Prenatal Exome Sequencing Analysis in Fetuses with Various Ultrasound Findings.

OBJECTIVES: To evaluate the use of Exome Sequencing (ES) for the detection of genome-wide Copy Number Variants (CNVs) and the frequency of SNVs-InDels in selected genes related to developmental disorders in a cohort of consecutive pregnancies undergoing invasive diagnostic procedures for minor or simple ultrasound findings with no indication of ES. METHODS: Women undergoing invasive diagnostic testing (chorionic villus sampling or amniocentesis) for QF-PCR and chromosomal microarray analysis (CMA) due to prenatal ultrasound findings without an indication for ES were selected over a five-month period (May-September 2021). ES was performed to compare the efficiency of genome-wide CNV detection against CMA analysis and to detect monogenic disorders. Virtual gene panels were selected to target genes related to ultrasound findings and bioinformatic analysis was performed, prioritizing variants based on the corresponding HPO terms. The broad Fetal Gene panel for developmental disorders developed by the PAGE group was also included in the analysis. RESULTS: A total of 59 out of 61 women consented to participate in this study. There were 36 isolated major fetal anomalies, 11 aneuploidy markers, 6 minor fetal anomalies, 4 multiple anomalies, and 2 other ultrasound signs. Following QF-PCR analysis, two uncultured samples were excluded from this study, and six (10%) common chromosome aneuploidies were detected. In the remaining 51 cases, no pathogenic CNVs were detected at CMA, nor were any pathogenic variants observed in gene panels only targeting the ultrasound indications. Two (3.9%) monogenic diseases, apparently unrelated to the fetal phenotype, were detected: blepharo-cheilo-odontic syndrome (spina bifida) and Duchenne muscular dystrophy (pyelocaliceal dilation). CONCLUSIONS: In our series of pregnancies with ultrasound findings, common aneuploidies were the only chromosomal abnormalities present, which were detected in 10% of cases. ES CNV analysis was concordant with CMA results in all cases. No additional findings were provided by only targeting selected genes based on ultrasound findings. Broadening the analysis to a larger number of genes involved in fetal developmental disorders revealed monogenic diseases in 3.9% of cases, which, although apparently not directly related to the indications, were clinically relevant.

Pion-Induced Radiative Corrections to Neutron ß Decay.

We compute the electromagnetic corrections to neutron ß decay using a low-energy hadronic effective field theory. We identify new radiative corrections arising from virtual pions that were missed in previous studies. The largest correction is a percent-level shift in the axial charge of the nucleon proportional to the electromagnetic part of the pion-mass splitting. Smaller corrections, comparable to anticipated experimental precision, impact the ß-ν angular correlations and the ß asymmetry. We comment on implications of our results for the comparison of the experimentally measured nucleon axial charge with first-principles computations using lattice QCD and on the potential of ß decay experiments to constrain beyond-the-standard-model interactions.

Toward Complete Leading-Order Predictions for Neutrinoless Double ß Decay.

The amplitude for the neutrinoless double ß (0νßß) decay of the two-neutron system nn→ppe^{-}e^{-} constitutes a key building block for nuclear-structure calculations of heavy nuclei employed in large-scale 0νßß searches. Assuming that the 0νßß process is mediated by a light-Majorana-neutrino exchange, a systematic analysis in chiral effective field theory shows that already at leading order a contact operator is required to ensure renormalizability. In this Letter, we develop a method to estimate the numerical value of its coefficient (in analogy to the Cottingham formula for electromagnetic contributions to hadron masses) and validate the result by reproducing the charge-independence-breaking contribution to the nucleon-nucleon scattering lengths. Our central result, while derived in dimensional regularization, is given in terms of the renormalized amplitude A_{ν}(|p|,|p^{'}|), matching to which will allow one to determine the contact-term contribution in regularization schemes employed in nuclear-structure calculations. Our results thus greatly reduce a crucial uncertainty in the interpretation of searches for 0νßß decay.

CP Violation in Higgs-Gauge Interactions: From Tabletop Experiments to the LHC.

