Rapid detection of chromosomes X and Y aneuploidies by quantitative fluorescent PCR

Privacy and ethical challenges of the Amelogenin sex test in forensic paternity/kinship analysis: Insights from a 13-year case history

The Amelogenin sex test included in forensic DNA typing kits has the potential to identify congenital conditions such as differences/disorders of sex development (DSD). It can also reveal mismatches between genotypic sex and gender marker in identity documents of transgender persons who obtained legal gender recognition. In a 13-year case history of paternity/kinship tests, involving n = 962 females and n = 1001 males, two mismatches between Amelogenin sex test (male) and gender marker (female), and three cases of chromosomal DSD (Klinefelter syndrome) were observed. The concrete risk of observing Amelogenin anomalies, their potential causes, and the context in which they occur (forensic, i.e. non-medical) mean that laboratory operators are called to strike a complex balance between privacy interests and individual health rights when providing preliminary information and reporting Amelogenin incidental findings. This case history argues for the need of a more responsible approach towards the Amelogenin sex test in the forensic community.

Detection of partial deletion and mosaicism using quantitative fluorescent polymerase chain reaction: Case reports and a review of the literature

Background

Aneuploidy of chromosomes 13, 18, 21, X, and Y can be detected by the quantitative fluorescence polymerase chain reaction (QF‐PCR) performed with short tandem repeat (STR) markers. Although QF‐PCR is designed to detect whole chromosome trisomy, the partial deletion or mosaic of chromosomes may also be detected.

Methods

Partial deletion or mosaic of chromosomes in three cases was detected by QF‐PCR. Karyotyping and chromosome microarray analysis(CMA) were performed. We further reviewed the clinical utility of QF‐PCR in detecting mosaicisms and deletions/duplications.

Results

QF‐PCR demonstrated structurally abnormal 21, X, and Y chromosomes in primary amniotic cells. QF‐PCR results in these three cases showed abnormal peak height/peak area, which could not be interpreted according to the kit instructions. QF‐PCR results suggested that there were partial deletions or mosaicism, which were confirmed by karyotyping and CMA.

Conclusion

In addition to detecting trisomies of whole chromosomes, QF‐PCR can also detect deletion and mosaicism of chromosomes 13, 18, 21, X, and Y, which could suggest the presence of copy number variants (CNVs). Additional testing with genetic technologies, such as karyotyping or microarrays, is recommended when an uninformative pattern is suspected.

High accuracy of quantitative fluorescence polymerase chain reaction combined with non-invasive pre-natal testing for mid-pregnancy diagnosis of common fetal aneuploidies: A single-center experience in China

Quantitative fluorescence polymerase chain reaction (QF-PCR) may be used as a mid-pregnancy test to confirm the diagnosis of common fetal aneuploidies, but its use is controversial. The present study aimed to determine the value of QF-PCR for diagnostic confirmation of karyotyping and the impact of parental origin and meiosis stage on the detected aneuploidy. The present prospective cohort study included pregnant women (age, 21-45 years; gestational age, 17-25 weeks) who consulted between May 2015 and December 2016. Women were screened and only consecutive high-risk individuals were included (n=428). QF-PCR analysis of amniocytes was performed. Karyotype analysis was considered the gold standard. Parental karyotyping was performed if the embryo exhibited any aneuploidy. GeneMapper 3.2 was used for data analysis. There were no false-negative or false-positive QF-PCR results, with 100% concordance with the karyotype. The aneuploidy distribution (n=105) was 68.6% for trisomy 21, 19.0% for trisomy 18, 7.6% for sex chromosome aneuploidy, 3.8% for trisomy 13 and 1.0% for 48,XXX,+18. Regarding trisomy 21, most cases (86.1%) were of maternal origin, 8.3% paternal and 6.5% undefined. Trisomy 18 was 88.2% maternal and 11.8% paternal. Maternal meiosis stage errors in trisomy 21 mainly occurred in meiosis I, while the origin of trisomy 18 exhibited similar proportions between meiosis I and II. The combination of non-invasive pre-natal testing and QF-PCR may become a rapid and effective method for fetal aneuploidy detection. QF-PCR may provide more genetic information for clinical diagnosis and treatment than karyotyping alone.

Rapid Prenatal Diagnosis of Aneuploidy Using Quantitative Fluorescence-PCR (QF-PCR)

Molecular cytogenetic aneuploidy testing for pregnant women at increased risk of chromosome abnormality leads to rapid reassurance for those with normal results and earlier decisions on pregnancy management in the case of abnormality. We tested 9080 prenatal samples using a one-tube QF-PCR test for trisomies 13, 18, and 21; the abnormality rate was 5.9%. There were no misdiagnoses for non-mosaic trisomy. A sex chromosome multiplex was developed that detects structural sex chromosome abnormalities as well as aneuploidies. The sex chromosome test was targeted at pregnancies (272) with specific abnormalities suggestive of Turner syndrome; 13.2% showed 45,X, confirmed by follow-up analysis.

