Incremental yield of whole-genome sequencing over chromosomal microarray analysis and exome sequencing for congenital anomalies in prenatal period and infancy: systematic review and meta-analysis.

OBJECTIVES: First, to determine the incremental yield of whole-genome sequencing (WGS) over quantitative fluorescence polymerase chain reaction (QF-PCR)/chromosomal microarray analysis (CMA) with and without exome sequencing (ES) in fetuses, neonates and infants with a congenital anomaly that was or could have been detected on prenatal ultrasound. Second, to evaluate the turnaround time (TAT) and quantity of DNA required for testing using these pathways. METHODS: This review was registered prospectively in December 2022. Ovid MEDLINE, EMBASE, MEDLINE (Web of Science), The Cochrane Library and ClinicalTrials.gov databases were searched electronically (January 2010 to December 2022). Inclusion criteria were cohort studies including three or more fetuses, neonates or infants with (i) one or more congenital anomalies; (ii) an anomaly which was or would have been detectable on prenatal ultrasound; and (iii) negative QF-PCR and CMA. In instances in which the CMA result was unavailable, all cases of causative pathogenic copy number variants > 50 kb were excluded, as these would have been detectable on standard prenatal CMA. Pooled incremental yield was determined using a random-effects model and heterogeneity was assessed using Higgins' I2 test. Subanalyses were performed based on pre- or postnatal cohorts, cases with multisystem anomalies and those meeting the NHS England prenatal ES inclusion criteria. RESULTS: A total of 18 studies incorporating 902 eligible cases were included, of which eight (44.4%) studies focused on prenatal cohorts, incorporating 755 cases, and the remaining studies focused on fetuses undergoing postmortem testing or neonates/infants with congenital structural anomalies, constituting the postnatal cohort. The incremental yield of WGS over QF-PCR/CMA was 26% (95% CI, 18-36%) (I2 = 86%), 16% (95% CI, 9-24%) (I2 = 85%) and 39% (95% CI, 27-51%) (I2 = 53%) for all, prenatal and postnatal cases, respectively. The incremental yield increased in cases in which sequencing was performed in line with the NHS England prenatal ES criteria (32% (95% CI, 22-42%); I2 = 70%) and in those with multisystem anomalies (30% (95% CI, 19-43%); I2 = 65%). The incremental yield of WGS for variants of uncertain significance (VUS) was 18% (95% CI, 7-33%) (I2 = 74%). The incremental yield of WGS over QF-PCR/CMA and ES was 1% (95% CI, 0-4%) (I2 = 47%). The pooled median TAT of WGS was 18 (range, 1-912) days, and the quantity of DNA required was 100 ± 0 ng for WGS and 350 ± 50 ng for QF-PCR/CMA and ES (P = 0.03). CONCLUSION: While WGS in cases with congenital anomaly holds great promise, its incremental yield over ES is yet to be demonstrated. However, the laboratory pathway for WGS requires less DNA with a potentially faster TAT compared with sequential QF-PCR/CMA and ES. There was a relatively high rate of VUS using WGS. © 2023 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.

Amniotic fluid gamma-glutamyl transferase for prediction of biliary atresia in cases of non-visualisation of the fetal gallbladder: a retrospective study using a validated analytical platform and local reference range.

INTRODUCTION: The level of amniotic fluid gamma-glutamyl transferase (AFGGT) may help identify biliary atresia (BA) in cases of non-visualisation of the fetal gallbladder (NVFGB). This study aimed to validate a serum/plasma matrix-based gamma-glutamyl transferase (GGT) assay for amniotic fluid (AF) samples, establish a local gestational age-specific AFGGT reference range, and evaluate the efficacy of AFGGT for predicting fetal BA in pregnancies with NVFGB using the constructed reference range. METHODS: The analytical performance of a serum/plasma matrix-based GGT assay on AF samples was evaluated using a Cobas c502 analyser. Amniotic fluid gamma-glutamyl transferase levels in confirmed euploid singleton pregnancies (16+0 to 22+6 weeks of gestation) were determined using the same analyser to establish a local gestational age-specific reference range (the 2.5th to 97.5th percentiles). This local reference range was used to determine the positive predictive value (PPV) and negative predictive value (NPV) of AFGGT level <2.5th percentile for identifying fetal BA in euploid pregnancies with NVFGB. RESULTS: The serum/plasma matrix-based GGT assay was able to reliably and accurately determine GGT levels in AF samples. Using the constructed local gestational age-specific AFGGT reference range, the NPV and PPV of AFGGT level <2.5th percentile for predicting fetal BA in pregnancies with NVFGB were 100% and 25% (95% confidence interval=0, 53), respectively. CONCLUSION: In pregnancies with NVFGB, AFGGT level ≥2.5th percentile likely excludes fetal BA. Although AFGGT level <2.5th percentile is not diagnostic of fetal BA, fetuses with AFGGT below this level should be referred for early postnatal investigation.

