLPA)

A female patient carrying a novel DMD mutation with non-random X-chromosome inactivation from a DMD family

OBJECTIVE

To analyze the clinical phenotype and genetic characteristics of a female proband carrying a novel mutation in the DMD gene with non-random X-chromosome inactivation in a large pedigree with pseudohypertrophic muscular dystrophy.

METHODS

Clinical information of the female proband, her monozygotic twin sister, and other family members were collected. Potential pathogenic variants were detected with Multiplex Ligation-dependent Probe Amplification (MLPA) and whole-exome sequencing (WES). Methylation-sensitive restriction enzyme (HhaI) was employed for X-chromosome inactivation analysis.

RESULTS

The proband was a female over 5 years old, displayed clinical manifestations such as elevated creatine kinase (CK) levels and mild calf muscle hypertrophy. Her monozygotic twin sister exhibited normal CK levels and motor ability. Her uncle and cousin had a history of DMD. WES revealed that the proband carried a novel variant in the DMD (OMIM: 300,377) gene: NM_004006.3: c.3051_3053dup; NP_003997.2: p.Tyr1018*. In this pedigree, five out of six female members were carriers of this variant, while the cousin and uncle were hemizygous for this variant. X-chromosome inactivation analysis suggested non-random inactivation in the proband.

CONCLUSION

The c.3051_3053dup (p.Tyr1018*) variant in the DMD gene is considered to be the pathogenic variant significantly associated with the clinical phenotype of the proband, her cousin, and her uncle within this family. Integrating genetic testing with clinical phenotype assessment can be a valuable tool for physicians in the diagnosis of progressive muscular dystrophies, such as Becker muscular dystrophy (BMD) and Duchenne muscular dystrophy (DMD).

Advances in Dystrophinopathy Diagnosis and Therapy

Dystrophinopathies are x-linked muscular disorders which emerge from mutations in the Dystrophin gene, including Duchenne and Becker muscular dystrophy, and dilated cardiomyopathy. However, Duchenne muscular dystrophy interconnects with bone loss and osteoporosis, which are exacerbated by glucocorticoids therapy. Procedures for diagnosing dystrophinopathies include creatine kinase assay, haplotype analysis, Southern blot analysis, immunological analysis, multiplex PCR, multiplex ligation-dependent probe amplification, Sanger DNA sequencing, and next generation DNA sequencing. Pharmacological therapy for dystrophinopathies comprises glucocorticoids (prednisone, prednisolone, and deflazacort), vamorolone, and ataluren. However, angiotensin-converting enzyme (ACE) inhibitors, angiotensin receptor blockers (ARBs), and β-blockers are the first-line to prevent dilated cardiomyopathy in dystrophinopathy patients. Duchenne muscular dystrophy gene therapy strategies involve gene transfer, exon skipping, exon reframing, and CRISPR gene editing. Eteplirsen, an antisense-oligonucleotide drug for skipping exon 51 from the Dystrophin gene, is available on the market, which may help up to 14% of Duchenne muscular dystrophy patients. There are various FDA-approved exon skipping drugs including ExonDys-51 for exon 51, VyonDys-53 and Viltolarsen for exon 53 and AmonDys-45 for exon 45 skipping. Other antisense oligonucleotide drugs in the pipeline include casimersen for exon 45, suvodirsen for exon 51, and golodirsen for exon 53 skipping. Advances in the diagnosis and therapy of dystrophinopathies offer new perspectives for their early discovery and care.

Large scale population screening for Duchenne muscular dystrophy - Predictable and unpredictable challenges

Objective

Large deletions and duplications account for 65%–80% of pathogenic Duchenne muscular dystrophy (DMD) variants. A nationwide carrier screening for DMD was initiated in Israel in 2020. We assessed the carrier rate and spectrum of variants detected in a cohort of women screened for DMD carrier status and analyzed screening efficacy and challenges related to DMD population screening.

Methods

A cohort of 12,362 women were tested at a single institute using multiplex ligation‐dependent probe amplification based copy number analysis of the 79 DMD exons. Consecutive sequencing of the primer region was performed when a single exon deletion was suspected.

Results

Deletions involving multiple exons were detected in seven cases and duplications involving multiple exons were found in four. Of these, nine were pathogenic based on previous reports and familial segregation testing, translating to a carrier rate of 1:1374. A family history was reported in three cases. Single exon deletions were suspected in 81 cases; further sequencing detected a single nucleotide variant affecting probe hybridization. These cases clustered according to ethnic origin.

Discussion

Population screening for DMD has a significant yield. Most carriers did not report a family history of dystrophinopathies. Screening should be adjusted for methodological limitations. Some cases may require extensive genetic counseling and work‐up.

What's already known about this topic?

Deletions and duplications account for 65%–80% of pathogenic Duchenne muscular dystrophy (DMD) variants.

About two‐thirds of DMD pathogenic variants are inherited from a female carrier.

A nationwide carrier screening for DMD was initiated in Israel in 2020.

What does this study add?

The carrier rate among 12,362 women tested for deletions and duplications in the DMD gene was 1:1374.

Screening should be adjusted for methodological limitations and may require extensive genetic counseling and work‐up.

Circulating MicroRNAs in Duchenne Muscular Dystrophy

OBJECTIVE

The diagnosis of Duchenne Muscular Dystrophy (DMD) currently depends on non-specific measures such as Creatine kinase (CK) levels. MicroRNAs (miRNAs) are a class of small, endogenous RNAs of 21-25 nucleotides, that are important regulators for numerous physiological and pathological processes. The aim of the current study is to assess the potential of miRNAs as non-invasive biomarker for the diagnosis of DMD and for identifying carriers.

PATIENTS AND METHODS

Thirty healthy subjects and 29 families with one member diagnosed with DMD were enrolled in the study. Peripheral blood samples were collected from all subjects where microRNAs were extracted from plasma followed by the quantification of miR-499, miR-103a-3p, miR-103a-5p, miR-206, miR-208a, miR-223 and miR-191-5p. MLPA and NGS were carried out as a gold standard technique to identify the mutations in the participants.

