应用多重连接依赖式探针扩增技术快速高通量诊断胎儿染色体非整倍体异常

Objective To assess the diagnostic value of multiplex ligation-dependent probe amplification (MLPA) for detection of common chromosome aneuploidy in amniotic fluid (AF) cells in order to obtain an accurate, rapid, cost-effective and high-throughput method in routine prenatal clinical practice.Methods The MLPA test was performed on 500 AF samples by using kit P095 and the results were obtained by using analysis software RH-MLPA-v511. The results were compared with that from fluorescence in situ hybridization (FISH) and traditional karyotyping (TK). The technical critical issues were analyzed in routine diagnostic application. Results The absolute specificity and sensitivity of the MLPA test to detect the aneuploidy were 100%. For the 500 AF samples, the success rate of the MLPA tests was 97%. Among them 92% were finished within three working days and 5% required more days for repeating. The test failure rate was 3%. The results confirmed that for the 38 detectable aneuploid samples,the probe reliability weighted mean ratio values were more than 4SD compared to normal diploids and the 2 suspected trisomy samples were more than 2SD. In this study, authors analyzed hybridization efficiencies of 8 probes for chromosome 21, and the presence of a trisomy was considered if at least 4 of the 8 probes gave probe ratio of ＞1.3. Conclusion The data suggested that MLPA is a rapid, simple and reliable method for large scale testing for aneuploidy of chromosomes 13, 18, 21, X, or Y in AF. The MLPA technology is complementary to AF culture and valuable for prenatal diagnosis.     

应用多重连接依赖式探针扩增技术快速高通量诊断胎儿染色体非整倍体异常

Objective To assess the diagnostic value of multiplex ligation-dependent probe amplification (MLPA) for detection of common chromosome aneuploidy in amniotic fluid (AF) cells in order to obtain an accurate, rapid, cost-effective and high-throughput method in routine prenatal clinical practice.Methods The MLPA test was performed on 500 AF samples by using kit P095 and the results were obtained by using analysis software RH-MLPA-v511. The results were compared with that from fluorescence in situ hybridization (FISH) and traditional karyotyping (TK). The technical critical issues were analyzed in routine diagnostic application. Results The absolute specificity and sensitivity of the MLPA test to detect the aneuploidy were 100%. For the 500 AF samples, the success rate of the MLPA tests was 97%. Among them 92% were finished within three working days and 5% required more days for repeating. The test failure rate was 3%. The results confirmed that for the 38 detectable aneuploid samples,the probe reliability weighted mean ratio values were more than 4SD compared to normal diploids and the 2 suspected trisomy samples were more than 2SD. In this study, authors analyzed hybridization efficiencies of 8 probes for chromosome 21, and the presence of a trisomy was considered if at least 4 of the 8 probes gave probe ratio of ＞1.3. Conclusion The data suggested that MLPA is a rapid, simple and reliable method for large scale testing for aneuploidy of chromosomes 13, 18, 21, X, or Y in AF. The MLPA technology is complementary to AF culture and valuable for prenatal diagnosis.     

应用多重连接依赖式探针扩增技术快速高通量诊断胎儿染色体非整倍体异常

目的 评价多重连接依赖式探针扩增技术(multiplex ligation-dependent probe amplification,MLPA)在染色体非整倍体诊断中的应用价值,为我国羊水染色体诊断提供一种快速、特异、高通量的分子诊断手段.方法 应用MLPA技术检测了500份羊水标本,所有标本均进行荧光原位杂交(fluorescence in situ hybridization,FISH)技术检测和常规染色体核型分析,应用RH-MLPA-v511数据分析软件获得MLPA结果,比较MLPA技术与FISH和染色体核型分析结果的准确性,总结MLPA技术临床应用过程中的关键要点.结果 在500份羊水标本中,MLPA检测成功率97%.3个工作日完成结果的为92%,需重复检测的为5%,失败为3%.对染色体非整倍体异常检测敏感性和准确性100%.证实38例非整倍体病例探针信号比值＞正常二倍体4s,2例疑似三体结果＞2s.分析了21号染色体8条探针的杂交效率,21三体患者8条探针中平均4条探针比值＞1.3.结论 MLPA技术具有快速、特异、敏感、高通量、成本低等特点,可用于产前染色体非整倍体数目的快速检测,是传统染色体培养方法的补充,临床应用价值较高.