We investigate the interplay between the high- and low-energy phenomenology of CP-violating interactions of the Higgs boson with gauge bosons. For this purpose, we use an effective field theory approach and consider all dimension-six operators arising in so-called universal theories. We compute their loop-induced contributions to electric dipole moments and the CP asymmetry in B→X_{s}γ and compare the resulting current and prospective constraints to the projected sensitivity of the LHC. Low-energy measurements are shown to generally have a far stronger constraining power, which results in highly correlated allowed regions in coupling space-a distinctive pattern that could be probed at the high-luminosity LHC.

Hadronic τ Decays as New Physics Probes in the LHC Era.

We analyze the sensitivity of hadronic τ decays to nonstandard interactions within the model-independent framework of the standard model effective field theory. Both exclusive and inclusive decays are studied, using the latest lattice data and QCD dispersion relations. We show that there are enough theoretically clean channels to disentangle all the effective couplings contributing to these decays, with the τ→ππν_{τ} channel representing an unexpected powerful new physics probe. We find that the ratios of nonstandard couplings to the Fermi constant are bound at the subpercent level. These bounds are complementary to the ones from electroweak precision observables and pp→τν_{τ} measurements at the LHC. The combination of τ decay and LHC data puts tighter constraints on lepton universality violation in the gauge boson-lepton vertex corrections.

New Leading Contribution to Neutrinoless Double-ß Decay.

Within the framework of chiral effective field theory, we discuss the leading contributions to the neutrinoless double-beta decay transition operator induced by light Majorana neutrinos. Based on renormalization arguments in both dimensional regularization with minimal subtraction and a coordinate-space cutoff scheme, we show the need to introduce a leading-order short-range operator, missing in all current calculations. We discuss strategies to determine the finite part of the short-range coupling by matching to lattice QCD or by relating it via chiral symmetry to isospin-breaking observables in the two-nucleon sector. Finally, we speculate on the impact of this new contribution on nuclear matrix elements of relevance to experiment.

Classical fragile-X phenotype in a female infant disclosed by comprehensive genomic studies.

BACKGROUND: We describe a female infant with Fragile-X syndrome, with a fully expanded FMR1 allele and preferential inactivation of the homologous X-chromosome carrying a de novo deletion. This unusual and rare case demonstrates the importance of a detailed genomic approach, the absence of which could be misguiding, and calls for reflection on the current clinical and diagnostic workup for developmental disabilities. CASE PRESENTATION: We present a female infant, referred for genetic testing due to psychomotor developmental delay without specific dysmorphic features or relevant family history. FMR1 mutation screening revealed a methylated full mutation and a normal but inactive FMR1 allele, which led to further investigation. Complete skewing of X-chromosome inactivation towards the paternally-inherited normal-sized FMR1 allele was found. No pathogenic variants were identified in the XIST promoter. Microarray analysis revealed a 439 kb deletion at Xq28, in a region known to be associated with extreme skewing of X-chromosome inactivation. CONCLUSIONS: Overall results enable us to conclude that the developmental delay is the cumulative result of a methylated FMR1 full mutation on the active X-chromosome and the inactivation of the other homologue carrying the de novo 439 kb deletion. Our findings should be taken into consideration in future guidelines for the diagnostic workup on the diagnosis of intellectual disabilities, particularly in female infant cases.

No-Go Theorem for Nonstandard Explanations of the τ→K_{S}πν_{τ} CP Asymmetry.

The CP asymmetry in τ→K_{S}πν_{τ}, as measured by the BABAR collaboration, differs from the standard model prediction by 2.8σ. Most nonstandard interactions do not allow for the required strong phase needed to produce a nonvanishing CP asymmetry, leaving only new tensor interactions as a possible mechanism. We demonstrate that, contrary to previous assumptions in the literature, the crucial interference between vector and tensor phases is suppressed by at least 2 orders of magnitude due to Watson's final-state-interaction theorem. Furthermore, we find that the strength of the relevant CP-violating tensor interaction is strongly constrained by bounds from the neutron electric dipole moment and D-D[over ¯] mixing. These observations together imply that it is extremely difficult to explain the current τ→K_{S}πν_{τ} measurement in terms of physics beyond the standard model originating in the ultraviolet.

