Rapid, high throughput prenatal detection of aneuploidy using a novel quantitative method (MLPA)

22q11 Copy Number Variations in a Brazilian Cohort of Children with Congenital Heart Disorders

Introduction

Congenital heart disease (CHD) is the most common type of congenital defect reported to be one of the leading causes of mortality in the first year of life. Microdeletion and microduplication syndromes (MMS) are associated with cardiac malformations. Understanding which genetic factors are involved in these conditions directly impacts treatment decisions. We aimed to identify the occurrence of genetic alterations and their association with MMS in CHD pediatric patients evaluated in a reference service of Southern Brazil.

Methods

Participants were recruited during 2010 in the intensive care unit of a pediatric hospital. MMs and regions of chromosome 22 were screened by SALSA MLPA Probemix P245 Microdeletion Syndromes-1A kit for detection of copy number variations (CNVs).

Results

MMS were detected in 11 from 207 patients (5.3%). Heterozygous deletion in the 22q11.2 chromosome region was the most prevalent CNV (5 from 11 patients). Also, atypical RTDR1 deletion and 22q11.2 duplication were detected. MLPA was able to reveal microdeletions in SNRPN and NF1 genes in patients with a normal karyotype and FISH.

Conclusion

Our study reports the prevalence and variability of genomic alterations associated with MMS in CHD pediatric patients. The results by MLPA are of great help in planning and specialized care.

MLPA as a genetic assay for the prenatal diagnosis of common aneuploidy: the first Egyptian experience

Background

The prenatal diagnosis of syndromes caused by chromosomal abnormality is a long-established part of obstetric care. Several DNA-based molecular approaches have provided rapid prenatal diagnosis of of cytogenomic abnormalities. MLPA has become available for rapid aneuploidy detection of the most common chromosome abnormalities.

Objectives

The aim of this study is to introduce the MLPA technique as a method for the prenatal detection of aneuploidy in Egypt by its validation compared to the FISH technique.

Methods

Fifty AF samples were collected for this study and were subjected to MLPA and FISH assays to detect the most common prenatal chromosomal abnormality.

Results and conclusions

Our study confirmed previous reports that MLPA is analogous to FISH for detecting common aneuploidies and could be a quick and dependable tool for prenatal diagnosis. Therefore, initial prompt testing of AF samples for the copy number of the most common occurring aneuploidies is recommended.

Clinicopathological Significance of BRCAness in Resectable Pancreatic Ductal Adenocarcinoma and Its Association With Anticancer Drug Sensitivity in Pancreatic Cancer Cells

OBJECTIVE

The concept of BRCAness has been proposed as a homologous recombination repair dysfunction triggered by a genetic defect in the BRCA pathway including the BRCA1/2 mutations. A certain number of pancreatic ductal adenocarcinoma (PDAC) patients have BRCAness. However, a large-scale analysis of BRCAness in PDAC has not been performed. In addition, no basic studies have examined the significance of BRCAness in PDAC cell lines.

METHODS

Ninety-two patients who underwent surgery for PDAC were enrolled. Formalin-fixed and paraffin-embedded specimens of resected PDACs were used to analyze BRCAness by multiplex ligation-dependent probe amplification. We also analyzed BRCAness in pancreatic cancer cell lines and the sensitivity to cisplatin and olaparib using a colony formation assay.

RESULTS

Of the 92 patients with PDAC, 6 were detected to have BRCAness-positive PDAC (6.5%). No significant differences in overall survival and progression-free survival were observed between the BRCAness-positive and BRCAness-negative groups. One PDAC cell line, KP-2, was positive for BRCAness and was more sensitive to cisplatin and olaparib than the BRCAness-negative cell lines.

CONCLUSIONS

Our results revealed that a considerable number of PDACs are positive for BRCAness, suggesting that BRCAness status could be a useful biomarker for selecting anticancer treatments for advanced or relapsed PDAC.

Evaluation of interpretation methods to improve accuracy of the prenatal BACs-on-Beads™ assay in prenatal diagnosis

Prenatal BACs-on-Beads™ (PNBoBs™) technology has been approved for use in routine clinical prenatal diagnosis in numerous countries. However, the influence of data interpretation on the accuracy of the results remains to be evaluated. The present study aimed to determine the accuracy of existing data interpretation approaches and develop an optimization method to improve the performance of the PNBoBs™ assay in prenatal diagnosis. A total of 2,289 prenatal cases with known karyotypes and raw ratio data from PNBoBs™ assays were recruited for the present study. Positive results, according to the data interpretation methods used for the PNBoBs™ test, were validated against current gold-standard approaches. Statistical analyses were then performed to evaluate the accuracy of existing methods in data interpretation to provide a basis for the optimization of a follow-up approach. Among the existing methods, the ‘trimmed standard deviation threshold’ approach had the highest sensitivity and false-positive rates, with 98.1 and 4.2%, respectively. The ‘n-1 or greater probes’ rule had the highest specificity (99.7%) and the second-highest false-negative rate (11.5%). The method optimized in the present study provided a reasonable balance between sensitivity (98.1%) and specificity (99.6%) with regards to the interpretation of the data obtained from the PNBoBs™ assay. The results indicated that the present optimization method outperforms existing approaches in data interpretation for the PNBoBs™ assay, and as a result, may reduce unnecessary verification turnaround time and cost in prenatal diagnosis.

Analysis of BRCAness with multiplex ligation-dependent probe amplification using formalin-fixed and paraffin-embedded pancreatic ductal adenocarcinoma tissue obtained via endoscopic ultrasound-guided fine-needle aspiration biopsy

BACKGROUND/OBJECTIVES

A breakthrough in chemotherapy for pancreatic ductal adenocarcinoma (PDAC) may be achieved using precision medicine, which involves identifying cases that are highly likely to respond to a certain treatment and then performing that treatment. BRCAness has been receiving attention as a novel predictor of anticancer drug sensitivity in PDAC, making the screening of BRCAness paramount.

METHODS

We conducted the first-ever examination of the feasibility of analyzing BRCAness using multiplex ligation-dependent probe amplification (MLPA). Formalin-fixed paraffin-embedded (FFPE) tissue samples obtained via endoscopic ultrasound-guided fine-needle aspiration biopsy (EUS-FNAB) from 20 patients with the highest pancreatic carcinoma cell counts in tissue samples out of 40 consecutive PDAC patients who underwent EUS-FNAB at our hospital were analyzed by MLPA for BRCAness.

RESULTS

We were able to accurately analyze BRCAness in 75% of the 20 cases of PDAC using FFPE tissue obtained by EUS-FNAB. BRCAness was observed in one of the 20 cases.