Establishment of a 10-Plex Quantitative Fluorescent-PCR Assay for rapid diagnosis of sex chromosome aneuploidies

Sex chromosome aneuploidies occur commonly in the general population, with an incidence of 1 in 400 newborns. However, no tests specifically targeting sex chromosomes have been carried out in prenatal diagnosis or newborn screening, resulting in late recognition of these diseases. In this study, a rapid diagnostic method for sex chromosome aneuploidies was established using Quantitative Fluorescent-PCR (QF-PCR). Ten markers were included in one multiplex QF-PCR assay, including two sex determination genes (AMXY and SRY), five X-linked short tandem repeats (STRs; DXS1053, DXS981, DXS6809, DXS1187, and DXS8377), one X/Y-common STR (X22), and two autosomal STRs (D13S305 and D21S11). Retrospective tests of 70 cases with known cytogenetic results indicated that the 10-plex QF-PCR assay could well determine sex chromosome copy numbers by both allelic peak numbers and a sex chromosome dosage calculation with the autosomal STRs as internal controls. Prospective comparison with cytogenetic karyotyping on 534 cases confirmed that the 10-plex QF-PCR assay could be well employed for sex chromosome aneuploidy diagnosis in at least the Chinese Han population. This is the first QF-PCR test for the diagnosis of sex chromosome aneuploidies in the Chinese population. This test is superior to previous designs by including up to 8 sex-linked markers covering different parts of sex chromosomes as well as employing internal controls for copy number dosage calculation in a single PCR reaction. Due to simple technique and data analysis, as well as easy implementation within routine clinical services, this method is of great clinical application value and could be widely applied.

Aneuploidy detection in paraffin embedded tissue from products of conception by mini-STR genotyping

Autosomal trisomy is the most common genetic abnormality observed in pregnancy loss. We designed a panel of mini-short tandem repeats (mini-STRs) for aneuploidy detection in chromosomes 13, 16, 18 and 21 from fresh and formalin fixed, paraffin embedded (FFPE) samples from products of conception (POC). FFPE POCs with trisomy 13 (n = 6), trisomy 18 (n = 6), trisomy 21 (n = 12), 6 euploid for the chromosomes of interest and two trisomy 16 samples from fresh tissue were tested. Concordance between cytogenetics and genotyping was 100% for non-mosaic samples. Mini-STR genotyping is a viable method for targeted aneuploidy detection in low quality DNA samples.

QF-PCR: application, overview and review of the literature

Quantitative fluorescent polymerase chain reaction has been in diagnostic use in the UK for over 10 years and has proved to be a cost-effective, robust and accurate rapid prenatal test for common aneuploidies. Specific advantages include detection of triploidy, mosaicism and maternal cell contamination. Its application at our centre is described, with developments including stand-alone testing and improvements in strategies for the preparation and testing of chorionic villus biopsies.

The high incidence of STR D21S1446 homozygosity in Han and She populations living in South Eastern China

PURPOSE

This study investigated the allelic frequency of 4 short terminal repeats (STRs) in Han and She populations from eastern China.

METHODS

DNA samples from Han (N = 110) and She (N = 110) healthy subjects were amplified using PCR and primers specific for the STRs. D21S11 and D21S1446 (chromosome 21) and D18S865 and D18S535 (chromosome 18). The frequency and homozygocity of different STRs were evaluated.

RESULTS

For both populations, D21S11 and D18S535 were more polymorphic than D21S1446 and D18S865, and the D21S1446 1 allele was very common (48.6% and 55.0% for the Han and She groups, respectively).The Han and She groups significantly differed from one another in respect to the distribution of D21S11, D18S865, and D18S535 allelic frequency (all P -values ≤ 0.48) but had a similar allelic distribution for D21S1446 (P = 0.106). D21S1446 was found to be homozygous about 50% of the time which was significantly greater compared to the other STRs analyzed.

CONCLUSION

This study found that the Han and She differ genetically at 3 autosomal STRs located on chromosome 18 and 21. The STR D21S1146 was often homozygous within these groups, indicating it would be poor marker for analyzing trisomy within these populations.

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).

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

BACKGROUND

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.

METHODS

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.

RESULTS

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.

CONCLUSIONS

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.

Preimplantation genetic diagnosis of X-linked retinoschisis

The aim of this study was to perform preimplantation genetic diagnosis (PGD) for X-linked retinoschisis using multiple displacement amplification (MDA) for whole genome amplification and linked markers to the RS1 gene. The study evaluates the ability of MDA to amplify the whole genome directly from a single blastomere. MDA products were used for polymerase chain reaction analysis of two polymorphic markers flanking the RS1 gene and a new X/Y marker, X22, to sex embryos in an X-linked retinoschisis PGD programme. Two couples in whom the wives were carriers of the RS1 gene mutation (599G-->A), previously identified in their families, were subjected to two PGD cycles each. The main outcome measure was the ability to analyse single blastomeres for X-linked retinoschisis using MDA. As a result, the development of an MDA-PGD protocol for X-linked retinoschisis allowed for the diagnosis of 20 embryos in the four PGD cycles performed. These were biopsied on day 3 of culture and analysed. Eight embryos were affected males and two embryos were female carriers. In summary, three healthy female and four healthy male embryos, and a female carrier embryo, were transferred 48 h after biopsy. One single pregnancy was achieved. This report shows that the MDA technique is useful for overcoming the problem of insufficient genomic DNA in PGD. It also allows the simultaneous amplification of different targets to perform diagnosis of any known gene defect and sexing test by standard methods and conditions.