RESULTS

Our data revealed that miR-499 was significantly upregulated in all DMD patients, and true carriers (mothers), while 78 % of potential carriers (sisters) exhibited high levels of this miRNA. Similarly, miR-103a-3p showed an increase in the patients' families although to a lesser extent. On the other hand, miR-206 and miR-191-5p were significantly downregulated in the majority of the DMD patients and the tested female family members. MicroRNA miR-103a-5p and miR-208a followed a comparable trend in patients and mothers.

CONCLUSIONS

Ourresults suggest that the plasma levels of miRNAs have the capability to diagnose DMD patients and more importantly, miRNAs can be used to identify female carriers.

Targeted sequencing of the DMD locus: A comprehensive diagnostic tool for all mutations

Background & objectives:

Duchenne muscular dystrophy (DMD) is an X-linked recessive disorder and is caused mainly by deletion, duplication and point mutations in the DMD gene. Diagnosis of DMD has been a challenge as the mutations in the DMD gene are heterogeneous and require more than one diagnostic strategy for the validation of the mutation. This study was planned to evaluate the targeted next-generation sequencing (NGS) as a single platform to detect all types of mutations in the DMD gene, thereby reducing the time and costs compared to conventional sequential testing and also provide precise genetic information for emerging gene therapies.

Methods:

The study included 20 unrelated families and 22 patients from an Indian population who were screened for DMD based on phenotypes such as scoliosis, toe walking and loss of ambulation. Peripheral blood DNA was isolated and subjected to multiplex ligation-dependent probe amplification (MLPA) and targeted NGS of the DMD gene to identify the nature of the mutation.

Results:

In the study patients, 77 per cent of large deletion mutations and 23 per cent single-nucleotide variations (SNVs) were identified. Novel mutations were also identified along with reported deletions, point mutations and partial deletions within the exon of the DMD gene.

Interpretation & conclusions:

Our findings showed the importance of NGS in the routine diagnostic practice in the identification of DMD mutations over sequential testing. It may be used as a single-point diagnostic strategy irrespective of the mutation type, thereby reducing the turnaround time and cost for multiple diagnostic tests such as MLPA and Sanger sequencing. Though MLPA is a sensitive technique and is the first line of a diagnostic test, the targeted NGS of the DMD gene may have an advantage of having a single diagnostic test. A study on a larger number of patients is needed to highlight NGS as a single, comprehensive platform for the diagnosis of DMD.

Molecular Analysis-Based Genetic Characterization of a Cohort of Patients with Duchenne and Becker Muscular Dystrophy in Eastern China

Background:

Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) are common X-linked recessive neuromuscular disorders caused by mutations in dystrophin gene. Multiplex polymerase chain reaction (multiplex PCR) and multiplex ligation-dependent probe amplification (MLPA) are the most common methods for detecting dystrophin gene mutations. This study aimed to contrast the two methods and discern the genetic characterization of patients with DMD/BMD in Eastern China.

Methods:

We collected 121 probands, 64 mothers of probands, and 15 fetuses in our study. The dystrophin gene was detected by multiplex PCR primarily in 28 probands, and MLPA was used in multiplex PCR-negative cases subsequently. The dystrophin gene of the remaining 93 probands and 62 female potential carriers was tested by MLPA directly. In fetuses, multiplex PCR and MLPA were performed on 4 fetuses and 10 fetuses, respectively. In addition, sequencing was also performed in 4 probands with negative MLPA.

Results:

We found that 61.98% of the subjects had genetic mutations including deletions (50.41%) and duplications (11.57%). There were 43.75% of mothers as carriers of the mutation. In 15 fetuses, 2 out of 7 male fetuses were found to be unhealthy and 2 out of 8 female fetuses were found to be carriers. Exons 3–26 and 45–52 have the maximum frequency in mutation regions. In the frequency of exons individually, exon 47 and exon 50 were the most common in deleted regions and exons 5, 6, and 7 were found most frequently in duplicated regions.

Conclusions:

MLPA has better productivity and sensitivity than multiplex PCR. Prenatal diagnosis should be applied in DMD high-risk fetuses to reduce the disease incidence. Furthermore, it is the responsibility of physicians to inform female carriers the importance of prenatal diagnosis.

Cost-Effectiveness Analysis of Diagnosis of Duchenne/Becker Muscular Dystrophy in Colombia

OBJECTIVES

To determine the cost-effectiveness ratio of different courses of action for the diagnosis of Duchenne or Becker muscular dystrophy in Colombia.

METHODS

The cost-effectiveness analysis was performed from the Colombian health system perspective. Decision trees were constructed, and different courses of action were compared considering the following tests: immunohistochemistry (IHC), Western blot (WB), multiplex polymerase chain reaction, multiplex ligation-dependent probe amplification (MLPA), and the complete sequencing of the dystrophin gene. The time horizon matched the duration of sample extraction and analysis. Transition probabilities were obtained from a systematic review. Costs were constructed with a type-case methodology using the consensus of experts and the valuation of resources from consulting laboratories and the 2001 Social Security Institute cost manual. Deterministic sensitivity and scenario analyses were performed with one or more unavailable alternatives. Costs were converted from Colombian pesos to US dollars using the 2014 exchange rate.

RESULTS

In the base case, WB was the dominant strategy, with a cost of US $419.07 and a sensitivity of 100%. This approach remains the dominant strategy down to a 98.2% sensitivity and while costs do not exceed US $837.38. If WB was not available, IHC had the best cost-effectiveness ratio, followed by MLPA and sequencing.

CONCLUSIONS

WB is a cost-effective alternative for the diagnosis of patients suspected of having Duchenne or Becker muscular dystrophy in the Colombian health system. The IHC test is rated as the second-best detection method. If these tests are not available, MLPA followed by sequencing would be the most cost-effective alternative.