CONCLUSIONS

In PDAC, analyzing BRCAness by MLPA using FFPE tissue obtained by EUS-FNAB offers the remarkable benefit of yielding results in a short period of time and at a low cost. In addition, this method of BRCAness analysis may prove to be a feasible and effective approach for performing precision medicine.

Clinical experience with multiplex ligation-dependent probe amplification for microdeletion syndromes in prenatal diagnosis: 7522 pregnant Korean women

Background

Conventional cytogenetic analysis using G-band karyotyping has been the method of choice for prenatal diagnosis, accurately detecting chromosomal abnormalities larger than 5 Mb. However, the method is inefficient for detecting the submicroscopic deletions and duplications that are associated with malformations and mental retardation. This study evaluated the results of the multiplex ligation-dependent probe amplification (MLPA) P245 assay used for prenatal diagnosis in cases with unusual ultrasonographic findings or specifically where parents wanted to be tested. The objective was to compare the results from MLPA with those from conventional cytogenetic testing in order to determine their concordance and the additional diagnostic yield of MLPA over G-band karyotyping.

Results

Of the 7522 prenatal cases analyzed, 124 were found to have genomic imbalances (1.6%). Of those 124 cases, 41 had gene loss (33.6%), and 83 had gene gain (66.4%). Most of the cases with genomic imbalances (64.5%) showed no abnormal karyotype. In particular, all cases with a 4p16.3 deletion (Wolf-Hirschhorn syndrome) showed an abnormal karyotype, whereas all of those with a 22q11–13 deletion showed a normal karyotype. In most of the cases with pathogenic deletions, the indication for invasive prenatal testing was an increase in the nuchal translucency (NT) alone (51.2%). Other indications observed in the remaining cases were abnormal serum screening markers (14.6%), other ultrasonographic findings (9.8%), pregnancy through in vitro fertilization and fertility assistance (9.8%), and advanced maternal age(2.4%).

Conclusions

These results show that for fetuses with an enlarged NT or abnormal ultrasonographic findings and normal conventional karyotype, additional genetic investigation like molecular testing would be for identifying the microscopic genomic aberrations (microdeletions, microduplications) responsible for syndromic associations including structural anomalies and mental retardation.

Multiplex Ligation-Dependent Probe Amplification (MLPA) for Prenatal Diagnosis of Common Aneuploidies

Multiplex Ligation-dependent Probe Amplification (MLPA) is a method to determine the copy number of up to 60 genomic DNA sequences in a single multiplex PCR based reaction.MLPA probes consist of two oligonucleotides that can hybridize next to each other on a certain DNA sequence of interest, where they are ligated. All ligated probes are subsequently amplified by PCR using a single set of primers. Each amplified MLPA probe has a unique length and can be visualized and quantified by capillary electrophoresis. As the primers are almost 100% consumed in the PCR reaction, the quantity of each PCR amplicon is proportional to the number of copies of each probe target sequence in the DNA sample. A trisomy 21 can therefore be detected by an approximately 50% increased signal of each chromosome 21 specific probe relative to reference samples.MLPA with the P095 Aneuploidy probemix for chromosomes 13, 18, 21, X and Y has been used as a rapid detection method on large numbers of samples from uncultured amniotic fluid or from chorionic villi. As compared to FISH and karyotyping, MLPA is more rapid, has a higher throughput, and is less expensive. MLPA however cannot detect low grade mosaicism, female triploidies, and copy number neutral chromosome abnormalities such as inversions and translocations.

Novel rapid molecular diagnosis of fetal chromosomal abnormalities associated with recurrent pregnancy loss

INTRODUCTION

Labor-intensive karyotyping is used as the reference standard diagnostic test to identify copy number variants (CNVs) in the fetal genome after recurrent pregnancy loss. Our aim was to present and evaluate a novel molecular assay called CNVplex that could potentially be used as an alternative method to conventional karyotyping for diagnosing fetal chromosomal abnormalities associated with recurrent pregnancy loss.

MATERIAL AND METHODS

Using karyotyping as the reference standard, CNVplex was performed to identify fetal chromosomal abnormalities in the chorionic villus samples from 76 women experiencing at least two pregnancy losses. Its diagnostic accuracy, sensitivity, and specificity were evaluated to detect aneuploidies associated with recurrent pregnancy loss. Turnaround time and costs of CNVplex were also measured.

RESULTS

Diagnostic accuracy of CNVplex in aneuploidies that are associated with recurrent pregnancy loss was 1.0 (95% CI 0.94-1.0), sensitivity was 100% (95% CI 0.89-1.0), and specificity was 100% (95% CI 0.875-1.0). Diagnostic accuracy of CNVplex was similar to that of karyotyping. Both karyotyping and CNVplex assay detected 27 autosomal trisomies, three 45,X monosomies, and three polyploidies. CNVplex also detected additional novel structural abnormalities of the fetal genome. Compared with karyotyping, CNVplex significantly (p = 0.001) reduced the waiting time by 13.98 days (95% CI 13.88-14.08) and the cost by US $241 (95% CI 234.53-247.47).

CONCLUSIONS

CNVplex is a novel effective assay for diagnosing fetal chromosomal abnormalities associated with recurrent pregnancy loss. In the routine clinical work-up of recurrent pregnancy loss, diagnostic accuracy of CNVplex is comparable to that of conventional karyotyping but it requires less waiting time and has lower cost.

"Down syndrome: an insight of the disease"

Down syndrome (DS) is one of the commonest disorders with huge medical and social cost. DS is associated with number of phenotypes including congenital heart defects, leukemia, Alzeihmer's disease, Hirschsprung disease etc. DS individuals are affected by these phenotypes to a variable extent thus understanding the cause of this variation is a key challenge. In the present review article, we emphasize an overview of DS, DS-associated phenotypes diagnosis and management of the disease. The genes or miRNA involved in Down syndrome associated Alzheimer's disease, congenital heart defects (AVSD), leukemia including AMKL and ALL, hypertension and Hirschprung disease are discussed in this article. Moreover, we have also reviewed various prenatal diagnostic method from karyotyping to rapid molecular methods -  MLPA, FISH, QF-PCR, PSQ, NGS and noninvasive prenatal diagnosis in detail.

Multiplex ligation-dependent probe amplification and array comparative genomic hybridization analyses for prenatal diagnosis of cytogenomic abnormalities

Background

The aims of this study were to evaluate the clinical utility of multiplex ligation-dependent probe amplification (MLPA) and array comparative genomic hybridization (aCGH) analyses on prenatal cases and to review prenatal ultrasound findings of cytogenomic syndromes.

