Search

Background: Next-generation sequencingbased molecular assessment has benefited the diagnosis of hereditary spastic paraplegia (HSP) subtypes. However, the clinical and genetic spectrum of HSP due to large fragment deletions/duplications has yet to be fully defined. Objective: We aim to better characterize the clinical phenotypes and genetic features of HSP and to provide new thoughts on diagnosis. Methods: Whole-exome sequencing (WES) was performed in patients with clinically suspected HSP, followed by multiple ligation-dependent probe amplification (MLPA) sequentially carried out for those with negative findings in known causative genes. Genotype–phenotype correlation analyses were conducted under specific genotypes. Results: We made a genetic diagnosis in 60% (162/270) of patients, of whom 48.9% (132/270) had 24 various subtypes due to point mutations (SPG4/SPG11/SPG35/SPG7/ SPG10/SPG5/SPG3A/SPG2/SPG76/SPG30/SPG6/SPG9A/ SPG12/SPG15/SPG17/SPG18/SPG26/SPG49/SPG55/ SPG56/SPG57/SPG62/SPG78/SPG80). Thirty patients were found to have causative rearrangements by MLPA (11.1%), among which SPG4 was the most prevalent (73.3%), followed by SPG3A (16.7%), SPG6 (3.3%), SPG7 (3.3%), and SPG11 (3.3%). Clinical analysis showed that some symptoms were often related to specific subtypes, and rearrangementrelated SPG3A patients seemingly had later onset. We observed a presumptive anticipation among SPG4 and SPG3A families due to rearrangement. Conclusions: Based on the largest known Asian HSP cohort, including the largest subgroup of rearrangementrelated pedigrees, we gain a comprehensive understanding of the clinical and genetic spectrum of HSP. We propose a diagnostic flowchart to sequentially detect the causative genes in practice. Large fragment mutations account for a considerable proportion of HSP, and thus, MLPA screening acts as a beneficial supplement to routine WES. © 2024 International Parkinson and Movement Disorder Society. [ABSTRACT FROM AUTHOR]

Abstract Background The discrepancy between the results of cytogenetics and the results of chromosome microarray analysis (CMA) has often led to confusion over genetic counselling for prenatal diagnosis. Case presentation The prenatal ultrasound results of a congenital heart defect (CHD) foetus displayed an apartial endocardial pad defect and permanently dilated coronary sinus and left superior vena cava at 21 weeks of gestation. Cytogenetic analysis, CMA, fluorescent in situ hybridization (FISH) and multiplex ligation-dependent probe amplification (MLPA) with foetal cord blood samples were used to detect the genetic aetiology. Routine G-binding cytogenetic analysis showed normal karyotypes in both the foetus’ and parents’ blood samples. CMA results demonstrated that there were 53.973-Mb recurrent CNVs at Xp22.33-p11.22, as confirmed by MLPA assay. Conclusions Herein, we described the CNV of six duplications at Xp22.33-p11.22 and the 53.973 Mb duplication CNV that was not found in foetal cord blood samples by conventional cytogenetic methods, and it was confirmed by CMA and MLPA. Our novel findings will provide helpful information for prenatal diagnosis and genetic counselling for foetal CHDs.

Background: The discrepancy between the results of cytogenetics and the results of chromosome microarray analysis (CMA) has often led to confusion over genetic counselling for prenatal diagnosis. Case presentation: The prenatal ultrasound results of a congenital heart defect (CHD) foetus displayed an apartial endocardial pad defect and permanently dilated coronary sinus and left superior vena cava at 21 weeks of gestation. Cytogenetic analysis, CMA, fluorescent in situ hybridization (FISH) and multiplex ligation-dependent probe amplification (MLPA) with foetal cord blood samples were used to detect the genetic aetiology. Routine G-binding cytogenetic analysis showed normal karyotypes in both the foetus' and parents' blood samples. CMA results demonstrated that there were 53.973-Mb recurrent CNVs at Xp22.33-p11.22, as confirmed by MLPA assay. Conclusions: Herein, we described the CNV of six duplications at Xp22.33-p11.22 and the 53.973 Mb duplication CNV that was not found in foetal cord blood samples by conventional cytogenetic methods, and it was confirmed by CMA and MLPA. Our novel findings will provide helpful information for prenatal diagnosis and genetic counselling for foetal CHDs. [ABSTRACT FROM AUTHOR]

