• Asian Pacific Journal of Cancer Prevention
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• v.16 no.17
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• pp.7997-8002
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• 2015

Gene amplification is an important mechanism in the development and progression of cancer. Currently, gene amplification status is generally determined by in situ hybridization (ISH). Multiplex ligation-dependent probe amplification (MLPA) is a PCR-based method that allows copy number detection of up to 50 nucleic acid sequences in one reaction. The aim of the present study was to compare results for HER2, CCND1, MYC and ESR1 gene amplification detected by MLPA with fluorescent in situ hybridization (FISH) and chromogenic in situ hybridization (CISH) as clinically approved methods. Tissue samples of 170 invasive breast cancers were collected. All were ER positive. Tissue samples had previously been tested for HER2 using immunohistochemistry. Amplification of the selected genes were assessed using MLPA, FISH and CISH and results were compared. HER2 MLPA and ISH results were also compared with HER2 immunohistochemistry (IHC) which detects protein overexpression. Amplification of HER2, CCND1, MYC and ESR1 by MLPA were found in 9%, 19%, 20% and 2% of samples, respectively. Amplification of HER2, CCND1, MYC and ESR1 by FISH was noted in 7%, 16%, 16% and 1% of samples, respectively. A high level of concordance was found between MLPA/FISH (HER2: 88%, CCND1: 88%, MYC: 86%, ESR1: 92%) and MLPA/CISH (HER2: 84%). Of all IHC 3+ cases, 91% were amplified by MLPA. In IHC 2+ group, 31% were MLPA amplified. In IHC 1+ group, 2% were MLPA amplified. None of the IHC 0 cases were amplified by MLPA. Our results indicate that there is a good correlation between MLPA, IHC and ISH results. Therefore, MLPA can serve as an alternative to ISH for detection of gene amplification.

• Journal of Genetic Medicine
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• v.6 no.2
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• pp.146-154
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• 2009

Multiplex ligation dependent probe amplification (MLPA) is a PCR-based method to detect gene dosage. Since its introduction, MLPA has been used to test a large number of genes for major deletions or duplications. Genetic testing, as a diagnostic tool for genetic disease, has been used primarily to identify point mutations, including base substitutions and small insertions/deletions, using PCR and sequence analysis. However, it is difficult to identify large deletions or duplications using routine PCR- gel based assays, especially in heterozygotes. The MLPA is a more feasible method for identification of gene dosage than another routine PCR-based methods, and better able to detect deleterious deletions or duplications. In addition to detection of gene dosage, MLPA can be applied to identify methylation patterns of target genes, aneuploidy during prenatal diagnoses, and large deletions or duplications that may be associated with various cancers. The MLPA method offers numerous advantages, as it requires only a small amount of template DNA, is applicable to a wide variety of applications, and is high-throughput. On the other hand, this method suffers from disadvantages including the possibility of false positive results affected by template DNA quality, difficulties identifying SNPs located in probe sequences, and analytical complications in quantitative aspects.

• Journal of Genetic Medicine
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• v.17 no.1
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• pp.27-33
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• 2020

Purpose: Duchenne muscular dystrophy (DMD) is the most common lethal muscular dystrophy and is caused by the genetic variants of DMD gene. Because DMD is X-linked recessive and shows familial aggregates, prenatal diagnosis is an important role in the management of DMD family. We present our experience of prenatal molecular diagnosis and carrier detection based on multiplex polymerase chain reaction (PCR), multiplex ligation-dependent probe amplification (MLPA), and linkage analysis. Materials and Methods: During study period, 34 cases of prenatal diagnosis and 21 cases of carrier detection were performed at the Seoul National University Hospital. Multiplex PCR and MLPA was used to detect the exon deletions or duplications. When the DMD pathogenic variant in the affected males is unknown and no DMD pathogenic variant is detected in atrisk females, linkage analysis was used. Results: The prenatal molecular diagnosis was offered to 34 fetuses. Twenty-five fetuses were male and 6 fetuses (24.0%) were affected. Remaining cases had no pathogenic mutation. We had 24 (80.0%) cases of known proband results; exon deletion mutation in 19 (79.2%) cases and duplication in 5 (20.8%) cases. Linkage analysis was performed in 4 cases in which 2 cases (50.0%) were found to be affected. In the carrier testing, among 21 cases including 15 cases of mother and 6 cases of female relative, 9 (42.9%) cases showed positive results and 12 (57.1%) cases showed negative results. Conclusion: Prenatal molecular diagnosis and carrier detection of DMD are effective and feasible. They are useful in genetic counseling for DMD families.