Results

Of the 54 prenatal cases analyzed, cytogenomic abnormalities were characterized in 14 cases. In four fetuses with abnormal ultrasound findings, a 40.701 Mb duplication of 8q22.3-q24.3 and a 23.839 Mb deletion of 7q33-q36.3 derived from a paternal balanced translocation, a de novo 13.062 Mb deletion of 11q24.1-q25 for Jacobsen syndrome, a de novo 19.971 Mb deletion of 7q11.23-q21.3 for type 1 split-hand/foot malformation (SHFM1), and a de novo 28.909 Mb duplication of 3q21.1-q25.1 were detected. A 699.8 Kb deletion at 5p15.33 for Cri du Chat syndrome was confirmed in a fetus with abnormal MLPA result. A fetus with abnormal maternal screening was detected with a de novo distal 1.747 Mb duplication at 2q37.1-q37.2 and a 6.664 Mb deletion at 2q37.2-q37.3. Of the eight cases referred by history of spontaneous abortions, derivative chromosomes 11 from paternal carriers of a balanced 8q/11q and a 10q/11q translocation were noted in two cases, simple aneuploids of trisomy 2 and trisomy 21 were seen in three cases, and compound aneuploids of two or three chromosomes were found in three cases. Post-test genetic counseling was performed with detailed genomic information and well characterized postnatal syndromic features.

Conclusions

These results demonstrated that coupling MLPA screening and aCGH analysis are a cost-effective approach to detect cytogenomic abnormalities in a prenatal setting. The aCGH analysis provided not only genomic maps of breakpoints and gene content of imbalanced regions but also better inference of related phenotypes for genetic counseling. Prenatal ultrasound findings reported in the literature for Jacobsen syndrome, SHFM and Cri du Chat syndrome were summarized for use as diagnostic references.

Subtelomeric multiplex ligation-dependent probe amplification as a supplement for rapid prenatal detection of fetal chromosomal aberrations

Background

Pregnant women with high-risk indications are highly suspected of fetal chromosomal aberrations. To determine whether Multiplex Ligation-dependent Probe Amplification (MLPA) using subtelomeric probe mixes (P036-E2 and P070-B2) is a reliable method for rapid detection of fetal chromosomal aberrations. The subtelomeric MLPA probe mixes were used to evaluate 50 blood samples from healthy individuals. 168 amniocytes and 182 umbilical cord blood samples from high-risk fetuses were analyzed using the same subtelomeric MLPA probe sets. Karyotyping was also performed in all cases of high-risk pregnancies, and single nucleotide polymorphism array analysis was used to confirm submicroscopic and ambiguous results from MLPA/karyotyping.

Results

Subtelomeric MLPA analysis of normal samples showed normal result in all cases by use of P036-E2 probe mix, while P070-B2 probe mix gave normal results for all but one case. In one normal control case P070-B2 produced a duplicated signal of probe for 13q34. In the high-risk group, totally 44 chromosomal abnormalities were found by karyotyping and MLPA, including 23 aneuploidies and 21 rearrangements or mosaics. MLPA detected all 23 aneuploidies, 12 rearrangements and 1 mosaic. Importantly, MLPA revealed 4 chromosomal translocations, 2 small supernumerary marker chromosomes (sSMCs), and 3 subtelomeric imbalances that were not well characterized or not detectable by karyotyping. However, MLPA showed negetive results for the remaining 8 rearrangements or mosaics, including 3 low mosaic aneuploidies, 1 inherited sSMC, and 4 paracentric inversions.

Conclusions

Results suggest that combined use of subtelomeric MLPA and karyotyping may be an alternative method for using karyotype analyses alone in rapid detection of aneuploidies, rearrangements, and sSMCs.

Electronic supplementary material

The online version of this article (doi:10.1186/s13039-014-0096-1) contains supplementary material, which is available to authorized users.

Rapid detection of Down's syndrome using quantitative real-time PCR (qPCR) targeting segmental duplications on chromosomes 21 and 11

OBJECTIVE

Development of a qPCR test for the detection of trisomy 21 using segmental duplications.

METHODS

Segmental duplications in the TTC3 gene on chromosome 21 and the KDM2A gene on chromosome 11 were selected as molecular markers for the diagnostic qPCR assay. A set of consensus primers selected from the conserved regions of these segmental duplications were used to amplify internal diverse sequences that were detected and quantified with different probes labeled with distinct fluorescence. The copy numbers of these two fragments were determined based on the ΔCq values of qPCR. The results of qPCR for prenatal and neonatal screening of Down's syndrome were compared with the conventional karyotype analysis by testing 82 normal individuals and 50 subjects with Down's syndrome.

RESULTS

The ΔCq values of segmental duplications on chr21 and 11 ranged between 0.33 and 0.75 in normal individuals, and between 0.91 and 1.18 in subjects with Down's syndrome. The ΔCq values of these two segmental duplications clearly discriminated Down's syndrome from normal individuals (P<0.001). Furthermore, the qPCR results were consistent with karyotype analysis.

CONCLUSION

Our qPCR can be used for rapid prenatal and neonatal screening of Down's syndrome.

The combined QF-PCR and cytogenetic approach in prenatal diagnosis

In this study, the importance of quantitative fluorescence polymerase chain reaction (QF-PCR) aneuploidy diagnosis test which provides earlier and easier results were discussed. The cell cultures and DNA isolations were performed on 100 amniotic fluids. DNA isolations were made from peripheral blood samples of mothers who had blood-stained amniotic fluid samples. The reasons of references of these pregnant women to our division were increased maternal age, positive double/triple screening test and fetal anomaly history. QF-PCR applied to 19 short tandem repeat markers in the chromosomes 13, 18, 21 and genes X and Y chromosomes. All electropherogram peaks were evaluated on ABI3130. Thirty two (32%) samples have high maternal age, seven (7%) have fetal anomaly and the others have double/triple screening test positivity. Ninety-nine (99%) of the 100 amniotic fluid samples were resulted, but one (1%) of them could not examined because of the culture failure. The maternal contamination rates were determined as 3%. Of 100 samples, 2 had trisomy 21 (2%), 1 had trisomy 13 (1%), 1 had structural abnormalities (1%) and the others (97%) have not any aneuploidy. The results of QF-PCR were in compatible with the results of cell culture and chromosome analysis. Although QF-PCR is an easier and an earlier test, it has a limitation of not to able to scan full genome. It is also sensitive for maternal contamination, so it should be tested together with maternal blood samples. QF-PCR aneuploidy test is the fastest diagnostic test for prenatal diagnosis and so it provides less stressful period for pregnant women.

