Is there a difference in the clinical profile and outcome of women using levonorgestrel IUD for abnormal uterine bleeding and those using it for contraception?: A comparative cross-sectional study.

Objective: The most common indications for Levonorgestrel intrauterine device (LNG-IUD) are contraception and management of abnormal uterine bleeding (AUB). This study was conducted with the aim of exploring the differences in the clinical profile and outcome of women using LNG-IUD for contraception and AUB. Materials and Methods: This was a retrospective comparative cross-sectional study of women who underwent LNG-IUD (52 mg) between 2012 and 2017. Their electronic health records were reviewed until the last documented follow-up or until December 2021. Results: A total of 235 women had LNG-IUD with an age range of 21 to 62 years and a mean of (37.98 years±6.76). Of these women, 153/235 (65.1%) had it for contraception and 82/235 (34.89%) had it for AUB. The follow-up was 1-94 months with (mean ± SEM) follow-up for the AUB group of (21.48±2.31) months and for contraception group was (20.74±1.76) months (p-value of 0.80). There was a significant difference between the two groups in the age and body mass index (BMI), where women who had LNG-IUD for AUB were older (mean of 42.54±6.49 years, p-value <0.001) and had higher BMI (31.88±7.52 kg/m2, p-value =0.011). All LNG-IUDs that were indicated for contraception were inserted in an outpatient setting. However, 68.3% in the AUB, the insertion was in the operating theater in conjunction with hysteroscopy. After combining both expulsion and removal of LNG-IUD during the follow-up period, there was no significant difference between the 2 groups in the overall retention rate during the follow-up (p-value =0.998). Conclusion: this study shows that women using LNG-IUD for the management of AUB are older and have a higher BMI compared with those using it for contraception. AUB women experienced more expulsion compared with the contraception group, but there was no difference between the 2 groups in the overall survival/retention of LNG-IUD.

Clinically significant findings in a decade-long retrospective study of prenatal chromosomal microarray testing.

BACKGROUND: Chromosomal microarray (CMA) is commonly utilized in the obstetrics setting. CMA is recommended when one or more fetal structural abnormalities is identified. CMA is also commonly used to determine genetic etiologies for miscarriages, fetal demise, and confirming positive prenatal cell-free DNA screening results. METHODS: In this study, we retrospectively examined 523 prenatal and 319 products-of-conception (POC) CMA cases tested at Nationwide Children's Hospital from 2011 to 2020. We reviewed the referral indications, the diagnostic yield, and the reported copy number variants (CNV) findings. RESULTS: In our cohort, the diagnostic yield of clinically significant CNV findings for prenatal testing was 7.8% (n = 41/523) compared to POC testing (16.3%, n = 52/319). Abnormal ultrasound findings were the most common indication present in 81% of prenatal samples. Intrauterine fetal demise was the common indication identified in POC samples. The most common pathogenic finding observed in all samples was isolated trisomy 21, detected in seven samples. CONCLUSION: Our CMA study supports the clinical utility of prenatal CMA for clinical management and identifying genetic etiology in POC arrays. In addition, it provides insight to the spectrum of prenatal and POC CMA results as detected in an academic hospital clinical laboratory setting that serves as a reference laboratory.

Clinical Cytogenetics: Current Practices and Beyond.

BACKGROUND: Throughout history, the field of cytogenetics has witnessed significant changes due to the constant evolution of technologies used to assess chromosome number and structure. Similar to the evolution of single nucleotide variant detection from Sanger sequencing to next-generation sequencing, the identification of chromosome alterations has progressed from banding to fluorescence in situ hybridization (FISH) to chromosomal microarrays. More recently, emerging technologies such as optical genome mapping and genome sequencing have made noteworthy contributions to clinical laboratory testing in the field of cytogenetics. CONTENT: In this review, we journey through some of the most pivotal discoveries that have shaped the development of clinical cytogenetics testing. We also explore the current test offerings, their uses and limitations, and future directions in technology advancements. SUMMARY: Cytogenetics methods, including banding and targeted assessments like FISH, continue to hold crucial roles in cytogenetic testing. These methods offer a rapid turnaround time, especially for conditions with a known etiology involving recognized cytogenetic aberrations. Additionally, laboratories have the flexibility to now employ higher-throughput methodologies to enhance resolution for cases with greater complexity.

