Screening For Chromosomal Abnormalities Research Articles

Low fetal fraction and adverse pregnancy outcomes- systematic review of the literature and metanalysis.

While cell-free DNA (cfDNA) screening has emerged as a screening modality for common aneuploidies, further research and several publications over the past decade suggested some correlation between the low concentrations of cfDNA and a number of pregnancy-related complications. The primarygoal of this systematic review and meta-analysis was to assess the potential value of low-ff levels in the prediction of subsequent PE/PIH, GDM, SGA/FGR, and PTB. The meta-analysis results aim atsummarizing the currently available literature data and determining the clinical relevance of this biochemical markerand the potentialnecessity for additional investigation of its utility in complications other than the detection of common aneuploidies. This systematic review and meta-analysis was designed according to the preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines. It included all observational studies that reported low -ff levels after the performance of non-invasive prenatal testing (NIPT) as part of the screening for chromosomal abnormalities and their association with adverse pregnancy outcomes, namely the subsequent development of hypertensive disorders of pregnancy, gestational diabetes, preterm birth, and the detection of small for gestational age fetuses or growth-restricted fetuses. The Medline (1966-2041), Scopus (2004-2024), Clinicaltrials.gov (2008-2024), EMBASE (1980-2024), Cochrane Central Register of Controlled Trials CENTRAL (1999-2024) and Google Scholar (2004-2024) databases were used in our primary search along with the reference lists of electronically retrieved full-text papers. The date of our last search was set at February 29, 2024. Our search identified 128 potentially relevant studies and,overall, 8 studies were included in the present systematic review that enrolled a total of 72,507 patients. Low ff of cfDNA cfDNA was positively associated with HDP (OR 1.66, 95% CI 1.34, 2.06, I-square test: 56%). Low ff of cfDNA was positively associated with GDM (OR 1.27, 95% CI 1.03, 1.56, I-square test: 76%). Furthermore, low ff levels were positively associated with SGA/FGR (OR 1.63, 95% CI 1.32, 2.03, I-square test: 0%). Low ff levels were positively correlated with the risk for PTB but the association did not manage to reach a statistical significant level (OR 1.22, 95% CI 0.89, 1.67, I-square test: 66%). Our study suggests that low ff is associated with increased risk of adverse perinatal outcomes, including PE/PIH, GDM, and SGA/FGR. However, the relationship between ff and PTB remains unclear due to conflicting evidence. It should be emphasized that further research is needed to reveal the underlying mechanisms behind the association of low ff with adverse pregnancy outcomes and explore its potential role in an overall prenatal screening, which could potentially not be limited to detecting aneuploidies.

Prenatal Screening and Diagnosis: Time for a Paradigm Shift.

Recent advances in genetics and imaging have ushered substantial breakthroughs in screening and diagnosis for chromosomal and structural abnormalities. Thus, it is imperative that health care providers caring for pregnant individuals should reexamine established practices in prenatal screening and diagnosis. In the past, screening for chromosomal abnormalities was based almost entirely on Down syndrome. Pregnant individuals aged > 35 years were considered at "high risk" or of "advanced maternal age" based on age alone; however, the advent of tests with high sensitivity for prenatal detection of chromosomal abnormalities should lead to abandoning that concept, at least from the perspective of chromosomal abnormalities. Given that first-trimester and second-trimester screenings will fail to detect between 5 and 20% of Down syndrome, in most situations, noninvasive testing with cell-free DNA should be the first-line screen for Down syndrome. The fact that over 99% of fetuses with Down syndrome will be detected prenatally with cell-free DNA gives other fetal chromosomal and structural abnormalities increasing prominence. Chromosomal microarray analysis (CMA) permits prenatal detection of several clinically important chromosomal aberrations that cannot be detected by karyotype and may exist in structurally normal fetuses with low-risk cell-free DNA screening. As such, CMA should be more readily conducted when invasive testing is performed, regardless of the presence of a structural abnormality. Isolated sonographic "soft markers" have no clinical significance in patients who have normal cell-free DNA screening, can cause unwarranted anxiety and a negative impact on pregnancy, and perhaps it is time to stop discussing them. Detailed first-trimester ultrasound allows early detection of several severe fetal anomalies and, therefore, in settings with adequately trained personnel and resources, should be used more frequently. This opinion traces the evolution of prenatal screening and diagnosis and advocates for a paradigm shift that aligns with recent developments in prenatal screening and diagnostic capabilities. KEY POINTS: · Noninvasive prenatal testing with cell-free DNA should be available to all pregnant individuals.. · Chromosomal microarray should be available to all pregnant individuals undergoing amniocentesis.. · Patients >35 years with low-risk screening are not at "high risk" for chromosomal abnormalities..

