Targeted long-read sequencing identifies missing disease-causing variation.

Despite widespread clinical genetic testing, many individuals with suspected genetic conditions lack a precise diagnosis, limiting their opportunity to take advantage of state-of-the-art treatments. In some cases, testing reveals difficult-to-evaluate structural differences, candidate variants that do not fully explain the phenotype, single pathogenic variants in recessive disorders, or no variants in genes of interest. Thus, there is a need for better tools to identify a precise genetic diagnosis in individuals when conventional testing approaches have been exhausted. We performed targeted long-read sequencing (T-LRS) using adaptive sampling on the Oxford Nanopore platform on 40 individuals, 10 of whom lacked a complete molecular diagnosis. We computationally targeted up to 151 Mbp of sequence per individual and searched for pathogenic substitutions, structural variants, and methylation differences using a single data source. We detected all genomic aberrations-including single-nucleotide variants, copy number changes, repeat expansions, and methylation differences-identified by prior clinical testing. In 8/8 individuals with complex structural rearrangements, T-LRS enabled more precise resolution of the mutation, leading to changes in clinical management in one case. In ten individuals with suspected Mendelian conditions lacking a precise genetic diagnosis, T-LRS identified pathogenic or likely pathogenic variants in six and variants of uncertain significance in two others. T-LRS accurately identifies pathogenic structural variants, resolves complex rearrangements, and identifies Mendelian variants not detected by other technologies. T-LRS represents an efficient and cost-effective strategy to evaluate high-priority genes and regions or complex clinical testing results.

Biallelic PI4KA Mutations Disrupt B-Cell Metabolism and Cause B-Cell Lymphopenia and Hypogammaglobulinemia.

PURPOSE: PI4KA-related disorder is a highly clinically variable condition characterized by neurological (limb spasticity, developmental delay, intellectual disability, seizures, ataxia, nystagmus) and gastrointestinal (inflammatory bowel disease and multiple intestinal atresia) manifestations. Although features consistent with immunodeficiency (autoimmunity/autoinflammation and recurrent infections) have been reported in a subset of patients, the burden of B-cell deficiency and hypogammaglobulinemia has not been extensively investigated. We sought to describe the clinical presentation and manifestations of patients with PI4KA-related disorder and to investigate the metabolic consequences of biallelic PI4KA variants in B cells. METHODS: Clinical data from patients with PI4KA variants were obtained. Multi-omics analyses combining transcriptome, proteome, lipidome and metabolome analyses in conjunction with functional assays were performed in EBV-transformed B cells. RESULTS: Clinical and laboratory data of 13 patients were collected. Recurrent infections (7/13), autoimmune/autoinflammatory manifestations (5/13), B-cell deficiency (8/13) and hypogammaglobulinemia (8/13) were frequently observed. Patients' B cells frequently showed increased transitional and decreased switched memory B-cell subsets. Pathway analyses based on differentially expressed transcripts and proteins confirmed the central role of PI4KA in B cell differentiation with altered B-cell receptor (BCR) complex and signalling. By altering lipids production and tricarboxylic acid cycle regulation, and causing increased endoplasmic reticulum stress, biallelic PI4KA mutations disrupt B cell metabolism inducing mitochondrial dysfunction. As a result, B cells show hyperactive PI3K/mTOR pathway, increased autophagy and deranged cytoskeleton organization. CONCLUSION: By altering lipid metabolism and TCA cycle, impairing mitochondrial activity, hyperactivating mTOR pathway and increasing autophagy, PI4KA-related disorder causes a syndromic inborn error of immunity presenting with B-cell deficiency and hypogammaglobulinemia.

Deletion rescue resulting in segmental homozygosity: A mechanism underlying discordant NIPT results.

With the increasing capabilities of non-invasive prenatal testing (NIPT), detection of sub-chromosomal deletions and duplications are possible. This case series of deletion rescues resulting in segmental homozygosity helps provide a biological explanation for NIPT discrepancies and adds to the dearth of existing literature surrounding segmental UPD cases and their underlying mechanisms. In the three cases presented here, NIPT reported a sub-chromosomal deletion (in isolation or as part of a complex finding). Diagnostic testing, however, revealed segmental homozygosity or UPD for the region reported deleted on NIPT. Postnatal placental testing was pursued in two cases and confirmed the NIPT findings. This discordance between the screening and diagnostic testing is suggestive of a corrective post-zygotic event, such as telomere capture and/or deletion rescue, ultimately resulting in segmental homozygosity and fetoplacental mosaicism. Imprinted chromosomes and autosomal recessive disease genes make homozygosity an important clinical consideration. Amniocentesis with SNP microarray is particularly useful in determining both copy number and UPD issues alike.