Multisite Verification of a Targeted CFTR Polymerase Chain Reaction/Capillary Electrophoresis Assay That Evaluates Pathogenic Variants Across Diverse Ethnic and Ancestral Groups.

CONTEXT.­: Existing targeted cystic fibrosis screening assays miss important pathogenic CFTR variants in the ethnically diverse US population. OBJECTIVE.­: To evaluate the analytic performance of a multiplex polymerase chain reaction (PCR)/capillary electrophoresis (CE) CFTR assay panel that simultaneously interrogates primary pathogenic variants of different ethnic/ancestral groups. DESIGN.­: Performance characteristic assessment and variant coverage comparison of the panel with a focus on ethnicity-specific CFTR variants were performed. Sample DNA was primarily from whole blood or cell lines. Detection of CFTR carriers was compared across several commercially available CFTR kits and recommended variant sets based on panel content. RESULTS.­: The panel interrogated 65 pathogenic CFTR variants representing 92% coverage from a recent genomic sequencing survey of the US population, including 4 variants with top 5 frequency in African or Asian populations not reflected in other targeted panels. In simulation studies, the panel represented 95% of carriers across the global population, resulting in 6.9% to 19.0% higher carrier detection rate compared with 10 targeted panels or variant sets. Precision and sensitivity/specificity were 100% concordant. Multisite sample-level genotyping accuracy was 99.2%. Across PCR and CE instruments, sample-level genotyping accuracy was 97.1%, with greater than 99% agreement for all variant-level metrics. CONCLUSIONS.­: The CFTR assay achieves 92% or higher coverage of CFTR variants in diverse populations and provides improved pan-ethnic coverage of minority subgroups of the US populace. The assay can be completed within 5 hours from DNA sample to genotype, and performance data exceed acceptance criteria for analytic metrics. This assay panel content may help address gaps in ancestry-specific CFTR genotypes while providing a streamlined procedure with rapidly generated results.

Papillary Hemangioma Harbors Somatic GNA11 and GNAQ Mutations.

Papillary hemangioma (PH) is a small, primarily dermal lesion occurring predominantly in the head and neck in both children and adults. Its signature characteristics are dilated thin-walled channels containing papillary clusters of mainly capillary-sized vessels and endothelial cytoplasmic eosinophilic inclusions. Given certain histopathologic similarities to congenital hemangioma which harbor mutations in GNAQ and GNA11 , we investigated whether similar mutations are present in PH. Seven PH specimens were studied. All presented in the first 4 years of life, with one being noted at birth. With the exception of one lesion, all were in the head and neck. Lesions were bluish and ranged in size from 0.5 to 2.8 cm. Four samples had GNA11 p.Q209L and 3 had GNAQ p.Q209L missense mutations. Mutations in GNA11 and GNAQ are associated with other types of somatic vascular lesions including capillary malformation, congenital hemangioma, anastomosing hemangioma, thrombotic anastomosing hemangioma, and hepatic small cell neoplasm. Shared mutations in GNA11 and GNAQ may account for some overlapping clinical and pathologic features in these entities, perhaps explicable by the timing of the mutation or influence of the germline phenotype.

Exome sequencing in the pediatric neuromuscular clinic leads to more frequent diagnosis of both neuromuscular and neurodevelopmental conditions.