Impact of choroid plexus size in prenatal diagnosis of normal and abnormal closure of fourth ventricle.

To assess the role of the choroid plexus (CP) of the fourth ventricle (4V) in fetuses with an open 4V and a normal cerebellar vermis. Two groups of patients were recruited in two fetal medicine referral centers. The prospectively collected control group included singleton pregnancies with a normal sonographic examination after first-trimester combined screening for chromosomal abnormalities and normal outcome, recruited in the period between 2019 and 2022. The study group was selected retrospectively by searching our databases to identify all cases with an isolated open 4V and normal anatomy and size of the cerebellar vermis. The inclusion criteria of the study group were: (1) gestational age between 20 and 22 weeks; (2) a brainstem-vermis angle ≥ 18° in the midsagittal plane with an otherwise normal cerebellum and vermis; (3) 4V-CP visible and seen separately from the vermis; (4) absence of other intra- and extracranial anomalies; and (5) available prenatal and/or postnatal magnetic resonance imaging (MRI) data. In 169 cases of the control group, the 4V-CP was seen separately from the cerebellar vermis and was noticed to progressively fill the space caudal to the 4V, between the vermis and brainstem. From 12 to 22 weeks, the surface areas of the vermis and medial portion of the 4V-CP increased progressively with advancing gestation (P < 0.0001). Intra- and interobserver correlation analysis showed good reproducibility for the measurements. Among the cases with an open 4V and a normal vermis, it was retrospectively feasible to visualize the 4V-CP separately from the inferior part of the vermis in 41 fetuses. In five of these cases, the open 4V was due to a small CP. In all 41 fetuses, the diagnosis on MRI was isolated upward rotation of the cerebellar vermis, and no additional anomaly was found. Closure of the 4V is dependent on the 4V-CP and not only the cerebellar vermis. In fact, a small CP may represent another cause of an open 4V. Therefore, separate visualization of the 4V-CP and cerebellar vermis is crucial to improve discrimination between the different causes of an open 4V at the anomaly scan and its clinical implications. © 2023 International Society of Ultrasound in Obstetrics and Gynecology.

Screening for Low Papp-A: Inconsistencies and Incongruities

Summary When women and birthing people are found to have low PAPP-A at the combined test for chromosomal abnormalities (Down’s syndrome, Edwards’ syndrome and Patau’s syndrome) it has major implications for their pregnancy, labour and delivery. However, neither women nor their midwives are informed that PAPP-A results will be looked at independently, or that recommendations of care will be based on these results, and neither is consent gained for this. In addition, the question arises of why screening for low PAPP-A is not offered to all women (regardless of their decision to have screening for chromosomal abnormalities) given its potentially serious implications.

Cytogenetic screening of chromosomal abnormalities and genetic analysis of FSH receptor Ala307Thr and Ser680Asn genes in amenorrheic patients.