Exploring the diagnostic utility of genome sequencing for fetal congenital heart defects.

OBJECTIVE: The diagnostic yield for congenital heart defects (CHD) with routine genetic testing is around 10%-20% when considering pathogenic CNVs or aneuploidies as positive findings. This is a pilot study to investigate the utility of genome sequencing (GS) for prenatal diagnosis of CHD. METHODS: Genome sequencing (GS, 30X) was performed on 13 trios with CHD for which karyotyping and/or chromosomal microarray results were non-diagnostic. RESULTS: Trio GS provided a diagnosis for 4/13 (30.8%) fetuses with complex CHDs and other structural anomalies. Findings included pathogenic or likely pathogenic variants in DNAH5, COL4A1, PTPN11, and KRAS. Of the nine cases without a genetic etiology by GS, we had outcome follow-up data on eight. For five of them (60%), the parents chose to keep the pregnancy. A balanced translocation [46,XX,t(14; 22)(q32.33; q13.31)mat] was detected in a trio with biallelic DNAH5 mutations, which together explained the recurrent fetal situs inversus and dextrocardia that was presumably due to de novo Phelan-McDermid syndrome. A secondary finding of a BRCA2 variant and carrier status of HBB, USH2A, HBA1/HBA2 were detected in the cohort. CONCLUSIONS: GS expands the diagnostic scope of mutation types over conventional testing, revealing the genetic etiology for fetal heart anomalies. Patients without a known genetic abnormality indicated by GS likely opted to keep pregnancy especially if the heart defect could be surgically repaired. We provide evidence to support the application of GS for fetuses with CHD.

Women with advanced pelvic organ prolapse and levator ani muscle avulsion would significantly benefit from mesh repair surgery.

OBJECTIVES: Mesh repair surgery for pelvic organ prolapse (POP) has been suspended in some countries owing to concerns about its associated complications. However, mesh repair has been shown to reduce the risk of prolapse recurrence after surgery. In view of this controversy, our aim was to assess the incidence of subjective and objective recurrence of POP following mesh repair surgery vs native-tissue repair in women with Stage-III or Stage-IV POP. METHODS: This was a prospective observational study of women who presented with Stage-III or Stage-IV POP and received primary prolapse surgery between 2013 and 2018. Transperineal ultrasound was performed before the operation and volumes were analyzed offline to assess the presence of levator ani muscle (LAM) avulsion. All women were counseled on either mesh repair or native-tissue reconstruction. The mesh-repair group was followed up for up to 5 years and the native-tissue-repair group for up to 2 years after the operation. Prolapse symptoms and POP quantification (POP-Q) staging were assessed at follow-up. Subjective recurrence of POP was defined as symptoms of prolapse (vaginal bulge sensation or dragging sensation) reported by the patient. Objective recurrence was defined as POP-Q ≥ Stage II. The subjective and objective recurrences of prolapse were compared between women with and those without mesh use. Multivariate regression analysis was used to identify risk factors for the recurrence of POP. RESULTS: A total of 154 Chinese women with Stage-III or Stage-IV prolapse were recruited. Of these, 104 (67.5%) underwent mesh repair (transabdominal in 57 women and transvaginal in 47 women) and 50 (32.5%) had native-tissue repair surgery. Ninety-five (61.7%) women had LAM avulsion. Both the subjective POP recurrence rate (4.8% vs 20.0%; P = 0.003) and the objective recurrence rate (20.2% vs 46.0%; P = 0.001) were significantly lower in the mesh-repair group than in the native-tissue-repair group. On multivariate logistic regression analysis, mesh repair was associated significantly with a reduced risk of subjective recurrence (odds ratio (OR), 0.20 (95% CI, 0.07-0.63)) and of objective recurrence (OR, 0.16 (95% CI, 0.07-0.55)) of prolapse. On subgroup analysis of women with LAM avulsion, mesh repair significantly reduced the risk of subjective recurrence (OR, 0.24 (95% CI, 0.07-0.87)) and objective recurrence (OR, 0.23 (95% CI, 0.09-0.57)) of POP. The incidence of mesh-related complications was low, and mesh exposure could be treated conservatively or by minor surgery. CONCLUSIONS: Mesh repair surgery, compared with native-tissue repair, was associated with a 5-fold reduction in the risk of subjective recurrence and a 6-fold reduction in the risk of objective recurrence of prolapse in women with Stage-III or Stage-IV POP. In women with concomitant LAM avulsion, mesh repair surgery was associated with a 4-fold reduction in both objective and subjective recurrence of POP. The rate of mesh-related complications was low, and mesh exposure could be treated conservatively or by minor surgery. The benefit of mesh surgery for these high-risk women appears to outweigh the risks of mesh complications, and it could be a treatment option for this group of women. © 2020 International Society of Ultrasound in Obstetrics and Gynecology.