Abstract：

Objective To assess the diagnostic value of multiplex ligation-dependent probe amplification (MLPA) for detection of common chromosome aneuploidy in amniotic fluid (AF) cells in order to obtain an accurate, rapid, cost-effective and high-throughput method in routine prenatal clinical practice.Methods The MLPA test was performed on 500 AF samples by using kit P095 and the results were obtained by using analysis software RH-MLPA-v511. The results were compared with that from fluorescence in situ hybridization (FISH) and traditional karyotyping (TK). The technical critical issues were analyzed in routine diagnostic application. Results The absolute specificity and sensitivity of the MLPA test to detect the aneuploidy were 100%. For the 500 AF samples, the success rate of the MLPA tests was 97%. Among them 92% were finished within three working days and 5% required more days for repeating. The test failure rate was 3%. The results confirmed that for the 38 detectable aneuploid samples,the probe reliability weighted mean ratio values were more than 4SD compared to normal diploids and the 2 suspected trisomy samples were more than 2SD. In this study, authors analyzed hybridization efficiencies of 8 probes for chromosome 21, and the presence of a trisomy was considered if at least 4 of the 8 probes gave probe ratio of ＞1.3. Conclusion The data suggested that MLPA is a rapid, simple and reliable method for large scale testing for aneuploidy of chromosomes 13, 18, 21, X, or Y in AF. The MLPA technology is complementary to AF culture and valuable for prenatal diagnosis.     

多重链接探针扩增技术在染色体非整倍体畸变诊断中的应用

目的 探讨多重连接探针扩增(multiplexligation-dependent probe amplification,MLPA)技术在13、18、21、X、Y染色体非整倍体畸变诊断中的应用价值.方法 收集本院经染色体核型分析确诊包括有上述5种染色体数目异常及正常的样本共44份,其中外周血30份、胎儿脐带血10份、羊水4份,提取标本DNA,采用MLPA技术对样本染色体数目进行分析,并与染色体核型分析结果进行比对.结果 42例样本检测结果与染色体核型分析结果一致,1例染色体核型分析未能作出判断的标记染色体片段被识别为Y染色体片段,1例21-三体嵌合体未能做出明确判断,临床检出率97.7%(43/44).结论 MLPA技术通过单管反应同时检测40多个不同靶基因序列的拷贝数,具有高通量、特异、便捷及成本较低等特点,可应用于常见染色体非整倍体畸变的临床诊断和产前诊断.     

多重链接探针扩增技术在染色体非整倍体畸变诊断中的应用

目的 探讨多重连接探针扩增(multiplexligation-dependent probe amplification,MLPA)技术在13、18、21、X、Y染色体非整倍体畸变诊断中的应用价值.方法 收集本院经染色体核型分析确诊包括有上述5种染色体数目异常及正常的样本共44份,其中外周血30份、胎儿脐带血10份、羊水4份,提取标本DNA,采用MLPA技术对样本染色体数目进行分析,并与染色体核型分析结果进行比对.结果 42例样本检测结果与染色体核型分析结果一致,1例染色体核型分析未能作出判断的标记染色体片段被识别为Y染色体片段,1例21-三体嵌合体未能做出明确判断,临床检出率97.7%(43/44).结论 MLPA技术通过单管反应同时检测40多个不同靶基因序列的拷贝数,具有高通量、特异、便捷及成本较低等特点,可应用于常见染色体非整倍体畸变的临床诊断和产前诊断.

Abstract：

Objective To investigate the application value of the multiplex ligation-dependent probe amplification (MLPA) technique in diagnosis and prenatal diagnosis of chromosomes 13, 18, 21, X and Yaneuploidy. Methods Forty-four cases including 30 peripheral blood samples, 10 fetal cord blood samples,and 4 amniotic fluid samples were collected in this study. DNA was isolated from the samples and detected by MLPA, followed by analyzing in ABI310 Genetic Analyzer. Analysis of copy number changes for chromosomes 13, 18, 21, X and Y was carried out with RH-MLPA-analysis software. The routine karyotype analyses were also done for all the samples. Results Of 44 samples, the results of 42 by MLPA method was consistent with that by chromosome karyotyping. Only one case with trisomy 21 chimerism was failed to reach conclusion. In addition, one case of mark chromosome segment was identified as Ychromosome segment by MLPA, while karyotyping failed to make judgment. The accurate rate of MLPA was 97. 7% (43/44). Conclusion The MLPA technique can simultaneously detect dozens of different target sequences and their copy number changes in a single reaction. It showed high specificity, good reproducibility, was fast and high-throughput. The MLPA technique can be applied to diagnosis and prenatal diagnosis of the common chromosomal aneuploidy.     