Background: Next-generation sequencing-based molecular assessment has benefited the diagnosis of hereditary spastic paraplegia (HSP) subtypes. However, the clinical and genetic spectrum of HSP due to large fragment deletions/duplications has yet to be fully defined., Objective: We aim to better characterize the clinical phenotypes and genetic features of HSP and to provide new thoughts on diagnosis., Methods: Whole-exome sequencing (WES) was performed in patients with clinically suspected HSP, followed by multiple ligation-dependent probe amplification (MLPA) sequentially carried out for those with negative findings in known causative genes. Genotype-phenotype correlation analyses were conducted under specific genotypes., Results: We made a genetic diagnosis in 60% (162/270) of patients, of whom 48.9% (132/270) had 24 various subtypes due to point mutations (SPG4/SPG11/SPG35/SPG7/SPG10/SPG5/SPG3A/SPG2/SPG76/SPG30/SPG6/SPG9A/SPG12/SPG15/SPG17/SPG18/SPG26/SPG49/SPG55/SPG56/SPG57/SPG62/SPG78/SPG80). Thirty patients were found to have causative rearrangements by MLPA (11.1%), among which SPG4 was the most prevalent (73.3%), followed by SPG3A (16.7%), SPG6 (3.3%), SPG7 (3.3%), and SPG11 (3.3%). Clinical analysis showed that some symptoms were often related to specific subtypes, and rearrangement-related SPG3A patients seemingly had later onset. We observed a presumptive anticipation among SPG4 and SPG3A families due to rearrangement., Conclusions: Based on the largest known Asian HSP cohort, including the largest subgroup of rearrangement-related pedigrees, we gain a comprehensive understanding of the clinical and genetic spectrum of HSP. We propose a diagnostic flowchart to sequentially detect the causative genes in practice. Large fragment mutations account for a considerable proportion of HSP, and thus, MLPA screening acts as a beneficial supplement to routine WES. © 2024 International Parkinson and Movement Disorder Society., (© 2024 International Parkinson and Movement Disorder Society.)

Background: Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited disease of the kidney. It occurs in adulthood but is also rarely diagnosed in early childhood. The majority of the disease-causing variants observed in ADPKD patients are in two genes: PKD1 and PKD2., Methods: 237 patients from 198 families with a clinical diagnosis of ADPKD were screened for PKD1 and PKD2 genetic variants using Sanger sequencing and multiple ligation-dependent probe amplification analysis., Results: Disease-causing (diagnostic) variants were identified in 173 families (211 patients), 156 on PKD1 and 17 on PKD2. Variants of unknown significance were detected in 6 additional families, while no mutations were found in the remaining 19 families. Among the diagnostic variants detected, 51 were novel. In ten families, seven large rearrangements were found and the molecular breakpoints of 3 rearrangements were identified. Renal survival was significantly worse for PKD1-mutated patients, particularly those carrying truncating mutations. In patients with PKD1 truncating (PKD1-T) mutations, disease onset was significantly earlier than in patients with PKD1 non-truncating variants or PKD2-mutated patients., Conclusions: Comprehensive genetic testing confirms its utility in diagnosing patients with ADPKD and contributes to explaining the clinical heterogeneity observed in this disease. Moreover, the genotype-phenotype correlation can allow for a more accurate disease prognosis., (© 2023 S. Karger AG, Basel.)

