Diagnosis Of Common Chromosomal Aneuploidies Research Articles

Assessment of multiple quantitative fluorescence PCR technique for common chromosome aneuploidies

Objective To evaluate the effectiveness of multiple quantitative fluorescence PCR (QF-PCR) as a rapid technique for prenatal diagnosis of common chromosome aneuploidies, in order to optimize the prenatal diagnosis and shorten the period of diagnosis. Methods Totally 731 amniotic fluid samples of pregnant subjects, who were referred to the Women′s Hospital School of Medicine Zhejiang University during August 2013 and September 2015, were analyzed with conventional karyotype and the QF-PCR technique by short tandem repeat(STR) markers to detect chromosomes 13, 18, 21, X and Y aneuploidies. There were 558 samples detected by single blind method, 173 samples detected by double blind method. Results All of the 731 amniotic fluid samples were tested in this study by QF-PCR and the results were compared to the conventional cytogenetic analysis results of the same sample. Totally 558 samples with single blind method detected 5 trisomy 21, 2 trisomy 18, 1 trisomy 13, 1(45, X), 1(47, XXY), 1(47, XYY), 1(47, XXX) and 1(69, XXX), 173 samples with double blind method detected 1 trisomy 21 and 1 trisomy 18. The rapid QF-PCR assay was successful to detect all aneuploidies involving chromosomes 21, 18, 13, X and Y in prenatal diagnosis, which were verified by chromosome karyotype analysis. The results of QF-PCR method were compared with the results of chromosome karyotype analysis, the positive rate was 15/16, the negative rate was 100% (715/715). Non chimeric chromosome abnormality detection rate was 15/15. Conclusions The multiple QF-PCR was a reliable method of detecting common chromosome aneuploidies for rapid prenatal diagnosis. As an important supplement of karyotype analysis, it was of great significance to optimize and improve the prenatal diagnosis system, and might provide more appropriate diagnostic methods for pregnant women. (Chin J Lab Med, 2017, 40: 50-54) Key words: Aneuploidy; Chromosome aberrations; Polymerase chain reaction; Prenatal diagnosis; Microsatellite repeats

Genetic variations of 21 STR markers on chromosomes 13, 18, 21, X, and Y in the south Iranian population

Quantitative fluorescent polymerase chain reaction (QF-PCR), in recent years, has been accepted as a rapid, high throughput, and sensitive method for prenatal diagnosis of common chromosomal aneuploidies. Since short tandem repeats (STRs) are the cornerstone of QF-PCR technique, selection of the most polymorphic STR markers is an essential step for a successful QF-PCR assay. The genetic variation parameters of each STR marker differ among different populations. In this study, we investigated the size, frequency, heterozygosity, polymorphism information content, power of discrimination, and other genetic polymorphism data for 21 STR markers on chromosomes 13, 18, 21, X, and Y in 1000 amniotic fluid samples obtained from south Iranian women. Our results showed that all the 21 STR markers are highly polymorphic and informative in our population. The heterozygosity, polymorphism information content, and power of discrimination of the markers were 62-91.1%, 0.61-0.91, and 0.830-0.976, respectively. The locus D18S386 was the most polymorphic STR, while the locus DXYS218 was the least polymorphic STR among all the studied STRs. The present study has provided extensive data regarding the efficiency of the 21 STR markers for diagnosis of chromosomes 13, 18, 21, X, and Y aneuploidies in the south Iranian population.

A new marker set that identifies fetal cells in maternal circulation with high specificity.

Fetal cells from the maternal circulation (FCMBs) have the potential to replace cells from amniotic fluid or chorionic villi in a diagnosis of common chromosomal aneuploidies. Good markers for enrichment and identification are lacking. Blood samples from 78 normal pregnancies were used for testing the marker-set CD105 and CD141 for fetal cell enrichment. Fetal cell candidates were subsequently stained by a cocktail of cytokeratin antibodies, and the gender of the fetal cells was explored by fluorescence in situ hybridization (FISH) of the X and Y chromosomes. Fetal cell candidates could be detected in 91% of the samples, and in 85% of the samples, it was possible to obtain X and Y chromosomal FISH results for gender determination. The concordance between gender determined by FISH on fetal cells in maternal blood and gender found at birth reached 100% if three or more fetal cells with FISH signals could be found in a sample. The marker set identifies fetal cells with specificity high enough to make cell-based noninvasive prenatal diagnosis realistic.

