Clinical Exome Research Articles

Clinical Exome Sequencing Identifies, Two Homozygous LOXHD1 Variants in Two Inbred Families With Pre-Lingual Hearing Loss From South India.

In recent years, numerous genetic variants have been linked with prelingual hearing loss (HL). Variants in the LOXHD1 gene (lipoxygenase homology domain-1) associated with DFNB77 are highly heterogeneous, with different auditory characteristics varying from stable to progressive and mild to profound. To date, 168 DFNB77 cases have been recorded worldwide. Forty-one hearing-impaired (HI) probands, who were previously excluded for a set of four common deafness-causing genes (viz., GJB2, GJB6, SLC26A4, and CDH23) from 33 HI families, were subjected to clinical exome sequencing (CES) involving 285 genes associated with HL. This was followed by a segregation analysis of the available members in the family. We identified two pathogenic LOXHD1 variants in two unrelated inbred families. One is a novel homozygous pathogenic nonsense variant (c.3999C>A; p.C1333X), whereas the other is a likely pathogenic missense variant (c.6046G>T; p.E2046K). In silico tools such as SIFT, PolyPhen-2, Mutation Taster, CADD, and REVEL scores were used to predict variant pathogenicity. Furthermore, American College of Medical Genetics and Genomics guidelines specific to HL were applied to finally classify a variant as pathogenic or otherwise. The frequency of LOXHD1 variants identified in our study is 4.88% (2/41). This is the first LOXHD1 report associated with non-syndromic HL in South Indian families.

Clinical Exome Sequencing in Pediatric Patients

Clinical Exome Sequencing in Pediatric Patients

Application of rapid clinical exome sequencing technology in the diagnosis of critically ill pediatric patients with suspected genetic diseases

PurposeThis study evaluates the efficacy of rapid clinical exome sequencing (CES) and mitochondrial DNA (mtDNA) sequencing for diagnosing genetic disorders in critically ill pediatric patients.MethodsA multi-centre investigation was conducted, enrolling critically ill pediatric patients suspected of having genetic disorders from March 2019 to December 2020. Peripheral blood samples from patients and their parents were analyzed using CES (proband-parent) and mtDNA sequencing (proband-mother) based on Next-Generation Sequencing (NGS) technology.ResultsThe study included 44 pediatric patients (24 males, 20 females) with a median age of 27 days. The median turnaround time for genetic tests was 9.5 days. Genetic disorders were diagnosed in 25 patients (56.8%): 5 with chromosome microduplication/deletion syndromes (11.3%), 1 with UPD-related disease (2.3%), and 19 with monogenic diseases (43.2%). De novo variants were identified in nine patients (36.0%). A neonate was diagnosed with two genetic disorders due to a homozygous SLC25A20 variant and an MT-TL1 gene variation.ConclusionRapid genetic diagnosis is crucial for critically ill pediatric patients with suspected genetic disorders. CES and mtDNA sequencing offer precise and timely results, guiding treatment and reducing mortality and disability, making them suitable primary diagnostic tools.

Pituitary stalk interruption with multiple pituitary hormone deficiencies associated with a roundabout guidance receptor 1 gene mutation

Pituitary stalk interruption syndrome (PSIS) is a rare condition characterized by multiple pituitary hormone deficiencies and a triad of distinctive features on imaging. We report a case of a 2.3-year-old male child who presented with hyponatremic seizures and was subsequently diagnosed with PSIS, identified to have a heterozygous mutation in the roundabout guidance receptor 1 (ROBO1) gene through clinical exome sequencing. This report emphasizes the importance of imaging in cases of hyponatremic seizures and represents the second documented case from India of classical PSIS associated with a novel ROBO1 gene mutation.