Screening for Sex Chromosome Aneuploidy by Cell-Free DNA Testing: Patient Choice and Performance.

OBJECTIVE: To study patient choice regarding testing for sex chromosome aneuploidy (SCA) and the performance of cell-free DNA (cfDNA) screening for SCA. METHODS: Patient choice regarding screening for SCA and factors influencing this choice were evaluated in a single center. In a subsequent two-center study, cases that screened positive for SCA were analyzed to determine the positive predictive value (PPV) for each SCA. RESULTS: In all, 1,957 (61.9%) of the 3,162 patients undergoing cfDNA testing opted for SCA screening. Regression analysis demonstrated that independent predictors of a patient's decision for SCA were earlier gestational age, spontaneous conception, and cfDNA chosen as a primary method of screening. A total of 161 cases screened positive for SCA and follow-up data were available for 118 (73.3%). Forty-six of the 61 cases of 45,X were false-positive results and 15 were concordant with the fetal karyotype (PPV = 24.6%). Seventeen of the 22 cases of 47,XXX were false positive and 5 concordant (PPV = 22.7%). Eleven of the 30 cases of 47,XXY were false positive and 19 concordant (PPV = 63.3%). All 5 cases of 47,XYY were correctly identified, thus yielding a PPV of 100%. CONCLUSION: More than half of the patients undergoing cfDNA aneuploidy screening also opted for SCA testing, but they were less likely to do so in the presence of an increased risk of trisomy. SCAs involving the X chromosome had a lower PPV than those involving the Y chromosome.

Neutron Electric Dipole Moment and Tensor Charges from Lattice QCD.

We present lattice QCD results on the neutron tensor charges including, for the first time, a simultaneous extrapolation in the lattice spacing, volume, and light quark masses to the physical point in the continuum limit. We find that the "disconnected" contribution is smaller than the statistical error in the "connected" contribution. Our estimates in the modified minimal subtraction scheme at 2 GeV, including all systematics, are g_{T}^{d-u}=1.020(76), g_{T}^{d}=0.774(66), g_{T}^{u}=-0.233(28), and g_{T}^{s}=0.008(9). The flavor diagonal charges determine the size of the neutron electric dipole moment (EDM) induced by quark EDMs that are generated in many new scenarios of CP violation beyond the standard model. We use our results to derive model-independent bounds on the EDMs of light quarks and update the EDM phenomenology in split supersymmetry with gaugino mass unification, finding a stringent upper bound of d_{n}<4×10^{-28} e cm for the neutron EDM in this scenario.

Three-Year Follow-Up of a Prenatally Ascertained Apparently Non-Mosaic sSMC(10): Delineation of a Non-Critical Region.

Small supernumerary marker chromosomes (sSMC) originating from chromosome 10 are rare and usually found in mosaic form. We present a de novo apparently non-mosaic sSMC(10) prenatally diagnosed in amniotic fluid and postnatally confirmed in peripheral blood. Characterization by array-CGH showed a pericentromeric duplication of 7.1 Mb of chromosome 10. The fetus did not show ultrasound abnormalities, and a normal female phenotype was observed during a 3-year postnatal follow-up. The absence of phenotypic abnormalities in the present case provides evidence of a non-critical pericentromeric region in 10p11.21q11.1 (hg19 35,355,570-42,448,569) associated with a duplication.

Prenatal invasive testing: a 13-year single institution experience.

OBJECTIVES: To analyze trends in screening and invasive prenatal diagnosis over a 13-year period in relation to changes in the national prenatal screening policy. METHODS: Fetal karyotypes obtained following 11 045 prenatal invasive procedures between January 1999 and December 2011 were retrospectively reviewed. Referral indications were classified as medical and non-medical (anxiety). The number of tests per relevant chromosomal abnormalities (CA) detected in both groups adjusted for indication was calculated. RESULTS: A total of 414 CA were detected (3.8%), 355 of which were considered clinically significant. The percentage of invasive procedures has declined from 49% to 12%, although cases referred by anxiety have increased from 22% to 55%. A total of 3129 invasive procedures did not have any medical indication (28%) and 13 relevant CA (0.42%) were found in this group. In this low-risk series, the index "number of invasive testing needed to detect 1 relevant CA" adjusted for indication was 241. CONCLUSIONS: Changes in our national prenatal policy through this 13-year period show an increasing efficiency of prenatal detection of CA. However, despite the intensifying screening policies, low-risk pregnant women show a growing demand for prenatal invasive testing and a baseline risk for cytogenetic abnormality of 1/241.