Novel Mutation of the Dystrophin Gene in a Child with Duchenne Muscular Dystrophy

INTRODUCTION

Duchenne muscular dystrophy (DMD) is an X-linked autosomal recessive genetic disorder caused by mutations in DMD gene. Approximately 70% of the mutations are caused by deletions or duplications of DMD exons, while the remaining were minor mutations.

CASE REPORT

We present a 5-year-old boy with typical clinical features of DMD. A novel mutation was identified as a c.9358_9359insA of DMD gene by next-generation sequencing. This mutation which was origined from mother, generated a frameshift mutation and resulted in abnormal synthesis of protein polypeptide chains.

CONCLUSION

We demonstrated a novel mutation of DMD gene and expanded the spectrum of mutations causing DMD.

Study of Dystrophinopathy in Eastern Uttar Pradesh Population of India

Introduction

The frequency and distribution of dystrophin gene deletions vary in patients with Duchene/Becker muscular dystrophy (DMD/BMD).

Objective

In this study, we aimed to analyze clinical, biochemical, and dystrophin gene deletion pattern, by using multiplex polymerase chain reaction (PCR) in the population of eastern Uttar Pradesh and the adjoining districts of Bihar and Madhya Pradesh.

Material and Method

After clinical assessment, 225 patients of DMD/BMD were analyzed for deletion in dystrophin gene. Clinical features and biochemical parameters were noted. For genetic study, all samples were tested for deletion from 25 exons of DMD gene by using multiplex PCR.

Result

Deletions were detected in 169 (75.1%) patients of DMD/BMD. Deletions were observed in both proximal and mid-distal hot spot regions with maximum deletion localized in the mid-distal hot spot region of the gene. The most frequent deletions were observed in exon 50 (14.9%) and exon 49 (10.8%).

Conclusion

This study concludes that mid-distal region of dystrophin is highly polymorphic in the population of eastern Uttar Pradesh and responsible for pathogenesis of DMD. The population of eastern Uttar Pradesh shows similar pattern of deletion in dystrophin gene when compared with other ethnic groups of the Indian population.

Homozygous and hemizygous CNV detection from exome sequencing data in a Mendelian disease cohort

We developed an algorithm, HMZDelFinder, that uses whole exome sequencing (WES) data to identify rare and intragenic homozygous and hemizygous (HMZ) deletions that may represent complete loss-of-function of the indicated gene. HMZDelFinder was applied to 4866 samples in the Baylor–Hopkins Center for Mendelian Genomics (BHCMG) cohort and detected 773 HMZ deletion calls (567 homozygous or 206 hemizygous) with an estimated sensitivity of 86.5% (82% for single-exonic and 88% for multi-exonic calls) and precision of 78% (53% single-exonic and 96% for multi-exonic calls). Out of 773 HMZDelFinder-detected deletion calls, 82 were subjected to array comparative genomic hybridization (aCGH) and/or breakpoint PCR and 64 were confirmed. These include 18 single-exon deletions out of which 8 were exclusively detected by HMZDelFinder and not by any of seven other CNV detection tools examined. Further investigation of the 64 validated deletion calls revealed at least 15 pathogenic HMZ deletions. Of those, 7 accounted for 17–50% of pathogenic CNVs in different disease cohorts where 7.1–11% of the molecular diagnosis solved rate was attributed to CNVs. In summary, we present an algorithm to detect rare, intragenic, single-exon deletion CNVs using WES data; this tool can be useful for disease gene discovery efforts and clinical WES analyses.

MLPA identification of dystrophin mutations and in silico evaluation of the predicted protein in dystrophinopathy cases from India

Background

Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) are X-linked recessive disorders caused by mutations in the DMD gene. The aim of this study was to predict the effect of gene mutations on the dystrophin protein and study its impact on clinical phenotype.

Methods

In this study, 415 clinically diagnosed patients were tested for mutations by Multiplex ligation dependent probe amplification (MLPA). Muscle biopsy was performed in 34 patients with negative MLPA. Phenotype-genotype correlation was done using PROVEAN, hydrophobicity and eDystrophin analysis. We have utilized bioinformatics tools in order to evaluate the observed mutations both at the level of primary as well as secondary structure.

Results

Mutations were identified in 75.42% cases, of which there were deletions in 91.6% and duplications in 8.30%. As per the reading frame rule, 84.6% out-of frame and 15.3% in-frame mutations were noted. Exon 50 was the most frequently deleted exon and the exon 45–52 region was the hot-spot for deletions in this cohort. There was no correlation noted between age of onset or creatine kinase (CK) values with extent of gene mutation. The PROVEAN analysis showed a deleterious effect in 94.5% cases and a neutral effect in 5.09% cases. Mutations in exon 45–54 (out of frame) and exon 46–54 (in-frame) regions in the central rod domain of dystrophin showed more negative scores compared to other domains in the present study. Hydrophobicity profile analysis showed that the hydrophobic regions I & III were equally affected. Analysis of deletions in hinge III hydrophobic region by the eDystrophin programme also predicted a hybrid repeat seen to be associated with a BMD like disease progression, thus making the hinge III region relatively tolerant to mutations.

Conclusions

We found that, while the predictions made by the software utilized might have overall significance, the results were not convincing on a case by case basis. This reflects the inadequacy of the currently available tools and also underlines the possible inadequacy of MLPA to detect other minor mutations that might enhance or suppress the effect of the primary mutation in this large gene. Next Generation Sequencing or targeted Sanger sequencing on a case by case basis might improve phenotype- genotype correlation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12881-017-0431-6) contains supplementary material, which is available to authorized users.