Diagnostic accuracy of the BACs-on-Beads™ assay versus karyotyping for prenatal detection of chromosomal abnormalities: a retrospective consecutive case series

OBJECTIVE

To evaluate the diagnostic performance of the BACs-on-Beads(™) (BoBs(™)) assay for prenatal detection of chromosomal abnormalities.

DESIGN

Retrospective study.

SETTING

Tertiary prenatal diagnosis centre.

POPULATION

Women referred for prenatal diagnosis.

METHODS

We retrieved 2153 archived DNA samples collected between January 2010 and August 2011 for the BoBs(™) assay. These samples had previously been tested by quantitative fluorescence polymerase chain reaction (QF-PCR) and karyotyping. In the BoBs(™) assay a sample was defined as normal disomic when the ratio of the fluorescence intensities in a chromosome locus lay within the threshold (mean ratio ± 2SD), and as deleted or duplicated when the ratio was below the lower threshold (0.6-0.8) or above the upper threshold (1.3-1.4), respectively. The BoBs(™) results were further validated by microarray and compared in a blinded manner with the original QF-PCR and karyotyping results.

MAIN OUTCOME MEASURES

Concordance of any numerical, structural, and submicroscopic chromosomal abnormalities between the methods.

RESULTS

BACs-on-Beads(™) was similar to karyotyping and QF-PCR in detecting trisomy 13, trisomy 18, trisomy 21, and sex chromosomal aneuploidies, and superior to QF-PCR in detecting major structural abnormalities (53.3 versus 13.3%) and mosaicism (28.6 versus 0%) involving chromosomal abnormalities other than the common aneuploidies. BoBs(™) detected six microdeletion syndromes missed by karyotyping and QF-PCR; however, BoBs(™) missed two cases of triploidy identified by QF-PCR. Therefore, the sensitivity of BoBs(™) is 96.7% (95% CI 92.6-98.7%), and its specificity is 100% (95% CI 99.8-100%).

CONCLUSIONS

BACs-on-Beads(™) can replace QF-PCR for triaging in prenatal diagnosis, and gives a better diagnostic yield than current rapid aneuploidy tests.

Can we rely on the multiplex ligation-dependent probe amplification method (MLPA) for prenatal diagnosis?

BACKGROUND

The major aneuploidies that are diagnosed prenatally involve the autosomal chromosomes 13, 18, and 21, as well as sex chromosomes, X and Y. Because multiplex ligation-dependent probe amplification (MLPA) is rapid and non-invasive, it has replaced traditional culture methods for the screening and diagnosis of common aneuploidies in some countries.

OBJECTIVE

To evaluate the sensitivity and specificity of MLPA in a cross-sectional descriptive study for the detection of chromosomal aneuploidies in comparison to other methods.

MATERIALS AND METHODS

Genomic DNA was extracted from the peripheral blood samples of 10 normal controls and the amniotic fluid of 55 patients. Aneuploidies screening of chromosomes 13, 18, 21, X and Y were carried out using specific MLPA probe mixes (P095-A2). For comparison purposes, samples were also tested by Quantitative Fluorescent-PCR (QF-PCR) and routine chromosomal culture method.

RESULTS

Using this specific MLPA technique and data-analyzing software (Genemarker v1.85), one case was diagnosed with 45, X (e.g. Monosomy X or Turner's Syndrome), and the remaining 54 cases revealed normal karyotypes. These results were concordant with routine chromosomal culture and QF-PCR findings.

CONCLUSION

The experiment demonstrates that MLPA can provide a rapid and accurate clinical method for prenatal identification of common chromosomal aneuploidies with 100% sensitivity and 100% specificity.

Rapid diagnosis of aneuploidy using segmental duplication quantitative fluorescent PCR

The aim of this study was use a simple and rapid procedure, called segmental duplication quantitative fluorescent polymerase chain reaction (SD-QF-PCR), for the prenatal diagnosis of fetal chromosomal aneuploidies. This method is based on the co-amplification of segmental duplications located on two different chromosomes using a single pair of fluorescent primers. The PCR products of different sizes were subsequently analyzed through capillary electrophoresis, and the aneuploidies were determined based on the relative dosage between the two chromosomes. Each primer set, containing five pairs of primers, was designed to simultaneously detect aneuploidies located on chromosomes 21, 18, 13, X and Y in a single reaction. We applied these two primer sets to DNA samples isolated from individuals with trisomy 21 (n = 36); trisomy 18 (n = 6); trisomy 13 (n = 4); 45, X (n = 5); 47, XXX (n = 3); 48, XXYY (n = 2); and unaffected controls (n = 40). We evaluated the performance of this method using the karyotyping results. A correct and unambiguous diagnosis with 100% sensitivity and 100% specificity, was achieved for clinical samples examined. Thus, the present study demonstrates that SD-QF-PCR is a robust, rapid and sensitive method for the diagnosis of common aneuploidies, and these analyses can be performed in less than 4 hours for a single sample, providing a competitive alternative for routine use.

Rapid prenatal diagnosis of common numerical chromosomal abnormalities by high-resolution melting analysis of segmental duplications

BACKGROUND

Rapid aneuploidy detection (RAD) methods constitute important complements to karyotyping in prenatal diagnosis. We evaluated the effectiveness of a method called high-resolution melting analysis of segmental duplications (SD-HRM) to serve as an alternative RAD method in prenatal diagnosis of common numerical chromosomal abnormalities (NCAs).

METHODS

We designed eight primary SD-HRM assays for the detection of chromosomes 13, 18, 21, X, and Y; 50 chorionic villus, 1105 amniotic fluid, and 395 cord blood samples were examined using these eight assays. For diagnosing samples that could not be diagnosed using primary assays, additional assays were designed for each target chromosome.

RESULTS

The success rate of eight primary SD-HRM assays ranged from 99.7% to 100%. For the distinguishable analyses, these eight assays attained high diagnostic sensitivities (100%) and specificities (99.9-100%). We differentiated 53 cases of NCAs from 1550 clinical samples; subsequent reference tests revealed that these assays attained 100% clinical sensitivity and specificity. The mosaic ratio of a 45,X/46,XX sample was also precisely calculated.

CONCLUSIONS

The SD-HRM method was able to effectively detect common NCAs in 1550 prenatal samples. We propose that SD-HRM could serve as an effective alternative option to the currently used prenatal RAD methods.

Slovenian five-year experiences with rapid prenatal diagnosis of common chromosome aneuploidies using quantitative-fluorescence polymerase chain reaction

OBJECTIVE

Quantitative-fluorescence polymerase chain reaction (QF-PCR) was used to detect common fetal aneuploidies in pregnancies with increased (maternal age) or high risk (increased nuchal translucency, abnormal fetal ultrasonography, positive biochemical hormone test, or positive family history) for fetal aneuploidy.