Application of multiple quantitative fluorescence polymerase chain reaction approach for rapid prenatal diagnosis of common chromosome aneuploidies

To assess the value of multiple quantitative fluorescence polymerase chain reaction (QF-PCR) approach for rapid prenatal diagnosis of common chromosomal aneuploidies. A total of 4760 amniotic samples from 4649 pregnant women were analyzed with QF-PCR for 21, 18, 13, X and Y aneuploidies, and the results were compared with those of karyotype analysis. The overall success rate for QF-PCR was 98.4%. All the 48 cases of 21, 18, 13, X and Y aneuploidies (including 2 case of 46, XY, rob(13:21), +21; 4 trisomy 21 in 4 twins) were detected by QF-PCR, with the overall sensibility and specificity both reaching 100%. One mosaicism of trisomy 21 and 4 mosaicisms of sex chromosome (1 misdiagnosed by karyotype analysis) were also detected by QF-PCR. Four mosaicisms of sex chromosome were verified as missed diagnosis. All the 64 cases failed by karyotype analysis were successfully analyzed by the QF-PCR approach. The total consistency rate for QF-PCR and karyotyping has reached 98.3%. QF-PCR approach can diagnose 21, 18, 13 as well as X and Y aneuploidies within 48 hours, in addition with a portion of mosaicisms. It is an efficient and reliable method for rapid prenatal diagnosis, and therefore provide an important supplement for karyotype analysis.

QF-PCR as a molecular-based method for autosomal aneuploidies detection

Objectives: The currently available methods for rapid prenatal diagnosis of common chromosomal aneuploidies are either Interphase-Fluorescence in Situ Hybridisation (I-FISH) or Quanti- tative Fluorescent Polymerase Chain Reaction (QF-PCR). QF-PCR represents a rapid, high throughput, cost-effective alternative for Interphase-FISH. The objective of the study was to evaluate the performance of QF-PCR, as a molecular-based technique for the detection of chromosome 21, 18 and 13 copy numbers. Study design: A retrospective cohort of 163 samples referred for screening of common chromosomal aneuploidies was blindly tested for chromosome 21, 18 and 13 copy numbers using QF-PCR and the results were compared with those of conventional cytogenetic analysis. Results: QF-PCR demonstrated optimal sensitivity and specificity (100%) for non mosaic trisomies. QF-PCR was able to consistently detect maternal cell contamination and mosaic trisomies when the trisomic cell line was present at an adequate level (23% or more). However, QF-PCR was unable to detect chromosomal rearrangements for which the primers were not designed. Conclusion: QF- PCR proved its superior performance as a molecular-based method for autosomal aneuploidy detection concerning both sensitivity and specificity.

Establishment of multiple quantitative fluorescent polymerase chain reaction assay and its application in rapid prenatal diagnosis of common chromosome aneuploidies