Preimplantation genetic diagnosis of X-linked adrenoleukodystrophy with gender determination using multiple displacement amplification

OBJECTIVE

To evaluate the use of multiple displacement amplification (MDA) for whole genome amplification in the preimplantation genetic diagnosis (PGD) of X-linked adrenoleukodystrophy.

DESIGN

MDA was used to amplify the whole genome directly from a single blastomere. MDA products were used for polymerase chain reaction (PCR) analysis of two polymorphic markers flanking the ABCD1 gene and a new X/Y marker, X22, to sex embryos in an X-linked adrenoleukodystrophy PGD program.

SETTING

Fertility and gynecology private center in Alicante, Spain.

PATIENT(S)

A couple in which the wife is a carrier of the ABCD1 gene mutation (676A-->C) that was previously identified in her family.

INTERVENTION(S)

MDA of single blastomere and PCR tests for PGD.

MAIN OUTCOME MEASURE(S)

The ability to analyze single blastomeres for X-linked adrenoleukodystrophy using MDA.

RESULT(S)

The development of an MDA-PGD protocol for X-linked adrenoleukodystrophy allowed for the diagnosis of five embryos. These were biopsied on day 3 of culture and analyzed. One embryo was an affected male and one embryo was a female carrier. Three healthy female embryos were transferred 48 hours after biopsy. Unfortunately, no pregnancy was achieved.

CONCLUSION(S)

The MDA technique is useful for overcoming the problem of insufficient genomic DNA in PGD and allows the simultaneous amplification of different targets to perform a diagnosis of any known gene defect and a sexing test by standard methods and conditions.

Application of QF-PCR for the prenatal assessment of discordant monozygotic twins for fetal sex

OBJECTIVE

To establish the utility of quantitative fluorescent polymerase chain reaction (QF-PCR) in order to determine the zygosity of multiple pregnancies, as well as to define the origin of the most frequent aneuploidies in amniotic fluid samples.

METHODS

We describe the case of a monochorionic (MC) diamniotic (DA) pregnancy with phenotypically discordant twins (nuchal cystic hygroma and non-immune hydrops in twin A and no anomalies in twin B). QF-PCR was performed for rapid prenatal diagnosis in uncultured amniocytes and subsequently in cultured cells. Polymorphic markers for chromosomes X, Y, 13, 18 and 21 were used for determination of zygosity as well as sex chromosome aneuploidy.

RESULTS

Twin A showed a Turner Syndrome (TS) mosaicism pattern by QF-PCR in uncultured amniocytes. The monozygotic origin of the pregnancy was determined. Interphase fluorescence in situ hybridization (I-FISH) in this sample showed a mosaicism X0/XY (83/17%). Cytogenetic analysis revealed a 45,X0 karyotype in twin A and a 46,XY karyotype in twin B.

CONCLUSIONS

QF-PCR is a reliable tool for the determination of the zygosity independently of the chorionicity and the fetal sex in case of twin pregnancy. Testing both direct and cultured cells can provide useful results for genetic counselling in chromosomal mosaicisms.

Rapid Detection of Sex Chromosomal Aneuploidies by QF-PCR: Application in 200 Men with Severe Oligozoospermia or Azoospermia

Klinefelter syndrome is the most common genetic cause of severe male factor infertility. Cytogenetic evaluation of metaphase chromosomes generally has a long turnaround time. We describe a reliable molecular genetic method that can be completed in 2 working days to identify the presence of any extra X chromosomes. The quantitative fluorescent (QF) 5-plex PCR includes the amplification of amelogenin, which is present on both sex chromosomes in a biallelic form, a polymorphic short tandem repeat (STR) on the pseudoautosomal region of X and Y (X22), two polymorphic X-specific STRs (DXS6803, DXS6809), and a Y-specific marker (SY134), in a single tube. The presence of an extra X chromosome is recognized either by a supernumerary peak or an increased peak area based on criteria we have developed. The application of the method on 200 patients resulted in the identification of 14 patients (7%) with Klinefelter syndrome or a variant form (2 SRY-positive 46,XX men), as well as an additional patient with 47,XYY karyotype. The QF-PCR method, along with Y chromosome microdeletion testing, can be used as a first-step genetic analysis in azoospermic or severely oligozoospermic patients for the rapid identification of sex chromosome aneuploidies.

Preimplantation genetic diagnosis of Marfan syndrome using multiple displacement amplification

OBJECTIVE

To evaluate the use of multiple displacement amplification (MDA) for whole-genome amplification in the preimplantation genetic diagnosis (PGD) of Marfan syndrome.

DESIGN

Multiple displacement amplification was used to amplify the whole-genome directly from a single cell. The MDA product was used for polymerase chain reaction (PCR) analysis of five different loci. At this point MDA was used to develop a PGD-Marfan syndrome program.

SETTING

Fertility and gynecology private center in Alicante, Spain.

PATIENT(S)

A couple in which the husband is affected by Marfan syndrome and carries a novel mutation in the FBN-1 gene.

INTERVENTION(S)

The MDA of single cells and PCR tests for PGD.