Clinical utility of expanded non-invasive prenatal screening and chromosomal microarray analysis in high-risk pregnancy.

OBJECTIVE: To evaluate the utility of expanded non-invasive prenatal screening (NIPS), compared with chromosomal microarray analysis (CMA), for the detection of chromosomal abnormalities in high-risk pregnancies. METHODS: This was a multicenter retrospective study of singleton pregnancies at high risk for chromosomal abnormality. Patients who underwent expanded NIPS and CMA sequentially during pregnancy from 2015 to 2019 were included in the analysis. Pregnancies with a positive result for sex chromosome aneuploidy were excluded as the full details could not be retrieved. The utility of expanded NIPS and CMA for detection of chromosomal abnormalities in this cohort was compared by assessing the concordance between the results. RESULTS: Of the 774 included high-risk pregnancies, 550 (71.1%) had a positive NIPS result, while a positive CMA result was detected in 308 (39.8%) cases. The rate of full or partial concordance between NIPS and CMA was 82.2%, 59.6% and 25.0% for trisomies 21, 18 and 13, respectively. For rare aneuploidies and segmental imbalances, NIPS and CMA results were fully or partially concordant in 7.5% and 33.3% of cases, respectively. Copy-number variants < 5 Mb were detected more often by CMA, with an incidence of 7.9% (61/774) compared with 3.1% (24/774) by NIPS. A genetic aberration was detected by CMA in 1 in 17 (5.8%) high-risk pregnancies that had a negative or non-reportable NIPS result. CONCLUSION: CMA allows for comprehensive detection of genome-wide chromosomal abnormalities in high-risk pregnancies. CMA should be offered instead of expanded NIPS for high-risk pregnancies. Copyright © 2020 ISUOG. Published by John Wiley & Sons Ltd.

Intermediate- to long-term outcomes of transvaginal mesh for treatment of Asian women with pelvic organ prolapse.

INTRODUCTION: Short-term follow-up analyses suggest that transvaginal mesh has limited application for pelvic organ prolapse (POP) treatment. This study evaluated the intermediate- and long-term outcomes of transvaginal mesh surgery. METHODS: This retrospective study included all women who underwent transvaginal mesh surgery in one urogynaecology centre. Inclusion criteria were women with stage III/IV POP, age ≥65 years, and (preferably) sexual inactivity. Concomitant sacrospinous fixation and mid-urethral slings were offered for stage III/IV apical POP and urodynamic stress incontinence, respectively. Women were followed up for 5 years. Subjective recurrence was defined as reported prolapse symptoms. Objective recurrence was defined as stage II prolapse or above. Mesh complications and patient satisfaction were reviewed. RESULTS: Of 183 women who underwent transvaginal mesh surgery, 156 had ≥1 year of follow-up (mean, 50 ± 22 months). Subjective and objective recurrence rates were 5.1% and 10.9%, respectively. The mesh erosion rate was 9.6%; all affected women received local oestrogen treatment or bedside surgical excision. Three women received transobturator tension-free transvaginal tape for de novo (n=1) or preoperative urodynamic stress incontinence who did not undergo concomitant surgery (n=2); 14% of the women had de novo urgency urinary incontinence. No women reported chronic pain. Overall, 98% were 'satisfied' or 'very satisfied' with the operation. CONCLUSION: During 50 months of follow-up, transvaginal mesh surgery for stage III/IV POP had low subjective and objective recurrence rates. The total re-operation rate was 9.6%. Most women were satisfied with the operation. Based on the risk-benefit profile, transvaginal mesh surgery may be suitable for women who have advanced POP.