Clinical RNA sequencing clarifies variants of uncertain significance identified by prior testing.

Purpose: Sequencing-based genetic testing often identifies variants of uncertain significance (VUS) or fails to detect pathogenic variants altogether. We evaluated the utility of RNA sequencing (RNA-seq) to clarify VUS or identify missing variants in a clinical setting. Methods: Over a 2-year period, genetics providers at a single institution referred 26 cases for clinical RNA-seq. Cases had either no candidate variant identified by prior testing or a VUS suspected to impact splicing or expression. A committee reviewed each submission to ensure it met study criteria. Results: Among 26 cases, 8 could not be sequenced because of poor expression in an accessible tissue, 2 did not meet inclusion criteria, 3 were solved prior to collection, and 4 families declined participation or did not complete sample collection. For the 9 cases sequenced, the clinical laboratory reported two positive, four negative, and three "indeterminate." For all three indeterminate cases, original RNA-seq data was manually evaluated and deemed explanatory. Conclusion: Clinical RNA-seq can clarify VUS, especially splice variants, but laboratory-specific interpretation guidelines may lead to indeterminate results. Identifying individuals likely to benefit from RNA-seq and providing appropriate counseling poses unique challenges.

The Strategies for Quantitative and Qualitative Remote Data Collection: Lessons From the COVID-19 Pandemic.

The COVID-19 pandemic has necessitated a rapid shift to web-based or blended design models for both ongoing and future clinical research activities. Research conducted virtually not only has the potential to increase the patient-centeredness of clinical research but may also further widen existing disparities in research participation among underrepresented individuals. In this viewpoint, we discuss practical strategies for quantitative and qualitative remote research data collection based on previous literature and our own ongoing clinical research to overcome challenges presented by the shift to remote data collection. We aim to contribute to and catalyze the dissemination of best practices related to remote data collection methodologies to address the opportunities presented by this shift and develop strategies for inclusive research.

Study protocol for a randomized trial of bridge: Person-centered collaborative care for serious mental illness and cancer.

BACKGROUND: Individuals with serious mental illness (SMI) experience inequities in cancer care that contribute to increased cancer mortality. Involving mental health at the time of cancer diagnosis may improve cancer care delivery for patients with SMI yet access to care remains challenging. Collaborative care is a promising approach to integrate mental health and cancer care that has not yet been studied in this marginalized population. METHODS/DESIGN: We describe a 24-week, two-arm, single-site randomized trial of person-centered collaborative care (Bridge) for patients with SMI (schizophrenia, bipolar disorder, or major depression with psychiatric hospitalization) and their caregivers. 120 patients are randomized 1:1 to Bridge or Enhanced Usual Care (EUC) along with their caregivers. Researchers proactively identify individuals with SMI and a new breast, lung, gastrointestinal, or head and neck cancer that can be treated with curative intent. EUC includes informing oncologists about the patient's psychiatric diagnosis, notifying patients about available psychosocial services, and tracking patient and caregiver outcomes. Bridge includes a proactive assessment by psychiatry and social work, a person-centered, team approach including collaboration between mental health and oncology, and increased access to evidence-based psycho-oncology care. The primary outcome is cancer care disruptions evaluated by a blinded panel of oncologists. Secondary outcomes include patient and caregiver-reported outcomes and healthcare utilization. Barriers to Bridge implementation and dissemination are assessed using mixed methods. DISCUSSION: This trial will inform efforts to systematically identify individuals with SMI and cancer and generate the first experimental evidence for the impact of person-centered collaborative care on cancer care for this underserved population.

Cerebrofacial vascular metameric syndrome is caused by somatic pathogenic variants in PIK3CA.

