Common Aneuploidies Research Articles

Fast Quantitative Real-Time PCR-Based Screening for Common Chromosomal Aneuploidies in Mouse Embryonic Stem Cells

SummaryChromosomal integrity has been known for many years to affect the ability of mouse embryonic stem cells (mESCs) to contribute to the germline of chimeric mice. Abnormal chromosomes are generally detected by standard cytogenetic karyotyping. However, this method is expensive, time consuming, and often omitted prior to blastocyst injection, consequently reducing the frequency of mESC-derived offspring. Here, we show a fast, accurate, and inexpensive screen for identifying the two most common aneuploidies (Trisomy 8 and loss of chromosome Y) in genetically manipulated mESCs using quantitative real-time PCR (qPCR). Screening against these two aneuploidies significantly increases the fraction of normal mESC clones. Our method is extremely sensitive and can detect as low as 10% aneuploidy among a large population of mESCs. It greatly expedites the generation of mutant mice and provides a quick tool for assessing the aneuploidy percentages of any mESC line.

Identification of Molecules with Altered Expression in the Brain of Mouse Model for Down Syndrome by Comprehensive Analyses

Down syndrome (DS), caused by triplication of human chromosome 21, is the most common aneuploidy. A mouse model of DS may be useful for the investigation of DS pathophysiology. Ts1Cje mouse, an established DS mouse model, is widely used in DS research. It carries a trisomic segment of mouse chromosome 16 that contains a syntenic region to human chromosome 21. The brain of the Ts1Cje mouse has been analyzed morphologically and biochemically to elucidate DS pathophysiology. We have also demonstrated some abnormal phenotypes of this mouse model, such as enlarged brain ventricles, reduced embryonic and adult neurogenesis, and increased lipid peroxidation. Elucidating the underlying molecular mechanisms in the Ts1Cje mouse may improve understanding of the etiology of the phenotypic abnormalities of DS, including cognitive impairment and developmental retardation, and aid in development of therapeutic strategy. High-throughput gene and protein expression analyses, such as transcriptomics and proteomics, are useful for identification of molecules associated with the development of DS symptoms. In this review, alteration of molecular expression in the brain of a DS mouse model is highlighted, and possible molecular mechanisms underlying DS phenotypic abnormalities such as cognitive impairment and developmental retardation are discussed.

The prevalence of non-detectable chromosomal abnormalities by QF-PCR in amniocentesis for certain referral indications: experience at a mainland Chinese hospital

To study the prevalence of non-detectable chromosomal abnormalities by quantitative fluorescent polymerase chain reaction (QF-PCR) in a Chinese population referred for amniocentesis. The karyotype results were reviewed in 8,466 amniotic fluid cultures performed for positive fetal Down syndrome screening or advanced maternal age between January 2002 and June 2012. The karyotype results were classified as detectable or not detectable by QF-PCR, using the assumption that all tests were conducted by this rapid molecular method. Of the 8,466 karyotypes obtained, 211 abnormal karyotypes were found (2.5%). Out of these, 168 cases of common aneuploidies were identified by QF-PCR, and 43 cases of chromosomal abnormalities were missed. The 43 cases missed by QF-PCR included 31 cases predicted to confer no increased risk and 12 with a potential clinical significance. When QF-PCR shows a normal result, the overall residual risk is 0.1% for any clinically significant chromosomal abnormality. A normal QF-PCR result predicts a very low residual risk for patients who are referred solely for an increased risk of a common trisomy.