Evaluation of sample stability and automated DNA extraction for fetal sex determination using cell-free fetal DNA in maternal plasma.

OBJECTIVE: The detection of paternally inherited sequences in maternal plasma, such as the SRY gene for fetal sexing or RHD for fetal blood group genotyping, is becoming part of daily routine in diagnostic laboratories. Due to the low percentage of fetal DNA, it is crucial to ensure sample stability and the efficiency of DNA extraction. We evaluated blood stability at 4°C for at least 24 hours and automated DNA extraction, for fetal sex determination in maternal plasma. METHODS: A total of 158 blood samples were collected, using EDTA-K tubes, from women in their 1st trimester of pregnancy. Samples were kept at 4°C for at least 24 hours before processing. An automated DNA extraction was evaluated, and its efficiency was compared with a standard manual procedure. The SRY marker was used to quantify cfDNA by real-time PCR. RESULTS: Although lower cfDNA amounts were obtained by automated DNA extraction (mean 107,35 GE/mL versus 259,43 GE/mL), the SRY sequence was successfully detected in all 108 samples from pregnancies with male fetuses. CONCLUSION: We successfully evaluated the suitability of standard blood tubes for the collection of maternal blood and assessed samples to be suitable for analysis at least 24 hours later. This would allow shipping to a central reference laboratory almost from anywhere in Europe.

Development and validation of multiplex real-time PCR assay for noninvasive prenatal assessment of fetal RhD status and fetal sex in maternal plasma.

OBJECTIVE: Noninvasive prenatal detection of RhD status and fetal sex is becoming part of daily practice in clinical laboratories. We evaluated a high throughput procedure for automated DNA extraction and developed a multiplex real-time PCR (rt-PCR) for the simultaneous detection of three fetal loci in a single reaction to assess fetal sex and RhD status in maternal plasma. METHODS: An automated DNA extraction method was evaluated together with a new multiplex rt-PCR assay for the simultaneous detection of exons 5 and 7 of the RHD gene together with the Y chromosome marker DYS14 in maternal plasma. The test was evaluated on 60 samples of known fetal genotype obtained from RhD-negative pregnant women before being applied prospectively on 158 consecutive clinical cases. Results were compared with newborn phenotypes. RESULTS: Automated DNA extraction allowed successful analysis of all samples. DYS14 was detected in 118 cases (male fetuses) and both RHD exon 5 and 7 were detected in 148 samples. In 70 samples neither RHD exon 5 nor RHD exon 7 were detected (RhD-negative fetuses). Absence of all three sequences (female RhD-negative fetuses) was assessed in 33 samples. All prenatal results were in concordance with postnatal RhD status and fetal sex without false- positive or -negative results. CONCLUSION: The automated DNA extraction procedure coupled with a novel multiplex rt-PCR assay proved accurate, efficient and reliable allowing rapid and high throughput noninvasive determination of fetal sex and RhD status in clinical samples.

Comparison of the f-HPV typing™ and Hybrid Capture II® assays for detection of high-risk HPV genotypes in cervical samples.

Human papillomavirus genotyping is being considered in cervical screening programs and for monitoring the effectiveness of HPV vaccination. Both approaches require access to fast, easy and high-throughput technology. The aim of this study was to compare a new commercial assay (f-HPV typing™) with the Hybrid Capture II® (HC2) to detect HPV infection. The F-HPV typing is a multiplex fluorescent PCR method recognizing E6 and E7 regions of 13 high-risk (HR) HPV types, the same set of HR-types targeted HC2 test. A subset of 157 cervical samples was tested with both assays. The percentage of positive HR-HPV DNA samples was 24% (37/155) by HC2 and 33% (49/155) by f-HPV typing. Concordant results were found in 133/155 (overall agreement, 85.8%; Cohen's kappa=0.65). The analytical sensitivity and specificity of f-HPV were 97.6 and 93, respectively. In conclusion, this study shows that the f-HPV assay provides a good alternative to HC2 to detect HPV infection, allowing simple and rapid HPV genotyping and detecting multiple infections.