Chromosomal abnormalities and neurological outcomes in fetal cerebral ventriculomegaly: a retrospective cohort analysis.

INTRODUCTION: This study investigated the incidences of chromosomal abnormalities and the neurological outcomes according to the degree of fetal cerebral ventriculomegaly. METHODS: All women with antenatal ultrasound diagnosis of fetal cerebral ventriculomegaly were retrospectively identified from two maternal-fetal medicine units in Hong Kong from January 2014 to December 2018. Degrees of fetal ventriculomegaly were classified as mild (10-11.9 mm), moderate (12-14.9 mm), or severe (≥15 mm). Genetic investigation results were reviewed, including conventional karyotyping and chromosomal microarray analysis (CMA); correlations between chromosomal abnormalities and the degree of fetal ventriculomegaly were explored. The neurological outcomes of subsequent live births were analysed to identify factors associated with developmental delay. RESULTS: Of 84 cases (ie, pregnant women and their fetuses) included, 46 (54.8%) exhibited isolated fetal ventriculomegaly, 55 (65.5%) had mild cerebral ventriculomegaly, and 29 (34.5%) had moderate or severe cerebral ventriculomegaly. Overall, 20% (14/70) of cases had chromosomal abnormalities. Moreover, 12% (3/25) of mild isolated ventriculomegaly cases had abnormal karyotype or CMA results. The CMA provided an incremental diagnostic yield of 8.6% (6/70), compared with conventional karyotyping; 4.3% exhibited pathogenic variants and 4.3% exhibited variants of uncertain significance. Among the 53 live births in the cohort, fewer cases of mild isolated ventriculomegaly were associated with developmental delay than more severe isolated ventriculomegaly (9.7% vs 41.7%, P<0.03). CONCLUSIONS: Chromosomal microarray analysis testing should be offered to all women with fetal cerebral ventriculomegaly, including women with isolated mild ventriculomegaly. The incidence of developmental delay after birth increases with the degree of prenatal cerebral ventriculomegaly.

Expanded carrier screening using next-generation sequencing of 123 Hong Kong Chinese families: a pilot study.

INTRODUCTION: To determine the carrier frequency and common mutations of Mendelian variants in Chinese couples using next-generation sequencing (NGS). METHODS: Preconception expanded carrier testing using NGS was offered to women who attended the subfertility clinic. The test was then offered to the partners of women who had positive screening results. Carrier frequency was calculated, and the results of the NGS panel were compared with those of a target panel. RESULTS: One hundred twenty-three women and 20 of their partners were screened. Overall, 84 (58.7%) individuals were identified to be carriers of at least one disease, and 68 (47.6%) were carriers after excluding thalassaemias. The most common diseases found were GJB2-related DFNB1 nonsyndromic hearing loss and deafness (1 in 4), alpha-thalassaemia (1 in 7), beta-thalassaemia (1 in 14), 21-hydroxylase deficient congenital adrenal hyperplasia (1 in 13), Pendred's syndrome (1 in 36), Krabbe's disease (1 in 48), and spinal muscular atrophy (1 in 48). Of the 43 identified variants, 29 (67.4%) were not included in the American College of Medical Genetics and Genomics or American College of Obstetrics and Gynecology guidelines. Excluding three couples with alpha-thalassaemia, six at-risk couples were identified. CONCLUSION: The carrier frequency of the investigated members of the Chinese population was 58.7% overall and 47.6% after excluding thalassaemias. This frequency is higher than previously reported. Expanded carrier screening using NGS should be provided to Chinese people to improve the detection rate of carrier status and allow optimal pregnancy planning.

TBX6 null variants and a common hypomorphic allele in congenital scoliosis.