Mosaicos cromosómicos en vellosidad corial

IntroductionThe study of chorionic villus samples comprises performing two cell cultures that may not have matching results. These discrepancies may be due to cytogenetic mosaics of in vivo or in vitro origin. This study included analysing the karyotypes in mosaics, associated with the cell culture and cytogenetic results. Material and methodsProspective study based on the analysis of 2,360 chorionic villus samples and 510 spontaneous abortion samples. Two cultures were routinely performed on the prenatal samples (short and long), as well as on the abortion samples. ResultsThe success rate was 99.9% in the prenatal group, and 87.1% in the abortion group. The percentage of chromosomal anomalies in the prenatal group was 10.6%, with the common aneuploidies (trisomy 13, 18, and 21) being the most frequent. In the abortions group there 55.1% anomalies, with uncommon aneuploidy the most frequent. The percentage of mosaicism in the prenatal group was 3.1%, and it was 6.8% in the abortion group. The confined placental mosaicism type ii was the most frequent. ConclusionsFor the study of the mosaicism in chorionic villi samples the best strategy is to perform 2 prenatal samples cultures in parallel, and 3 abortion samples cultures. Given the risk to the mother and child using this invasive test, it is our duty to give the most comprehensive cytogenetic results achievable.

Slovenian Five-Year Experiences with Rapid Prenatal Diagnosis of Common Chromosome Aneuploidies Using Quantitative-Fluorescence Polymerase Chain Reaction

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. 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. 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. 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.

Noninvasive prenatal testing of fetal aneuploidies by massively parallel sequencing in a prospective Chinese population

The recently developed noninvasive prenatal test (NIPT) presents a new era of prenatal screening. Previously reported studies were primarily conducted on high-risk and advanced maternal age (AMA) pregnancies. We sought to evaluate the performance of NIPT for detection of fetal aneuploidies in a Chinese cohort of women younger than 35 years old in a prospective clinical setting. Maternal plasma samples were sequenced to identify the aneuploidies. The results were compared against the serum screening results and validated by karyotyping through invasive procedures and birth follow-up. A total of 1916 prospectively collected maternal plasma samples were sequenced, among which 73 samples (3.8%) failed the sequencing quality control. Birth follow-up missed 111 samples (5.8%). The remaining 1741 samples were analyzed. Sequencing reported 15 aneuploidy samples, including all the T21, T18, and T13 cases. Sequencing performed moderately in identifying sex chromosome aneuploidies, detecting two out of four samples, with a specificity of 99.88% (95% CI 99.53% to 99.98%). Noninvasive prenatal detection of common fetal aneuploidies is a more sensitive and specific method than triple maternal serum screening. It has a remarkable low false positive rate and is applicable to women younger than 35 years old.

The impact of maternal plasma DNA fetal fraction on next generation sequencing tests for common fetal aneuploidies

Maternal plasma contains circulating cell-free DNA fragments originating from both the mother and the placenta. The proportion derived from the placenta is known as the fetal fraction. When measured between 10 and 20 gestational weeks, the average fetal fraction in the maternal plasma is 10% to 15% but can range from under 3% to over 30%. Screening performance using next-generation sequencing of circulating cell-free DNA is better with increasing fetal fraction and, generally, samples whose values are less than 3% or 4% are unsuitable. Three examples of the clinical impact of fetal fraction are discussed. First, the distribution of test results for Down syndrome pregnancies improves as fetal fraction increases, and this can be exploited in reporting patient results. Second, the strongest factor associated with fetal fraction is maternal weight; the false negative rate and rate of low fetal fractions are highest for women with high maternal weights. Third, in a mosaic, the degree of mosaicism will impact the performance of the test because it will reduce the effective fetal fraction. By understanding these aspects of the role of fetal fraction in maternal plasma DNA testing for aneuploidy, we can better appreciate the power and the limitations of this impressive new methodology.