Meckel–Gruber syndrome due to homozygous c.16del (p.Leu6SerfsTer15) variant in the TCTN1: first case from Türkiye

Introduction: Meckel–Gruber syndrome (MKS) is a clinically and genetically heterogeneous ciliopathy characterized by a triad of occipital encephalocele, polycystic kidneys, and postaxial polydactyly. Almost all of them are lethal in the prenatal or first postnatal periods. It is usually diagnosed clinically with a detailed prenatal ultrasound examination. Variants have been reported in at least 14 different genes. Case Presentation: We report a male fetus with oligohydramnios, large kidneys with microcysts covering the entire abdomen, postaxial polydactyly of the hands, bilateral pes equinovarus, encephalocele, microphthalmia, short extremities, and a mass lesion under the diaphragm. Termination was recommended to the family due to severe findings. Fetal skin biopsy and parental peripheral blood samples were obtained to investigate the potential pathogenic variants associated with MKS via clinical exome sequencing and Sanger sequencing. Results and Conclusion: The fetus was homozygous for the c.16del (p.Leu6SerfsTer15) variant in the TCTN1 (NM_001082538.3), and both parents were heterozygous for the variant. Genetic diagnosis is very important in terms of counseling for subsequent pregnancies. To our knowledge, this is the third Meckel Gruber case in the literature caused by the TCTN1, and a novel likely pathogenic variant was detected.

Molecular insights into genodermatoses: Genetic findings from 43 patients.

Genodermatoses, a group of inherited skin disorders, are characterized by significant genetic heterogeneity and clinical variability, often posing diagnostic and therapeutic challenges. Advances in next-generation sequencing (NGS) technologies, such as whole exome sequencing (WES) and clinical exome sequencing (CES), have transformed the diagnostic landscape by enabling comprehensive genetic analysis. This study aimed to investigate the molecular spectrum and clinical relevance of genetic findings in 43 patients diagnosed with genodermatoses. Demographic, clinical, and molecular data were collected, and genetic testing was performed using the MGI-Seq platform. Variants were analyzed for pathogenicity, zygosity, and novelty. Neurofibromatosis Type 1 (27.9%) and Epidermolysis Bullosa (23.2%) were the most common diagnoses, followed by Ichthyosis (16.2%) and Oculocutaneous Albinism (13.9%). Less frequent conditions included Ectodermal Dysplasia (6.9%) and single cases of Palmoplantar Keratoderma, PTEN Hamartoma Syndrome, Rothmund-Thomson Syndrome, Xeroderma Pigmentosum, and Megaconial Congenital Muscular Dystrophy (each 2.3%). Molecular findings underscored the genetic complexity of genodermatoses, with 42 distinct variants identified across 19 genes. Of these, 13 variants (31%) were novel, expanding the known molecular spectrum. The novel variants were detected in genes including NF1, COL7A1, ITGB4, COL17A1, NIPAL4, ALOX12B, KRT10, ST14, OCA2, and PTEN, highlighting the diagnostic value of comprehensive genetic analysis. The mean age at diagnosis varied significantly among conditions, reflecting the diagnostic challenges and clinical variability of genodermatoses. This study emphasizes the critical role of WES and CES in diagnosing genodermatoses and understanding their molecular basis, which enhances diagnostic accuracy and supports personalized management strategies.

CSF1R-related adult-onset leukoencephalopathy with axonal spheroids: A case series of four Asian Indian patients.

Colony stimulating factor 1 receptor-related leukoencephalopathy (CSF1R-L) is a rare, adult onset leukoencephalopathy. Descriptions from the Indian subcontinent remain limited. To report four patients with genetically confirmed CSF1R-L from four Asian Indian families, describing clinical, molecular and radiological features. All patients underwent clinical examination, MRI brain, and whole exome sequencing to identify causative variants in CSF1R gene. We also reviewed published Indian cases with CSF1R-L. Age at enrolment ranged from 34-40 years. Duration of symptoms ranged from 11 months to 2 years. The chief clinical phenotype in three patients was a rapidly evolving cognitive-behavioural syndrome combined with atypical parkinsonism, and asymmetrical spastic tetraparesis in one patient. We identified four different variants (three missense, one inframe deletion). Radiological findings demonstrated white matter involvement, and diffusion restriction involving subcortical white matter and pyramidal tracts. We expand the literature from India with four new cases of CSF1R-L.