BACKGROUND: Congenital scoliosis is a common type of vertebral malformation. Genetic susceptibility has been implicated in congenital scoliosis. METHODS: We evaluated 161 Han Chinese persons with sporadic congenital scoliosis, 166 Han Chinese controls, and 2 pedigrees, family members of which had a 16p11.2 deletion, using comparative genomic hybridization, quantitative polymerase-chain-reaction analysis, and DNA sequencing. We carried out tests of replication using an additional series of 76 Han Chinese persons with congenital scoliosis and a multicenter series of 42 persons with 16p11.2 deletions. RESULTS: We identified a total of 17 heterozygous TBX6 null mutations in the 161 persons with sporadic congenital scoliosis (11%); we did not observe any null mutations in TBX6 in 166 controls (P<3.8×10(-6)). These null alleles include copy-number variants (12 instances of a 16p11.2 deletion affecting TBX6) and single-nucleotide variants (1 nonsense and 4 frame-shift mutations). However, the discordant intrafamilial phenotypes of 16p11.2 deletion carriers suggest that heterozygous TBX6 null mutation is insufficient to cause congenital scoliosis. We went on to identify a common TBX6 haplotype as the second risk allele in all 17 carriers of TBX6 null mutations (P<1.1×10(-6)). Replication studies involving additional persons with congenital scoliosis who carried a deletion affecting TBX6 confirmed this compound inheritance model. In vitro functional assays suggested that the risk haplotype is a hypomorphic allele. Hemivertebrae are characteristic of TBX6-associated congenital scoliosis. CONCLUSIONS: Compound inheritance of a rare null mutation and a hypomorphic allele of TBX6 accounted for up to 11% of congenital scoliosis cases in the series that we analyzed. (Funded by the National Basic Research Program of China and others.).

Women's preference for non-invasive prenatal DNA testing versus chromosomal microarray after screening for Down syndrome: a prospective study.

OBJECTIVE: To examine preferences for follow-up testing in women screened with high or intermediate risk for Down syndrome in the first or second trimester. DESIGN: Prospective cohort study. SETTING: Three public hospitals in Hong Kong, China. SAMPLE: Women with pregnancies termed as high risk (≥1:250; HR) or intermediate risk (1:251-1200; IR) for Down syndrome. METHODS: Women with pregnancies screened as HR were offered the choices of: (1) an invasive test plus chromosomal microarray (CMA) to obtain more detailed fetal genetic information; (2) non-invasive cell-free prenatal DNA screening (NIPT) to detect trisomies 13, 18 and 21, and to avoid procedure-related miscarriage; and (3) to decline any further testing. Women received standardised counselling informing them that the reporting times were identical, the procedure miscarriage risk was 0.1-0.2% and that there was no charge for screening. Women with IR pregnancies (1:251-1200) were offered NIPT as a secondary screening test. MAIN OUTCOME MEASURES: Uptake rate for NIPT. RESULTS: Three hundred and forty-seven women had pregnancies deemed as HR; 344 (99.1%) women opted for follow-up testing, 216 (62.2%) of whom chose NIPT. Five hundred and seven of 614 women (82.6%) with IR risk chose NIPT. Seven (21%) of 34 women with nuchal translucency ≥3.5 mm opted for NIPT. CONCLUSION: In a setting where reporting times are similar and there is no cost difference between options, approximately 60% of women with pregnancies classed as HR would opt for NIPT, offering simple but limited aneuploidy assessment, over a diagnostic procedure with comprehensive and more detailed assessment. TWEETABLE ABSTRACT: 60% of pregnant Chinese women prefer NIPT over CMA when screened as high risk for Down syndrome.

Identification of fragile X pre-mutation carriers in the Chinese obstetric population using a robust FMR1 polymerase chain reaction assay: implications for screening and prenatal diagnosis.

INTRODUCTION: There is significant morbidity associated with fragile X syndrome. Unfortunately, most maternal carriers are clinically silent during their reproductive years. Because of this, many experts have put forward the notion of preconception or prenatal fragile X carrier screening for females. This study aimed to determine the prevalence of fragile X syndrome pre-mutation and asymptomatic full-mutation carriers in a Chinese pregnant population, and the distribution of cytosine-guanine-guanine (CGG) repeat numbers using a robust fragile X mental retardation 1 (FMR1) polymerase chain reaction assay. METHODS: This was a cross-sectional survey in prospectively recruited pregnant women from a university hospital in Hong Kong. Chinese pregnant women without a family history of fragile X syndrome were recruited between April 2013 and May 2015. A specific FMR1 polymerase chain reaction assay was performed on peripheral blood to determine the CGG repeat number of the FMR1 gene. Prenatal counselling was offered to full-mutation and pre-mutation carriers. RESULTS: In 2650 Chinese pregnant women, two individuals with pre-mutation alleles (0.08%, one in 1325) and one asymptomatic woman with full-mutation (0.04%, one in 2650) alleles were identified. The overall prevalence of pre-mutation and full-mutation alleles was 0.11% (1 in 883). Furthermore, 30 (1.1%) individuals with intermediate alleles were detected. In the 2617 women with normal CGG repeats, the most common CGG repeat allele was 30. CONCLUSIONS: The overall prevalence of pre-mutation and asymptomatic full-mutation carriers in the Chinese pregnant population was one in 883, detected by a new FMR1 polymerase chain reaction assay.