MAIN OUTCOME MEASURE(S)

Allele drop-out (ADO), amplification efficiency rates, and the ability to detect Marfan syndrome using MDA.

RESULT(S)

We report that isothermal whole-genome amplification from single cells allowed analysis of five different loci using standard conditions. The development of a MDA-PGD protocol for Marfan syndrome allowed for the diagnosis of seven embryos. These were biopsied on day 3 of culture and analyzed. Two healthy embryos were transferred 48 hours after culture, resulting in a singleton ongoing pregnancy and the birth of a healthy child.

CONCLUSION(S)

The MDA technique is useful for overcoming the problem of insufficient genomic DNA in PGD. The use of MDA as a universal step marks a new cycle for PGD as it allows for the diagnosis of any known gene defect by standard methods and conditions.

Rapid Prenatal Diagnosis by QF-PCR: Evaluation of 30,000 Consecutive Clinical Samples and Future Applications

Rapid prenatal diagnoses of major chromosome abnormalities can be performed on a large scale using highly polymorphic short tandem repeats (STRs) amplified by the quantitative fluorescent polymerase chain reaction (QF-PCR). The assay was introduced as a preliminary investigation to remove the anxiety of the parents waiting for the results by conventional cytogenetic analysis using amniotic fluid or chorionic cells. However, recent studies, on the basis of the analyses of several thousand samples, have shown that this rapid approach has a very high rate of success and could reduce the need for cytogenetic investigations. Its high efficiency, for example, allows early interruption of affected fetuses without the need of waiting for completion of fetal karyotype. The main advantages of the QF-PCR are its accuracy, speed, automation, and low cost that allows very large number of samples to be analyzed by few operators. Here, we report the results of using QF-PCR in a large series of consecutive clinical cases and discuss the possibility that, in a near future, it may even replace conventional cytogenetic analyses on selected samples.

Prenatal detection of a de novo Yqh-acrocentric translocation

OBJECTIVES

To identify the extra chromosomal material on 46,XX,21p+ for prenatal diagnosis.

DESIGN AND METHODS

Conventional cytogenetic studies using GTG (G bands by trypsin using Giemsa) and CBG (C bands by barium hydroxide using Giemsa) techniques were performed on chromosomes at metaphase obtained from cultured amniocytes and parental blood lymphocytes. Molecular cytogenetic techniques, QF-PCR (quantitative fluorescent polymerase chain reaction), FISH (fluorescent in-situ hybridization), and DA-DAPI (Distamycin A and 4,6-diamino-2-phenylindole) staining, were then used to clarify the extra material present on fetal chromosome 21 p.

RESULTS

The extra material on fetal chromosome 21 p has originated from Yqh, most likely at PAR2 (the secondary pseudoautosomal region). The karyotype should be 46,XX,der(21)t(Y;21)(q12;p13)de novo.ish der(21)t(Y;21)(q12;p13) (EST Cdy16c07+).

CONCLUSION

This case demonstrates the usefulness of molecular techniques in the investigation of rare chromosomal rearrangements.

Non-invasive diagnosis of fetal sex; utilisation of free fetal DNA in maternal plasma and ultrasound

Non-invasive prenatal diagnosis is now a clinical reality, using both early ultrasound and molecular DNA methods. Technical advances in the sensitivity of the polymerase chain reaction (PCR), coupled with the finding that significant levels of fetal DNA (ffDNA) are found in maternal plasma and serum, has enabled the ready detection of paternally inherited genes or polymorphisms. Routine maternal plasma-based genotyping is now available for the determination of fetal sex and RHD blood group status (Van der Schoot et al., 2003). This review touches briefly on the ultrasound diagnoses and then focuses on the application of free ffDNA for fetal sex determination, indicating the Y-chromosome targets exploited in this strategy and the merits of their utilisation.

Clinical, hormonal and cytogenetic evaluation of 46,XX males and review of the literature

The main factor influencing the sex determination of an embryo is the genetic sex determined by the presence or absence of the Y chromosome. However, some individuals carry a Y chromosome but are phenotypically female (46,XY females) or have a female karyotype but are phenotypically male (46,XX males). 46,XX maleness is a rare sex reversal syndrome affecting 1 in 20,000 newborn males. Molecular analysis of sex-reversed patients led to the discovery of the SRY gene (sex-determining region on Y). The presence of SRY causes the bipotential gonad to develop into a testis. The majority of 46, SRY-positive XX males have normal genitalia; in contrast SRY-negative XX males usually have genital ambiguity. A small number of SRY-positive XX males also present with ambiguous genitalia. Phenotypic variability observed in 46,XX sex reversed patients cannot be explained only by the presence or absence of SRY despite the fact that SRY is considered to be the major regulatory factor for testis determination. There must be some other genes either in the Y or other autosomal chromosomes involved in the definition of phenotype. In this article, we evaluate four patients with 46,XX male syndrome with various phenotypes. Two of these cases are among the first reported to be diagnosed prenatally.