• Journal of Genetic Medicine
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• v.14 no.1
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• pp.43-47
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• 2017

Cat eye syndrome (CES) is a very rare chromosomal syndrome characterized by various malformations such as anal atresia, preauricular malformation, coloboma of the iris, and congenial heart and renal defects. This genetic disorder is caused by partial duplication of chromosome 22, mostly as a result of a supernumerary isodicentric marker chromosome idic(22)(q11.2). Various congenital abnormalities and extreme phenotypic variability in CES patients have been reported, which have made prenatal diagnosis of CES difficult. We report the first case diagnosed with CES prenatally by multiplex ligation-dependent probe amplification in a woman who was referred to our hospital, for a fetus presenting with heart anomaly.

• Journal of Genetic Medicine
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• v.15 no.1
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• pp.13-16
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• 2018

X-linked juvenile retinoschisis (XLRS) is characterized by the progressive loss of visual acuity and vitreous hemorrhage. XLRS is caused by a mutation of retinoschisin 1 (RS1) gene at Xp22.13. In the current report, a 2-year-old Korean patient with XLRS was described. The germline deletion of exon 1 was identified in the RS1 gene. Considering X-linked inheritance pattern, validation of a carrier state of a patient's mother is important for the genetic counseling of other family members and for the future reproductive plan. To confirm the carrier state of his mother, the multiplex ligation-dependent probe amplification analysis was done using peripheral leukocytes and found the heterozygous deletion of exon 1 in his mother.

• Journal of Genetic Medicine
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• v.20 no.2
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• pp.46-51
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• 2023

Exonic copy number variation (CNV), involving deletions and duplications at the gene's exon level, presents challenges in detection due to their variable impact on gene function. The study delves into the complexities of identifying large CNVs and investigates less familiar but recurrent exonic CNVs, notably enriched in East Asian populations. Examining specific cases like DRC1, STX16, LAMA2, and CFTR highlights the clinical implications and prevalence of exonic CNVs in diverse populations. The review addresses diagnostic challenges, particularly for single exon alterations, advocating for a strategic, multi-method approach. Diagnostic methods, including multiplex ligation-dependent probe amplification, droplet digital PCR, and CNV screening using next-generation sequencing data, are discussed, with whole genome sequencing emerging as a powerful tool. The study underscores the crucial role of ethnic considerations in understanding specific CNV prevalence and ongoing efforts to unravel subtle variations. The ultimate goal is to advance rare disease diagnosis and treatment through ethnically-specific therapeutic interventions.

• Journal of Genetic Medicine
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• v.10 no.2
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• pp.94-98
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• 2013

Dystrophinopathy, caused by mutations in the DMD gene, presents with variable clinical phenotypes ranging from the severe Duchenne muscular dystrophy (DMD) to the milder Becker muscular dystrophy(BMD) forms. DMD is a recessive X-linked form of muscular dystrophy. Two-thirds of mothers of affected males are thought to be DMD carriers. Approximately 2.5-7.8% of female DMD carriers have muscle weakness and are categorized as manifesting DMD carriers. The symptoms of female carriers of DMD range from mild muscle weakness to severe gait problems. The most commonly presented symptom is mild proximal muscle weakness, which is often asymmetric and progressive, but shows variable clinical spectrum with BMD of more severe DMD-like phenotype. Atypical presentations in manifesting carriers are myalgia or cramps without limb weakness, isolated cardiomyopathy and camptocormia. Multiplex PCR and MLPA analysis are common techniques to identify mutations in the DMD gene. Relationship between X-chromosome inactivation and clinical severity is not clear. Female carriers of DMD are not less common, and they have an important role of birth of a male DMD.