SNaPshot reveals high mutation and carrier frequencies of 15 common hearing loss mutants in a Chinese newborn cohort.

Genetic causes account for more than half of congenital hearing loss cases. The most frequent mutations found in non-syndromic hearing loss patients occur in GJB2 and SLC26A4. Mitochondrial genome mutations are also prevalent. However, the frequency of common hearing loss mutations in the Chinese population has not yet been well estimated. Here, we implemented the SNaPshot genotyping method to investigate the carrier frequency of 15 commonly reported hearing loss mutations in GJB2, SLC26A4 and the mitochondrial genome based on a cohort of 5800 neonates in China. Up to 15.9% (923/5800) of the newborns carry at least one mutant allele. The top three were GJB2-c.109G>A, GJB2-c.235delC, and SLC26A4-c.919A>G, with notably high carrier frequencies of 1/10, 1/53 and 1/62 respectively, and mt-7444G>A with 1/141 was the most frequent allele in the mitochondrial genome. In this cohort, 0.48% (28/5800) of neonates were genetically diagnosed with hearing loss, from which seven cases failed an OAE test. This is the first epidemiological study of non-syndromic hearing loss in Chinese newborns indicating a notably high carrier frequency (1 per 6.3 newborns) among these 15 mutant alleles. Our carrier frequency data also aid in effective risk assessment and genetic counseling for hearing loss patients in the Chinese population.

Role of adrenal vein sampling in primary aldosteronism: the Monash Health experience.

BACKGROUND: Adrenal vein sampling (AVS) is useful for distinguishing unilateral versus bilateral hypersecretion in primary aldosteronism (PA), but is technically challenging. Furthermore, the use of adrenocorticotropic hormone (ACTH)-stimulation in AVS is controversial. We implemented a Monash Health-specific AVS protocol in 2010. AIM: The audit aimed to: (i) examine the impact of a dedicated protocol on success rates of AVS at a tertiary referral centre; (ii) evaluate the impact of AVS on sub-typing of PA; and (iii) assess the utility of ACTH stimulation in AVS. METHODS: AVS was performed on patients with PA confirmed by positive saline suppression testing (aldosterone level >140 pmol/L post-saline infusion), with sequential sampling of adrenal and peripheral veins, pre- and post-ACTH infusion. Patients with unilateral aldosterone-producing adenoma diagnosed on successful AVS were referred for adrenalectomy. RESULTS: Between 2010 and 2014 inclusive, a total of 28 AVS procedures was performed, with complete pre- and post-ACTH data for 19 procedures. Bilateral successful cannulation rates improved post-implementation of our protocol (61% vs 41%). Of the patients, 32% had discordant imaging and AVS results: four patients with unilateral adenomas did not lateralise on AVS and were managed medically; four patients with bilateral or no adenomas on imaging, lateralised on AVS and had surgery. Overall, use of ACTH did not increase successful cannulation and tended to mask lateralisation. CONCLUSION: AVS is crucial in subtype classification of PA and should be performed by a dedicated radiologist with a standardised protocol. AVS outcomes were not improved with the use of ACTH stimulation.

Congenital hydrocephalus and hemivertebrae associated with de novo partial monosomy 6q (6q25.3→qter).

This study was conducted to describe a prenatal case of congenital hydrocephalus and hemivertebrae with a 6q terminal deletion and to investigate the possible correlation between the genotype and phenotype of the proband. We performed an array-based comparative genomic hybridization (aCGH) analysis on a fetus diagnosed with congenital hydrocephalus and hemivertebrae. The deletion, spanning 10.06 Mb from 6q25.3 to 6qter, was detected in this fetus. The results of aCGH, karyotype and fluorescent in situ hybridization (FISH) analyses in the healthy parents were normal, which confirmed that the proband's copy-number variant (CNV) was de novo. This deleted region encompassed 97 genes, including 28 OMIM genes. We discussed four genes (TBP, PSMB1, QKI and Pacrg) that may be responsible for hydrocephalus while the T gene may have a role in hemivertebra. We speculate that five genes in the 6q terminal deletion region were potentially associated with hemivertebrae and hydrocephalus in the proband.