Expanding the Clinical Spectrum Associated with the Recurrent Arg203Trp Variant in PACS1: An Italian Cohort Study.

Background/Objectives: Schuurs-Hoeijmakers syndrome (SHMS), also known as PACS1 neurodevelopmental disorder, is a rare condition characterized by intellectual disability, distinctive craniofacial abnormalities, and congenital malformations. SHMS has already been associated with variants in the PACS1 gene in 63 patients. In this study, we describe 10 new Italian SHMS patients all harboring the common de novo p.(Arg203Trp) variant. Methods: The 10 patients we studied were evaluated by clinical geneticists and child neurologists and a detailed description of clinical features was recorded. Data were then coded using the Human Phenotype Ontology (HPO) terms. The recurrent p.(Arg203Trp) variant in PACS1 was identified by clinical exome sequencing or whole exome sequencing in trio using standard methodologies. To facilitate mutation identification, we designed a new PCR-RFLP strategy adopting the endonuclease DpnII. Results: We define a detailed clinical phenotyping in patients with intellectual disability and facial characteristics (thick eyebrows, down-slanting palpebral fissures, ocular hypertelorism, low-set ears, a thin upper lip, and a wide mouth) that can help clinicians form a more efficient diagnosis of SHMS even through neuroimaging and neuropsychological evaluation. Conclusions: Our series of 10 newly affected Italian children highlights specific clinical features that may help clinicians recognize and better manage this syndrome, contributing to precision medicine approaches in medical genetics.

Monogenic disorders associated with motor speech phenotypes in children and adolescents undergoing clinical exome sequencing.

Monogenic disorders associated with motor speech phenotypes in children and adolescents undergoing clinical exome sequencing.

Congenital Ataxia with Progressive Cerebellar Atrophy, Camptodactyly, and Hypertrichosis: A Novel Recognizable Phenotype for NALCN Heterozygous Variants.

Non-selective sodium leak channel (NALCN) protein encoded by the NALCN gene is of key importance for neuronal cell excitability. Previous reports showed that biallelic NALCN pathogenic variants cause infantile hypotonia with psychomotor retardation and characteristic facies 1 (IHPRF1) while monoallelic variants lead to congenital contractures of the limbs and face, hypotonia, and developmental delay (CLIFAHDD). In our work, we aimed to expand the heterozygous NALCN-related clinical spectrum, presenting two affected individuals and a literature review. We describe two new unrelated subjects harboring monoallelic NALCN pathogenic variants identified through clinical exome sequencing and review the current literature of other heterozygous NALCN patients. The c.3542G > A (p.Arg1181Gln) and the novel c.3423C > A (p.Phe1141Leu) heterozygous missense variants were disclosed in two subjects manifesting a similar phenotype characterized by congenital ataxia with progressive cerebellar atrophy, camptodactyly, and hypertrichosis of the arms (CAPCACH). Other NALCN subjects with overlapping features have already been reported. A combination of these clinical and neuroimaging findings suggests the definition of the new CAPCACH phenotype. We expand the heterozygous NALCN-related clinical spectrum from the more severe CLIFFAHDD to the milder CAPCACH phenotype. These conditions should be considered in the differential diagnosis of syndromic congenital ataxias, and the presence of camptodactyly and/or hypertrichosis may represent peculiar diagnostic clues.

Two de novo UBR1 variants in trans as a cause of Johanson-Blizzard syndrome.