Noninvasive prenatal detection of sex chromosomal aneuploidies by sequencing circulating cell‐free DNA from maternal plasma

Whole-genome sequencing of circulating cell free (ccf) DNA from maternal plasma has enabled noninvasive prenatal testing for common autosomal aneuploidies. The purpose of this study was to extend the detection to include common sex chromosome aneuploidies (SCAs): [47,XXX], [45,X], [47,XXY], and [47,XYY] syndromes. Massively parallel sequencing was performed on ccf DNA isolated from the plasma of 1564 pregnant women with known fetal karyotype. A classification algorithm for SCA detection was constructed and trained on this cohort. Another study of 411 maternal samples from women with blinded-to-laboratory fetal karyotypes was then performed to determine the accuracy of the classification algorithm. In the training cohort, the new algorithm had a detection rate (DR) of 100% (95%CI: 82.3%, 100%), a false positive rate (FPR) of 0.1% (95%CI: 0%, 0.3%), and nonreportable rate of 6% (95%CI: 4.9%, 7.4%) for SCA determination. The blinded validation yielded similar results: DR of 96.2% (95%CI: 78.4%, 99.8%), FPR of 0.3% (95%CI: 0%, 1.8%), and nonreportable rate of 5% (95%CI: 3.2%, 7.7%) for SCA determination Noninvasive prenatal identification of the most common sex chromosome aneuploidies is possible using ccf DNA and massively parallel sequencing with a high DR and a low FPR.

Fetal aneuploidy detection by maternal plasma DNA sequencing: a technology assessment

The American College of Obstetricians and Gynecologists currently recommends that all pregnant women be offered screening for chromosomal abnormalities, regardless of maternal age. Traditional screening tests have detection rates ranging from 85% to 90% and false-positive rates of 3% to 5%. A woman with an abnormal noninvasive test is offered a diagnostic test, but diagnostic tests are associated with a risk of pregnancy loss. Recently, analysis of cell-free fetal DNA (cffDNA) in maternal blood has been shown to have potential for the accurate detection of some of the common fetal autosomal aneuploidies. As part of a technology assessment for the California Technology Assessment Forum, we critically reviewed the evidence for the use of cffDNA as a prenatal screening test. We evaluated the evidence for its use as either a 'primary' or an 'advanced' screening test and for its use in screening for three different trisomies: 21, 18, and 13. We evaluated whether the use of cffDNA met established technology assessment criteria and established conclusions about evidence-based use of this new technology.

Noninvasive prenatal testing creates an opportunity for antenatal treatment of Down syndrome

Trisomy 21 (T21) is the most common autosomal aneuploidy that is associated with intellectual disability. It is the focus of many prenatal screening programs across the globe. Pregnant women who receive a prenatal diagnosis of T21 in their fetus currently have the option of continuing or terminating their pregnancy, but no fetal treatment is available. In this paper, we review compelling morphogenetic, cellular, and molecular studies that, taken together, suggest that there is an important window of opportunity during fetal life to positively impact brain development to improve postnatal neurocognition and behavior. Although substantial progress has been made in understanding the basic neurobiology of Down syndrome (DS), the majority of pre-clinical trials is currently focused on adults. There are a number of challenges in the identification and development of novel antenatal therapies for DS, including the lack of toxicity and teratogenicity for the pregnant woman and the fetus, evidence that the compounds can cross the placenta and achieve therapeutic levels, and the demonstration of clinical improvement. Preliminary experiments in mouse models suggest that prenatal treatment of DS is an achievable goal.

The clinical implementation of non‐invasive prenatal diagnosis for single‐gene disorders: challenges and progress made

Recently, we have witnessed the rapid translation into clinical practice of non-invasive prenatal testing for the common aneuploidies, most notably within the United States and China. This represents a lucrative market with testing being driven by companies developing and offering their services. These tests are currently aimed at women with high/medium-risk pregnancies identified by serum screening and/or ultrasound scanning. Uptake has been impressive, albeit limited to the commercial sector. However, non-invasive prenatal diagnosis (NIPD) for single-gene disorders has attracted less interest, no doubt because this represents a much smaller market opportunity and in the majority of cases has to be provided on a bespoke, patient or disease-specific basis. The methods and workflows are labour-intensive and not readily scalable. Nonetheless, there exists a significant need for NIPD of single-gene disorders, and the continuing advances in technology and data analysis should facilitate the expansion of the NIPD test repertoire. Here, we review the progress that has been made to date, the different methods and platform technologies, the technical challenges, and assess how new developments may be applied to extend testing to a wider range of genetic disorders.