Diagnostic accuracy of the BACs-on-Beads™ assay versus karyotyping for prenatal detection of chromosomal abnormalities: a retrospective consecutive case series.

OBJECTIVE: To evaluate the diagnostic performance of the BACs-on-Beads(™) (BoBs(™)) assay for prenatal detection of chromosomal abnormalities. DESIGN: Retrospective study. SETTING: Tertiary prenatal diagnosis centre. POPULATION: Women referred for prenatal diagnosis. METHODS: We retrieved 2153 archived DNA samples collected between January 2010 and August 2011 for the BoBs(™) assay. These samples had previously been tested by quantitative fluorescence polymerase chain reaction (QF-PCR) and karyotyping. In the BoBs(™) assay a sample was defined as normal disomic when the ratio of the fluorescence intensities in a chromosome locus lay within the threshold (mean ratio ± 2SD), and as deleted or duplicated when the ratio was below the lower threshold (0.6-0.8) or above the upper threshold (1.3-1.4), respectively. The BoBs(™) results were further validated by microarray and compared in a blinded manner with the original QF-PCR and karyotyping results. MAIN OUTCOME MEASURES: Concordance of any numerical, structural, and submicroscopic chromosomal abnormalities between the methods. RESULTS: BACs-on-Beads(™) was similar to karyotyping and QF-PCR in detecting trisomy 13, trisomy 18, trisomy 21, and sex chromosomal aneuploidies, and superior to QF-PCR in detecting major structural abnormalities (53.3 versus 13.3%) and mosaicism (28.6 versus 0%) involving chromosomal abnormalities other than the common aneuploidies. BoBs(™) detected six microdeletion syndromes missed by karyotyping and QF-PCR; however, BoBs(™) missed two cases of triploidy identified by QF-PCR. Therefore, the sensitivity of BoBs(™) is 96.7% (95% CI 92.6-98.7%), and its specificity is 100% (95% CI 99.8-100%). CONCLUSIONS: BACs-on-Beads(™) can replace QF-PCR for triaging in prenatal diagnosis, and gives a better diagnostic yield than current rapid aneuploidy tests.

Is high fetal nuchal translucency associated with submicroscopic chromosomal abnormalities on array CGH?

OBJECTIVE: To examine the possible association between high fetal nuchal translucency thickness (NT) and pathogenic chromosomal copy number variants (CNVs) detected by array comparative genomic hybridization (CGH) in pregnancies with normal fetal karyotype. METHODS: Array CGH was carried out in stored samples of chorionic villi from 215 singleton pregnancies resulting in live births in which chorionic villus sampling at 11-13 weeks' gestation for high fetal NT (≥ 3.5 mm) had demonstrated normal karyotype. RESULTS: Median fetal NT was 4.0 (range, 3.5-9.5) mm. Array CGH detected additional CNVs in 1.4% (95% CI, 0.5-4.0) of the cases, but none of these was a known pathogenic CNV. CONCLUSION: High fetal NT in the absence of sonographically detectable defects may not be associated with pathogenic CNVs.

Non-invasive prenatal testing for fetal chromosomal abnormalities by low-coverage whole-genome sequencing of maternal plasma DNA: review of 1982 consecutive cases in a single center.