To establish the multiple quantitative fluorescent polymerase chain reaction (QF-PCR) assay and evaluate its clinical application in prenatal diagnosis. Totally 170 samples were collected between May 2008 and July 2009 in prenatal center of Peking Union Medical College Hospital; 123 of them were amniotic fluid, 9 were chorionic villous samples, 20 were fetal blood and 18 were villi from aborted fetuses. All samples were from women of Han nationality, with mean age of (34.1 ± 4.6) years old, and with mean gestational age of (19.6 ± 1.0) weeks. Cytogenetic cultures and karyotyping were made to every sample. Genomic DNA was extracted from the samples. The sequences of twenty short tandem repeat (STR) markers were designed according to the GenBank and references, including 6 STR markers in chromosome 21, 4 in chromosome 18, 4 in chromosome 13, 4 in chromosome X, 1 in chromosome Y and 1 universal marker in both X and Y chromosome. Each sample was amplified by two sets of multiple QF-PCR, which included 4 STR markers in each of 21, 18, 13 and sex chromosomes. If the result was uninformative, the third set of another 4 STR markers was added. (1) Karyotyping. Cytogenetic analysis were made for all the 170 samples, 151 (89%) of which were normal, and 19 (11%) were abnormal. (2) QF-PCR assay. 167 (98%) samples were detected by QF-PCR. The results were obtained within 2 - 3 days after sampling. 134 samples were proved normal by QF-PCR, which was consistent with karyotyping. Among the 19 abnormal karyotype samples, 18 were detected as abnormal(eight were 21-trisomy, three were 18-trisomy)by QF-PCR. Among the 167 samples, 150 (90%) were detected using the first and second set of STR mixtures, and 3 (2%) were detected when the third set of STR was added. The remain 14 (8%) were uninformative. (3) The diagnostic efficiency of QF-PCR. The sensitivity of QF-PCR in prenatal diagnosis of common aneuploidities was 95%, the specificity, the false positive rate, the false negative rate, the positive predictive value and negative predictive value were 100%, 0, 5%, 100% and 99%, respectively. (4) Autosome and sex chromosome detection by QF-PCR. Among all the STR markers, D21S1270 and D21S1411 had the highest heterozygosities in chromosome 21, and DXS8377 had the highest in sex chromosome. The amplifications were stable. Multiple QF-PCR assay is a valid alternative in rapid prenatal diagnosis of common chromosome aneuploidies. With high accuracy, it can be used for numerous sample test in large-scale laboratories.

Validation of QF-PCR for Rapid Prenatal Diagnosis of Common Chromosomal Aneuploidies in Korea

Sung-Hee Han, M.D., Jae-Song Ryu, M.S., Jeong-Wook An, M.T., Ok-Kyoung Park, M.T., Hye-Ryoung Yoon, M.D., Young-Ho Yang, M.D. and Kyoung-Ryul Lee, M.D.. J Genet Med 2010;7:59-66. https://doi.org/10.5734/JGM.2010.7.1.59

Rapid prenatal diagnosis of common chromosome aneuploidies by QF‐PCR, results of 9 years of clinical experience

Despite being deliberately targeted to common chromosome aneuploidies, the rapid quantitative fluorescent polymerase chain reaction (QF-PCR) tests can detect the majority of chromosome abnormalities in prenatal diagnosis. The main advantages of this assay are low cost, speed and automation allowing large-scale application. We developed a QF-PCR test that was applied on 43 000 clinical samples reporting results in 24 h. Most common indications were biochemical risk (32%) and advanced maternal age (30%). Samples were also tested by cytogenetic analysis and the results compared. Aneuploidies involving chromosomes 21, 18, 13, X and Y were detected with 100% specificity. Several cases of partial trisomies and mosaicism were also identified. Overall 95% of clinically relevant abnormalities were readily detected and termination of affected pregnancies could be performed without waiting for the cytogenetic results. Our study supports the possibility of reducing the load of prenatal cytogenetic tests if the pregnancies are carefully monitored by non-invasive screening. In case of abnormal QF-PCR results, medical action can be taken within few hours from sampling. In cases of negative QF-PCR results, cytogenetic analyses might only be performed for fetuses with ultrasound abnormalities. In countries where large-scale cytogenetic tests are not available, QF-PCR may be used as the only prenatal diagnostic procedure.

Rapid prenatal diagnosis of common chromosome aneuploidies by QF-PCR: Evaluation of two in vitro diagnostic test kits (Chromoquant and Aneufast)

Rapid prenatal diagnosis of common aneuploidies (21, 18, 13 trisomy and sex chromosome) can be performed by the Quantitative Fluorescence Polymerase Chain Reaction (QF-PCR) of Short Tandem Repeat (STR). The main advantages of the QF-PCR are its rapidity (24–48 h), accuracy and automation. Furthermore, its provides an additional and useful contribution for the karyotype analysis. Recently, three kits are commercially available for the in vitro diagnosis of common chromosome aneuploidies by QF-PCR. In this study we have evaluated two of these kits: Chromoquant Version 2 and Aneufast.

Rapid prenatal diagnosis of common chromosome aneuploidies by QF-PCR: large scale clinical application and future implications

Rapid prenatal diagnosis of common chromosome aneuploidies by QF-PCR: large scale clinical application and future implications

Strategies for the rapid prenatal diagnosis of chromosome aneuploidy.