多重链接探针扩增技术在染色体非整倍体畸变诊断中的应用

目的 探讨多重连接探针扩增(multiplexligation-dependent probe amplification,MLPA)技术在13、18、21、X、Y染色体非整倍体畸变诊断中的应用价值.方法 收集本院经染色体核型分析确诊包括有上述5种染色体数目异常及正常的样本共44份,其中外周血30份、胎儿脐带血10份、羊水4份,提取标本DNA,采用MLPA技术对样本染色体数目进行分析,并与染色体核型分析结果进行比对.结果 42例样本检测结果与染色体核型分析结果一致,1例染色体核型分析未能作出判断的标记染色体片段被识别为Y染色体片段,1例21-三体嵌合体未能做出明确判断,临床检出率97.7%(43/44).结论 MLPA技术通过单管反应同时检测40多个不同靶基因序列的拷贝数,具有高通量、特异、便捷及成本较低等特点,可应用于常见染色体非整倍体畸变的临床诊断和产前诊断.     

Multiplex ligation-dependent probe amplification assay for diagnosis of congenital adrenal hyperplasia

Mutations in the CYP21A2 gene encoding the 21-hydroxylase enzyme account for >90% of congenital adrenal hyperplasia (CAH) cases. Approximately 20% of mutant alleles carrying large deletion/duplication have also been reported. Herein, we describe the use of the multiplex ligation-dependent probe amplification (MLPA) method for convenient and rapid detection of deletions/duplications in the CYP21A2 gene. We used MLPA to analyze the gene dose of CYP21A2 MLPA in 13 Korean patients who previously underwent direct sequencing for the molecular diagnosis of CAH. The MLPA assays identified 5 patients with CYP21A2 deletions; all 5 patients carried a single mutant allele peak in sequence analysis. These results demonstrate the diagnostic usefulness of MLPA to detect CYP21A2 deletions/duplications for diagnosis of CAH.     

应用多重连接依赖探针扩增技术快速检测胎儿染色体非整倍体异常

目的 探讨多重连接依赖探针扩增(multiplex ligation-dependent probe amplification,MLPA)技术在常见染色体非整倍体异常检测及其在产前诊断中的应用价值.方法 应用MLPA技术检测561份产前诊断样本和20例已知染色体异倍体标本,所有样本均进行常规染色体核型分析,比较MLPA结果和染色体核型分析结果,评价MLPA技术的临床符合率.结果 MLPA技术能够在48 h内出具检测结果,共检测出38例染色体异倍体,包括20例21-三体,10例18-三体,1例13-三体,4例Turner综合征,1例Klinefelter综合征,1例超雄综合征,1例48,XYY,+18双三体综合征.MLPA结果与染色体核型结果一致,检测结果100％准确.在561份产前诊断样本中,有550份样本的MLPA分析结果和细胞染色体核型的结果一致,临床符合率达到98.04％.结论 MLPA技术具有快速、简单、稳定等优点,可检测常见非整倍体异常,能作为产前诊断的可靠方法,具有临床实际应用价值.     

采用多重连接探针扩增技术检测智力低下儿童的基因缺陷

目的 探讨原因不明智力低下儿童的发病与染色体亚端粒基因重组间的关系.方法 采用多重连接探针扩增(multiplex ligation-dependent probe amplification,MLPA)技术检测30名原因不明的综合征性智力低下患儿的染色体亚端粒区域.结果 检测到5例患儿存在染色体亚端粒的基因缺失或重复突变,分别为4p缺失,21q重复,10p重复、4p缺失,15p重复,3p重复、9p缺失.结论 不明原因智力低下儿童的发病与染色体亚端粒基因重组密切相关.MLPA技术可以作为一种高效、特异的方法对智能障碍儿童进行基因缺陷筛查.     