METHODS

The QF-PCR testing was performed on 642 prenatal samples (73.3% amniotic fluids, 26.7% chorionic villus). DNA from prenatal samples were analyzed using an in-house-developed QF-PCR method with 20 micro-satellite markers located on the chromosomes 13, 18, 21, X and Y. Karyotyping of the 392 samples was done and both results were compared.

RESULTS

634/642 samples were successfully analyzed. In 7.1% of 634 cases numerical chromosome abnormalities were detected. Results of QF-PCR and karyotyping were compared in 392 cases. In the group, with increased risk of fetal trisomy the specificity and sensitivity of QF-PCR method was 100%. Among cases with high risk for fetal aneuploidy, sensitivity was 100% (86.6%-100%); however, the specificity was lower, 91.1% to 100%, depending on the referral reason.

CONCLUSIONS

In women, at advanced age QF-PCR can be used alone without karyotyping. In cases with higher risk, especially those with abnormal ultrasound findings, analysis performed only with QF-PCR is not a sufficient diagnostic method.

Rapid detection of aneuploidy and unbalanced chromosomal rearrangements by subtelomeric multiplex ligation-dependent probe amplification in fetuses with congenital heart disease

OBJECTIVE

To validate multiplex ligation-dependent probe amplification (MLPA) with subtelomeric probe mixes as a tool for diagnosis of aneuploidy and unbalanced terminal chromosomal rearrangements in fetuses with congenital heart disease.

METHODS

A prospective study of 117 fetuses found to have structural heart defects by ultrasound at 17-40 weeks' gestation. MLPA with P036E and P070B probe mixes was performed and compared to traditional karyotyping by cell culture and to findings of quantitative fluorescence-polymerase chain reaction (QF-PCR).

RESULTS

MLPA was able to define the fetal karyotype in 99% of cases whereas cell culture only defined the karyotype in 64% of cases. Consequently, the overall number of chromosomal abnormalities that were detected increased. The majority of these affected chromosomes, 21, 18, 13, X or Y, were also confirmed by QF-PCR. Two (5%) cases had atypical aneuploidy that was confirmed by MLPA but not by QF-PCR. In 4 cases, structural rearrangements or mosaicism were not detected by MLPA.

CONCLUSIONS

Subtelomeric MLPA may be a valuable adjunct to QF-PCR and/or conventional cytogenetics for the investigation of chromosomal abnormalities in fetuses with congenital heart disease.

Current mutation discovery approaches in Retinitis Pigmentosa

With a worldwide prevalence of about 1 in 3500-5000 individuals, Retinitis Pigmentosa (RP) is the most common form of hereditary retinal degeneration. It is an extremely heterogeneous group of genetically determined retinal diseases leading to progressive loss of vision due to impairment of rod and cone photoreceptors. RP can be inherited as an autosomal-recessive, autosomal-dominant, or X-linked trait. Non-Mendelian inheritance patterns such as digenic, maternal (mitochondrial) or compound heterozygosity have also been reported. To date, more than 65 genes have been implicated in syndromic and non-syndromic forms of RP, which account for only about 60% of all RP cases. Due to this high heterogeneity and diversity of inheritance patterns, the molecular diagnosis of syndromic and non-syndromic RP is very challenging, and the heritability of 40% of total RP cases worldwide remains unknown. However new sequencing methodologies, boosted by the human genome project, have contributed to exponential plummeting in sequencing costs, thereby making it feasible to include molecular testing for RP patients in routine clinical practice within the coming years. Here, we summarize the most widely used state-of-the-art technologies currently applied for the molecular diagnosis of RP, and address their strengths and weaknesses for the molecular diagnosis of such a complex genetic disease.

Multiplex ligation-dependent probe amplification (MLPA) and prenatal diagnosis

Multiplex ligation-dependent probe amplification (MLPA) is a recent technique for the relative quantitation of up to 40 to 45 nucleic acid targets. Due to its relative simplicity, low cost, and availability of laboratory-developed and more than 300 commercially-developed assays, MLPA has become more widely used for both research and diagnostic applications. The MLPA platform is now extensively applied for postnatal diagnosis of genetic disorders and has recently been used for prenatal diagnosis. The published uses of MLPA for prenatal diagnosis include detection of aneuploidies, common microdeletion syndromes and subtelomeric copy-number changes, identification of marker chromosomes, and detection of familial copy-number changes in single genes. This review describes the technique of MLPA in detail and offers considerations for the interpretation of results in the clinical diagnostic setting. © 2012 John Wiley & Sons, Ltd.

Rapid Diagnosis of Aneuploidy by High-Resolution Melting Analysis of Segmental Duplications

BACKGROUND

Several molecular methods, such as quantitative fluorescence PCR and multiplex ligation-dependent probe amplification, currently serve as important adjuncts to traditional karyotyping for the diagnosis of aneuploidy; however, the performance or throughput limitations of these methods hinder their use for routine prenatal diagnosis and population-based postnatal screening. We developed a novel approach, called “high-resolution melting analysis of segmental duplications,” to detect common aneuploidies.

METHODS

In this method, similar sequences located on different chromosomes are amplified simultaneously with a single primer set; the PCR products are then analyzed by high-resolution melting. Aneuploidy-associated dosage abnormalities produce different ratios of similar amplicons, which produce melting curves that are detectably different from those of samples from unaffected individuals. We applied this method to DNA samples isolated from individuals with trisomy 21 (n = 48), trisomy 18 (n = 10), trisomy 13 (n = 3), 45,X (n = 8), and 47,XXY (n = 14), and from unaffected controls (n = 48).

RESULTS

As judged by the karyotyping results, our method attained 100% diagnostic sensitivity and 99.6% diagnostic specificity. Moreover, our method was able to detect a change in chromosome dosage as low as 1.05-fold.

CONCLUSIONS

This novel method clearly differentiates samples of patients with common aneuploidies from those of unaffected controls, while markedly simplifying the assays and reducing time and costs. The assay has sufficient throughput to meet the demands of large-scale testing, such as population-based postnatal screening, and is thus suitable for routine use.

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.