Feasibility Study of Semiconductor Sequencing for Noninvasive Prenatal Detection of Fetal Aneuploidy

Noninvasive prenatal detection of common fetal aneuploidies with cell-free DNA from maternal plasma has been achieved with high-throughput next-generation sequencing platforms. Turnaround times for previously tested platforms are still unsatisfactory for clinical applications, however, because of the time spent on sequencing. The development of semiconductor sequencing technology has provided a way to shorten overall run times. We studied the feasibility of using semiconductor sequencing technology for the noninvasive detection of fetal aneuploidy. Maternal plasma DNA from 13 pregnant women, corresponding to 4 euploid, 6 trisomy 21 (T21), 2 trisomy 18 (T18), and 1 trisomy 13 (T13) pregnancies, were sequenced on the Ion Torrent Personal Genome Machine sequencer platform with 318 chips. The data were analyzed with the T statistic method after correcting for GC bias, and the T value was calculated as an indicator of fetal aneuploidy. We obtained a mean of 3 524 401 high-quality reads per sample, with an efficiency rate of 77.9%. All of the T21, T13, and T18 fetuses could be clearly distinguished from euploid fetuses, and the time spent on library preparation and sequencing was 24 h. Semiconductor sequencing represents a suitable technology for the noninvasive prenatal detection of fetal aneuploidy. With this platform, sequencing times can be substantially reduced; however, a further larger-scale study is needed to determine the imprecision of noninvasive fetal aneuploidy detection with this system.

Secondary findings from non‐invasive prenatal testing for common fetal aneuploidies by whole genome sequencing as a clinical service

To report secondary or additional findings arising from introduction of non-invasive prenatal testing (NIPT) for aneuploidy by whole genome sequencing as a clinical service. Five cases with secondary findings were reviewed. In Case 1, NIPT revealed a large duplication in chromosome 18p, which was supported by arrayCGH of amniocyte DNA, with final karyotype showing mosaic tetrasomy 18p. In Case 2, a deletion in the proximal long arm of chromosome 18 of maternal origin was suspected and confirmed by arrayCGH of maternal white cell DNA. In Case 3, NIPT was negative for trisomies 21 and 18. In-depth analysis for deletions/duplications was requested when fetal structural anomalies were detected at routine scan. A deletion in the proximal long arm of chromosome 3 was found and confirmed by karyotyping. In Case 4, NIPT correctly predicted confined placental mosaicism with triple trisomy involving chromosomes X, 7 and 21. In Case 5, NIPT correctly detected a previously unknown maternal mosaicism for 45X. Non-invasive prenatal testing is able to detect a wide range of fetal, placental and maternal chromosomal abnormalities. This has important implications on patient counseling when an abnormality is detected by NIPT.

Analysis of 89 amniotic samples using fluorescent in situ hybridization

To assess the association between 2 single nucleotide polymorphisms (SNPs) of ETS1 gene and susceptibility to systemic lupus erythematosus (SLE) in a northern Chinese Han population. Two SNPs within the ETS1 gene mapped to 11q23 were selected based on HapMap data. Genotyping was conducted with Taqman method in 231 patients with SLE and 474 healthy controls from Qilu Hospital, Shandong and analyzed with PLINK1.07 software. Haplotypes were analyzed with SHEsis software. A statistically significant difference was detected in the distribution of rs1128334 and rs4937333 genotypes between the two groups (all P< 0.01). For rs1128334, the frequency of the minor allele was 0.291 and 0.428 in controls and cases, respectively. For rs4937333, the minor allele frequency was 0.381 and 0.476 in controls and cases respectively. An A-C haplotype was found to be strongly associated with increased risk for SLE, while another haplotype G-C may reduce this risk. Our study has suggested that rs1128334 and rs4937333 are strongly associated with the risk for SLE in northern Chinese Han population.