INTRODUCTION/AIMS: Exome sequencing (ES) has proven to be a valuable diagnostic tool for neuromuscular disorders, which often pose a diagnostic challenge. The aims of this study were to investigate the clinical outcomes associated with utilization of ES in the pediatric neuromuscular clinic and to determine if specific phenotypic features or abnormal neurodiagnostic tests were predictive of a diagnostic result. METHODS: This was a retrospective medical record review of 76 pediatric neuromuscular clinic patients who underwent ES. Based upon clinical assessment prior to ES, patients were divided into two groups: affected by neuromuscular (n = 53) or non-neuromuscular (n = 23) syndromes. RESULTS: A diagnosis was made in 28/76 (36.8%), with 29 unique disorders identified. In the neuromuscular group, a neuromuscular condition was confirmed in 78% of those receiving a genetic diagnosis. Early age of symptom onset was associated with a significantly higher diagnostic yield. The most common reason neuromuscular diagnoses were not detected on prior testing was due to causative genes not being present on disease-specific panels. Changes to medical care were made in 57% of individuals receiving a diagnosis on ES. DISCUSSION: These data further support ES as a powerful diagnostic tool in the pediatric neuromuscular clinic and highlight the advantages of ES over gene panels, including the ability to identify diagnoses regardless of etiology, identify genes newly associated with disease, and identify multiple confounding diagnoses. Rapid and accurate diagnosis by ES can not only end the patient's diagnostic odyssey, but often impacts patients' medical management and genetic counseling of families.

Expanding the Clinical Utility of Targeted RNA Sequencing Panels beyond Gene Fusions to Complex, Intragenic Structural Rearrangements.

Gene fusions are a form of structural rearrangement well established as driver events in pediatric and adult cancers. The identification of such events holds clinical significance in the refinement, prognostication, and provision of treatment in cancer. Structural rearrangements also extend beyond fusions to include intragenic rearrangements, such as internal tandem duplications (ITDs) or exon-level deletions. These intragenic events have been increasingly implicated as cancer-promoting events. However, the detection of intragenic rearrangements may be challenging to resolve bioinformatically with short-read sequencing technologies and therefore may not be routinely assessed in panel-based testing. Within an academic clinical laboratory, over three years, a total of 608 disease-involved samples (522 hematologic malignancy, 86 solid tumors) underwent clinical testing using Anchored Multiplex PCR (AMP)-based RNA sequencing. Hematologic malignancies were evaluated using a custom Pan-Heme 154 gene panel, while solid tumors were assessed using a custom Pan-Solid 115 gene panel. Gene fusions, ITDs, and intragenic deletions were assessed for diagnostic, prognostic, or therapeutic significance. When considering gene fusions alone, we report an overall diagnostic yield of 36% (37% hematologic malignancy, 41% solid tumors). When including intragenic structural rearrangements, the overall diagnostic yield increased to 48% (48% hematologic malignancy, 45% solid tumor). We demonstrate the clinical utility of reporting structural rearrangements, including gene fusions and intragenic structural rearrangements, using an AMP-based RNA sequencing panel.

Deep Brain Stimulation for the Management of AIFM1-Related Disabling Tremor: A Case Series.

The AIFM1 gene encodes a mitochondrial protein that acts as a flavin adenine dinucleotide-dependent nicotinamide adenine dinucleotide oxidase and apoptosis regulator. Monoallelic pathogenic AIFM1 variants result in a spectrum of X-linked neurological disorders, including Cowchock syndrome. Common features in Cowchock syndrome include a slowly progressive movement disorder, cerebellar ataxia, progressive sensorineural hearing loss, and sensory neuropathy. We identified a novel maternally inherited hemizygous missense AIFM1 variant, c.1369C>T p.(His457Tyr), in two brothers with clinical features consistent with Cowchock syndrome using next-generation sequencing. Both individuals had a progressive complex movement disorder phenotype, including disabling tremor poorly responsive to medications. Deep brain stimulation (DBS) of the ventral intermediate thalamic nucleus ameliorated contralateral tremor and improved their quality of life; this suggests the beneficial role for DBS in treatment-resistant tremor within AIFM1-related disorders.

Pacific Biosciences Fusion and Long Isoform Pipeline for Cancer Transcriptome-Based Resolution of Isoform Complexity.