Highlights • We validated that the combined usage of direct sequencing and MLPA can achieve a high detection rate in Chinese Han PJS patients. • We found significantly more splice mutations in Chinese Han PJS patients. • We suggest that wide usage of enteroscopy would be helpful in PJS surveillance. Abstract Background The combination of direct sequencing and multiple ligation-dependent probe amplification (MLPA) has resulted in an 80% detection rate of serine/threonine kinase 11 (STK11) gene mutations in Peutz-Jeghers syndrome (PJS); however, this rate varies in different ethnicities. Aims To test the efficacy of the combination in Chinese patients with PJS. Methods PJS probands visiting our center during one year were enrolled. Sanger sequencing and MLPA were used to detect STK11 mutations. Associations between the occurrence of severe complications and risk factors were analyzed statistically. Results We identified 47 PJS probands. Among them, 34 received an STK11 mutation test, revealing 23 point mutations and 2 exonic deletions. Nine of the mutations were splicing errors, reflecting a significantly higher proportion (p < 0.05). Laparotomy history existed for 33 of the probands, and seven families had a history of cancer. Statistical analysis revealed no associations between the occurrence of severe complications or cancers and risk factors. Conclusion The strategy achieved a high detection rate in Chinese people, validating its effectiveness. This cohort comprised a significantly higher proportion of splicing errors, reflecting the unique genetic characteristics Chinese people. No specific genotype-phenotype relationship was noted, while the wide usage of enteroscopy would benefit PJS surveillance. [ABSTRACT FROM AUTHOR]

Purpose: Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) are similar genetic disorders whose patterns of mutation and disease phenotypes might be expected to show differences among different countries. We analyzed multiplex ligation-dependent probe amplification (MLPA) data in a large number of Korean patients with DMD/BMD. Materials and Methods: We obtained 130 positive MLPA results (86 DMD, 27 BMD, and 17 female carriers) from 272 candidates (237 clinically suspected patients and 35 possible female carriers) who took part in this study. We analyzed the mutation patterns among 113 patients diagnosed by MLPA and calculated deletion/duplication percentages from a total of 128 patients, including 15 patients who were diagnosed using methods other than MLPA. We also analyzed hot spot locations among the 130 MLPA-positive results. Results: Most mutations were detected in a central hot spot region between exons 44 and 55 (80 samples, 60.6%). Unlike previous reports, a second frequently observed hot spot near the 5'-end was not distinctive. MLPA detected deletions in specific exons in 92 patients with DMD/BMD (71.8%) and duplications in 21 patients (16.4%). Conclusion: Our MLPA study of a large number of Korean patients with DMD/BMD identified the most frequent mutation hot spot, as well as a unique hot spot pattern. DMD gene mutation patterns do not appear to show significant ethnic differences. [ABSTRACT FROM AUTHOR]

Duchenne muscular dystrophy (DMD) is an X-linked recessive neuromuscular disease caused by mutation in the DMD gene. A 38-year-old woman was referred to our hospital with her son who was diagnosed with DMD. Multiplex PCR failed to detect DMD mutations in the affected child. The female carrier underwent preimplantation genetic diagnosis by linkage analysis and gender determination. Eight embryos were biopsied after in vitro fertilization. Two healthy embryos determined both as females (E1 and E3) were transferred. Although the paternal allele was absent in E3, it was considered to be a result of allele dropout for the STR-49 marker. Surprisingly, a female and a male baby were delivered at 38 gestational weeks, suggesting that E3 was a male embryo with the allele dropout occurring at the SRY gene. Exon 2 duplication was detected in the DMD patient and the carrier mother using next-generation sequencing and multiple ligation-dependent probe amplification. Next, we verified the duplication of exon 2 by real-time PCR, using a special primer at 3′ of intron 1, very close to exon 2. Finally, we confirmed that both newborns inherited the normal allele, using quantitative real-time PCR and linkage analysis. © 2014 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]