Non‐invasive prenatal testing with cell‐free DNA: US physician attitudes toward implementation in clinical practice

The aim of this study was to assess awareness, potential adoption, and current utilization of non-invasive prenatal testing (NIPT) analysis for common fetal aneuploidies among obstetricians. A 36-item web-based survey was designed to assess the current practice of fetal aneuploidy screening and knowledge and utilization of NIPT for fetal trisomy. Practicing obstetricians in the United States were invited via email to participate in the survey. Of the 101 obstetricians that completed the survey (27% academic-based, 73% private practice), 97% offer screening to high-risk patients and 91% offer screening to average-risk patients. With regard to current screening tests, the top three advantages were as follows: recommendation by professional societies, no risk to the pregnancy, and long history/experience with the test, whereas the top three limitations were as follows: patient anxiety, risks of follow-up invasive testing, and high false positives. NIPT had been used by 32% of respondents and 22% were familiar with NIPT and the associated clinical data. The majority of physicians predicted that they would offer NIPT to high-risk women (86.1%) and average-risk women (76.2%) within 12 months. Obstetricians plan to increase their utilization of NIPT and expect that the majority of both high-risk and average-risk patients will be offered NIPT as an option.

Trisomy 21 and facial developmental instability

The most common live-born human aneuploidy is trisomy 21, which causes Down syndrome (DS). Dosage imbalance of genes on chromosome 21 (Hsa21) affects complex gene-regulatory interactions and alters development to produce a wide range of phenotypes, including characteristic facial dysmorphology. Little is known about how trisomy 21 alters craniofacial morphogenesis to create this characteristic appearance. Proponents of the "amplified developmental instability" hypothesis argue that trisomy 21 causes a generalized genetic imbalance that disrupts evolutionarily conserved developmental pathways by decreasing developmental homeostasis and precision throughout development. Based on this model, we test the hypothesis that DS faces exhibit increased developmental instability relative to euploid individuals. Developmental instability was assessed by a statistical analysis of fluctuating asymmetry. We compared the magnitude and patterns of fluctuating asymmetry among siblings using three-dimensional coordinate locations of 20 anatomic landmarks collected from facial surface reconstructions in four age-matched samples ranging from 4 to 12 years: (1) DS individuals (n = 55); (2) biological siblings of DS individuals (n = 55); 3) and 4) two samples of typically developing individuals (n = 55 for each sample), who are euploid siblings and age-matched to the DS individuals and their euploid siblings (samples 1 and 2). Identification in the DS sample of facial prominences exhibiting increased fluctuating asymmetry during facial morphogenesis provides evidence for increased developmental instability in DS faces. We found the highest developmental instability in facial structures derived from the mandibular prominence and lowest in facial regions derived from the frontal prominence.

Prenatal microarray analysis as second‐tier diagnostic test: single‐center prospective study

To evaluate the usefulness of chromosome microarrays as a second-tier test in prenatal genetic testing. We prospectively analyzed 75 high-risk pregnancies undergoing invasive prenatal genetic testing in which the karyotype either was normal or had findings other than a common non-mosaic autosomal aneuploidy. Chromosomal microarray analysis (CMA) was performed successfully in all cases. Pathological copy-number variations (CNVs) explaining the phenotypes were found in 11 cases (14.7%). Four cases were detected with an unbalanced translocation. In three of these cases, subsequent genetic analysis demonstrated that a parent was an unknown carrier of a balanced translocation. Among the 67 cases with normal karyo-types, submicroscopic rearrangements with pathological significance were detected in five (7.5%) and CNVs of unclear significance were detected in one (1.5%). CMA was able to discriminate correctly between true mosaicism and confined or pseudomosaicism in all six mosaic cases. CMA is a valuable second-tier test in high-risk pregnancies for which identification or further delineation of genetic aberrations is important. Its higher resolution results in a higher detection rate of aberrant cases, with a clear clinical benefit for estimation of risk of recurrence.