Amenorrhea is a rare reproductive medical condition defined by the absence of menstruation during puberty or later life. This study aims to establish the frequency and pattern of chromosomal abnormalities (CA) in both primary amenorrhea (PA) and secondary amenorrhea (SA), and further to detect the genetic changes in exon 10 at nucleotide positions 919 and 2039 of the genotypes Thr307Ala, and Asn680Ser, respectively. This cross-sectional study was conducted on a sample of seventy amenorrhoeic women according to the Helsinki declaration rules of medical ethics, as divided into 40 (57.14%) with PA and 30 (42.86%) with SA, and 30 healthy women with normal menstruation as the control. The chromosomal karyotyping was performed according to the ISCN, 2020. PCR products were submitted to RFLP and Sanger sequencing for women with normal karyotype and high FSH serum levels. The classical Turner Syndrome was the most common CA in PA, followed by isochromosome X [46, Xi(X)(q10)], mosaicism of Turner and isochromosome X [45, X /46, Xi(X)(q10)], sex reversal (46, XY) and (46, XX,-3,+der3,-19,del 19 p). Abnormal SA cases were characterized by mosaicism Turner syndrome (45,X/46,XX) and (46,XX,-3,+der3,X,+derX). The homozygous genotypes AA and GG of Ala307Thr (rs6165) in the FSHR gene are most common in PA, while the homozygous genotype AA is more common in SA. GG and AG genotypes of Ser680Asn (rs6166) are more frequent in Iraqi patients with PA and SA compared to the healthy control women. Both PCR-RFLP and Sanger sequencing indicated a marked matching between genotypes. The study emphasizes the need for cytogenetic analysis to determine the genetic basis of PA and SA. Further, genotyping for women with normal karyotype and high FSH serum concentrations via PCR-RFLP should be considered for the precise diagnosis and development of appropriate management of and counselling for these patients.

Basic sonographic examination of the fetal brain at 11–13 weeks' gestation: Rationale for a simple and reliable four‐step technique

The widespread incorporation of first-trimester scanning between 11 and 13 weeks' gestation has shifted from the screening of chromosomal abnormalities, mainly by measuring nuchal translucency thickness and visualization of the nasal bone, to a more detailed study of the fetal anatomy leading to early detection of several structural congenital anomalies. This goal can be improved by the routine and focused sonographic assessment of specific anatomic planes and the identification of distinctive landmarks that can help disclosing a particular, non-evident condition. In this article we present the basis for a basic, early examination of the fetal brain during screening using a four-step technique, which can be readily incorporated during the first-trimester scan. The technique includes the focused visualization of the cranial contour, choroid plexuses of the lateral ventricles and midline, aqueduct of Sylvius, brainstem, fourth ventricle, and the choroid plexus of the fourth ventricle. The rationale for this approach is presented and discussed.

A Prospective Study of Genetic Variants in Infants with Congenital Unilateral Sensorineural Hearing Loss.

Children with unilateral sensorineural hearing loss (uSNHL) have a high risk of speech-language delays and academic difficulties. Still, challenges remain in the diagnosis of uSNHL. With a prospective cross-sectional design, 20 infants were consecutively recruited from a universal newborn hearing screening program and invited to genetic testing. Eighteen of the subjects agreed to genetic testing, 15 subjects with OtoSCOPE® v.9 screening 224 genes, and four subjects underwent targeted testing, screening for chromosomal abnormalities or 105-137 gene mutations. The genetic results were described together with the 20 infants' previously published auditory profiles and imaging results. Genetic causes for the uSNHL were found in 28% of subjects (5/18) including CHARGE syndrome (CHD7), autosomal recessive non-syndromic hearing loss (GJB2), Townes-Brocks syndrome (SALL1), Pendred Syndrome (SLC26A4) and Chromosome 8P inverted duplication and deletion syndrome. In subjects with comorbidities (malformation of fingers, anus, brain, and heart), 100% were diagnosed with a genetic cause for uSNHL (3/3 subjects), while 13% (2/15 subjects) were diagnosed without comorbidities observed at birth (p = 0.002). Genetic testing for congenital uSNHL is currently efficient for alleged syndromes, whereas genetic variants for non-syndromic congenital uSNHL need further research.