Johanson-Blizzard syndrome (JBS) is a rare autosomal recessive disease caused by pathogenic variants in the UBR1 gene. JBS is usually suspected based on characteristic anomalies, but only genetic testing provides a definitive diagnosis. Since most variants are inherited from the parents, we aimed to identify the causal variants in a Czech proband with clinically suspected JBS and perform segregation analysis. A proband with clinically suspected JBS underwent clinical exome sequencing (CES). Sanger sequencing was used for the validation, characterization, and segregation of variants in the family. The variants were also characterized using quantitative real-time PCR (qPCR) and in silico analysis. Using CES in the proband, we identified two novel causal variants in the UBR1 gene, c.3482A>C and c.3509+6T>C. Although the variants were found in trans, neither was detected in the parents. Sanger sequencing of the cDNA revealed that the novel variant c.3509+6T>C caused activation of the non-canonical GC donor splice site. The inclusion of 70 bp of the intronic sequence generated a frameshift and a premature termination codon leading to nonsense-mediated decay, as detected by qPCR. In silico protein structural analysis showed that the novel missense variant c.3482A>C in the zinc-stabilized domain RING-H2 altered a highly conserved zinc-coordinating histidine by proline. To the best of our knowledge, we report the first molecular confirmation of JBS in the Czech Republic and the first identification of two de novo causal variants in two alleles. Our findings also expand the spectrum of pathogenic variants in the UBR1 gene.

Two Novel Protein-Truncating Variants in NLRP2 and Their Functional Impacts on the Subcortical Maternal Complex.

Female infertility is a prevalent reproductive disorder with high genetic heterogeneity. Previous reports have demonstrated the causal role of biallelic pathogenic variants in the Subcortical Maternal Complex (SCMC) genes in female reproductive failure with some leading to infertility, early embryonic loss, and molar pregnancies, while others are compatible with live birth with and without multilocus imprinting disorders (MLID). Here, we report two deleterious protein-truncating variants, c.1326delG, p.Leu443Phefs*78 and c.2802_2803del, p.Arg935Metfs*15, in heterozygous state in the NLRP2 gene of a patient with primary infertility, four early miscarriages, and one failed attempt of intracytoplasmic sperm injection. We show that the two variants mediate mRNA decay in EBV-transformed lymphoblastoid cells from the patient, lead to decreased NLRP2 protein levels, and alter NLRP2 interactions with other members of the SCMC invitro. This study emphasizes the importance of performing clinical exomes for patients with recurrent reproductive failure and reporting their variants and reproductive histories to improve patient counseling.

A missense variant in the SOX5 gene (c.221C > T) is associated with intellectual disability

ObjectivesThe SOX5 gene has been identified as the pathogenic gene responsible for Lamb-Shaffer syndrome. In this study, we examined the SOX5 variant (c.221C > T, p.Thr74Met) within a Chinese family presenting with intellectual disability and evaluated the functional implications of SOX5 by in vitro experiment.Materials and methodsThe family underwent a clinical assessment of intellectual development, which included precise clinical exome sequencing to identify causative genetic variants. The potential deleterious effects and pathogenicity of the variant were predicted using bioinformatics tools such as Mutation Taster, PROVEAN, and SIFT. Additionally, protein stability was evaluated using I-Mutant, and 3D protein structures were modeled with I-TASSER. Western blots and QPCR were employed to assess gene expression and protein stability. Flow cytometry was utilized to compare the cell cycle dynamics between wild-type and mutant cells.ResultsA previously identified missense variant (c.221C > T) in the SOX5 gene was determined to be the underlying cause of intellectual disability in a Chinese family. Functional assays demonstrated that mutant cells exhibited increased levels of SOX5 mRNA and protein relative to wild-type cells, accompanied by enhanced protein stability. Additionally, the mutant SOX5 protein was found to alter the cell cycle and downregulate the mRNA expression levels of the ACAN, AXIN2, SOX9, and PDGFRA genes.ConclusionsWe confirmed that the SOX5 p.Thr74Met variant is associated with intellectual disability in a second-generation Chinese family. This mutant protein potentially exhibits increased stability, influences the cell cycle, and downregulates genes related to bone and neural functions.

Genomic Testing in Adults With Undiagnosed Rare Conditions: Improvement of Diagnosis Using Clinical Exome Sequencing as a First-Tier Approach.