Noninvasive Prenatal Testing/Noninvasive Prenatal Diagnosis: the Position of the National Society of Genetic Counselors

The 1997 discovery of free fetal DNA in maternal plasma launched clinical researchers' efforts to establish a reliable method for non-invasive prenatal testing for fetal genetic conditions. Various methods, including, but not limited to, massively parallel sequencing (MPS) and selective analysis of cell-free fetal DNA in maternal plasma, have recently been developed as highly sensitive and specific noninvasive screening tools for common fetal chromosome aneuploidies. Incorporating these new noninvasive technologies into clinical practice will impact the current prenatal screening paradigm for fetal aneuploidy, in which genetic counseling plays an integral role. The National Society of Genetic Counselors (NSGC) currently supports Noninvasive Prenatal Testing/Noninvasive Prenatal Diagnosis (NIPT/NIPD) as an option for patients whose pregnancies are considered to be at an increased risk for certain chromosome abnormalities. NSGC urges that NIPT/NIPD only be offered in the context of informed consent, education, and counseling by a qualified provider, such as a certified genetic counselor. Patients whose NIPT/NIPD results are abnormal, or who have other factors suggestive of a chromosome abnormality, should receive genetic counseling and be given the option of standard confirmatory diagnostic testing.

Neurocognitive variance and neurological underpinnings of the X and Y chromosomal variations

X and Y chromosomal variations including tetrasomy and pentasomy conditions are rare and occur in 1:18,000-1:100,000 male births. The most common sex chromosome aneuploidy is 47, XXY for which there is a rich literature delineating the physical and neurobehavioral phenotype. Although the more complex chromosome aneuploidies 48, XXYY, 48, XXXY, and 49, XXXXY are often compared with 47, XXY (Klinefelter syndrome) because of shared features including tall stature and hypergonadotropic hypogonadism, there is a wider spectrum of physical and cognitive abilities that have recently been delineated. The phenotypic presentation of the boys with more severe aneuploidy shares some characteristics with 47, XXY, but there are also other unique and distinctive features. Previously unappreciated intact nonverbal skills have been demonstrated in association with severe developmental dyspraxia. MRI findings of white matter hyperintensities may underlie cognitive deficits and deserve further study. This report discusses what is known about clinical variability in the XY syndromes collectively evaluated through careful multidisciplinary clinical evaluation including the clinical and neurobehavioral aspects of these conditions. Variability in clinical and cognitive functioning may reflect skewed X inactivation, mosaicism, or epigenetic factors that warrant further investigation.

Timing of diagnosis of 47,XXY and 48,XXYY: A survey of parent experiences

47,XXY/Klinefelter syndrome is the most common sex chromosomal aneuploidy, yet 64% of males with this condition go undiagnosed. 48,XXYY is less common and there is less known about the diagnosis. The objective of this study is to describe the diagnosis experiences of parents of males with 47,XXY and 48,XXYY. Parents of 89 males with 47,XXY and 76 males with 48,XXYY completed a survey that gathered data about their experiences leading to a diagnosis, including the current age of the child, age at diagnosis, reasons for initial concern, and the specialists providing the diagnosis. In the 47,XXY cohort diagnosed postnatally, 59% presented with developmental delay, with a mean age at first parental concern of 5.2 years and mean age of diagnosis at 10.0 years. The remaining 41% presented with endocrinologic issues with a mean age at first concern of 19.1 years and mean age of diagnosis at 21.1 years. In the 48,XXYY group, 93% presented with developmental delay, with mean age at first parental concern of 2.4 years and mean age of diagnosis at 7.6 years. Hence, the average time from initial parental concern to diagnosis of 47,XXY or 48,XXYY ranges from 2 to 5 years, with those presenting with developmental issues having a longer lag to diagnosis compared to those presenting with endocrinologic issues. Increased awareness of the developmental, psychological, and medical features of 47,XXY and 48,XXYY is important to facilitate timely diagnosis and initiation of appropriate screenings and treatments that are important for optimal outcomes.