Genomic profiling using short-read sequencing has utility in detecting disease-associated variation in both DNA and RNA. However, given the frequent occurrence of structural variation in cancer, molecular profiling using long-read sequencing improves the resolution of such events. For example, the Pacific Biosciences long-read RNA-sequencing (Iso-Seq) transcriptome protocol provides full-length isoform characterization, discernment of allelic phasing, and isoform discovery, and identifies expressed fusion partners. The Pacific Biosciences Fusion and Long Isoform Pipeline (PB_FLIP) incorporates a suite of RNA-sequencing software analysis tools and scripts to identify expressed fusion partners and isoforms. In addition, sequencing of a commercial reference (Spike-In RNA Variants) with known isoform complexity was performed and demonstrated high recall of the Iso-Seq and PB_FLIP workflow to benchmark our protocol and analysis performance. This study describes the utility of Iso-Seq and PB_FLIP analysis in improving deconvolution of complex structural variants and isoform detection within an institutional pediatric and adolescent/young adult translational cancer research cohort. The exemplar case studies demonstrate that Iso-Seq and PB_FLIP discover novel expressed fusion partners, resolve complex intragenic alterations, and discriminate between allele-specific expression profiles.

A Decade's Experience in Pediatric Chromosomal Microarray Reveals Distinct Characteristics Across Ordering Specialties.

Chromosomal microarray (CMA) is a testing modality frequently used in pediatric patients; however, published data on its utilization are limited to the genetic setting. We performed a database search for all CMA testing performed from 2010 to 2020, and delineated the diagnostic yield based on patient characteristics, including sex, age, clinical specialty of providers, indication of testing, and pathogenic finding. The indications for testing were further categorized into Human Phenotype Ontology categories for analysis. This study included a cohort of 14,541 patients from 29 different medical specialties, of whom 30% were from the genetics clinic. The clinical indications for testing suggested that neonatology patients demonstrated the greatest involvement of multiorgan systems, involving the most Human Phenotype Ontology categories, compared with developmental behavioral pediatrics and neurology patients being the least. The top pathogenic findings for each specialty differed, likely due to the varying clinical features and indications for testing. Deletions involving the 22q11.21 locus were the top pathogenic findings for patients presenting to genetics, neonatology, cardiology, and surgery. Our data represent the largest pediatric cohort published to date. This study is the first to demonstrate the diagnostic utility of this assay for patients seen in the setting of different specialties, and it provides normative data of CMA results among a general pediatric population referred for testing because of variable clinical presentations.

Phenotypic Spectrum in a Family Sharing a Heterozygous KCNQ3 Variant.

BACKGROUND AND PURPOSE: Mutations in KCNQ3 have classically been associated with benign familial neonatal and infantile seizures and more recently identified in patients with neurodevelopmental disorders and abnormal electroencephalogram (EEG) findings. We present 4 affected patients from a family with a pathogenic mutation in KCNQ3 with a unique constellation of clinical findings. METHODS: A family of 3 affected siblings and mother sharing a KCNQ3 pathogenic variant are described, including clinical history, genetic results, and EEG and magnetic resonance imaging (MRI) findings. RESULTS: This family shows a variety of clinical manifestations, including neonatal seizures, developmental delays, autism spectrum disorder, and anxiety. One child developed absence epilepsy, 2 children have infrequent convulsive seizures that have persisted into childhood, and their parent developed adult-onset epilepsy. An underlying c.1091G>A (R364H) variant in KCNQ3 was found in all affected individuals. CONCLUSIONS: The phenotypic variability of KCNQ3 channelopathies continues to expand as more individuals and families are described, and the variant identified in this family adds to the understanding of the manifestations of KCNQ3-related disorders.

Somatic variation as an incidental finding in the pediatric next-generation sequencing era.

The methodologic approach used in next-generation sequencing (NGS) affords a high depth of coverage in genomic analysis. Inherent in the nature of genomic testing, there exists potential for identifying genomic findings that are incidental or secondary to the indication for clinical testing, with the frequency dependent on the breadth of analysis and the tissue sample under study. The interpretation and management of clinically meaningful incidental genomic findings is a pressing issue particularly in the pediatric population. Our study describes a 16-mo-old male who presented with profound global delays, brain abnormality, progressive microcephaly, and growth deficiency, as well as metopic craniosynostosis. Clinical exome sequencing (ES) trio analysis revealed the presence of two variants in the proband. The first was a de novo variant in the PPP2R1A gene (c.773G > A, p.Arg258His), which is associated with autosomal dominant (AD) intellectual disability, accounting for the proband's clinical phenotype. The second was a recurrent hotspot variant in the CBL gene (c.1111T > C, p.Tyr371His), which was present at a variant allele fraction of 11%, consistent with somatic variation in the peripheral blood sample. Germline pathogenic variants in CBL are associated with AD Noonan syndrome-like disorder with or without juvenile myelomonocytic leukemia. Molecular analyses using a different tissue source, buccal epithelial cells, suggest that the CBL alteration may represent a clonal population of cells restricted to leukocytes. This report highlights the laboratory methodologic and interpretative processes and clinical considerations in the setting of acquired variation detected during clinical ES in a pediatric patient.