Mirror extreme BMI phenotypes associated with gene dosage at the chromosome 16p11.2 locus

Both obesity and being underweight have been associated with increased mortality. Underweight, defined as a body mass index (BMI) ≤ 18.5 kg per m(2) in adults and ≤ -2 standard deviations from the mean in children, is the main sign of a series of heterogeneous clinical conditions including failure to thrive, feeding and eating disorder and/or anorexia nervosa. In contrast to obesity, few genetic variants underlying these clinical conditions have been reported. We previously showed that hemizygosity of a ∼600-kilobase (kb) region on the short arm of chromosome 16 causes a highly penetrant form of obesity that is often associated with hyperphagia and intellectual disabilities. Here we show that the corresponding reciprocal duplication is associated with being underweight. We identified 138 duplication carriers (including 132 novel cases and 108 unrelated carriers) from individuals clinically referred for developmental or intellectual disabilities (DD/ID) or psychiatric disorders, or recruited from population-based cohorts. These carriers show significantly reduced postnatal weight and BMI. Half of the boys younger than five years are underweight with a probable diagnosis of failure to thrive, whereas adult duplication carriers have an 8.3-fold increased risk of being clinically underweight. We observe a trend towards increased severity in males, as well as a depletion of male carriers among non-medically ascertained cases. These features are associated with an unusually high frequency of selective and restrictive eating behaviours and a significant reduction in head circumference. Each of the observed phenotypes is the converse of one reported in carriers of deletions at this locus. The phenotypes correlate with changes in transcript levels for genes mapping within the duplication but not in flanking regions. The reciprocal impact of these 16p11.2 copy-number variants indicates that severe obesity and being underweight could have mirror aetiologies, possibly through contrasting effects on energy balance.

Molecular identification of Clonorchis sinensis and discrimination with other opisthorchid liver fluke species using multiple Ligation-depended Probe Amplification (MLPA)

BACKGROUND

Infections with the opisthorchid liver flukes Clonorchis sinensis, Opisthorchis viverrini, and O. felineus cause severe health problems globally, particularly in Southeast Asia. Early identification of the infection is essential to provide timely and appropriate chemotherapy to patients.

RESULTS

In this study we evaluate a PCR-based molecular identification method, Multiplex Ligation-dependent Probe Amplification (MLPA), which allows rapid and specific detection of single nucleotide acid differences between Clonorchis sinensis, Opisthorchis viverrini and O. felineus. Three probe pairs were derived from the Internally Transcribed Spacer 1 (ITS1) of three opisthorchid liver flukes using a systematic phylogenetic analysis. Specific loci were detected in all three species, yielding three amplicons with 198,172 and 152 bp, respectively, while no cross reactions were observed. A panel of 66 C. sinensis isolates was screened using MLPA. All species were positively identified, and no inhibition was observed. The detection limit was 10(3) copies of the ITS gene for the three liver flukes, or about 60 pg genomic DNA for Clonorchis sinensis. Amplification products can be detected by electrophoresis on agarose gel or in a capillary sequencer. In addition, genomic DNA of Clonorchis sinensis in fecal samples of infected rats was positively amplified by MLPA.

CONCLUSION

The flexibility and specificity make MLPA a potential tool for specific identification of infections by opisthorchid liver flukes in endemic areas.

Economic evaluation of multiplex ligation-dependent probe amplification and karyotyping in prenatal diagnosis: a cost-minimization analysis

Purpose

To assess the cost-effectiveness of Multiplex Ligation-dependent Probe Amplification (MLPA, P095 kit) compared to karyotyping.

Methods

A cost-minimization analysis alongside a nationwide prospective clinical study of 4,585 women undergoing amniocentesis on behalf of their age (≥36 years), an increased risk following first trimester prenatal screening or parental anxiety.

Results

Diagnostic accuracy of MLPA (P095 kit) was comparable to karyotyping (1.0 95% CI 0.999–1.0). Health-related quality of life did not differ between the strategies (summary physical health: mean difference 0.31, p = 0.82; summary mental health: mean difference 1.91, p = 0.22). Short-term costs were lower for MLPA: mean difference €315.68 (bootstrap 95% CI €315.63–315.74; −44.4%). The long-term costs were slightly higher for MLPA: mean difference €76.42 (bootstrap 95% CI €71.32–81.52; +8.6%). Total costs were on average €240.13 (bootstrap 95% CI €235.02–245.23; −14.9%) lower in favor of MLPA. Cost differences were sensitive to proportion of terminated pregnancies, sample throughput, individual choice and performance of tests in one laboratory, but not to failure rate or the exclusion of polluted samples.

Conclusion

From an economic perspective, MLPA is the preferred prenatal diagnostic strategy in women who undergo amniocentesis on behalf of their age, following prenatal screening or parental anxiety.

Electronic supplementary material

The online version of this article (doi:10.1007/s00404-011-1921-y) contains supplementary material, which is available to authorized users.

Rapid screening for chromosomal aneuploidies using array-MLPA

Background

Chromosome abnormalities, especially trisomy of chromosome 21, 13, or 18 as well as sex chromosome aneuploidy, are a well-established cause of pregnancy loss. Cultured cell karyotype analysis and FISH have been considered reliable detectors of fetal abnormality. However, results are usually not available for 3-4 days or more. Multiplex ligation-dependent probe amplification (MLPA) has emerged as an alternative rapid technique for detection of chromosome aneuploidies. However, conventional MLPA does not allow for relative quantification of more than 50 different target sequences in one reaction and does not detect mosaic trisomy. A multiplexed MLPA with more sensitive detection would be useful for fetal genetic screening.

Methods

We developed a method of array-based MLPA to rapidly screen for common aneuploidies. We designed 116 universal tag-probes covering chromosomes 13, 18, 21, X, and Y, and 8 control autosomal genes. We performed MLPA and hybridized the products on a 4-well flow-through microarray system. We determined chromosome copy numbers by analyzing the relative signals of the chromosome-specific probes.

Results

In a blind study of 161 peripheral blood and 12 amniotic fluid samples previously karyotyped, 169 of 173 (97.7%) including all the amniotic fluid samples were correctly identified by array-MLPA. Furthermore, we detected two chromosome X monosomy mosaic cases in which the mosaism rates estimated by array-MLPA were basically consistent with the results from karyotyping. Additionally, we identified five Y chromosome abnormalities in which G-banding could not distinguish their origins for four of the five cases.

Conclusions

Our study demonstrates the successful application and strong potential of array-MLPA in clinical diagnosis and prenatal testing for rapid and sensitive chromosomal aneuploidy screening. Furthermore, we have developed a simple and rapid procedure for screening copy numbers on chromosomes 13, 18, 21, X, and Y using array-MLPA.

A fast and accurate method to detect allelic genomic imbalances underlying mosaic rearrangements using SNP array data

Background

Mosaicism for copy number and copy neutral chromosomal rearrangements has been recently identified as a relatively common source of genetic variation in the normal population. However its prevalence is poorly defined since it has been only studied systematically in one large-scale study and by using non optimal ad-hoc SNP array data analysis tools, uncovering rather large alterations (> 1 Mb) and affecting a high proportion of cells. Here we propose a novel methodology, Mosaic Alteration Detection-MAD, by providing a software tool that is effective for capturing previously described alterations as wells as new variants that are smaller in size and/or affecting a low percentage of cells.