The Incidence of the Agenesis of Fetal Ductus Venosus at the 11-13 Weeks' Ultrasound Examination.

The objective is to examine the incidence of agenesis offetal ductus venosus (DV) at the routine ultrasound examination at 11-13 weeks. This is a retrospective study on women presenting for screening for chromosomal abnormalities. The fetal DV was routinely examined by color Doppler in the sagittal view. Out of 8,304 fetuses examined, there were 13 cases of DV agenesis (0.15%). The umbilical vein drainage was intra-hepatic in two-thirds of the cases, and all resulted in normal live births. In the remaining one-third of cases, the umbilical vein drained to the inferior vena cava and all had a poor outcome because of aneuploidies, cardiac defects, and Noonan syndrome. Fetal DV agenesis occurs in about one in 650 fetuses and the majority of cases have a benign course and a favorable outcome. Failure to identify the DV should prompt a detailed ultrasound examination, identification of the drainage site of the umbilical vein, and genetic testing.

First trimester low maternal serum pregnancy associated plasma protein-A (PAPP-A) as a screening method for adverse pregnancy outcomes.

To evaluate different cut-off values of first trimester pregnancy associated plasma protein-A (PAPP-A) in screening for adverse pregnancy outcomes in a retrospective cohort study. During the study period of 1.1.2014-31.12.2018, total of 23,482 women with singleton pregnancies participated in first trimester combined screening for chromosomal abnormalities. Maternal serum PAPP-A multiple of medians (MoM) levels were measured, and study population was divided into three study groups of PAPP-A≤0.40 (n=1,030),≤0.35 (n=630) and≤0.30 (n=363) MoM. Small for gestational age (SGA), preterm birth (PTB) and composite outcome (SGA, hypertensive disorder of pregnancy (HDP) and/or PTB) were more frequent in all three PAPP-A MoM study groups and pre-eclampsia in≤0.40 and≤0.35 study groups than in their control groups (p<0.05). The odds ratio (OR) for SGA varied from 3.7 to 5.4 and sensitivity and specificity from 6.9 to 13.8% and from 95.9 to 98.6%, between study groups. Using PAPP-A≤0.30 MoM as a screening cut-off instead of PAPP-A≤0.40 MoM, resulted in approximately 50% reduction in screening detection of SGA and PTB. PAPP-A≤0.40 MoM should be considered asa primary screening cut-off for adverse pregnancy outcomes as approximately 23% will develop either SGA, HDP or PTB. It seems to be the best cut-off to screen for SGA.

Hemoglobinopathies and preimplantation diagnostics.

Hemoglobinopathies constitute some of the most common inherited disorders worldwide. Manifestations are very severe, patient management is difficult and treatment is not easily accessible. Preimplantation genetic testing for monogenic disorders (PGT-M) is a valuable reproductive option for hemoglobinopathy carrier-couples as it precludes the initiation of an affected pregnancy. PGT-M is performed on embryos generated by assisted reproductive technologies and only those found to be free of the monogenic disorder are transferred to the uterus. PGT-M has been applied for 30 years now and β-thalassemia is one of the most common indications. PGT may also be applied for human leukocyte antigen typing to identify embryos that are unaffected and also compatible with an affected sibling in need of hemopoietic stem cell transplantation. PGT-M protocols have evolved from PCR amplification-based, where a small number ofloci were analysed, to whole genome amplification-based, the latter increasing diagnostic accuracy, enabling the development of more generic strategies and facilitating multiple diagnoses in one embryo. Currently, numerous PGT-M cycles are performed for the simultaneous diagnosis of hemoglobinopathies and screening for chromosomal abnormalities in the embryo in an attempt to further improve success rates and increase deliveries of unaffected babies.