Background Ornithine transcarbamylase deficiency, an inborn error of metabolism, is the most common urea cycle disorder and is caused by mutations in the OTC gene located on Xp21. In this study, the clinical and genetic characteristics of seven Korean patients with ornithine transcarbamylase deficiency were analyzed. Methods During 2009-2012, a total of seven patients (three male and four female patients) from six unrelated families were diagnosed with ornithine transcarbamylase deficiency by biochemical or molecular analysis. OTC gene sequencing analysis was performed in six of these patients. Clinical manifestations, clinical courses, and the results of genetic studies were reviewed retrospectively. Results The median follow-up period for the seven patients with ornithine transcarbamylase deficiency was 44 months (11.9-150 months). Clinical manifestations of ornithine transcarbamylase deficiency included vomiting and seizure, which were the most frequent signs at admission. Two of the four heterozygous female patients (50%) experienced severe neurological sequelae. The early onset male patient characterized severe neurological deficits. The late-onset male patient recovered completely from acute encephalopathy and coma without any neurological deficits. Direct sequencing and multiplex ligation-dependent probe amplification analysis of OTC gene revealed five different mutations. Of these mutations, two were novel (c.867-3T>C and c.664_667delinsAC). Conclusions Ornithine transcarbamylase deficiency was genetically heterogeneous in the seven Korean patients with confirmed ornithine transcarbamylase deficiency diagnosis by biochemical findings and/or genetic analysis, together with two novel mutations in the OTC gene. We hope that these data will contribute to a better understanding of the clinical course and distinct molecular genetic characteristics of Korean patients with ornithine transcarbamylase deficiency. [ABSTRACT FROM AUTHOR]

Objective: The presence of numerical and/or structural chromosomal abnormalities is a frequent finding in clonal hematopoietic malignant disease, typically diagnosed through routine karyotyping and/or fluorescent in situ hybridization (FISH) analysis. Recently, the application of array comparative genomic hybridization (aCGH) has uncovered many new cryptic genomic copy number imbalances, most of which are now recognized as clinically useful markers of haematological malignancies. In view of the limitations of both FISH and aCGH techniques, in terms of their routine application as a first line screening test, we designed a new multiple ligation-dependent probe amplification (MLPA) probemix for use in addition to classic karyotype analysis. Methods: A novel MLPA probemix was developed to interrogate copy number changes involving chromosomal regions: 2p23-24 (MYCN, ALK), 5q32-34 (MIR145A, EBF1, MIR146A), 6q21-27, 7p12.2 (IKZF1), 7q21-36, 8q24.21 (MYC), 9p24 (JAK2 V617F point mutation), 9p21.3 (CDKN2A/2B), 9p13.2 (PAX5), 10q23 (PTEN), 11q22.3 (ATM), 12p13.2 (ETV6), 13q14 (RB1, MIR15A, DLEU2, DLEU1), 17p13.1 (TP53), and 21q22.1 (RUNX1/AML1) and was applied to DNA extracted from 313 consecutive bone marrow patient samples, referred for routine karyotype analysis. Results: More than half of the samples originated from newly investigated patients. We discovered clinically relevant genomic aberrations, involving a total of 24 patients (8%) all with a normal karyotype, which would have remained undiagnosed. Discussion: Our data clearly indicate that routine application of this MLPA screening panel, as an adjunct to karyotype analysis, provides a sensitive, robust, rapid and low-cost approach for uncovering clinically important genomic abnormalities, which would have otherwise remained undetected. [ABSTRACT FROM AUTHOR]

Conclusion: Various biomarkers might ultimately prove to have prognostic value and could be clinically relevant. It is mandatory confirm the prognostic power of these markers in large, well-designed, and prospective studies. Objective: The aim of this study was to investigate the possible role of specific genes and proteins in laryngeal tumorigenesis. Methods: Genetic analysis by multiple ligation-dependent probe amplification and analysis of protein expression by immunohistochemistry were carried out in a series of 50 tissue samples. Results: In the smoker normal mucosa group TP53 loss was predominant, whereas in the epithelial precursor lesions (EPLs) CDKN2A loss and BCL2L1 gain were most frequent. EPL with progression presented CTNNB1 loss. Positivity at cytoplasm for β-catenin, cyclin D1 and p53 was detected in all EPL cases with progression to invasive carcinoma. Multivariate analysis showed that expression of β-catenin and loss of CTTNB1 were associated with laryngeal cancer risk. [ABSTRACT FROM AUTHOR]

The article presents a case study of a four-year-old male with suspected Sotos syndrome or cerebral gigantism. It utilizes the multiple ligation-dependent probe amplification (MLPA) analysis and messenger RNA (mRNA) analysis to determine and analyze the case of the patient. Result shows the deletion of exon 14 in nuclear receptor binding SET domain protein 1 (NSD1) confirming the suspicion of the genetic disorder Sotos syndrome in the child.