Results

The developed method identified all previously known mosaic abnormalities reported in SNP array data obtained from controls, bladder cancer and HapMap individuals. In addition MAD tool was able to detect new mosaic variants not reported before that were smaller in size and with lower percentage of cells affected. The performance of the tool was analysed by studying simulated data for different scenarios. Our method showed high sensitivity and specificity for all assessed scenarios.

Conclusions

The tool presented here has the ability to identify mosaic abnormalities with high sensitivity and specificity. Our results confirm the lack of sensitivity of former methods by identifying new mosaic variants not reported in previously utilised datasets. Our work suggests that the prevalence of mosaic alterations could be higher than initially thought. The use of appropriate SNP array data analysis methods would help in defining the human genome mosaic map.

Rapid methods for targeted prenatal diagnosis of common chromosome aneuploidies

Improvements in non-invasive screening methods for trisomy 21 (Down syndrome) and other aneuploidies during the first and second trimester of pregnancy have radically changed the indications for prenatal diagnosis over the last decade. Consequently, there was a need for rapid tests for the detection of common chromosome aneuploidies resulting in the development of molecular methods for the rapid, targeted detection of (an)euploidies of the chromosomes 13, 18, 21 and the sex chromosomes. The analysis of large series of prenatal samples has shown that such tests can detect the great majority of chromosome abnormalities in prenatal diagnosis. This resulted in lively discussions on whether conventional karyotyping should remain the standard method for the majority of prenatal cases or can be replaced by rapid tests only. This review gives an overview of different aspects of the three most common tests for rapid, targeted prenatal detection of (an)euploidies, i.e. interphase fluorescence in-situ hybridisation (iFISH), quantitative fluorescent polymerase chain reaction (QF-PCR) and multiplex ligation-dependent probe amplification (MLPA).

Molecular diagnosis of Down syndrome using quantitative APEX-2 microarrays

OBJECTIVE

To develop a new rapid and high-throughput microarray-based prenatal diagnostic test for the detection of trisomy 21 (T21).

METHODS

The T21 arrayed primer extension-2 (APEX-2) assay discriminates between trisomy and euploid DNA samples by comparing the signal intensities of allelic fractions of heterozygous single nucleotide polymorphisms (SNPs) after APEX reaction. After preliminary validation using DNA samples from Down syndrome patients, we analyzed DNA samples from cultured and uncultured amniocytes and chorionic villus for 90 SNPs with high heterozygosity from the 21(q21.1q22.2) region. Differences in allelic ratios of heterozygous SNPs in normal and T21 individuals were verified by t-test.

RESULTS

Analysis of the T21 APEX-2 assay results revealed that 90 SNPs were sufficient for reliable discrimination between T21 and euploid DNA samples (P≤0.05 for one or both strands). Using 134 clinical samples from cultured or uncultured fetal cells, both the sensitivity and the specificity of the assay were 100%.

CONCLUSION

Our study provides a proof of principle demonstration of the use of the modified APEX-2 assay as a new, fast and reliable method for prenatal diagnosis of fetal T21.

Rapid identification and characterization of Penicillium marneffei using multiplex ligation-dependent probe amplification (MLPA) in paraffin-embedded tissue samples

Penicillium marneffei infection is a deadly disease and early diagnosis leads to prompt and appropriate antifungal therapy. To develop a sensitive method to diagnose P. marneffei infection, a multiplex ligation-dependent probe amplification (MLPA) assay was adapted. This method can rapidly and specifically detect P. marneffei DNA in cultured cells and paraffin-embedded tissue samples. Three pairs of probes were designed for amplifying the internally (intergenic) transcribed spacer (ITS) region of P. marneffei rRNA using a systematic phylogenetic analysis. These three probe sets produced three amplicons of 198, 166, and 152 bp, respectively, specific for P. marneffei. In contrast, there was only one 198 bp amplicon produced for Talaromyces stipitatus, and one 152 bp amplicon for P. funiculosum, T. intermedius and T. derxii. The probes did not amplify any other reference strains. An array of 40 P. marneffei strains isolated from human patients, bamboo rat, and the local environment was tested by using MLPA, and all were positively identified. Most importantly, P. marneffei in paraffin-embedded tissue specimens from infected human patients was positively amplified by MLPA. The sensitivity and specificity of the MLPA assay could be a useful tool for prompt diagnosis, pathogen characterization, and epidemiological studies of fungal infections.

Rapid and novel prenatal molecular assay for detecting aneuploidies and microdeletion syndromes

OBJECTIVES

To develop a targeted aneuploidy and microdeletion detection platform for use in the prenatal setting, to assess the integrity of the platform with a robust validation system, and to prospectively determine the performance of the platform under routine clinical conditions.

METHODS

To generate proxies for the various disorders assessed by the assay for analytical validation purposes, cells from ten microdeletion syndromes as well as from common aneuploidies were spiked into cleared amniotic fluid. Genomic DNA was isolated, labeled, and hybridized to microbeads that have been coupled to DNA derived from Bacterial Artificial Chromosome (BAC) from the relevant regions targeted by the array. Beads were read using a flow cytometric multiplex bead array detection system. In the prospective part of the study, 104 amniotic fluid samples were collected and analyzed.

RESULTS

All microdeletion syndromes and aneuploidies were validated in a blinded fashion. In the prospective study, the total number of readable samples was 101 of 104 (97%). All sample results were confirmed independently.

CONCLUSION

The bead array approach is a rapid and reliable test for detecting aneuploidies and microdeletions. This assay has the potential to provide the benefit of expanded molecular cytogenetic testing to pregnant women undergoing invasive prenatal diagnosis. This approach may be especially useful in parts of the world where cytogenetic personnel and facilities may be limited.

[New technologies for genome analysis: Which use in prenatal diagnosis]

Array-CGH emergence allowed important diagnosis progress, and a better care of patients in postnatal. So, there is a great temptation to use it also in prenatal diagnosis. The point of view objective is to make a rapid overview of cytogenetic diagnosis evolution during the last 50 years, and to show all questions raised by the use of array-CGH, and problems that could arise in prenatal diagnosis. While array-CGH just comes in genetic laboratories, new diagnosis approaches emerged like whole genome sequencing or non-invasive prenatal diagnosis. The 2nd objective will be to review all these techniques for a probably close future.

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.