Prenatal Diagnosis of Chromosome Abnormalities: A 13-Year Institution Experience.

OBJECTIVE: To analyze trends in screening and invasive prenatal diagnosis of chromosome abnormalities (CA) over a 13-year period and correlate them to changes in the national prenatal screening policy. METHODS: We retrospectively reviewed Down syndrome (DS) screening tests and fetal karyotypes obtained by prenatal invasive testing (IT) in our fetal medicine unit between January 1999 and December 2011. RESULTS: A total of 24,226 prenatal screening tests for DS and 11,045 invasive procedures have been analyzed. Over a 13-year period, utilization of non-invasive screening methods has significantly increased from 57% to 89%. The percentage of invasive procedures has declined from 49% to 12%, although the percentage of IT performed for maternal anxiety has increased from 22% to 55%. The percentage of detected CA increased from 2.5% to 5.9%. Overall, 31 invasive procedures are needed to diagnose 1 abnormal case, being 23 procedures in medical indications and 241 procedures in non-medical indications. CONCLUSIONS: Our experience on screening and invasive prenatal diagnostic practice shows a decrease of the number of IT, with a parallel decline in medical indications. There is an increasing efficiency of prenatal screening program to detect CA. Despite the increasing screening policies, our population shows a growing request for prenatal IT. The a priori low risk population shows a not negligible residual risk for relevant CA. This observation challenges the current prenatal screening strategy focused on DS; showing that the residual risk is higher than the current cut-off used to indicate an invasive technique.

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).

Prospective validation of quantitative fluorescent polymerase chain reaction for rapid detection of common aneuploidies.

PURPOSE: To prospectively validate a quantitative fluorescent polymerase chain reaction (PCR) assay as a method of rapid prenatal aneuploidy detection for chromosomes 13, 18, 21, X, and Y. METHODS: A commercial quantitative fluorescent PCR kit was validated on 200 known, blinded, prenatal DNA specimens. The kit was then validated prospectively on 1069 amniotic fluid specimens, and the results were compared with the karyotype results and the results of interphase fluorescence in situ hybridization testing, when performed in the course of standard care. Turnaround time was monitored in a subset of the prospective specimens. RESULTS: The analytical sensitivity and specificity of testing in the validation specimens were 98.9% and 100%, respectively. There were no false positives and a single false negative, a mosaic sex chromosome aneuploidy interpreted as normal. In the prospective study, the analytical sensitivity and specificity were 98% and 100%, respectively. No false positives and a single false negative, again a sex chromosome mosaic, were detected. Overall, 72.5% of all chromosomal anomalies and 87.7% of clinically significant chromosome anomalies were detected by quantitative fluorescent PCR. The average and median turnaround times were 30.5 and 25.1 hours, respectively. CONCLUSIONS: Quantitative fluorescent PCR is a robust and accurate method of rapid prenatal aneuploidy detection.

Superfluid heat conduction and the cooling of magnetized neutron stars.

We report on a new mechanism for heat conduction in the neutron star crust. We find that collective modes of superfluid neutron matter, called superfluid phonons, can influence heat conduction in magnetized neutron stars. They can dominate the heat conduction transverse to the magnetic field when the magnetic field B> approximately 10(13) G. At a density of rho approximately 10(12)-10(14) g/cm3, the conductivity due to superfluid phonons is significantly larger than that due to lattice phonons and is comparable to electron conductivity when the temperature approximately 10(8) K. This new mode of heat conduction can limit the surface anisotropy in highly magnetized neutron stars. Cooling curves of magnetized neutron stars with and without superfluid heat conduction could show observationally discernible differences.

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.