Adult patients with undiagnosed genetic disorders suffer most from diagnostic delay and seldom appear in cohort studies investigating the diagnostic yield in medical genetic clinical practice. Here we present the results of the diagnostic activity performed in a referral center on 654 consecutive, unselected adult subjects presenting with molecularly unsolved conditions. More than 50% of the referred individuals were affected by syndromic or isolated intellectual disability. Different molecular approaches, including clinical/whole exome sequencing (CES/WES), chromosomal microarray analysis (CMA), and/or targeted gene or gene panel sequencing were used to analyze patients' DNA. Definitive diagnosis was obtained in over 30% of individuals. The most sensitive methodology was CES/WES, which allowed us to reach a diagnosis in over 50% of the 162 solved cases. Despite the great variety of clinical presentations, our results represent a reliable picture of the "real world" daily routine in an outpatient medical genetics clinic dedicated to diagnostic activity, and contribute to better understand the great value of a definitive molecular diagnosis in adults, either for the affected individuals and their families. This retrospective analysis demonstrates the importance of adopting a genomic-first approach within the diagnostic process for adults affected with unsolved rare conditions.

Clinical exome sequencing for carrier screening in assisted reproductive technology and sperm donation.

To assess the efficacy of clinical exome sequencing (CES) in individuals involved in assisted reproductive technology (ART) or sperm donor programs, with a specific focus on its impact on clinical decision-making. A total of 3991 individuals without a family history of genetic disorders underwent CES targeting 5595 genes at a reproductive center between December 2022 and April 2024. The cohort comprised 217 sperm donors, 232 female recipients, and 1771 couples (3542 patients) undergoing ART with their own gametes. At-risk couples (ARCs) were identified when both partners had a pathogenic or likely pathogenic variant (P/LP) in the same autosomal recessive gene or X-linked variants in females. The analysis primarily examined carrier frequencies, reproductive choices, and outcomes of ARCs. Among the 3991 individuals screened, 3895 (97.6%) were found to carry at least one P/LP variant, with an average carrier burden of 3.8 variants per individual, showing no significant disparity in carrier status between individuals with infertility and sperm donors/recipients. Within the screened couples, 9.3% were identified as ARCs and 2.3% opted for preimplantation genetic testing for monogenic diseases (PGT-M). As of now, 31 ARCs proceeded with the transfer of euploid and unaffected blastocysts, resulting in 8 healthy live births and 13 ongoing pregnancies. The findings reveal a significant prevalence of carrier status for autosomal recessive and X-linked diseases, irrespective of fertility status. This highlights the critical importance of integrating genetic risk counseling and informed reproductive decision-making into fertility clinics and sperm banks.

Diagnostic efficiency of exome-based sequencing in pediatric patients with epilepsy.

Epilepsy, a prevalent neurological disorder, has multifaceted etiologies. Next-generation sequencing (NGS) has emerged as a robust diagnostic tool for this condition. This study aims to evaluate the detection efficiencies of different exome-based sequencing techniques. Exome-based epilepsy panel tests, clinical exome sequencing (CES), and whole exome sequencing (WES) were conducted on 259 pediatric patients diagnosed with epilepsy. Single-nucleotide variants (SNVs) and copy number variants (CNVs) were interpreted based on each patient's phenotypic presentation. Additionally, data concerning clinical symptoms, neuroimaging findings, treatment responses, and prognostic outcomes were collected and analyzed. The overall diagnostic yield was 32.8% (85/259), with a diagnostic yield of 40.0% for exome-based epilepsy panels, 30.1% for CES, and 27.8% for WES. We identified 82 cases with pathogenic or likely pathogenic SNVs and 4 cases with pathogenic CNVs, of which one case with both SNV and CNV. The most frequently detected gene was PRRT2, present in 10.0% (9/82) of cases. Epileptic syndromes were diagnosed in 66 patients, predominantly West Syndrome, Dravet Syndrome and Genetic Epilepsy with Febrile Seizures plus. NGS is an effective method for uncovering the genetic foundations of pediatric epilepsy, with diagnostic yields varying based on the sequencing approach used. The growing preference for WES underscores its utility in complex cases, pointing to a trend towards more tailored diagnostic strategies.