Application of quantitative fluorescent PCR with short tandem repeat markers to the study of aneuploidies in spontaneous miscarriages

BACKGROUND

Aneuploidies involve approximately 80% of chromosomal anomalies found in spontaneous miscarriages. Since cytogenetic studies show high rates of failure, we have incorporated the quantitative fluorescent polymerase chain reaction (QF-PCR) technique to the study of numerical chromosome anomalies in miscarriages.

METHODS

Multiplex and simple QF-PCR assays have been performed on 160 miscarriage and 34 parental DNA samples analysing specific short tandem repeat (STR) markers for chromosomes 2, 7, 13, 15, 16, 18, 21, 22 and X. Cases successfully karyotyped were used as controls in our study.

RESULTS

While maternal contamination could be detected in such cases, a molecular result was obtained for 94% of miscarriages without a cytogenetic one. Thirty-six per cent of them were diagnosed with numerical chromosome anomalies. Parental origin of the extra chromosome and the error stage of meiosis could be also determined.

CONCLUSIONS

QF-PCR represents a useful and reliable tool to diagnose aneuploidies in spontaneous miscarriages. It provides information about parental and meiotic origin of anomaly, allowing an appropriate genetic counselling.

Detection of mosaicism for primary trisomies in prenatal samples by QF-PCR and karyotype analysis

OBJECTIVES

QF-PCR can be used to rapidly diagnose primary trisomy in prenatal samples. Our objectives were to estimate the prevalence of primary trisomy mosaicism for chromosomes 13, 18 or 21 in a cohort of prenatal samples, and to compare and contrast the detection of this mosaicism using both QF-PCR and karyotype analysis.

METHODS

Data was collated from all prenatal samples displaying mosaicism for a primary trisomy between June 2000 and March 2004. Levels of mosaicism were estimated and samples were categorised according to the cell population in which the mosaicism was detected.

RESULTS

In a total of 8983 samples, 18 samples (0.20%) displaying mosaicism were detected, including trisomy 13 (three samples), trisomy 18 (seven samples), trisomy 21 (seven samples) and mosaic triploidy (one sample). This included 7 amniotic fluid and 11 chorionic villus samples. Mosaicism was detected by QF-PCR in 12 samples and by karyotype analysis in 8 samples.

CONCLUSIONS

QF-PCR can detect mosaicism when the abnormal cell line contributes at least 15% of the whole sample. Use of both karyotype and QF-PCR analysis leads to the detection of more cases of mosaicism than either test alone.

Prenatal Diagnosis of Common Aneuploidies Using Multiplex Quantitative Fluorescent Polymerase Chain Reaction

OBJECTIVE

Prenatal diagnosis of foetal trisomies is usually performed by cytogenetic analysis. This requires lengthy laboratory procedures and it is expensive. Here, we report a retrospective study of quantitative fluorescent polymerase chain reaction (QF-PCR) for prenatal detection of trisomies 13, 18 and 21.

METHODS

QF-PCR was performed on a total of 447 amniotic fluids blindly analysed without any knowledge of the cytogenetic results and 43 samples with known karyotype. All samples were tested with at least 4 small tandem repeat markers specific for each chromosome 13, 18 or 21.

RESULTS

QF-PCR results on amniotic fluid were consistent with conventional cytogenetic data. QF-PCR detected 5 cases of trisomy 21, 2 cases of trisomy 18, 1 case of trisomy 13 and 1 case with Klinefelter's syndrome.

CONCLUSIONS

QF-PCR has proved to be very useful in clinical settings, since it allows the detection of major numerical disorders in a few hours after sampling and thus reduces parental anxiety.

Rapid prenatal diagnosis of common chromosome aneuploidies by QF-PCR. Assessment on 18 000 consecutive clinical samples

The quantitative fluorescent PCR (QF-PCR) assay, introduced during the last few years, allows prenatal diagnoses of common chromosome aneuploidies in a few hours after sampling. We report the first assessment of QF-PCR performed on a large cohort of 18,000 consecutive clinical specimens analysed in two different Centres. All samples were analysed by QF-PCR using several selected STR markers together with amelogenin and, occasionally, SRY for fetal sexing. Results were compared with those obtained by conventional cytogenetic analysis. In 17,129 tests, normal fetuses were detected by QF-PCR. No false positives were observed. All 732 cases of trisomy 21, 18, 13, triploidies, double trisomies as well as all but one fetuses with X and Y aneuploidies were correctly diagnosed. Chromosome mosaicism could also be suspected in several samples. In some cases of in vitro culture failures, QF-PCR was the only evidence of fetal X, Y, 21, 18 and 13 chromosome complement. QF-PCR proved to be efficient and reliable in detecting major numerical chromosome disorders. The main advantages of the molecular assay are its very low cost, speed and automation enabling a single operator to perform up to 40 assays per day. QF-PCR relieves anxiety of most parents within 24 h from sampling and accelerates therapeutic interventions in the case of an abnormal result. In countries where large scale conventional cytogenetics is hampered by its high cost and lack of technical expertise, QF-PCR may be used as the only prenatal diagnostic test.