Reducing the Anxiety and Concern of Pregnant Women during Antenatal Anomaly Screening Tests: A Systematic Review

Objectives: Although antenatal anomaly screening tests (AAST) provide valuable information about fetal health, performed to prevent the birth of children with chromosomal abnormalities, uncontrolled stress while performing such tests may negatively affect the mother’s mental health. This study aimed to systematically review clinical trial studies in which reducing pregnant women’s anxiety and concern in the process of performing AAST was among their objectives. Materials and Methods: In this systematic review, six electronic databases (Scopus, Cochrane Library, Science Direct, PubMed, Google Scholar, and CINAHL) were searched. Data extraction was performed through randomized controlled trials (RCTs) in English, which the core fell onto designing an intervention to reduce pregnant women’s anxiety and concern associated with performing AAST. Results: Out of the 1946 studies, six were included in this systematic review. In most studies, a positive impact on knowledge and satisfaction with the information received was observed. However, no effect was reported regarding decreasing or increasing the anxiety and concern of pregnant women in the process of performing AAST. Studies were heterogeneous in terms of intervention type and gestational age of participants. Conclusions: Interventions aimed at providing pregnant women with specific information about prenatal screening for chromosomal abnormalities have no impact on reducing their anxiety and concern. Therefore, designing educational-psychological interventions to prevent and reduce anxiety and concern of pregnant women in this period is recommended.

First Trimester Combined Aneuploidy Screening for Trisomy 21: A Three Years Retrospective Study

Introduction: Prenatal testing also known as maternal screening is primarily performed to screen out most common chromosomal anomalies in the foetus using maternal blood. It provides an accurate and sensitive assessment of a patient’s risk of carrying a foetus with chromosomal anomalies. Aim: To study the first trimester prenatal screening using a Foetal Medicine Foundation (FMF) certified platform to estimate the risk of foetal trisomy 21. Materials and Methods: This retrospective study was conducted at Global Reference Laboratory, Mumbai, Maharashtra, India, from January 2018 to March 2021, samples of 86118 pregnant Asian women with respect to age, the risk cut-off was set at 1:250 for trisomy 21. The study included determination of free β- human Chorionic Gonadotropin (β-hCG) and PregnancyAssociated Plasma Protein-A (PAPP-A) in maternal serum, ultrasound studies of Crown Rump Length (CRL), Nuchal Translucency (NT) and nasal bone and maternal characteristics. Concentration of biochemical parameters was expressed in Multiple of Medians (MoM) respective to gestation age. Risk assessment of trisomy 21 was analysed using lifecycle software cut-off being 1:250 at sampling. Results: The overall positive risk (high risk) for Trisomy 21 obtained was 2.58%, association with advanced maternal age, history of Insulin dependent diabetes mellitus and absent nasal bone status. Biochemically, the MoMs were in accordance with published studies of mean free β-hCG MoM&gt;1.5 and PAPP-A MoM of ≤0.6. Conclusion: This study enabled us to understand the importance of prenatal testing, a non invasive screening of chromosomal disorders like trisomy 21 which gives the advantages of early counseling and of diagnosis quite as early as in the first trimester of pregnancy. It helps in drastically reducing the use of invasive procedures associated with risk of miscarriages. It is suggested that screening for chromosomal abnormalities be offered in all antenatal women irrespective of age and parity.

Low torcular Herophili position and large brainstem-tentorium angle in fetuses with open spinal dysraphism at 11-13 weeks' gestation.