• Clinical and Experimental Pediatrics
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• v.53 no.3
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• pp.397-407
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• 2010

Purpose : The F9 gene is known to be the causative gene for hemophilia B, but unfortunately the detection rate for restriction fragment length polymorphism-based linkage analysis is only 55.6%. Direct DNA sequencing can detect 98% of mutations, but this alternative procedure is very costly. Here, we conducted multiplex polymerase chain reactions (PCRs) and conformation sensitive gel electrophoresis (CSGE) to perform a screened DNA sequencing for the F9 gene, and we compared the results with direct sequencing in terms of accuracy, cost, simplicity, and time consumption. Methods : A total of 27 unrelated hemophilia B patients were enrolled. Direct DNA sequencing was performed for 27 patients by a separate institute, and multiplex PCR-CSGE screened sequencing was done in our laboratory. Results of the direct DNA sequencing were used as a reference, to which the results of the multiplex PCR-CSGE screened sequencing were compared. For the patients whose mutation was not detected by the 2 methods, multiplex ligation-dependent probe amplification (MLPA) was conducted. Results : With direct sequencing, the mutations could be identified from 26 patients (96.3%), whereas for multiplex PCRCSGE screened sequencing, the mutations could be detected in 23 (85.2%). One patient's mutation was identified by MLPA. A total of 21 different mutations were found among the 27 patients. Conclusion : Multiplex PCR-CSGE screened DNA sequencing detected 88.9% of mutations and reduced costs by 55.7% compared with direct DNA sequencing. However, it was more labor-intensive and time-consuming.

• Journal of Genetic Medicine
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• v.13 no.1
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• pp.36-40
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• 2016

Tuberous sclerosis complex (TSC, MIM#191100) is an autosomal dominant neurocutaneous syndrome caused by mutation or deletion of TSC1 encoding hamartin or TSC2 encoding tuberin and characterized by seizure, mental retardation, and multiple hamartomas or benign tumors in the skin, brain, retina, heart, kidney, and lungs. The TSC2 gene on chromosome 16p13.3 lies adjacent to the PKD1 gene which is responsible for autosomal dominant polycystic kidney disease (MIM#173900). The TSC2/PKD1 contiguous gene syndrome (TSC2/PKD1 CGDS, MIM#600273) is caused by deletion of both TSC2 and PKD1 gene. We recently experienced a 15 month-old boy and a 26 month-old girl with TSC2/PKD1 CGDS confirmed by multiplex ligation-dependent probe amplification (MLPA) analysis. They showed not only typical neurologic manifestations of TSC such as epilepsy, subependymal nodules, and subcortical tubers, but also polycystic kidney disease. The contiguous gene syndrome involving PKD1 and TSC2 should be suspected in children with enlarged polycystic kidneys and TSC. MLPA analysis is a useful method for the genetic confirmation of TSC2/PKD1 CGDS.

• Journal of Genetic Medicine
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• v.16 no.2
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• pp.49-54
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• 2019

Purpose: Potocki-Lupski syndrome (PTLS), is a recently identified, rare genomic disorder. The patients are affected by infantile hypotonia, poor growth and developmental delay. Facial dysmorphism may not be obvious in some patients. PTLS is associated with microduplication at chromosome 17p11.2. In the current study, three Korean patients are reported with their clinical and genetic features. Materials and Methods: The clinical findings of each patient were reviewed. Karyotyping and multiplex ligation-dependent probe amplification (MLPA) analyses were done for genetic diagnoses. Results: All the patients did not have the characteristic dysmorphic features, such as broad forehead, triangular face, asymmetric smile and palpebral fissures. On the other hand, all three patients were affected by variable degree of developmental delay, poor oral intake, failure to thrive, and language development disorders. Chromosome 17p11.2 duplication was identified by conventional karyotyping analysis only in one patient, whereas the other confirmed by MLPA analyses. Conclusion: Delayed development was mostly commonly observed in our patients without distinct dysmorphic facial features. In this respect, genomic screening in patients with developmental delay would identify more cases with PTLS to understand their long-term clinical courses with the development of adequate psychological and rehabilitation education program.