Rapid determination of trisomy 21 from amniotic fluid cells using single-nucleotide polymorphic loci

Rapid prenatal diagnosis of aneuploidy for chromosomes 21, 18, 13, X, and Y using segmental duplication quantitative fluorescent PCR (SD-QF-PCR)

BACKGROUND

In our previous studies, the rapid diagnosis of aneuploidy has been achieved using the segmental duplication molecular markers-based SD-QF-PCR technique. However, it is also insufficient due to the drawbacks including less detection loci and incompetence in single-tube detection.

METHODS

In this paper, we developed 13 new segmental duplications as molecular markers, as well as designed 13 pairs of primers and 1 fluorescence-labeled universal primer, which could detect chromosome aneuploidies in one PCR tube.

RESULTS

Two hundred and thirty samples were detected using SD-QF-PCR, the samples were collected from individuals with trisomy 21 (n=16); trisomy 18 (n=4); trisomy 13 (n=3); 45,X (n=3); 47,XXY (n=2); 47,XYY (n=2); suspected mosaic 46,XX/46,XY (n=2); and unaffected controls (n=198).

CONCLUSIONS

The detection results of SD-QF-PCR were consistent with those of conventional karyotype analysis. SD-QF-PCR based on the newly developed segmental duplications enables the single-tube and multi-locus simultaneous detection on the number of chromosomes 13, 18, 21, X and Y. Therefore, this technique offers a new alternative for the diagnosis of chromosome aneuploidies.

Rapid and simultaneous detection of common aneuploidies by quadruplex real-time polymerase chain reaction combined with melting curve analysis

BACKGROUND

During the prenatal period, the number variation of chromosomes 13, 18, 21, X and Y accounts for more than 80% of the clinically significant chromosomal abnormalities diagnosed. Rapid tests for prenatal diagnosis of these abnormalities can improve pregnancy management and alleviate parental anxiety. Here, we present a molecular alternative method for detecting common aneuploidies.

METHODS

This method is based on co-amplification of segmental duplications located on two different chromosomes using a single pair of primers. Segmental duplications have a high degree of sequence identity, but have single-nucleotide differences in some regions. These sequence differences can be quantified using melting curve analysis of dual-labeled probes to estimate the relative dosages of different chromosomes. We designed two quadruplex real-time PCR assays to detect aneuploidies of chromosomes 13, 18, 21, X and Y.

RESULTS

We examined 75 aneuploid DNA samples and 56 unaffected DNA control samples using these two assays and correctly identified all samples. Four cases of unbalanced translocation were also accurately detected. The observed averaged ratio for each chromosomal disorder was similar to the theoretically expected value.

CONCLUSIONS

Our real-time assay is a robust, rapid, and easy to conduct technique for prenatal diagnosis of common aneuploidies, representing a competitive alternative for use in diagnostic laboratories.

Prenatal diagnosis of single gene disorders using amniotic fluid as the starting material for PCR

A rapid and inexpensive method for fetal genetic diagnosis using amniotic fluid (AF) as the starting material was demonstrated in this study.

Detection of sex chromosome aneuploidies using quantitative fluorescent PCR in the Hungarian population

BACKGROUND

Aneuploidies are the most frequent chromosomal abnormalities at birth. Autosomal aneuploidies cause serious malformations like trisomy 21, trisomy 18 and trisomy 13. However sex chromosome aneuploidies are causing less severe syndromes. For the detection of these aneuploidies, the "gold standard" method is the cytogenetic analysis of fetal cells, karyograms show all numerical and structural abnormalities, but it takes 2-4 weeks to get the reports. Molecular biological methods were developed to overcome the long culture time, thus, FISH and quantitative fluorescent PCR were introduced. In this work we show our experience with a commercial kit for the detection of sex chromosome aneuploidies.

METHODS

We analyzed 20.173 amniotic fluid samples for the period of 2006-2013 in our department. A conventional cytogenetic analysis was performed on the samples. We checked the reliability of quantitative fluorescent PCR and DNA fragment analysis on those samples where sex chromosomal aneuploidy was diagnosed.

RESULTS

From the 20.173 amniotic fluid samples we found 50 samples with sex chromosome aneuploidy. There were 19 samples showing 46, XO, 17 samples with 46, XXY, 9 samples with 47, XXX and 5 samples with 47, XYY karyotypes. The applied quantitative fluorescent PCR and DNA fragment analyses method are suitable to detect all abnormal sex chromosome aneuploidies.

CONCLUSIONS

Quantitative fluorescent PCR is a fast and reliable method for detection of sex chromosome aneuploidies.

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.

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.