To evaluate whether in fetuses with open spina bifida (OSB) the tentorium can be seen to be displaced downwards and vertically oriented by the time of the 11-13-week scan and whether this is reflected in an alteration of the brainstem-tentorium (BST) angle. The study population was recruited between 2015 and 2020 from three fetal medicine referral centers and comprised a control group and a study group of pregnancies with OSB. The control group was recruited prospectively and included singleton pregnancies with a normal sonographic examination after first-trimester combined screening for chromosomal abnormalities and normal outcome. The study group was selected retrospectively and included all cases with OSB between 2015 and 2020. All cases underwent detailed ultrasound assessment at 11 + 0 to 13 + 6 weeks' gestation. The position of the torcular Herophili (TH) was identified in the midsagittal view of the fetal brain with the use of color Doppler and was considered as a proxy for the insertion of the tentorium on the fetal skull. The BST angle was calculated in the same view and was compared between the two groups. Sixty normal fetuses were included in the control group and 22 fetuses with OSB in the study group. In both groups, the BST angle was found to be independent of gestational age or crown-rump length (P = 0.8815, R2 = 0.0003861 in the controls, and P = 0.2665, R2 = 0.00978 in the OSB group). The mean BST angle was 48.7 ± 7.8° in controls and 88.1 ± 1.18°, i.e. close to 90°, in fetuses with OSB. Comparison of BST-angle measurements between the control group and cases with OSB showed a statistically significant difference (P = 0.0153). In all fetuses with OSB, the downward displacement of the TH and tentorium was clearly visible at the 11-13-week scan. In fetuses with OSB, the BST angle is significantly larger than in normal controls, with the tentorium being almost perpendicular to the brainstem. This sign confirms the inferior displacement of the tentorium cerebelli with respect to its normal insertion on the occipital clivus as early as the first trimester of pregnancy and is useful in the diagnosis of Chiari-II malformation at this early stage. In fetuses with OSB, the low position of the tentorium and TH is clearly visible, even subjectively, at the 11-13-week scan. © 2021 International Society of Ultrasound in Obstetrics and Gynecology.

Сytogenetic techniques in current biomedical research. part i: history and theoretical basis of human cytogenetics

Cytogenetics is an essential part of human genetics which studies the structure of chromosomes and their collection which is called karyotype. Cytogenetic techniques are employed while interrogating DNA organisation and compaction. Analysis of the chromosomal structure contributes to uncovering the molecular basis of various cellular processes in normal and pathological conditions. Furthermore, spectrum and frequency of chromosome abnormalities serves as an indicator of mutagenic effects. Cytogenetic techniques became indispensable for discovering the genetic causes of human diseases at different stages of ontogenesis. Genetic abnormalities are a common cause of impaired reproductive function, abnormal pregnancy, and neonatal malformations. Genetic screening for chromosomal abnormalities and congenital anomalies is a powerful tool for reducing the genetic load in human populations as well as disease, psychological and social burden on families and societies. This paper begins the cycle of lectures on molecular basis of human cytogenetics, cytogenetic techniques, and the corresponding research and clinical applications. The lecture is primarily aimed at biomedical students and physicians who often have an unmet need to analyse and interpret the results of cytogenetic analyses.

Fetal Screening for Chromosomal Abnormalities.

With more and more reproductive-aged women opting to pursue genetic screening during pregnancy, health care professionals must understand the variety of testing options available as well as the advantages and limitations of each testing option. Presently, no single screening test is universally believed to be superior because the combination of the specific test and the population being tested determines the range of potential identifiable conditions as well as the positive predictive values. As a result, pre- and posttest counseling are not always straightforward and may require discussions with multiple specialists including genetic counselors, obstetricians, and pediatricians/neonatologists. The purpose of this review is to summarize the screening options currently available to pregnant women to determine their risk of having a child affected by a chromosomal disorder. Screening for chromosomal abnormalities using ultrasonography, maternal serum analytes, cell-free DNA, and preimplantation genetic testing will be discussed here. Advances in the field, including the possible future use of cell-based noninvasive prenatal screening (NIPS) as a more accurate method for genetic screening and the incorporation of screening for copy number variants (microdeletions and duplications) into traditional cell-free NIPS will also be reviewed.

Different Cutoff Values for Increased Nuchal Translucency in First-Trimester Screening to Predict Fetal Chromosomal Abnormalities.