Genetic diagnosis of Duchenne and Becker muscular dystrophy using multiplex ligation-dependent probe amplification in Rwandan patients

Duchenne and Becker muscular dystrophies are the most common clinical forms of muscular dystrophies. They are genetically X-linked diseases caused by a mutation in the dystrophin (DMD) gene. A genetic diagnosis was carried out in six Rwandan patients presenting a phenotype of Duchenne and Becker muscular dystrophies and six asymptomatic female carrier relatives using multiplex ligation-dependent probe amplification (MLPA). Our results revealed deletion of the exons 48-51 in one patient, an inherited deletion of the exons 8-21 in two brothers and a de novo deletion of the exons 46-50 in the fourth patient. No copy number variation was found in two patients. Only one female carrier presented exon deletion in the DMD gene. This is the first cohort of genetic analysis in Rwandan patients affected by Duchenne and Becker muscular dystrophies. This report confirmed that MLPA assay can be easily implemented in low-income countries.

Development of MLPA for human ACAT1 gene and identification of a heterozygous Alu-mediated deletion of exons 3 and 4 in a patient with mitochondrial acetoacetyl-CoA thiolase (T2) deficiency

Mitochondrial acetoacetyl-CoA thiolase deficiency is an autosomal recessive disorder, characterized by intermittent ketoacidosis. We developed a multiplex ligation-dependent probe amplification method for mutation detection in the ACAT1 gene, which encodes this enzyme, and validated it using DNAs from two previously reported patients having partial deletion and duplication in this gene. Using this method, we identified a heterozygous deletion including exons 3-4 in a third patient, likely due to Alu-mediated non-equal homologous recombination between Alu sequences.

Use of the MLPA assay in the molecular diagnosis of gene copy number alterations in human genetic diseases

Multiplex Ligation-dependent Probe Amplification (MLPA) assay is a recently developed technique able to evidence variations in the copy number of several human genes. Due to this ability, MLPA can be used in the molecular diagnosis of several genetic diseases whose pathogenesis is related to the presence of deletions or duplications of specific genes. Moreover, MLPA assay can also be used in the molecular diagnosis of genetic diseases characterized by the presence of abnormal DNA methylation. Due to the large number of genes that can be analyzed by a single technique, MLPA assay represents the gold standard for molecular analysis of all pathologies derived from the presence of gene copy number variation. In this review, the main applications of the MLPA technique for the molecular diagnosis of human diseases are described.

Genetic analysis of dystrophin gene for affected male and female carriers with Duchenne/Becker muscular dystrophy in Korea

Duchenne and Becker muscular dystrophy (DMD/BMD) are X-linked recessive disorders caused by mutation in dystrophin gene. We analyzed the results of a genetic test in 29 DMD/BMD patients, their six female relatives, and two myopathic female patients in Korea. As the methods developed, we applied different procedures for dystrophin gene analysis; initially, multiplex polymerase chain reaction was used, followed by multiplex ligation-dependent probe amplification (MLPA). Additionally, we used direct DNA sequencing for some patients who had negative results using the above methods. The overall mutation detection rate was 72.4% (21/29) in DMD/BMD patients, identifying deletions in 58.6% (17/29). Most of the deletions were confined to the central hot spot region between exons 44 and 55 (52.9%, 7/19). The percentage of deletions and duplications revealed by MLPA was 45.5% (5/11) and 27.2% (3/11), respectively. Using the MLPA method, we detected mutations confirming their carrier status in all female relatives and symptomatic female patients. In one patient in whom MLPA revealed a single exon deletion of the dystrophin gene, subsequent DNA sequencing analysis identified a novel nonsense mutation (c.4558G > T; Gln1520X). The MLPA assay is a useful quantitative method for detecting mutation in asymptomatic or symptomatic carriers as well as DMD/BMD patients.

Diagnostic work-up and risk stratification in X-linked dilated cardiomyopathies caused by dystrophin defects

OBJECTIVES

We sought to describe the diagnostic work-up, phenotype, and long-term evolution of dilated cardiomyopathy (DCM) associated with Dystrophin (DYS) defects.

BACKGROUND

X-linked DCM associated with DYS defects can be clinically indistinguishable from other types of DCM.

METHODS

The series comprises 436 consecutive male patients diagnosed with DCM. Patients underwent endomyocardial biopsy (EMB). Genetic testing employed multiplex polymerase chain reaction and multiple ligation dependent probe assay for deletions and direct sequencing of the 79 exons and flanking regions of the gene for point mutations or small rearrangements.

RESULTS

We identified DYS defects in 34 of 436 patients (7.8%) (onset age 34 ± 11 years, age range 17 to 54 years); 30 had proven X-linked inheritance. The 2 phenotypes included DCM with mild skeletal myopathy and/or increased serum creatine phosphokinase (n = 28) or DCM only (n = 6). The EMB showed defective dystrophin immunostain. The DYS defects consisted of 21 in-frame deletions and 11 out-of-frame deletions as well as 1 stop and 1 splice-site mutation. During a median follow-up of 60 months (interquartile range: 11.25 to 101.34 months) we observed 17 events, all related to heart failure (HF) (median event-free survival: 83.5 months). Eight patients (23%) underwent transplantation, and 9 (26%) died of HF while waiting for transplantation. Eight patients received an implantable cardioverter-defibrillator, although none had device intervention during a median follow-up of 14 months (interquartile range: 5 to 25 months). No patient died suddenly, suffered syncope, or developed life-threatening ventricular arrhythmias.

CONCLUSIONS

DYS-related DCM should be suspected in male patients with increased serum creatine phosphokinase (82%) and X-linked inheritance. The disease shows a high risk of end-stage HF but a lower risk of life-threatening arrhythmias.

Comprehensive copy number variant (CNV) analysis of neuronal pathways genes in psychiatric disorders identifies rare variants within patients

BACKGROUND

Copy number variations (CNV) have become an important source of human genome variability noteworthy to consider when studying genetic susceptibility to complex diseases. As recent studies have found evidences for the potential involvement of CNVs in psychiatric disorders, we have studied the dosage effect of structural genome variants as a possible susceptibility factor for different psychiatric disorders in a candidate gene approach.

METHODS

After selection of 68 psychiatric disorders' candidate genes overlapping with CNVs, MLPA assays were designed to determine changes in copy number of these genes. The studied sample consisted of 724 patients with psychiatric disorders (accounting for anxiety disorders, mood disorders, eating disorders and schizophrenia) and 341 control individuals.