Rapid diagnosis of common chromosome aneuploidies in raised risk pregnancies, usually prior to full karyotype analysis, is now carried out in a number of European genetic centres; several techniques for detecting genomic copy number changes have been described. Prenatal diagnosis of genetic disease requires accurate and robust assays; the invasive procedures are associated with a risk of pregnancy loss and an abnormal result may lead to termination of the pregnancy. The testing of prenatal material (amniotic fluid, chorionic villi or, more rarely, fetal blood) is associated with specific problems, including the quality and quantity of the tissue and difficulties of interpretation due to phenomena such as maternal cell contamination and mosaicism. In addition, there are 24-h, high-throughput demands on centres offering such a service. The extent to which existing and proposed strategies, including different PCR-based assays, a multiplex ligation-dependent probe amplification approach, and microarrays, fulfil the requirements of rapid prenatal testing is discussed. In the past 3 years, we have tested 7720 prenatal samples for trisomies 13, 18 and 21 using a quantitative fluorescence-PCR (QF-PCR) approach. The abnormality rate was 5.7%. There were no misdiagnoses for nonmosaic trisomy, the amplification failure rate was 0.09% of samples, and 97% of samples received a report on the working day following sample receipt. Maternal cell contamination and mosaicism were also detected. Our data recommend a QF-PCR approach as the current method of choice for rapid aneuploidy testing.

Rapid prenatal diagnosis of Down Syndrome using quantitative fluorescent PCR in uncultured amniocytes.

Rapid prenatal diagnosis of common chromosome aneuploidies have been successful through quantitative fluoresent PCR (QF-PCR) assays and small tandem repeat (STR) markers. The purpose of our study was to investigate the clinical feasibility for rapid prenatal detection of Down syndrome using the quantitative fluorescent PCR in uncultured amniocytes. DNA was extracted from uncultured amniotic fluid of normal karyotype (n=200) and of Down syndrome (n=21). It was amplified using QF-PCR with four STR markers located on chromosome 21. Among normal samples, the ranges of diallelic peaks for at least one STR marker were 1.0-1.3 for D21S11, 1.0-1.4 for D21S1411 and 1.0-1.5 for D21S1270. Down syndrome samples showed trisomic triallelic patterns or trisomic diallelic patterns. The sensitivity, specificity, and efficiency of the assay for detecting Down syndrome were 95.4%, 100%, and 99.5%, respectively. Rapid prenatal diagnosis of Down syndrome using QF-PCR is a reliable technique that aids clinical management of pregnancy.

Two years' prospective experience using fluorescencein situ hybridization on uncultured amniotic fluid cells for rapid prenatal diagnosis of common chromosomal aneuploidies

A probe was generated from the YAC clone 831B9 that was suitable for the prenatal detection of trisomy 21 using fluorescence in situ hybridization (FISH). This probe was initially tested on a series of 650 unselected amniotic fluid samples prior to the karyotype being available. 630 were correctly identified as having two copies and 13 samples were correctly scored as having three copies of chromosome 21. Seven samples failed to produce a result. A trial was then initiated, reporting to clinicians the interphase FISH results before cytogenetic analysis had been performed. During the first 18 months of this trial 1504 samples were tested: 1467 were correctly identified as disomic and 35 samples were correctly scored as trisomic for chromosome 21. Two samples failed to produce a result. A chromosome 18 specific probe (LI.84) was employed where there was a relevant clinical indication (181 samples) and 10 samples were correctly scored as having three copies of chromosome 18. Thus, this approach appears to be reliable and is popular with both clinicians and patients due to the speed of the result. However, it does not replace chromosomal analysis on cultured cells, which detected a range of abnormalities besides the trisomies and triploidies detected by FISH.

Two years' prospective experience using fluorescence in situ hybridization on uncultured amniotic fluid cells for rapid prenatal diagnosis of common chromosomal aneuploidies

Two years' prospective experience using fluorescence in situ hybridization on uncultured amniotic fluid cells for rapid prenatal diagnosis of common chromosomal aneuploidies