IntroductionIncreased nuchal translucency (NT) is closely related to an increased risk of chromosomal abnormalities. However, the criterion of increased NT for invasive prenatal diagnosis remains controversial, as the cutoff values are inconsistent among countries. This study was conducted to compare the various cutoff values of increased NT and calculate the incidence of chromosomal abnormalities to determine the predictive ability of these cutoff values in conventional chromosome analysis.MethodsA total of 3223 invasive samples with increased nuchal translucency (NT) or other non-ultrasound indications were collected from singleton pregnant women. Samples with isolated increased NT were divided into five groups based on the NT thickness: 909 samples in the NT ≥2.5 mm group, 819 samples in the NT ≥95th group, 547 samples in the NT ≥99th group, 527 samples in the NT ≥3.0 mm group, and 253 samples in the NT ≥3.5 mm group; 2301 samples with normal NT were considered as the control group. All five groups were karyotyped and the results were compared. The accuracy of the NT cutoff value for the screening of chromosomal abnormalities was assessed using receiver operating characteristic curve analysis.ResultsDetection of all chromosomal aberrations and trisomy 21 showed that the sensitivity and false-positive rate decreased sequentially in the NT ≥2.5 mm, NT ≥95th, NT ≥3 mm, NT ≥99th, and NT ≥3.5 mm groups, whereas the specificity, positive predictive value, and false-negative rates increased sequentially. Comprehensive analysis of various factors, including sensitivity and specificity, revealed values equal to or higher than the calculated 95th percentile of NT distribution, which showed a sensitivity of 49.2% and specificity of 75.67% for detecting all aneuploidies and a sensitivity of 64% and specificity of 75.45% for trisomy 21, exhibiting the highest ability for the screening of chromosomal defects in first-trimester screening.ConclusionFor different thresholds of NT thickness, values equal to or higher than the calculated 95th percentile of the NT distribution showed the highest ability for the screening of chromosomal defects in first-trimester screening.

NiPTUNE: an automated pipeline for noninvasive prenatal testing in an accurate, integrative and flexible framework.

Noninvasive prenatal testing (NIPT) consists of determining fetal aneuploidies by quantifying copy number alteration from the sequencing of cell-free DNA (cfDNA) from maternal blood. Due to the presence of cfDNA of fetal origin in maternal blood, in silico approaches have been developed to accurately predict fetal aneuploidies. Although NIPT is becoming a new standard in prenatal screening of chromosomal abnormalities, there are no integrated pipelines available to allow rapid, accurate and standardized data analysis in any clinical setting. Several tools have been developed, however often optimized only for research purposes or requiring enormous amount of retrospective data, making hard their implementation in a clinical context. Furthermore, no guidelines have been provided on how to accomplish each step of the data analysis to achieve reliable results. Finally, there is no integrated pipeline to perform all steps of NIPT analysis.To address these needs, we tested several tools for performing NIPT data analysis. We provide extensive benchmark of tools performances but also guidelines for running them. We selected the best performing tools that we benchmarked and gathered them in a computational pipeline. NiPTUNE is an open source python package that includes methods for fetal fraction estimation, a novel method for accurate gender prediction, a principal component analysis based strategy for quality control and fetal aneuploidies prediction. NiPTUNE is constituted by seven modules allowing the user to run the entire pipeline or each module independently. Using two cohorts composed by 1439 samples with 31 confirmed aneuploidies, we demonstrated that NiPTUNE is a valuable resource for NIPT analysis.

Performance of non-invasive prenatal testing for foetal chromosomal abnormalities in 1048 twin pregnancies