Diagnosis of hereditary ataxias: a real-world single center experience.

This study aims to evaluate our experience in the diagnosis of hereditary ataxias (HAs), to analyze data from a real-world scenario. This is a retrospective, cross-sectional, descriptive study conducted at a single Italian adult neurogenetic outpatient clinic, in 147 patients affected by ataxia with a suspicion of hereditary forms, recruited from November 1999 to February 2024. A stepwise approach for molecular diagnostics was applied: targeted gene panel (TP) next-generation sequencing (NGS) and/or clinical exome sequencing (CES) were performed in the case of inconclusive first-line genetic testing, such as short tandem repeat expansions (TREs) testing for most common spinocerebellar ataxias (SCA1-3, 6-8,12,17, DRPLA), other forms [Fragile X-associated tremor/ataxia syndrome (FXTAS), Friedreich ataxia (FRDA) and mitochondrial DNA-related ataxia, RFC1-related ataxia/CANVAS] or inconclusive phenotype-guided specific single gene sequencing. A definitive diagnosis was reached in 36.7% of the cases. TREs testing was diagnostic in 30.4% of patients. The three most common TREs ataxias were FRDA (36.1%), SCA2 (27.8%), and RFC1-related ataxia/CANVAS (11.1%). In five patients, the molecular diagnosis was achieved by single gene sequencing and causative mutations were identified in POLG (2), SACS (1), DARS2 (1), MT-ATP6 (1). Of 94 patients with a suspicion of HAs of indeterminate genetic origin, 68 underwent new molecular evaluation using the NGS approach. In 28 of these cases, CES was performed after the TP sequencing resulted negative. In 13 patients, the diagnosis was achieved by NGS approach. In 7 of these 13 patients, the diagnosis was made by CES. Genes mutations identified as causative of HAs were found in SPG7 (4), SACS (1), CACNA1A (1), CACNA1G (1), EEF2 (1), PRKCG (1), KCNC3 (1), ADCK3 (1), SYNE1 (1), ITPR1 (1). A positive family history of ataxia and early onset of symptoms were associated with a higher likelihood of obtaining a definite diagnosis. The molecular diagnosis of HAs remains a significant challenge for neurologists. Our data indicate that, in most cases, a diagnosis of HA can be established through first line genetic testing, particularly TREs testing. However, for patients with a clinical diagnosis of HA who do not achieve a molecular diagnosis through initial genetic tests, the use of NGS proves to be a valuable tool, providing a definitive diagnosis in approximately 20% of cases. Therefore, when feasible in clinical practice, integrating NGS testing, especially exome sequencing, into the diagnostic decision-making process for unsolved cases is crucial.

Clinical follow-up of 2 families with glomerulopathy caused by COQ8B gene variants and literature review.

Primary coenzyme Q10 (CoQ10) deficiency is an autosomal recessive genetic disease caused by mitochondrial dysfunction. Variants in Coenzyme Q8B (COQ8B) can cause primary CoQ10 deficiency. COQ8B-related glomerulopathy is a recently recognized glomerular disease that most often presents as steroid-resistant nephrotic syndrome (SRNS) in childhood. The disease often progresses to kidney failure and the renal histopathology is most commonly focal segmental glomerulosclerosis (FSGS). Four SRNS cases (2 females and 2 males) from 2 unrelated families who were followed clinically for nearly 3 years. Clinical exome testing and analyses were performed by MyGenostics Laboratory in China to evaluate unexplained proteinuria given the strong family history of glomerular disease and histologic evidence of SRNS. Pathogenic variants were identified in COQ8B in the exome studies and confirmed by direct sequencing. Clinical exome sequencing revealed biallelic variants of the COQ8B gene in 2 families. In the Family 1, the oldest of three affected siblings died of renal failure at 11 years of age. Based on the results of genetic testing which identified a homozygous variant of COQ8B, the other two affected siblings with mild proteinuria and normal renal function were treated with CoQ10 oral supplementation at an early stage. Coenzyme Q10 treatment was effective in reducing proteinuria levels in both patients from Family 1 over the first 6 months and the two patients still have low-level proteinuria and normal renal function at nearly three years. In Family 2, clinical exome sequencing revealed a compoundheterozygous variants of COQ8B in a patient with biopsy- proven FSGS. His disease was unresponsive to prior treatment with glucocorticoids and cyclosporine. Oral CoQ10 was initiated based on his genetic diagnosis and was it was effective in reducing proteinuria over the first 5 months months of therapy. However after 1 year, his disease progressed tokidney failure. Kidney transplantation was performed at 5 years of age and his condition has been stable without rejection and no recurrence of disease. COQ8B gene variant-related glomerulopathy often presents as SRNS without obvious extrarenal manifestations. The histopathology is mainly FSGS and follows an autosomal recessive mode of inheritance. Some patients may benefit from early coenzyme Q10 supplementation. For patients whose disease progresses to kidney failure, kidney transplantation can be an effective treatment. For children with unexplained proteinuria and abnormal renal function, genetic testing should be performed early in the course of disease to guide therapy where possible and improve prognosis.