Association of common copy number variants at the glutathione S-transferase genes and rare novel genomic changes with schizophrenia

Copy number variants (CNVs) are a substantial source of human genetic diversity, influencing the variable susceptibility to multifactorial disorders. Schizophrenia is a complex illness thought to be caused by a number of genetic and environmental effects, few of which have been clearly defined. Recent reports have found several low prevalent CNVs associated with the disease. We have used a multiplex ligation-dependent probe amplification-based (MLPA) method to target 140 previously reported and putatively relevant gene-containing CNV regions in 654 schizophrenic patients and 604 controls for association studies. Most genotyped CNVs (95%) showed very low (<1%) population frequency. A few novel rare variants were only present in patients suggesting a possible pathogenic involvement, including 1.39 Mb overlapping duplications at 22q11.23 found in two unrelated patients, and duplications of the somatostatin receptor 5 gene (SSTR5) at 16p13.3 in three unrelated patients. Furthermore, among the few relatively common CNVs observed in patients and controls, the combined analysis of gene copy number genotypes at two glutathione S-transferase (GST) genes, GSTM1 (glutathione S-transferase mu 1) (1p13.3) and GSTT2 (glutathione S-transferase theta 2) (22q11.23), showed a statistically significant association of non-null genotypes at both loci with an additive effect for increased vulnerability to schizophrenia (odds ratio of 1.92; P=0.0008). Our data provide complementary evidences for low prevalent, but highly penetrant chromosomal variants associated with schizophrenia, as well as for common CNVs that may act as susceptibility factors by disturbing glutathione metabolism.

The impact of rapid aneuploidy detection (RAD) in addition to karyotyping versus karyotyping on maternal quality of life

OBJECTIVE

To assess the impact of rapid aneuploidy detection (RAD) combined with fetal karyotyping versus karyotyping only on maternal anxiety and health-related quality of life.

METHODS

Women choosing to undergo amniocentesis were selected into group 1, i.e. receiving a karyotype result only (n = 132) or to group 2, i.e. receiving both the result of RAD and karyotyping (n = 181).

RESULTS

There were no systematic differences in time of RAD combined with karyotyping versus karyotyping only in terms of anxiety (P = 0.91), generic physical health (P = 0.76, P = 0.46), generic mental health (P = 0.52, P = 0.72), personal perceived control (P = 0.91) and stress (P = 0.13). RAD combined with karyotyping reduced anxiety and stress two weeks earlier compared to karyotyping only.

CONCLUSION

RAD as add-on to karyotyping reduces anxiety and stress in the short term but it does not influence overall anxiety, stress, personal perceived control, and generic mental and physical health when compared to a karyotype-only strategy.

Simultaneous Detection of Trisomies 13, 18, and 21 with Multiplex Ligation-Dependent Probe Amplification–Based Real-Time PCR

BACKGROUND

Trisomies 13, 18, and 21 account for the majority of chromosomal aneuploidies detected in prenatal diagnosis. Diagnosis of these trisomies relies mainly on karyotype analysis. Several molecular methods have been developed for trisomy detection, but performance or throughput limitations of these methods currently constrain their use in routine testing.

METHODS

We developed multiplex ligation-dependent probe amplification–based real-time PCR (MLPA/rtPCR) to simultaneously detect these 3 trisomy conditions with a single reaction. We applied the method to DNA isolated from 144 blinded clinical samples that included 32 cases of trisomy 21, 11 cases of trisomy 18, 1 case of trisomy 13, and 100 unaffected control samples; results were compared with karyotype analysis.

RESULTS

As judged by the results of the karyotype analysis, MLPA/rtPCR correctly detected all 44 cases of trisomy in the analysis of the blinded clinical samples. The method was able to detect a change in chromosome dosage as low as 1.2-fold.

CONCLUSIONS

This novel PCR-based technology simultaneously identified 3 types of trisomy in a single reaction and accurately detected trisomy with mosaicism, while reducing assay times and costs compared with conventional methods. The MLPA/rtPCR approach may have applicability in noninvasive prenatal diagnosis with maternal blood samples.

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.

[Molecular biology usefulness for rapid diagnosis of Down's syndrome and common aneuploidies]

OBJECTIVE

Trisomy of chromosome 13, 18, 21 and sex chromosome aneuploidies are the most common chromosomal abnormalities encountered in prenatal screening and are responsible for polymaformative syndrome associated with severe mental retardation. This high degree of morbidity justifies the prenatal diagnosis of these aneuploidies. Fetal nuchal translucency measurement and maternal serum biochemical marker assessment are the method of choice used for antenatal screening of aneuploidies. This prenatal screening leads to numerous maternal samplings followed by karyotyping which is cost-effective, time consuming, while results are generally returned between 2 and 3 weeks. Our study describes the research of common aneuploidies by molecular biology. We have used on one hand the MLPA kit (MRC Holland) based on amplification of specific DNA probes that hybridize with chromosomes 13, 18, 21, X, Y. On the other hand we have developed multiplex fluorescent PCR, amplifying microsatellite DNA sequences.

PATIENTS AND METHODS

We have evaluated the efficiency of these two techniques to detect chromosomal abnormalities by screening 400 amniotic fluids or chorionic villi samples obtained from pregnant women presenting a high risk of chromosomal aneuploidy.

RESULTS

We have found four trisomies 21, one trisomy 13, one monosomy 13, one trisomy 18, two triploidies, one trisomy X and one Klinefelter syndrome.

DISCUSSION AND CONCLUSION

In our study we have detected by molecular biology, in less than 48 h, 100% of common chromosomal aneuploidies without false positive or false negative results which could lead molecular biology as a method of choice for the rapid detection of common aneuploidies in addition to fetal karyotyping.

Microfluidic digital PCR enables rapid prenatal diagnosis of fetal aneuploidy

OBJECTIVE

The purpose of this study was to demonstrate that digital polymerase chain reaction (PCR) enables rapid, allele independent molecular detection of fetal aneuploidy.

STUDY DESIGN

Twenty-four amniocentesis and 16 chorionic villus samples were used for microfluidic digital PCR analysis. Three thousand and sixty PCR reactions were performed for each of the target chromosomes (X, Y, 13, 18, and 21), and the number of single molecule amplifications was compared to a reference. The difference between target and reference chromosome counts was used to determine the ploidy of each of the target chromosomes.

RESULTS

Digital PCR accurately identified all cases of fetal trisomy (3 cases of trisomy 21, 3 cases of trisomy 18, and 2 cases of triosmy 13) in the 40 specimens analyzed. The remaining specimens were determined to have normal ploidy for the chromosomes tested.

CONCLUSION

Microfluidic digital PCR allows detection of fetal chromosomal aneuploidy utilizing uncultured amniocytes and chorionic villus tissue in less than 6 hours.