ObjectiveTo investigate the clinical value of non-invasive prenatal testing (NIPT) to screen for chromosomal abnormalities in twin pregnancies and to provide further data on NIPT manifestations in twin pregnancies.Materials and methodsIn a 4-year period, 1048 women with twin pregnancies were voluntarily prospectively tested by NIPT to screen for chromosomal abnormalities by sequencing cell-free foetal DNA (cffDNA) in maternal plasma. Positive NIPT results were confirmed by karyotyping, while negative results were followed up 42 days after delivery.ResultsThirteen women had positive NIPT results as follows: 2 cases of trisomy 21 (T21), 1 of trisomy 18 (T18), 7 of sex chromosome aneuploidy (SCA), 1 of microdeletion, and 2 of microduplication. Of these 13 cases, 2 were true-positive cases confirmed by foetal karyotype analysis, namely, 1 case of T21 and 1 of microdeletion. Furthermore, the remaining 11 high-risk pregnant women were confirmed as false positive by foetal karyotyping. Thus, the combined positive predictive value (PPV) of NIPT screening for chromosomal abnormalities in twin pregnancies was 15.4% (2/13). There were no false-negative case via our follow-up results.ConclusionSafe and rapid NIPT has a certain clinical application value; however, the PPV is limited, and the screening efficiency is not stable. Careful use should be made in the screening of chromosomal abnormalities in twin pregnancies.

Structure and signifi cance of cytogenetic abnormalities in patients with multiple myeloma

Introduction. Cytogenetic and genomic traits of tumour cells are considered the key mediating factors in multiple myeloma (MM). Selected chromosomal abnormalities are prognostic of therapeutic response and patient survival in MM.Aim — to assess of the diversity and rate of chromosomal abnormalities in MM patients and their association with the disease course.Materials and methods. The study enrolled 134 MM patients with pre-treatment bone marrow FISH assay screening for chromosomal abnormalities: t(11;14), t(4;14), t(14;16), t(14;20), t(6;14), hyperdiploidy, del13q14/-13, del17p13/TP53, amp1q21, t(8q24)/cMYC. The studied criteria at the MM onset were: hemogram, lactate dehydrogenase (LDH) activity, calcium, β2-microglobulin and creatinine concentrations, punctate cytology, bone marrow trephine biopsy and/or soft tissue biopsy histology, bone X-ray, immunochemical variant of MM, disease staging. A median follow-up was 20 months (3.2–77.4).Results. The primary chromosomal abnormality rate was 82.9 %, among them t(14q32)/IGH — 29.1 %, multiple trisomies — 46.3 % and their combination — 7.5 %. The rates of particular t(14q32)/IGH): t(11;14) — 16.4 %, t(4;14) — 12.7 %, t(14;16) and t(14;20) — 3.7 and 2.2 %, respectively. The secondary chromosomal abnormality rate was 69.4 %, among them del13q14/-13 — 40.3 %, amp1q21 — 39.6 %, t(8q24)/cMYC — 17.2 %, del17p13/TP53 — 12.7 %, del1p32 — 2.2 %. Analyses of the primary–secondary abnormality combinations showed that del13q14/-13 is more frequently combined with t(4;14) and less frequently with trisomies (p &lt; 0.05). Amp1q21 occurs more frequently with t(4;14) and less — with t(11;14) (p&lt;0.05). Patients with t(4;14) more frequently (p &lt; 0.05) had anemia at a hemoglobin level&lt;100 g/L, and the presence of amp1q21 and del17p13/TP53-enhanced serum LDH activity (p &lt; 0.05). Abnormality t(8q24)/cMYC more often co-occurred with higher serum β2-microglobulin concentrations (p &lt; 0.05). A three-year overall survival (OS) in del17p13/TP53-positive patients was 35.5 vs. 71.3 % in the negative (p = 0.002) and 50.8 vs. 67 % — in t(8q24)/cMYC-positive and negative patients, respectively (p = 0.001). Patients without amp1q21, with one, with two or more additional 1q21 copies had a five-year OS 79.4, 67.3 and 20.9 %, respectively (p = 0.0016), and a two-year progression-free survival (PFS) 83, 50 and 0 %, respectively (p = 0.005).Conclusion. We establish a negative impact of del17p13/TP53 and t(8q24)/cMYC on patients’ OS in MM, as well as unfavourable effect of amp1q21 on OS and PFS in the presence of two or more additional copies of 1q21 loci.

First-trimester fetal heart evaluation: time to move forward.

First-trimester fetal heart evaluation: time to move forward.