Systematic Ultrasound Evaluation of Olfactory Sulci in Fetuses with Congenital Heart Defects: A Clue for CHARGE Syndrome Diagnosis

Introduction: Arhinencephaly have been identified as a significant feature in CHARGE syndrome. This study aimed to evaluate the diagnostic role of olfactory sulci (OS) in identifying CHARGE syndrome among fetuses with major congenital heart defects (CHDs). Methods: We prospectively evaluated OS development in fetuses diagnosed with CHDs from 2017 to 2021. Neurosonography was performed using transabdominal and transvaginal approaches after 30 weeks of gestation. OS assessment was conducted in the trans-frontal coronal plane, classifying their appearance as fully developed, hypoplastic, or absent. Abnormal OS cases underwent MRI and trio-based clinical exome sequencing (CES). Results: The study included 147 fetuses with CHD. Abnormal OS were found in 4 fetuses (2.7%) which also exhibited other additional anomalies. OS were absent in cases 1–3 and hypoplastic in case 4. MRI confirmed OS abnormalities in all cases, and trio-based CES identified a CHD7 gene mutation in cases 1, 2, and 4, supporting the diagnosis of CHARGE syndrome. Case 3 had normal trio-based CES results. No other CHARGE syndrome cases were diagnosed postnatally among the cases with normal OS. Conclusions: Systematic evaluation of OS in fetuses with major CHD might contribute to the diagnosis of CHARGE syndrome. Our findings support the inclusion of OS assessment in the prenatal evaluation of fetuses with major CHDs.

Return of Clinically Actionable Pharmacogenetic Results From Molecular Tumor Board DNA Sequencing Data: Workflow and Estimated Costs.

Pharmacogenetic testing can prevent severe toxicities from several oncology drug therapies; it also has the potential to improve the outcomes from supportive care drugs. Paired tumor and germline sequencing is increasingly common in oncology practice; these include sequencing of pharmacogenes, but the germline pharmacogenetic variants are rarely included in the clinical reports, despite many being clinically actionable. We established an informatics workflow to evaluate the clinical sequencing results for pharmacogenetic variants. We used the Aldy computational tool, which we have previously shown to determine the variant alleles in 14 pharmacogenes in clinical sequencing data with >99% accuracy, to identify pharmacogenetic variants in the clinical whole exome sequencing from our molecular tumor board. Patients with genetic variants that are clinically actionable for their individual therapy programs, including both treatment and supportive care, are referred to a clinical pharmacogenetics testing laboratory for confirmation. Through an evaluation of our weekly informatics workflow, we determined it took approximately 3.25 hours to complete the analysis of the sequencing data from approximately 20 patients. Using a United States pharmacist's median salary, we estimated the incremental added cost of the process to be only ~$15 per patient. This adds only a minor increase to the patient's cost of testing and has the potential to improve the safety and efficacy of their treatment.