RESULTS

CNVs were detected in 30 out of the 68 genes screened, indicating that a considerable proportion of neuronal pathways genes contain CNVs. When testing the overall burden of rare structural genomic variants in the different psychiatric disorders compared to control individuals, there was no statistically significant difference in the total amount of gains and losses. However, 14 out of the 30 changes were only found in psychiatric disorder patients but not in control individuals. These genes include GRM7, previously associated to major depression disorder and bipolar disorder, SLC6A13, in anxiety disorders, and S100B, SSTR5 and COMT in schizophrenia.

CONCLUSIONS

Although we have not been able to found a clear association between the studied CNVs and psychiatric disorders, the rare variants found only within the patients could account for a step further towards understanding the pathophysiology of psychiatric disorders.

Reverse protein arrays as novel approach for protein quantification in muscular dystrophies

The definite molecular diagnosis in patients with muscular dystrophies often requires the assessment of muscular expression of multiple proteins in small amounts of muscle tissue. The sample material obtained in muscle biopsies is limited and the measurement of multiple proteins is often restricted to conventional, non-quantitative assays, i.e. immunohistochemistry and immunoblotting. Here, we demonstrate that reverse protein arrays are a novel and excellent material-saving method for the measurement and quantification of changes in protein expression between healthy and diseased muscle tissue as well as cultured primary myotubes. We evaluated a set of antibodies and found reproducible differences between Duchenne muscular dystrophy/limb-girdle muscular dystrophy patients and control samples for dystrophin, the sarcoglycans and the dystroglycans. As little as 10 mg of tissue is sufficient for the analysis of all diagnostically relevant proteins. The average coefficient of variation calculated for the sample signals confirmed that the method is highly reproducible. Thus, our experiments provide strong evidence that quantitative protein detection from very small amounts of muscle tissue is possible using reverse protein arrays. This technology may not only be of interest for diagnostic purposes, but also for protein quantification of multiple, follow-up biopsies during clinical trials when protein expression in muscle is considered an important outcome measure or biomarker.

Interventions for muscular dystrophy: molecular medicines entering the clinic

Muscular dystrophies are individually rare genetic disorders that cause much chronic disability, affecting young children and adults. In the past 20 years, more than 30 genetic types of muscular dystrophy have been defined. During this time, precise diagnosis, genetic counselling, and medical management have improved. These advances in medical practice have occurred while definitive therapies based on an improved knowledge of disease pathogenesis are awaited. A wide range of therapeutic options have been tested in animal models, and some are being tested in clinical trials. Various therapeutic targets are being investigated, from personalised medicines targeting specific mutations and drugs targeting cellular pathways to gene-based and cell-based therapies.

Multiplex ligation-dependent probe amplification technique for copy number analysis on small amounts of DNA material

The multiplex ligation-dependent probe amplification (MLPA) technique is a sensitive technique for relative quantification of up to 50 different nucleic acid sequences in a single reaction, and the technique is routinely used for copy number analysis in various syndromes and diseases. The aim of the study was to exploit the potential of MLPA when the DNA material is limited. The DNA concentration required in standard MLPA analysis is not attainable from dried blood spot samples (DBSS) often used in neonatal screening programs. A novel design of MLPA probes has been developed to permit for MLPA analysis on small amounts of DNA. Six patients with congenital adrenal hyperplasia (CAH) were used in this study. DNA was extracted from both whole blood and DBSS and subjected to MLPA analysis using normal and modified probes. Results were analyzed using GeneMarker and manual Excel analysis. A total number of 792 ligation events were analyzed. In DNA extracted from dried blood spot samples, 99.1% of the results were accurate compared to 99.9% of the results obtained in DNA from whole blood samples. This study clearly demonstrates that MLPA reactions with modified probes are successful and reliable with DNA concentrations down to 0.3 ng/microL (1.6 ng total). This broadens the diagnostic perspectives of samples of DBSS allowing for copy number variation analysis in general and particularly testing for CAH.

Small mutations detected by multiplex ligation-dependent probe amplification of the dystrophin gene

Currently, multiplex ligation-dependent probe amplification (MLPA) has been recognized as the most powerful and convenient method to identify exon deletions or duplications in the dystrophin gene, the mutation of which causes Duchenne and Becker muscular dystrophies (DMD/BMD). The mutation diagnosis is easily done by assessing the amounts amplified by MLPA (loss, single, or double). However, an ambiguous amount of amplified product has never been reported. When 77 Japanese DMD/BMD patients were examined by MLPA from MRC-Holland (Amsterdam, The Netherlands), deletions/duplications in the dystrophin gene were identified in 64.8%. Ten male patients showed loss of a single exon by MLPA, but one of them was found to have not an exon deletion, but a four-nucleotide deletion (c.3347-3350delAGAA) within the exon. Remarkably, two patients showed ambiguous amounts of product with less than half of that of a single copy, making the genetic diagnosis impossible. In one patient, a novel single-nucleotide change (c.4303G>T) leading to a nonsense mutation was identified. In another patient, a novel five-nucleotide deletion (c.4536-4540delGAGTG) was identified. It was considered that these two mutations partially disturbed MLPA amplification, resulting in ambiguous amplification. These results show that MLPA can serve as a tool for screening small mutations, as well as for detecting exon deletions or duplications.

Identification of medicinal plants and plant sequences: multiplexed MLPA assay

Recognition of medicinal plant species or plant characters can be accomplished through the use of genomic DNA sequences unique to a species, a group of species, or a species variant. An assay well-suited to this application is the Multiplexed Ligase-dependent Probe Amplification (MLPA) assay. It uses the sensitivity of the polymerase chain reaction, but increases the specificity by including a key ligation step for those MLPA probes that hybridize to a DNA sequence. The MLPA can be used to perform multiple tests in one tube, but the number of tests is limited when the amplified products are separated by chromatography. The use of hybridization to a microarray as part of the MLPA allows for a potentially greater number of tests to be performed on one sample. We describe the method for the MLPA procedure in detail, including the microarray hybridization protocol.