Refined quantitative fluorescent PCR of Y-chromosome DNA sequences mosaics in Turner's syndrome patients—alternative to real-time PCR

BACKGROUND

Real-time polymerase chain reactions (PCRs) are the most frequently used techniques for gonosomal mosaics quantification. The primary aim of this work is to assess and optimize the refined technique of quantitative fluorescent polymerase chain reaction (RQF PCR) in the quantification of Y-chromosome sequences in gonosomal mosaics. The method was applied to the analysis of Y-chromosome sequences (amelogenin gene, AMELX/Y-loci) in peripheral lymphocytes and gonadal tissues in Y-positive Turner's syndrome (TS) patients.

METHODS

RQF PCR was used for molecular quantification, and fluorescent in situ hybridization (FISH) technique was used for comparison.

RESULTS

Based on a formulated calibration curve, DNA mosaics from six Y-positive patients and gonads from one patient were deducted. For calculation of rare mosaics, it is possible to take advantage of a new empirical formula. FISH results were comparable to RQF PCR.

CONCLUSION

The sensitivity of RQF PCR brings significant progress in the analysis of gonosomal aberrations. RQF PCR also finds applications in prenatal diagnostics of maternal contaminations of amniotic fluid and foetal DNA in maternal blood and analysis of chimerism in patients after bone marrow transplantation. The method is very convenient for determining the number of testis-specific protein, Y-linked (TSPY) gene repetitions.

Sex chromosome analysis in Turner Syndrome by a pentaplex PCR assay

In this study, we describe a pentaplex PCR to determine the parental origin of the X chromosome and the presence of mosaicism, via amplification of four polymorphic markers located along the X chromosome (DXS10011, DXS6807, HUMARA, DXS101) and the X-Y amelogenin marker, in 41 families having a daughter with Turner Syndrome. Our results confirmed the cytogenetic findings and we found that the parental origin of the single X chromosome to be maternal in 84% of cases.

Comparison between fluorescence in situ hybridization (FISH) and quantitative-fluorescent polymerase chain reaction (QF-PCR) for the detection of aneuploidies in single blastomeres

OBJECTIVES

The aim of our investigation was to compare the efficiencies of the fluorescence in situ hybridization (FISH) and the quantitative-fluorescent PCR (QF-PCR) methods for the detection of sexing and numerical chromosome disorders in single blastomeres collected from the same preimplantation human embryos.

METHODS

FISH analysis was carried out on 145 blastomeres from the 79 surplus embryos with probes specific for chromosomes 13, 18, 21, X, and Y. QF-PCR was performed with each one or two of the primers specific for the same chromosomes on 151 blastomeres from the same embryos obtained from patients undergoing IVF treatment.

RESULTS

Analyses were possible on 135 blastomeres (93%) by FISH and on 117 blastomeres (77%) by QF-PCR. Of 65 embryos, which could be analyzed by both methods, 20 embryos (31%) were diagnosed as abnormal.

CONCLUSION

The present study shows that FISH tests are more accurate than QF-PCR assays for the detection of numerical chromosome disorders when performed on single blastomeres.

Rapid prenatal diagnosis of aneuploidies and zygosity in multiple pregnancies by amniocentesis with single insertion of the needle and quantitative fluorescent PCR

OBJECTIVE

To investigate amniotic fluid (AF) samples retrieved in multiple pregnancies by single insertion of the needle, for rapid assessment of chromosome copy number, zygosity, and cross-contamination between fetuses, using Quantitative Fluorescent Polymerase Chain Reaction (QF-PCR) amplification of highly polymorphic microsatellite markers.

METHODS

Fifty-two multiple pregnancies were selected (47 twins, 5 triplets) and 108 samples of amniotic fluid were sampled between 12 to 20 weeks of gestation (mean 15.5) using the single-needle technique. Aneuploidy screening by QF-PCR amplification of short tandem repeats (STRs) on chromosomes X, Y, 21, 13, and 18 was carried out within 24 h of collection. Owing to the sampling procedure, the eventual presence of contamination between fetuses was also evaluated in every case.

RESULTS

Normal and aneuploid fetuses were readily identified by QF-PCR. Fetal reduction was made available, for trisomic fetuses, without further waiting for completion of fetal karyotyping. In twin gestations, the ultrasound examination of chorionicity was always in agreement with the molecular assessment of zygosity. Contamination between fetuses due to the sampling procedure with a single puncture was never observed.

CONCLUSION

Rapid prenatal diagnosis of aneuploidies by QF-PCR is a sensitive, efficient, and reliable assay. When applied in multiple pregnancies, it has the added value of allowing the assessment of zygosity in all cases, independently of chorionicity and fetal sex.

Development and targeted application of a rapid QF-PCR test for sex chromosome imbalance

OBJECTIVES

A QF-PCR test has been developed to diagnose sex chromosome imbalances in prenatal samples and has been applied to a diagnostic service.

METHODS

The test uses a PCR multiplex with eight primer pairs: six X-chromosome polymorphic markers, including two markers from Xp (a region not included in previously published sex chromosome aneuploidy tests), one polymorphic marker for a locus common to the long arms of the X and Y chromosomes, and the non-polymorphic amelogenin marker. Homozygosity for all X-chromosome markers and the absence of the Y-chromosome amelogenin marker is highly likely (907 : 1) to represent monosomy X (Turner syndrome), but interphase FISH is always used to confirm such a result.