Pathogenic variants in SMARCA5, a chromatin remodeler, cause a range of syndromic neurodevelopmental features.

Intellectual disability encompasses a wide spectrum of neurodevelopmental disorders, with many linked genetic loci. However, the underlying molecular mechanism for more than 50% of the patients remains elusive. We describe pathogenic variants in SMARCA5, encoding the ATPase motor of the ISWI chromatin remodeler, as a cause of a previously unidentified neurodevelopmental disorder, identifying 12 individuals with de novo or dominantly segregating rare heterozygous variants. Accompanying phenotypes include mild developmental delay, frequent postnatal short stature and microcephaly, and recurrent dysmorphic features. Loss of function of the SMARCA5 Drosophila ortholog Iswi led to smaller body size, reduced sensory dendrite complexity, and tiling defects in larvae. In adult flies, Iswi neural knockdown caused decreased brain size, aberrant mushroom body morphology, and abnormal locomotor function. Iswi loss of function was rescued by wild-type but not mutant SMARCA5. Our results demonstrate that SMARCA5 pathogenic variants cause a neurodevelopmental syndrome with mild facial dysmorphia.

Ocular manifestations in a case of Wernicke's encephalopathy due to hyperemesis gravidarum.

Wernicke's Encephalopathy (WE) is a potentially devastating disorder, which if not diagnosed and treated at the earliest, could lead to dangerous neurological and ophthalmological complications. We report the ocular manifestations of WE in a pregnant woman with hyperemesis gravidarum.

Decisions to Perform Emergency Caesarean Sections at a University Hospital: Do obstetricians agree?

OBJECTIVES: This study was undertaken to assess the degree of agreement amongst obstetricians regarding decisions to perform emergency Caesarean section (CS) procedures at a university hospital. METHODS: This retrospective clinical audit was carried out on 50 consecutive emergency CS procedures performed between November 2012 and March 2013 on women with singleton pregnancies at the Sultan Qaboos University Hospital in Muscat, Oman. Data on each procedure were collected from electronic patient records and independently reviewed by six senior obstetricians to determine agreement with the decision. RESULTS: Of the 50 women who underwent CS procedures, the mean age was 28.9 ± 5.1 years and 48% were primigravidae. A total of 65% of the CS procedures were category I. The most common indications for a CS was a non-reassuring fetal heart trace (40%) and dystocia (32%). There was complete agreement on the decision to perform 62% of the CS procedures. Five and four obstetricians agreed on 80% and 95% of the procedures, respectively. The range of disagreement was 4-20%. Disagreement occurred primarily with category II and III procedures compared to category I. Additionally, disagreement occurred in cases where the fetal heart trace pattern was interpreted as an indication for a category II CS. CONCLUSION: The majority of obstetricians agreed on the decisions to perform 94% of the emergency CS procedures. Obstetric decision-making could be improved with the implementation of fetal scalp pH testing facilities, fetal heart trace interpretation training and cardiotocography review meetings.

Idiopathic intracranial hypertension presenting as postpartum headache.

Postpartum headache is described as headache and neck or shoulder pain during the first 6 weeks after delivery. Common causes of headache in the puerperium are migraine headache and tension headache; other causes include pre-eclampsia/eclampsia, post-dural puncture headache, cortical vein thrombosis, subarachnoid hemorrhage, posterior reversible leukoencephalopathy syndrome, brain tumor, cerebral ischemia, meningitis, and so forth. Idiopathic intracranial hypertension (IIH) is a rare cause of postpartum headache. It is usually associated with papilledema, headache, and elevated intracranial pressure without any focal neurologic abnormality in an otherwise healthy person. It is more commonly seen in obese women of reproductive age group, but rare during pregnancy and postpartum. We present a case of IIH who presented to us 18 days after cesarean section with severe headache and was successfully managed.