Characteristics of dystrophin gene mutations among Chinese patients as revealed by multiplex ligation-dependent probe amplification

AIMS

To verify whether dystrophin gene mutations among Chinese patients feature different types and frequencies from other populations.

METHODS

Multiplex ligation-dependent probe amplification (MLPA) in combination with multiplex PCR (mPCR) and/or short tandem repeat (STR)-based linkage analysis were applied in a large series of Chinese families affected with Duchenne muscular dystrophy (DMD) or Becker muscular dystrophy (BMD). There were a total of 19 cases seeking prenatal diagnosis during their second pregnancies.

RESULTS

Of the 59 family trios (51 with DMD and 8 with BMD), 40 were found to have carried various mutations of the dystrophin gene. In addition to deletions and duplications within the mutational hotspots identified by both methods, 10 mutations missed by mPCR were detected by MLPA, among which at least 3 were of rare types. Combined MLPA and linkage analysis also achieved prenatal diagnoses in all of the 19 amniocentesis samples.

CONCLUSIONS

Mutations of dystrophin gene among Chinese patients showed a diverse spectrum, with similarity to as well as discrepancies from other populations. For the comprehensive coverage of all exons of the dystrophin gene, MLPA should be the method of choice for initial screening of DMD/BMD patients. When combined with STR-based analysis, it can achieve diagnosis in as much as 70-80% of all referred cases.

Multiplex ligation-dependent probe amplification (MLPA) assay for the detection of CYP21A2 gene deletions/duplications in congenital adrenal hyperplasia: first technical report

BACKGROUND

More than 90% of the cases of Congenital Adrenal Hyperplasia (CAH) are associated with mutations in 21-hydroxylase gene (CYP21A2). Up to now, large CYP21A2 rearrangements have been mainly detected by Southern blot analysis, although more rapid methods have been alternatively proposed. In this paper, we report the use of a multiplex ligation-dependent probe amplification (MLPA) method for easy and rapid detection of deletions/duplications in the CYP21A2 gene.

METHODS

We collected 18 CAH Italian patients previously analyzed by gene sequencing and Southern blot technique. In addition, a prenatal diagnosis study was performed.

RESULTS

Of the 7 known subjects with CYP21A2 deletions and 2 with gene duplications previously characterized in our laboratory, all were successfully identified by the MLPA analysis. In the prenatal diagnosis study, the MLPA assay was able to identify the presence of a CYP21A2 gene duplication in the fetus, as well in other two family members.

CONCLUSION

MLPA analysis represents a simple, rapid and sensitive tool for the detection of CYP21A2/CYP21A1P deletions/duplications in CAH molecular diagnosis. Compared to Southern blot, MLPA may be considered a high throughput analysis, allowing the simultaneous study of several samples in the same experiment and the investigation of both gene (CYP21A2) and pseudogene (CYP21A1P) in each patient.

[Evaluation of multiplex PCR assay using dual priming oligonucleotide system for detection mutation in the Duchenne muscular dystrophy gene]

BACKGROUND

Exon deletions of Duchenne muscular dystrophy (DMD) gene account for most of the alterations found in DMD and Becker muscular dystrophy (BMD). This study was to evaluate the usefulness of dual priming oligonucleotide multiplex PCR (DPO PCR) in detection of exon deletions of DMD gene.

METHODS

Thirty-seven DMD or BMD patients who had known exon deletions detected by conventional multiplex PCR (conventional PCR) and nine control subjects were enrolled in this study. When a discrepancy was shown between the results of conventional PCR and DPO PCR, the multiplex ligation-dependent probe amplification (MLPA) technique was performed as a confirmation test.

RESULTS

The same deletions previously identified by conventional PCR in 32 out of 37 subjects were also detected by DPO PCR. For the five subjects (13.5%) showing discrepant results between the conventional PCR and DPO PCR, MLPA was performed and its results were found to correlate better with those of DPO PCR. The discrepancies were due to false positive or false negative results of the conventional PCR.

CONCLUSIONS

DPO PCR shows a high agreement of results with the conventional PCR and is considered an adequate method to be used as a primary genetic test for the diagnosis of DMD. Because of an improved accuracy, especially for determining the boundaries of DMD gene deletions, DPO PCR can be very useful as a supplement to the conventional PCR.

Detection of exonic copy-number changes using a highly efficient oligonucleotide-based comparative genomic hybridization-array method

Genomic copy-number variations (CNVs) involving large DNA segments are known to cause many genetic disorders. Depending on the changes, they are predicted to lead either to decreased or an increased gene expression. However, the ability to detect smaller exonic copy-number changes has not been explored. Here we describe a new oligonucleotide-based comparative genomic hybridization (CGH)-array approach for high-throughput detection of exonic deletions or duplications and its application to deletion/duplication analyses of the genes encoding CFTR, six sarcoglycans (SGCA, SGCB, SGCG, SGCD, SGCE, and SGCZ), and DMD. In this work we show the successful development of an array format containing 158 exons that collectively span eight genes and its clinical application for the rapid screening of deletions and duplications in a diagnostic setting. We have analyzed a series of 35 DNA samples from patients affected with cystic fibrosis (CF), Duchenne and Becker muscular dystrophies (DMD/BMD), or sarcoglycanopathies, and have characterized exonic copy-number changes that have been validated with other methods. Interestingly, even heterozygous deletions and duplications of only one exon, as well as mosaic deletions, were detected by this CGH approach. Our results showed that the resolution is very high, as abnormalities of about 1.5-2 kb could be detected. Since this approach is completely scalable, this new molecular tool will allow the screening of combinations of genes involved in a particular group of clinically and genetically heterogeneous disorders such as mental retardation, muscular dystrophies and brain malformations.