OBJECTIVE: To review the performance of non-invasive prenatal testing (NIPT) by low-coverage whole-genome sequencing of maternal plasma DNA at a single center. METHODS: The NIPT result and pregnancy outcome of 1982 consecutive cases were reviewed. NIPT was based on low coverage (0.1×) whole-genome sequencing of maternal plasma DNA. All subjects were contacted for pregnancy and fetal outcome. RESULTS: Of the 1982 NIPT tests, a repeat blood sample was required in 23 (1.16%). In one case, a conclusive report could not be issued, probably because of an abnormal vanished twin fetus. NIPT was positive for common trisomies in 29 cases (23 were trisomy 21, four were trisomy 18 and two were trisomy 13); all were confirmed by prenatal karyotyping (specificity=100%). In addition, 11 cases were positive for sex-chromosomal abnormalities (SCA), and nine cases were positive for other aneuploidies or deletion/duplication. Fourteen of these 20 subjects agreed to undergo further investigations, and the abnormality was found to be of fetal origin in seven, confined placental mosaicism (CPM) in four, of maternal origin in two and not confirmed in one. Overall, 85.7% of the NIPT-suspected SCA were of fetal origin, and 66.7% of the other abnormalities were caused by CPM. Two of the six cases suspected or confirmed to have CPM were complicated by early-onset growth restriction requiring delivery before 34 weeks. Fetal outcome of the NIPT-negative cases was ascertained in 1645 (85.15%). Three chromosomal abnormalities were not detected by NIPT, including one case each of a balanced translocation, unbalanced translocation and triploidy. There were no known false negatives involving the common trisomies (sensitivity=100%). CONCLUSIONS: Low-coverage whole-genome sequencing of maternal plasma DNA was highly accurate in detecting common trisomies. It also enabled the detection of other aneuploidies and structural chromosomal abnormalities with high positive predictive value.

A pilot study of urine cytokines in ketamine-associated lower urinary tract symptoms.

INTRODUCTION AND HYPOTHESIS: The aim of this study was to investigate urine cytokine and chemokine levels in symptomatic ketamine abusers compared with age-matched controls. METHODS: Midstream urine specimens were collected in a prospective study of 23 ketamine abusers and 27 controls who had never used ketamine. Their basic demographic and urinary symptoms were compared. The urine was analyzed by a multiplex panel screen for 19 cytokines/chemokines: EGF, GM-CSF, GRO, IL-1Ra, IL-5, IL-6, IL-7, IL-8, IL-10, IL-12p40, IL-12p70, IP-10, MCP-1, MIP-1b, sCD40L, sIL-2Ra, VEGF, MCP-4, and TARC using Luminex™ xMAP® technology. Protein concentration values were normalized to urine creatinine concentrations. RESULTS: Mean age of the control group was 21.1 ± 4.3 years (n = 27) and of the ketamine group was 20.6 ± 3.7 years (n = 23). All participants were women. The urine cytokine analysis showed a significant elevation in EGF levels in the ketamine group with lower urinary tract symptoms (LUTS) compared with the control group (p < 0.005). Levels of the remaining 18 proteins tested were not different from control values. CONCLUSIONS: Urinary EGF levels were increased among symptomatic ketamine abusers. This suggests inflammation and epithelial repair may play a role in ketamine-associated LUTS, and this may in turn help in understanding the pathophysiology of this disease entity, leading to better treatment options.

Prevalence of levator ani muscle injury in Chinese women after first delivery.

OBJECTIVES: To assess the prevalence of levator ani muscle injury in Chinese women after their first delivery and investigate associated factors. METHODS: A prospective observational study was conducted involving Chinese nulliparous women recruited in the first trimester of pregnancy. Translabial ultrasound was performed at 35-38 weeks' gestation and 8 weeks postpartum and three-dimensional volume datasets were obtained. Offline analysis to detect levator ani muscle injury was performed by investigators blinded to the delivery details. RESULTS: 339 women, with a mean age of 30.6 ± 3.9 years, completed the study. Overall, 201 (59.3%) had a spontaneous vaginal delivery, 62 (18.3%) an operative vaginal delivery (48 ventouse extraction and 14 forceps delivery), 14 (4.1%) an elective Cesarean section and 62 (18.3%) an emergency Cesarean section. No levator ani muscle injury was detected in any woman antenatally. After vaginal delivery, 57 (21.7% (95% CI, 16.7-26.7%)) women had levator ani muscle injury. The rates of injury for spontaneous vaginal delivery, ventouse extraction and forceps delivery were 15.4%, 33.3% and 71.4%, respectively. There was no levator ani muscle injury in the Cesarean section groups. Logistic regression analysis showed that only operative vaginal delivery (odds ratio, 3.09) was associated with an independent increase in the likelihood of levator ani muscle injury. Intrapartum epidural analgesics, duration of second stage of labor and infant birth weight were not independently associated with levator ani muscle injury. CONCLUSIONS: The prevalence of levator ani muscle injury in Chinese women after their first vaginal delivery was 21.7% (95% CI, 16.7-26.7%). Operative vaginal delivery was found to increase the likelihood of women suffering such injury. A longer follow-up of these women and future studies on the effects of episiotomy are proposed.