Investigation of gene dosage imbalances in patients with Noonan syndrome using multiplex ligation-dependent probe amplification analysis

The RAS-MAPK syndromes are a group of clinically and genetically related disorders caused by dysregulation of the RAS-MAPK pathway. A member of this group of disorders, Noonan syndrome (NS), is associated with several different genes within the RAS-MAPK pathway. To date, mutations in PTPN11, SOS1, KRAS, RAF1 and SHOC2 are known to cause NS and a small group of patients harbour mutations in BRAF, MEK1 or NRAS. The majority of the mutations are predicted to cause an up-regulation of the pathway; hence they are gain-of-function mutations. Despite recent advances in gene identification in NS, the genetic aetiology is still unknown in about ¼ of patients.To investigate the contribution of gene dosage imbalances of RAS-MAPK-related genes to the pathogenesis of NS, a multiplex ligation-dependent probe amplification (MLPA) assay was developed. Two probe sets were designed for seven RAS-MAPK-syndrome-related candidate genes: PTPN11, SOS1, RAF1, KRAS, BRAF, MEK1 and MEK2. The probe sets were validated in 15 healthy control individuals and in glioma tumour cell lines. Subsequently, 44 NS patients negative for mutations in known NS-associated genes were screened using the two probe sets. The MLPA results for the patients revealed no gene dosage imbalances. In conclusion, the present results exclude copy number variation of PTPN11, SOS1, RAF1, KRAS, BRAF, MEK1 and MEK2 as a common pathogenic mechanism of NS. The validated and optimised RAS-MAPK probe sets presented here enable rapid high throughput screening of further patients with RAS-MAPK syndromes.     

应用多重连接探针扩增技术行脊髓性肌萎缩症产前诊断的结果分析与遗传咨询指导

目的:对脊髓性肌萎缩症(spinal muscular atrophy, SMA)家系进行产前诊断,为SMA产前分子诊断提供遗传咨询指导意见。方法:纳入2016年至2019年在本院产前诊断中心就诊的21个家系开展研究,应用多重连接探针扩增(multiplex ligation-dependent probe ampli...     

Subtelomeric deletions detected in patients with idiopathic mental retardation using multiplex ligation-dependent probe amplification (MLPA)

Subtelomeric rearrangements are responsible for 5% to 10% of cases of unexplained mental retardation. Despite their clinical relevance, methods to screen for these cytogenetically invisible abnormalities on a routine base are scarce. We screened patients with idiopathic mental retardation for subtelomeric aberrations using multiplex ligation-dependent probe amplification (MLPA). This recently developed technique is based on PCR amplification of ligated probes hybridized to chromosome ends. Currently, 41 telomeres can be screened in just two multiplex reactions. Four subtelomeric rearrangements (5.3%) were detected in a group of 75 patients with mild to severe mental retardation in combination with dysmorphic features and/or a familial history of mental retardation: two terminal 1p deletions, a terminal 1q deletion, and a terminal 3p deletion. Deletions could be verified by FISH and marker analysis. In one case the MLPA indicated a terminal 21q deletion due to a 3-bp deletion at the site of the probe, giving a false-positive rate of 1.3%. This study demonstrates that MLPA is a fast and reliable screening method, potentially suitable for use in routine diagnostics.     

多重连接探针扩增检测Williams综合征微缺失

MLPA是一种简便快速检测缺失及重复突变的方法,该技术弥补了荧光原位杂交技术的不足,可用于实验室对Williams综合征的快速检测,具有一定临床诊断价值.     

Two-color multiplex ligation-dependent probe amplification: detecting genomic rearrangements in hereditary multiple exostoses

Genomic deletions and duplications play an important role in the etiology of human disease. Versatile tests are required to detect these rearrangements, both in research and diagnostic settings. Multiplex ligation-dependent probe amplification (MLPA) is such a technique, allowing the rapid and precise quantification of up to 40 sequences within a nucleic acid sample using a one-tube assay. Current MLPA probe design, however, involves time-consuming and costly steps for probe generation. To bypass these limitations we set out to use chemically synthesized oligonucleotide probes only. The inherent limitations of this approach are related to oligonucleotide length, and thus the number of probes that can be combined in one assay is also limited. This problem was tackled by designing a two-color assay, combining two sets of probes, each amplified by primers labeled with a different fluorophore. In this way we successfully combined 28 probes in a single reaction. The assay designed was used to screen for the presence of deletions and duplications in patients with hereditary multiple exostoses (HME). Screening 18 patients without detectable point mutations in the EXT1 and EXT2 genes revealed five cases with deletions of one or more exons: four in EXT1 and one in EXT2. Our results show that a two-color MLPA assay using only synthetic oligonucleotides provides an attractive alternative for probe design. The approach is especially suited for cases in which the number of patients to be tested is limited, making it financially unattractive to invest in cloning.     