Multiplex ligation-dependent probe amplification identification of whole exon and single nucleotide deletions in the CFTR gene of Hispanic individuals with cystic fibrosis

A disparity between Caucasian and Hispanic mutation detection for cystic fibrosis continues to exist, although the carrier frequency is only moderately lower in Hispanics. We aimed to identify exonic rearrangements that remained undetected by conventional methods. In seven of 32 cystic fibrosis-affected self-identified Hispanics for whom only one or no mutations were identified by extensive molecular testing, exon deletions appeared to be present with a multiplex ligation-dependent probe amplification (MLPA) assay. Two recurrent deletions (of exons 2-3 and exons 22-23) were identified in one and three patients, respectively (12.5%, 11.1% of unidentified alleles). Two apparently novel deletions (exons 6b and 20) were identified in three additional patients. Subsequent sequencing to characterize deletion breakpoints, however, identified single nucleotide deletions at the probe binding sites close to the ligation point. All resulted in false positive MLPA deletion signals. Interestingly, these mutations were not common in Caucasians, and one (935delA) was common in U.S. Hispanics. On examination of all probe binding sites, we identified a total of 76 reported mutations and five silent variants that immediately surrounded the MLPA ligation sites, with 22 occurring in non-Caucasians. These mutations are not all rare. Thus, apparent exon deletions by MLPA may indicate the presence of both large deletions and point mutations, with important implications for pan-ethnic MLPA testing in cystic fibrosis and other genetic conditions.

Probe-specific mixed-model approach to detect copy number differences using multiplex ligation-dependent probe amplification (MLPA)

Background

MLPA method is a potentially useful semi-quantitative method to detect copy number alterations in targeted regions. In this paper, we propose a method for the normalization procedure based on a non-linear mixed-model, as well as a new approach for determining the statistical significance of altered probes based on linear mixed-model. This method establishes a threshold by using different tolerance intervals that accommodates the specific random error variability observed in each test sample.

Results

Through simulation studies we have shown that our proposed method outperforms two existing methods that are based on simple threshold rules or iterative regression. We have illustrated the method using a controlled MLPA assay in which targeted regions are variable in copy number in individuals suffering from different disorders such as Prader-Willi, DiGeorge or Autism showing the best performace.

Conclusion

Using the proposed mixed-model, we are able to determine thresholds to decide whether a region is altered. These threholds are specific for each individual, incorporating experimental variability, resulting in improved sensitivity and specificity as the examples with real data have revealed.

Cognitive and psychological profile of males with Becker muscular dystrophy

Duchenne and Becker muscular dystrophy are allelic X-linked disorders causing progressive muscle weakness in males. Duchenne muscular dystrophy is caused by absence of dystrophin in muscle and brain; boys with Duchenne muscular dystrophy have a static cognitive impairment with mean Full Scale IQ approximately 1 standard deviation below the mean. Less is known of the cognitive profile of males with Becker muscular dystrophy, which is associated with variable alterations in the amount or size of the dystrophin protein. The aim of this study was to describe the cognitive and psychological profile of males with Becker muscular dystrophy. This was a prospective cohort study. Clinical data collected included age at diagnosis and assessment, socioeconomic status, serum creatine kinase level, and site of gene deletion/mutation (by exon number). The following psychological tests were used to assess general intellectual functioning, academic achievement, incidence and nature of behavioral problems: The Wechsler Intelligence Scales, The Wide Range Achievement Test-Revised, The Developmental Test of Visual-Motor Integration, The Child Behavior Checklist, and The Conner's Parent Rating Scale. Twenty-four males were enrolled. The Wechsler Full Scale IQ was normally distributed with a mean of 95.6 (SD 23.3), which did not differ significantly from the population mean. The frequency of learning difficulties for reading was 21%, for spelling was 32%, and for arithmetic was 26%, significantly higher than the frequency in the general population. The frequency of total behavioral problems in the clinical range was 67%, and the frequency of autism was 8.3%. Patients with Becker muscular dystrophy demonstrate a less homogeneous cognitive phenotype than that seen in Duchenne muscular dystrophy. Males with Becker muscular dystrophy have a high incidence of learning difficulties. Autism and behavioral and attention problems are also more common in Becker muscular dystrophy than in the general population.

An ABCC8 gene mutation and mosaic uniparental isodisomy resulting in atypical diffuse congenital hyperinsulinism

OBJECTIVE

Congenital hyperinsulinism (CHI) may be due to diffuse or focal pancreatic disease. The diffuse form is associated with an increase in the size of beta-cell nuclei throughout the whole of the pancreas and most commonly results from recessive ATP-sensitive K(+) channel (K(ATP) channel) mutations. Focal lesions are the consequence of somatic uniparental disomy for a paternally inherited K(ATP) channel mutation with enlargement of the beta-cell nuclei confined to the focal lesion. Some "atypical" cases defy classification and show pancreatic beta-cell nuclear enlargement confined to discrete regions of the pancreas. We investigated an atypical case with normal morphology within the tail of the pancreas but occasional enlarged endocrine nuclei in parts of the body and head.

RESEARCH DESIGN AND METHODS

The KCNJ11 and ABCC8 genes encoding the K(ATP) channel subunits and microsatellite markers on chromosome 11 were analyzed in DNA samples from the patient and her parents.

RESULTS

A mosaic ABCC8 nonsense mutation (Q54X) was identified in the proband. The paternally inherited mutation was present at 90% in lymphocytes and 50% in normal pancreatic sections but between 64 and 74% in abnormal sections. Microsatellite analysis showed mosaic interstitial paternal uniparental isodisomy (UPD) for chromosome 11p15.1.

CONCLUSIONS

We report a novel genetic mechanism to explain atypical histological diffuse forms of CHI due to mosaic UPD in patients with dominantly inherited ABCC8 (or KCNJ11) gene mutations.