Disorganized morphogenesis of arteries, veins, capillaries, and lymphatic vessels results in vascular malformations. Most individuals with isolated vascular malformations have postzygotic (mosaic), activating pathogenic variants in a handful of oncogenes within the PI3K-RAS-MAPK pathway (Padia et al., Laryngoscope Investig Otolaryngol 4: 170-173 [2019]). Activating pathogenic variants in the gene PIK3CA, which encodes for the catalytic subunit of phosphatidylinositol 3-kinase, are present in both lymphatic and venous malformations as well as arteriovenous malformations in other complex disorders such as CLOVES syndrome (congenital, lipomatous, overgrowth, vascular malformations, epidermal anevi, scoliosis) (Luks et al., Pediatr Dev Pathol 16: 51 [2013]; Luks et al., J Pediatr 166: 1048-1054.e1-5 [2015]; Al-Olabi et al., J Clin Invest 128: 1496-1508 [2018]). These vascular malformations are part of the PIK3CA-related overgrowth spectrum, a spectrum of entities that have regionalized disordered growth due to the presence of tissue-restricted postzygotic PIK3CA pathogenic variants (Keppler-Noreuil et al., Am J Med Genet A 167A: 287-295 [2015]). Cerebrofacial vascular metameric syndrome (CVMS; also described as cerebrofacial arteriovenous metameric syndrome, Bonnet-Dechaume-Blanc syndrome, and Wyburn-Mason syndrome) is the association of retinal, facial, and cerebral vascular malformations (Bhattacharya et al., Interv Neuroradiol 7: 5-17 [2001]; Krings et al., Neuroimaging Clin N Am 17: 245-258 [2007]). The segmental distribution, the presence of tissue overgrowth, and the absence of familial recurrence are all consistent with CVMS being caused by a postzygotic mutation, which has been hypothesized by previous authors (Brinjiki et al., Am J Neuroradiol 39: 2103-2107 [2018]). However, the genetic cause of CVMS has not yet been described. Here, we present three individuals with CVMS and mosaic activating pathogenic variants within the gene PIK3CA We propose that CVMS be recognized as part of the PIK3CA-related overgrowth spectrum, providing justification for future trials using pharmacologic PIK3CA inhibitors (e.g., alpelisib) for these difficult-to-treat patients.

Computational fluid dynamics modeling aiding surgical planning in a toddler with Parkes Weber syndrome.

Parkes Weber syndrome is a fast-flow and slow-flow vascular anomaly with limb overgrowth that can lead to congestive heart failure and limb ischemia. Current management strategies have focused on symptom management with focal embolization. A pediatric case with early onset heart failure is reported. We discuss the use of computational fluid dynamics (CFD) modeling to guide a surgical management strategy in a toddler with an MAP2K1 mutation.

Maternal Parvovirus B19 Infection Causing First-Trimester Increased Nuchal Translucency and Fetal Hydrops.

This is a case report of a 31-year-old primigravida who was diagnosed with an asymptomatic acute parvovirus B19 infection in the second trimester of pregnancy and its suspected association with an increased nuchal translucency (NT) measurement. Parvovirus B19 is a single-stranded DNA virus that is cytotoxic to erythroid progenitor cells, causing inhibition of erythropoiesis. While maternal disease is usually mild, fetal infection can result in spontaneous abortion, aplastic anemia, nonimmune fetal hydrops, and fetal demise. This fetus had an increased NT of 3.2 mm at 11 weeks' gestation with a normal male karyotype and microarray analysis on chorionic villi sampling, in addition to a normal fetal echocardiogram at 15 weeks' gestation. The anatomy scan at 20 weeks' and 1-day gestation revealed fetal ascites, pleural effusion, and increased middle cerebral artery peak systolic velocity suspicious for fetal anemia. At this time, maternal serology for parvovirus was positive for IgM and IgG. Amniocentesis, cordocentesis, and intrauterine transfusion were performed. The amniocentesis revealed elevated parvovirus B19 DNA, quantitative PCR (2,589,801 copies/mL, reference range <100 copies/mL). The patient delivered a viable male fetus at 37 weeks' and 6-day gestation, without sequelae of the previously noted hydrops. Parvovirus B19 infection should be a consideration when evaluating increased NT and hydrops fetalis. It warrants close antepartum surveillance and possible intrauterine fetal transfusions. With prompt recognition, proper treatment, and surveillance, these patients can go on to achieve healthy term deliveries. Long-term outcomes of delivered infants require further study.