RESULTS

Blind studies were carried out to validate the test and the first year of clinical use has been reported. Results are usually issued within one working day, and the test is more efficient than interphase FISH.

CONCLUSIONS

The sex chromosome imbalance test has been targeted to prenatal samples displaying a clear ultrasound indication consistent with Turner syndrome, and has also been used to identify fetal sex in pregnancies at risk of inheriting a sex-linked molecular disorder. No misdiagnoses were made. It is concluded that QF-PCR can rapidly and accurately diagnose sex chromosome status and imbalances, reducing maternal anxiety and aiding in efficient pregnancy management.

A comparative genomic hybridization study in a 46,XX male

OBJECTIVE

To identify Y chromosome material in an azoospermic male with an XX karyotype.

DESIGN

Case report.

SETTING

Faculty of medicine and Centro de Patologia Celular (CPC) medical center.

PATIENT(S)

A 33-year-old man with infertility.

INTERVENTION(S)

G-banding, fluorescence in situ hybridization (FISH), polymerase chain reaction (PCR), and comparative genomic hybridization (CGH).

MAIN OUTCOME MEASURE(S)

FISH for X and Y chromosomes, PCR for the SRYgene and amelogenin gene in the Xp (AMGX) and (AMGY), and losses or gains with CGH.

RESULT(S)

FISH analysis using X and Y chromosome-specific probes showed an X chromosome containing Y chromosome sequences on the top of the short arm; this Y chromosome region was not visible by conventional cytogenetic analysis. PCR amplification of DNA showed the presence of the sex-determining region of the Y chromosome (SRY) and the amelogenin gene in the pseudoautosomal boundary of the X chromosome (AMGX). CGH confirmed the presence of the chromosome region Yp11.2-pter and detected the presence of the two otherwise normal X chromosomes.

CONCLUSION(S)

The two Xpter (XPAR1) pseudoautosomal regions present in this XX male suggest the need to reevaluate XX males using CGH and PCR to characterize the clinical variability in XX males due to genes other than those located on the Y chromosome.

Prenatal diagnosis of common aneuploidies using quantitative fluorescent PCR

OBJECTIVE

Quantitative fluorescence-polymerase chain reaction (QF-PCR) has recently been used for the detection of common chromosomal aneuploidies in prenatal diagnosis. Here we describe our experience in prenatal diagnosis of 1100 samples.

METHODS

Extraction of DNA was performed from amniotic fluid, chorionic villus samples (CVS), fetal blood and fetal tissue samples, using a simple, rapid protocol. Fluorescent multiplex PCR products of single tandem repeats (STRs) located on chromosomes 13, 18, 21, X and Y were then analyzed on an automated laser fluorescent sequencer. All samples were analyzed with at least two polymorphic markers for chromosomes 13, 18 and 21 and one for the X chromosome. The amelogenin locus was used for sexing. Analysis was performed twice on affected samples. When miscellaneous results were obtained extra markers were used.

RESULTS

We evaluated the usefulness of different markers in the Greek population. In a total of 1100 samples, 25 chromosome aberrations were identified, including trisomy 13, 18 and 21, XYY, triploidies 69,XXX and 69,XXY and one Turner mosaic. All results but three were consistent with conventional cytogenetic analysis. One mosaic was missed. Most bloodstained samples were successfully analyzed.

CONCLUSION

Successful analysis of a large number of prenatal samples proves QF-PCR to be an efficient adjunct in routine prenatal diagnosis.

Enrichment, immunomorphological, and genetic characterization of fetal cells circulating in maternal blood

Fetal cells circulating in the peripheral blood of pregnant women are a potential target for noninvasive genetic analyses. They include epithelial (trophoblastic) cells, which are larger than peripheral blood leukocytes. We enriched circulating trophoblastic cells using the isolation by size of epithelial tumor cells (ISET) method. Peripheral blood was obtained at 11 to 12 weeks of pregnancy. Cells isolated by ISET were stained by hematoxylin and eosin or by immunohistochemistry. Large epithelial cells were microdissected and fetal cell identification was obtained by polymerase chain reaction with short tandem repeats and/or Y-specific primers. By analyzing only 2 ml of blood, we found a variable number (n = 1 to 7) of Y-positive cells (overall 15 of 23) in all of the six mothers carrying a male fetus. In contrast, none of the 26 cells isolated from seven mothers carrying a female fetus scored positive. Eleven cells were analyzed by using short tandem repeat-specific markers: six of them showed a fetal profile and five showed a maternal profile consistently with Y-specific results. Only one-fifth of the single cell DNA was used for fetal cell assessment, leaving enough material for further genetic tests. We also show that the ISET approach allows the performance of fluorescence in situ hybridization analyses and the detection of DNA point mutations in single microdissected cells. We conclude that this is a powerful approach to enrich circulating fetal cells and prove their fetal origin, and that it may have implications for noninvasive prenatal diagnosis of genetic disorders.

Development and implementation of a new rapid aneuploidy diagnostic service within the UK National Health Service and implications for the future of prenatal diagnosis

BACKGROUND

Prenatal diagnosis for chromosome abnormality is routinely undertaken by full karyotype analysis of chromosomes from cultured cells; pregnant women must wait on average 13-14 days for their results. Autosomal trisomies, which account for around 80% of significant abnormalities, can be detected by quantitative fluorescence (QF) PCR. We report on the development and implementation of this technique as the first such routine service within a diagnostic department of the UK National Health Service (NHS).