[Carrier detection in families affected by Duchenne/Becker muscular dystrophy]

Duchenne/Becker muscular dystrophy is a severe, recessive, X-linked neuromuscular disease with an incidence of 1/3500 (Duchenne type) and 1/30,000 (Becker type) in newborn boys. The gene responsible for the Duchenne/Becker muscular dystrophy phenotype is located at Xp21 and its 427 kD protein product is called dystrophin. Deletions, point mutations and rarely duplications can occur almost anywhere in the DMD gene, which makes the molecular diagnosis difficult. Multiple polymerase chain reactions detect 95% of deletions in affected males [2, 4], but are not suitable for carrier detection in female relatives. Southern-blot analysis with six different cDNA probes covers the whole 14 kb dystrophin transcript and allows the detection of female carriers by comparing the intensity of the signals corresponding to the different exons. This method is time consuming compared to the newly introduced multiple ligation-dependent probe amplification method. Multiple ligation-dependent probe amplification is a method suitable for relative quantification of several DNA sequences in one reaction. The authors report results on 93 cases where the carrier status was analysed simultaneously by cDNA hybridisation and multiple ligation-dependent probe amplification technique. In 42 cases the carrier state was confirmed and in this carrier population the authors additionally detected two cases with duplication, two cases with one copy of the whole dystrophin gene and three manifest carrier females. On the basis of these results the MLPA technique, which has been newly introduced in Hungary, proved to be a sensitive and quick method for the detection of carrier state in the DMD/BMD disease. Moreover, the exact deletion or duplication border can be detected and as a result, prediction on the phenotype can be given. This will provide the right therapeutic intervention for the affected patients in the future.

Copy number analysis of survival motor neuron genes by multiplex ligation-dependent probe amplification

PURPOSE

To determine the copy number of survival motor genes using multiplex ligation-dependent probe amplification.

METHODS

Three hundred seventy-three subjects were recruited and divided into three groups. Group 1 included 310 subjects without a history of muscular atrophy, Group 2 consisted of 18 patients and 45 carriers of spinal muscular atrophy, and Group 3 included 20 subjects who were previously tested with denatured high-performance liquid chromatography. The copy number of survival motor neuron 1 and survival motor neuron 2 genes was determined with a commercially available multiplex ligation-dependent probe amplification kit.

RESULTS

Twenty-one genotypes of the survival motor neuron genes could be clearly defined in this series. The whole process of genotyping took <48 hours. In Group 1, 2:2 (survival motor neuron 1:survival motor neuron 2) was most common (52.90%), followed by 2:1 (30.32%); six (1.94%) subjects were found to be carriers of 1:2 or 1:3. In Group 2, all 18 patients had zero copies of the survival motor neuron 1 gene and variable copies of the survival motor neuron 2 gene. In Group 3, three subjects who had been told they were carriers of spinal muscular atrophy turned out to be noncarriers by multiplex ligation-dependent probe amplification. All 51 carriers from Groups 1 and 2 had one copy of the survival motor neuron 1 gene and one to four copies of the survival motor neuron 2 gene.

CONCLUSION

Multiplex ligation-dependent probe amplification is a simple and efficient method for copy number analysis of survival motor neuron genes. It can be used to detect the homozygous and heterozygous survival motor neuron deletion of spinal muscular atrophy.

Multiplex Ligation-dependent Probe Amplification Identification of Deletions and Duplications of the Duchenne Muscular Dystrophy Gene in Taiwanese Subjects

BACKGROUND/PURPOSE

Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) are X-linked recessive disorders caused by mutations in the DMD gene. We intended to determine the distribution of DMD gene deletions and duplications in local Taiwanese male patients and potential female carriers.

METHODS

A total of 102 unrelated subjects, including 89 unrelated DMD/BMD male patients and another 13 unrelated potential female carriers, were recruited for this study. Multiplex ligation-dependent probe amplification (MLPA) was employed to detect DMD gene deletions and duplications in the 102 subjects.

RESULTS

MLPA was informative in 60.7% (54/89) of these patients, identifying deletions in 36.0% (32/89) and duplications in 24.7% (22/89) of these patients. This assay revealed deletions in 30.8% (4/13) and duplications in 30.8% (4/13) of the 13 potential carriers. Deletions and duplications were detected in 35.3% (36/102) and 25.5% (26/102) of a total of 102 affected families, respectively in this series. The "hotspot" regions of the duplications were close to those of the deletions.

CONCLUSION

MLPA was proven to be a powerful tool for the detection of DMD gene deletions and duplications in male patients and female carriers. There was a relatively lower frequency of deletion and a higher frequency of duplication of DMD gene in this population compared to previous reports.

Deletions in CCM2 are a common cause of cerebral cavernous malformations

Cerebral cavernous malformations (CCMs) are vascular abnormalities of the brain that can result in a variety of neurological disabilities, including hemorrhagic stroke and seizures. Mutations in the gene KRIT1 are responsible for CCM1, mutations in the gene MGC4607 are responsible for CCM2, and mutations in the gene PDCD10 are responsible for CCM3. DNA sequence analysis of the known CCM genes in a cohort of 63 CCM-affected families showed that a high proportion (40%) of these lacked any identifiable mutation. We used multiplex ligation-dependent probe analysis to screen 25 CCM1, -2, and -3 mutation-negative probands for potential deletions or duplications within all three CCM genes. We identified a total of 15 deletions: 1 in the CCM1 gene, 0 in the CCM3 gene, and 14 in the CCM2 gene. In our cohort, mutation screening that included sequence and deletion analyses gave disease-gene frequencies of 40% for CCM1, 38% for CCM2, 6% for CCM3, and 16% with no mutation detected. These data indicate that the prevalence of CCM2 is much higher than previously predicted, nearly equal to CCM1, and that large genomic deletions in the CCM2 gene represent a major component of this disease. A common 77.6-kb deletion spanning CCM2 exons 2-10 was identified, which is present in 13% of our entire CCM cohort. Eight probands exhibit an apparently identical recombination event in the CCM2 gene, involving an AluSx in intron 1 and an AluSg distal to exon 10. Haplotype analysis revealed that this CCM2 deletion occurred independently at least twice in our families. We hypothesize that these deletions occur in a hypermutable region because of surrounding repetitive sequence elements that may catalyze the formation of intragenic deletions.