Rapid diagnosis of fetal chromosomal abnormalities by fluorescence in situ hybridization

A Down-kór noninvazív, maternális szűrése során azonosított fokozott kockázatú esetekben a magzati aneuploidiák diagnosztizálására gyors molekuláris módszerek állnak rendelkezésre, ezek diagnosztikus értéke azonban vitatott. Célkitűzés: A szerzők a prospektív vizsgálattal adatokat kívántak szerezni arra a kérdésre, hogy milyen a megbízhatósága az egyik gyors tesztnek, az interfázis fluoreszcens in situ hibridizációnak (FISH). Módszerek: 2002. május és 2006. szeptember között az összes beérkezett 1279 magzati mintát megvizsgálták mind interfázis-FISH-sel, mind tenyésztést követő kariotipizálással. Eredmények: Interfázis-FISH-vizsgálattal 47 esetben (3,7%) észleltek többlet- vagy hiányzó szignált (32 esetben 21-triszómia, 15 esetben egyéb számbeli rendellenesség), ezek mindegyike megegyezett a tenyésztés során talált eredménnyel. Tizenkilenc esetben interfázis-FISH-sel normális eredményt kaptak, azonban a tenyésztés után nyert készítményekben rendellenesség mutatkozott (a 19-ből 12-ben kiegyensúlyozott transzlokáció). Tovább elemezve ezeket az eseteket, azt az eredményt kapták, hogy az 1279 terhességből 4 (0,3%) volt olyan (3 magzat szám feletti kromoszómával, 1 kiegyensúlyozatlan de novo transzlokációval), amelyből új mutációval rendellenes fenotípusú újszülött született volna, ha nem készül metafázisos vizsgálat. A 4-ből kettőben kóros magzati ultrahangjelek mutatkoztak. Következtetés: Noha további összehasonlító elemzésekre van szükség, a szerzők véleménye szerint a Down-szindróma szűrési protokolljában az interfázis-FISH kizárólagos alkalmazása a diagnosztikus fázisban elfogadható lehet, ha ezt csupán emelkedett anyai életkor és az anyai szérummarkerek alapján kiszűrt esetekben alkalmazzák. Amennyiben az indikáció familiáris transzlokáció vagy 2. trimeszterbeli kóros ultrahanglelet, a metafázisos készítmények értékelésére van szükség.

Reliable detection of Trisomy 21 using MALDI-TOF mass spectrometry

PURPOSE

Current diagnostic methods for chromosomal abnormalities rely mainly on karyotyping and occasionally fluorescent in situ hybridization or quantitative polymerase chain reaction. We describe an alternative molecular method for the detection of trisomy 21 involving mass spectrometric analysis of single nucleotide polymorphisms.

METHODS

In collaboration with Sequenom, Inc., 350 blinded amniotic fluid, amniocyte culture, chorionic villus, or amniotic fluid supernatant samples were analyzed for trisomy 21 using SNP analysis and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. Peak ratios were calculated for heterozygous genotypes and compared to control values generated from known euploid samples. An analytical algorithm using standard deviations from control values was used to determine the probability of a sample being affected or unaffected.

RESULTS

Seventy-three trisomy 21 samples from among the 350 blinded samples were correctly identified. There were no false-positive or false-negative results among the complete trisomy 21 samples. One sample exhibiting mosaicism for trisomy 21 was identified as being unaffected.

CONCLUSIONS

MALDI-TOF mass spectrometry is a robust and reproducible method for the detection of trisomy 21. Its amenability to high-throughput analysis and high degree of multiplexing make it a potential future diagnostic tool for the detection of other aneuploidies as well.

Detection of DeltaF508del using quantitative real-time PCR, comparison of the results obtained by fluorescent PCR

OBJECTIVE

Cystic fibrosis (CF) is the most common autosomal recessive genetic disorder in the Caucasian population. The molecular diagnosis is difficult since there are about 1,000 mutations in the CF transmembrane regulator gene. The DeltaF508del is the cause of the CF in 64% of the cases in Hungary. Our aim was to compare two polymerase chain reaction (PCR)-based method for the detection of DeltaF508del.

METHODS

One hundred and sixteen DNA samples isolated from different tissues (84 blood samples, 18 chorionic villus samples and 14 amniotic fluid samples) were involved in the study. Fluorescent PCR with DNA fragment analysis and quantitative real-time PCR with melting curve analysis were performed on the DNA samples for the detection of DeltaF508del.

RESULTS

Sixty-five healthy normal samples, 43 heterozygous samples, 6 DeltaF508del homozygous samples and 2 DeltaF508C homozygous samples were detected by using quantitative real-time PCR combined with melting curve analysis. The fluorescent PCR method did not detect the DeltaF508C mutation and these two samples were diagnosed as normal healthy ones.

CONCLUSIONS

The quantitative real-time PCR with melting curve analysis is a reliable and fast method for the detection of DeltaF508del. The results are ready in 1 h following the DNA isolation. The applied primer-probe set with melting curve analysis gives additional information for the presence of other mutations in the DeltaF508del region.