METHODS

We designed a "one-tube test" comprising four primer pairs for polymorphic tetranucleotide repeat sequences on chromosome 21, four primer pairs for sequences on chromosome 18, three primer pairs for sequences on chromosome 13, and one primer pair to identify the sex chromosomes. All prenatal samples received by our NHS diagnostic department between April, 2000, and April, 2001, were tested. After DNA extraction, PCR amplification was done and the products separated on a capillary-based genetic analyser; the results were interpreted with dedicated software. Follow-up karyotype analysis was done on all samples.

FINDINGS

1148 amniotic fluid samples, 188 chorionic villus samples, and 37 fetal tissue samples were tested; the amplification failure rate was zero with our current protocol. QF-PCR results were obtained and reported on 1314 (98%) of the prenatal samples; the remaining 22 (2%) were uninformative because of maternal-cell contamination. One case of mosaicism in a chorionic villus sample, and two cases indicating somatic expansion of a tetranucleotide repeat were found. No false positive or false negative results were obtained. The mean reporting time for the last 4 months of data collection was 1.25 working days.

INTERPRETATION

QF-PCR aneuploidy testing is an efficient and accurate technique for the detection of autosomal trisomies in prenatal samples. Implementation of this service has led to the rapid diagnosis of abnormalities and early reassurance for women with normal results.

Embryonic and fetal globins are expressed in adult erythroid progenitor cells and in erythroid cell cultures

The understanding of human hemoglobin ontogeny during development is of biological and clinical importance. Molecular and immunocytological techniques were used to study the expression of embryonic zeta (zeta), epsilon (epsilon), and fetal gamma (gamma) globin genes in newborn cord blood, peripheral blood from men, pregnant and non-pregnant women, and in vitro mononuclear cell cultures. We have shown that embryonic and fetal globin mRNA and peptides are expressed in cultured erythroid cells and in circulating blood cells from newborns, adult non-pregnant women and from men. The findings suggest that during erythroid cell differentiation in newborns and adults, there is a transient recapitulation of sequential globin chain expression as found during embryonic and fetal development. Furthermore, these findings underscore the need for caution in using embryonic and fetal globin chains as markers to identify erythroid cells of fetal origin in maternal circulation for prenatal diagnosis.

A large-scale evaluation of amnio-PCR for the rapid prenatal diagnosis of fetal trisomy

OBJECTIVE

Traditional chromosome preparation from amniotic fluid samples often involves lengthy culture procedures in order to obtain cells for analysis. Multiplex quantitative fluorescent polymerase chain reaction (PCR) is a new molecular biological technique capable of quantifying in-situ DNA without the need for cell culture. Our objective was to test the reliability of PCR using fetal DNA from amniotic fluid (amnio-PCR) for the rapid prenatal diagnosis of the common trisomies.

DESIGN

This was a large prospective study of 5000 amniocentesis specimens. Multiplex quantitative fluorescent PCR was performed specifically for short tandem repeat sequences within chromosomes 21, 18, 13, X and Y. All amniocentesis samples were subsequently analyzed by traditional karyotyping methods.

RESULTS

Amnio-PCR detected all 89 major autosomal trisomies in this cohort. Diagnosis of sex chromosome anomalies was accurate for cases involving first meiotic division nondisjunction. However, further markers were necessary to detect sex chromosome anomalies arising from second meiotic division nondisjunction, highlighting the importance of using specific markers that enable the quantification of both the X and the Y chromosomes simultaneously.

CONCLUSIONS

Rapid prenatal diagnosis of trisomies 21, 18, and 13 and the sex chromosome anomalies using amnio-PCR is a reliable technique that aids the clinical management of pregnancy. The speed of the methodology will help to minimize the period of parental anxiety in the wait for a diagnostic test result.

Prenatal diagnosis and genetic analysis of X chromosome polysomy 49, XXXXY

We report on the prenatal diagnosis, genetic analysis and clinical manifestations of a 49,XXXXY fetus. A 31-year-old, primigravida woman was referred for genetic counselling at 17 weeks' gestation with the sonographic findings of intrauterine growth retardation, generalized oedema, a large septated cystic hygroma colli measuring 5x4 cm, and abnormal posturing of the lower extremities. Quantitative fluorescent polymerase chain reaction (QF-PCR) with small tandem repeat (STR) markers specific for chromosome X and a pentanucleotide marker X22 for the Xq/Yq pseudoautosomal region PAR2 rapidly detected the X-chromosome polysomy from amniotic fluid cells. This abnormality appeared to arise from successive non-disjunction during maternal meiosis I and meiosis II. Cytogenetic analysis revealed a karyotype of 49,XXXXY. Our case shows that a 49,XXXXY fetus in the second trimester may demonstrate hydrops fetalis and a large septated cystic hygroma colli by prenatal ultrasound. Our case also shows that QF-PCR assays with sex chromosome specific STR markers provide rapid prenatal diagnosis of numerical sex chromosome aneuploidy as well as its genetic cause in fetal cystic hygroma.