Deletions of NF1 gene and exons detected by multiplex ligation-dependent probe amplification

To estimate the contribution of single and multi-exon NF1 gene copy-number changes to the NF1 mutation spectrum, we analysed a series of 201 Italian patients with neurofibromatosis type 1 (NF1). Of these, 138 had previously been found, using denaturing high-performance liquid chromatography or protein truncation test, to be heterozygous for intragenic NF1 point mutations/deletions/insertions, and were excluded from this analysis. The remaining 63 patients were analysed using multiplex ligation-dependent probe amplification (MLPA), which allows detection of deletions or duplications encompassing >or=1 NF1 exons, as well as entire gene deletions. MLPA results were validated using real-time quantitative PCR (qPCR) or fluorescent in situ hybridisation. MLPA screening followed by real-time qPCR detected a total of 23 deletions. Of these deletions, six were single exon, eight were multi-exon, and nine were of the entire NF1 gene. In our series, deletions encompassing >or=1 NF1 exons accounted for approximately 7% (14/201) of the NF1 gene mutation spectrum, suggesting that screening for these should now be systematically included in genetic testing of patients with NF1.     

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.     

多重连接探针扩增技术在肿瘤相关基因缺失/重复检测中的应用进展

多重连接探针扩增(MLPA)技术应用于检测肿瘤相关基因大片段缺失/重复,不仅有助于了解潜在的肿瘤发展分子机制,而且为肿瘤的诊断和预后提供重要信息,成为肿瘤学研究的主要方向。     

Rapid aneuploidy detection with multiplex ligation-dependent probe amplification: a prospective study of 4000 amniotic fluid samples

The introduction of prenatal screening requires rapid high-throughput diagnosis of common aneuploidies. Multiplex ligation-dependent probe amplification (MLPA) allows for quick, easily automated multiplex testing of these aneuploidies in one polymerase chain reaction. We performed a large prospective study using MLPA on 4000 amniotic fluid (AF) samples including all indications and compared its value to karyotyping and fluorescence in situ hybridization (FISH). MLPA can reliably determine common aneuploidies with 100% sensitivity and 100% specificity. Moreover, some mosaic cases and structural chromosome aberrations were detected as well. In cases of a male fetus, triploidies can be detected by an aberrant pattern of probe signals, which mimics maternal cell contamination (MCC). Macroscopic blood contamination was encountered in 3.2% of the AF samples. In 20% of these samples, an MLPA pattern was found consistent with MCC, although there were no false negatives of the most common aneuploidies. As the vast majority of inconclusive results (1.7%) is due to potential MCC, we designed a protocol in which we determine whether MLPA can be performed on blood-contaminated AF samples by testing if blood is of fetal origin. Then, the number of inconclusive results could be theoretically reduced to 0.05%. We propose an alternative interpretation of relative probe signals for rapid aneuploidy diagnosis (RAD). We discuss the value of MLPA for the detection of (submicroscopic) structural chromosome anomalies. MLPA is a reliable method that can replace FISH and could be used as a stand-alone test for RAD instead of karyotyping.     

High frequency of down-regulation of E-cadherin detected in benign sporadic insulinomas by multiplex ligation-dependent probe amplification

Insulinomas are the most common functioning pancreatic endocrine tumors, and the previous studies showed that the chromosomal aberrations of Chr.9q, 11q, and 22q were associated with the development and progression of insulinoma. To analyze the genetic alterations in sporadic insulinoma, we tested 23 tumor samples using multiplex ligation-dependent probe amplification. The results showed that 20 (87%) of the 23 patients had lost CDH1, a tumor suppressor gene. Immunofluorescence analysis of the E-cadherin and β-catenin proteins further confirmed the impaired expression of E-cadherin and the translocation of β-catenin in sporadic insulinomas. It was found that the cytoplasmic accumulation of β-catenin coincided with the decrease or loss of E-cadherin synthesis during the tumorigenesis of sporadic insulinomas. Our study suggests that the inactivation of CDH1 is an important and early event in the development of these tumor types.