A letter to the editor is presented in response to an article related to the application of MLPA method in severe von Willebrand disease that was published in a previous issue.

Purpose: Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) are similar genetic disorders whose patterns of mutation and disease phenotypes might be expected to show differences among different countries. We analyzed multiplex ligation-dependent probe amplification (MLPA) data in a large number of Korean patients with DMD/BMD., Materials and Methods: We obtained 130 positive MLPA results (86 DMD, 27 BMD, and 17 female carriers) from 272 candidates (237 clinically suspected patients and 35 possible female carriers) who took part in this study. We analyzed the mutation patterns among 113 patients diagnosed by MLPA and calculated deletion/duplication percentages from a total of 128 patients, including 15 patients who were diagnosed using methods other than MLPA. We also analyzed hot spot locations among the 130 MLPA-positive results., Results: Most mutations were detected in a central hot spot region between exons 44 and 55 (80 samples, 60.6%). Unlike previous reports, a second frequently observed hot spot near the 5'-end was not distinctive. MLPA detected deletions in specific exons in 92 patients with DMD/BMD (71.8%) and duplications in 21 patients (16.4%)., Conclusion: Our MLPA study of a large number of Korean patients with DMD/BMD identified the most frequent mutation hot spot, as well as a unique hot spot pattern. DMD gene mutation patterns do not appear to show significant ethnic differences., Competing Interests: The authors have no financial conflicts of interest., (© Copyright: Yonsei University College of Medicine 2017)

CYP21A2 mutation analysis of congenital adrenal hyperplasia (CAH) is challenging because of the genomic presence of a homologous CYP21A2 pseudogene and the significant incidence of pseudogene conversion and large deletions. The objective of this study was to accurately analyze the CYP21A2 genotype in Korean CAH patients using a combination of complementary methods. Long-range PCR and restriction fragment length polymorphism analyses were performed to confirm valid amplification of CYP21A2 and to detect large gene conversions and deletions before direct sequencing. Multiple ligation-dependent probe amplification (MLPA) analysis was conducted concurrently in 14 CAH-suspected patients and six family members of three patients. We identified 27 CYP21A2 mutant alleles in 14 CAH-suspected patients. The c.293-13A>G (or c.293-13C>G) was the most common mutation, and p.Ile173Asn was the second, identified in 25% and 17.9% of alleles, respectively. A novel frame-shift mutation of c.492delA (p.Glu 164Aspfs*24) was detected. Large deletions were detected by MLPA in 10.7% of the alleles. Mutation studies of the six familial members for three of the patients aided in the identification of haplotypes. In summary, we successfully identified CYP21A2 mutations using both long-range PCR and sequencing and dosage analyses. Our data correspond relatively well with the previously reported mutation spectrum analysis.

Microduplications of 22q11.2 have been recently characterized as a new genomic duplication syndrome showing an extremely variable phenotype ranging from normal or mild learning disability to multiple congenital defects and sharing some overlapping features with DiGeorge/Velocardiofacial syndrome (DGS/VCFS). We report on the prenatal diagnosis of a 22q11.2 microduplication in a fetus with normal development that was referred for chromosomal analysis at 17 weeks of gestation because of advanced maternal age. Pregnancy was the result of an IVF-ICSI attempt after 4 years of infertility, mainly due to severe oligoasthenoteratospermia of the father. Amniocentesis was undertaken and cytogenetic analysis revealed an apparently normal male karyotype. Multiple Ligation-dependent Probe Amplification (MLPA) revealed a microduplication in the 22q11.2 chromosome region. Parental analysis showed that the 22q11.2 microduplication has been inherited from the otherwise healthy mother. Analysis with high resolution array-CGH showed that the size of the microduplication is 2.5 Mb and revealed the genes that are duplicated, including the TBX1 gene. The parents elected to continue with the pregnancy and the infant is now five months old and shows normal development., (Copyright © 2013 Elsevier B.V. All rights reserved.)