Gestational and Pregestational Diabetes Mellitus in Omani Women: Comparison of obstetric and perinatal outcomes.

OBJECTIVES: The aim of this study was to assess the prevalence of gestational diabetes mellitus (GDM) and pregestational diabetes mellitus (PGDM) among pregnant women in Oman and compare their obstetric and perinatal outcomes. METHODS: This retrospective study assessed the obstetric and perinatal outcomes of pregnant Omani women with GDM or PGDM who delivered at the Sultan Qaboos University Hospital in Muscat, Oman, between January 2009 and December 2010. RESULTS: There were a total of 5,811 deliveries during the study period. Of the 5,811 women who gave birth, 639 women were found to have diabetes mellitus (11.0%). A total of 581 of the diabetic women had GDM (90.9%) and only 58 (9.1%) had PGDM. Women with PGDM had a significantly higher incidence of pre-eclampsia (P = 0.022), preterm deliveries (P <0.001) and Caesarean sections (P <0.001). Neonatal complications, such as respiratory distress syndrome (RDS), neonatal hypoglycaemia, neonatal jaundice and subsequent admission to a neonatal intensive care unit (NICU) were significantly higher for neonates born to mothers with PGDM compared to those born to mothers with GDM (P <0.001). The corrected perinatal mortality rates for women with PGDM and GDM were 34.5 and 13.7 per 1,000 live births, respectively. CONCLUSION: In this Omani cohort, women with PGDM were at higher risk of developing obstetric and perinatal complications such as pre-eclampsia, preterm delivery and Caesarean delivery compared to women with GDM. In addition, neonates who had mothers with PGDM had higher rates of RDS, neonatal hypoglycaemia, neonatal jaundice and admission to the NICU.

Twin Pregnancy with a Complete Hydatidiform Mole and a Coexisting Live Fetus: Rare entity.

A hydatidiform mole with a coexisting live fetus is a rare occurrence and the optimal management for this condition is not yet known. We report the case of a 32-year-old woman (gravida 3, para 2) who presented to the Sultan Qaboos University Hospital, Muscat, Oman, in March 2012 at 13 gestational weeks with abdominal pain and vaginal bleeding. An ultrasound examination revealed a hydatidiform mole pregnancy coexisting with a live fetus. After extensive counselling, the patient and her husband opted for a conservative management approach. Unfortunately, a hysterotomy had to be performed at 17 gestational weeks due to severe haemorrhage. The postoperative period was uneventful and histopathology results confirmed one complete mole with a coexisting fetus and normal placenta. The patient's serum ß-human chorionic gonadotropin level remained normal for 18 months following her surgery.

Ruptured Rudimentary Horn Pregnancy Diagnosed by Preoperative Magnetic Resonance Imaging Resulting in Fetal Salvage.

Pregnancy in a rudimentary horn is very rare. The rupture of the horn during pregnancy is an obstetric emergency which can be life-threatening for both the mother and fetus. Preoperative diagnosis of such pregnancies can be challenging and they are usually diagnosed intraoperatively. We report a unique case of a 31-year-old multiparous woman who presented to the Sultan Qaboos University Hospital in Muscat, Oman, in January 2013 at 32 gestational weeks with abdominal pain. Ultrasonography was inconclusive. A rudimentary horn pregnancy was subsequently diagnosed via magnetic resonance imaging (MRI). An emergency laparotomy revealed haemoperitoneum and a ruptured rudimentary horn pregnancy. A live baby with an Apgar score of 2 at one minute and 7 at five minutes was delivered. The rudimentary horn with the placenta in situ was excised and a left salpingo-oophorectomy was performed. The postoperative period was uneventful. The authors recommend MRI as an excellent diagnostic modality to confirm rudimentary horn pregnancies and to expedite appropriate management.