"Why did I choose genetics?": A survey of current and recent medical genetics and genomics residents provides insight into recruitment efforts.

There is a shortage of clinical geneticists, even with concerted recruitment efforts. Previously, no data had been collected about why young career geneticists chose this specialty. To investigate this question, we carried out a survey of current and recent medical genetics and genomics residents. The goal of this survey was to understand their reasons for pursuing medical genetics and genomics as a specialty. Results demonstrate that, for most, interest in genetics begins in medical school and was largely influenced by mentorship. This suggests that placing greater focus on introducing medical genetics as a clinical specialty and fostering robust mentorship of students in preclinical years may increase recruitment into medical genetics residencies.

DLG2 intragenic exonic deletions reinforce the link to neurodevelopmental disorders and suggest a potential association with congenital anomalies and dysmorphism.

PURPOSE: Multiple studies suggest an association between DLG2 and neurodevelopmental disorders and indicate the haploinsufficiency of this gene; however, few cases have been thoroughly described. We performed additional studies to confirm this clinical association and DLG2 haploinsufficiency. METHODS: Chromosomal microarray analysis was performed on 11,107 patients at the Cytogenetics Laboratory at the University of Alabama at Birmingham. The Database of Genomic Variants-Gold Standard Variants and the Genome Aggregation Database were selected for the association analysis. Fifty-nine patients from the literature and DECIPHER, all having DLG2 intragenic deletions, were included for comprehensive analysis of the distribution of these deletions. RESULTS: A total of 13 patients with DLG2 intragenic deletions, from 10 families in our cohort, were identified. Nine of 10 probands presented with clinical features of neurodevelopmental disorders. Congenital anomalies and dysmorphism were common in our cohort of patients. Association analysis showed that the frequency of DLG2 deletions in our cohort is significantly higher than those in the Database of Genomic Variants-Gold Standard Variants and the Genome Aggregation Database. Most of DLG2 intragenic deletions identified in 69 unrelated patients from our cohort, the literature, and DECIPHER map to the 5' region of the gene, with a hotspot centered around HPin7, exon 8, and HPin8. CONCLUSION: Our findings reinforce the link between DLG2 intragenic deletions and neurodevelopmental disorders, strongly support the haploinsufficiency of this gene, and indicate that these deletions might also have an association with congenital anomalies and dysmorphism.

HNRNPC haploinsufficiency affects alternative splicing of intellectual disability-associated genes and causes a neurodevelopmental disorder.

Heterogeneous nuclear ribonucleoprotein C (HNRNPC) is an essential, ubiquitously abundant protein involved in mRNA processing. Genetic variants in other members of the HNRNP family have been associated with neurodevelopmental disorders. Here, we describe 13 individuals with global developmental delay, intellectual disability, behavioral abnormalities, and subtle facial dysmorphology with heterozygous HNRNPC germline variants. Five of them bear an identical in-frame deletion of nine amino acids in the extreme C terminus. To study the effect of this recurrent variant as well as HNRNPC haploinsufficiency, we used induced pluripotent stem cells (iPSCs) and fibroblasts obtained from affected individuals. While protein localization and oligomerization were unaffected by the recurrent C-terminal deletion variant, total HNRNPC levels were decreased. Previously, reduced HNRNPC levels have been associated with changes in alternative splicing. Therefore, we performed a meta-analysis on published RNA-seq datasets of three different cell lines to identify a ubiquitous HNRNPC-dependent signature of alternative spliced exons. The identified signature was not only confirmed in fibroblasts obtained from an affected individual but also showed a significant enrichment for genes associated with intellectual disability. Hence, we assessed the effect of decreased and increased levels of HNRNPC on neuronal arborization and neuronal migration and found that either condition affects neuronal function. Taken together, our data indicate that HNRNPC haploinsufficiency affects alternative splicing of multiple intellectual disability-associated genes and that the developing brain is sensitive to aberrant levels of HNRNPC. Hence, our data strongly support the inclusion of HNRNPC to the family of HNRNP-related neurodevelopmental disorders.

Abrogation of MAP4K4 protein function causes congenital anomalies in humans and zebrafish.

We report 21 families displaying neurodevelopmental differences and multiple congenital anomalies while bearing a series of rare variants in mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4). MAP4K4 has been implicated in many signaling pathways including c-Jun N-terminal and RAS kinases and is currently under investigation as a druggable target for multiple disorders. Using several zebrafish models, we demonstrate that these human variants are either loss-of-function or dominant-negative alleles and show that decreasing Map4k4 activity causes developmental defects. Furthermore, MAP4K4 can restrain hyperactive RAS signaling in early embryonic stages. Together, our data demonstrate that MAP4K4 negatively regulates RAS signaling in the early embryo and that variants identified in affected humans abrogate its function, establishing MAP4K4 as a causal locus for individuals with syndromic neurodevelopmental differences.

Clinical evaluation and etiologic diagnosis of hearing loss: A clinical practice resource of the American College of Medical Genetics and Genomics (ACMG).

Hearing loss is a common and complex condition that can occur at any age, can be inherited or acquired, and is associated with a remarkably wide array of etiologies. The diverse causes of hearing loss, combined with the highly variable and often overlapping presentations of different forms of hearing loss, challenge the ability of traditional clinical evaluations to arrive at an etiologic diagnosis for many deaf and hard-of-hearing individuals. However, identifying the etiology of hearing loss may affect clinical management, improve prognostic accuracy, and refine genetic counseling and assessment of the likelihood of recurrence for relatives of deaf and hard-of-hearing individuals. Linguistic and cultural identities associated with being deaf or hard-of-hearing can complicate access to and the effectiveness of clinical care. These concerns can be minimized when genetic and other health care services are provided in a linguistically and culturally sensitive manner. This clinical practice resource offers information about the frequency, causes, and presentations of hearing loss and suggests approaches to the clinical and genetic evaluation of deaf and hard-of-hearing individuals aimed at identifying an etiologic diagnosis and providing informative and effective patient education and genetic counseling.

Near complete deletion of KMT2D in a college student.

Pathogenic variants in KMT2D are typically associated with Kabuki syndrome (KS), a rare multisystem disorder. KS is characterized by facial dysmorphisms, intellectual disability, skeletal and dermatoglyphic differences, and poor growth. Seventy percent of individuals with clinically diagnosed KS have a confirmed pathogenic variant in KMT2D or less commonly KDM6A. The majority of mutations found in KMT2D are de novo nonsense or frameshift, with deletions and duplications rarely reported in the literature. Here, we present the case of near complete deletion of KMT2D in a college student with normal intelligence discovered via exome sequencing and EpiSign methylation testing. This case provides evidence that large deletions in KMT2D are compatible with normal intelligence and presents EpiSign as a method for discovering molecular causes of KS not identified by traditional molecular testing.

The natural history of OTOF-related auditory neuropathy spectrum disorders: a multicenter study.

Pathogenic variations in the OTOF gene are a common cause of hearing loss. To refine the natural history and genotype-phenotype correlations of OTOF-related auditory neuropathy spectrum disorders (ANSD), audiograms and distortion product otoacoustic emissions (DPOAEs) were collected from a diverse cohort of individuals diagnosed with OTOF-related ANSD by comprehensive genetic testing and also reported in the literature. Comparative analysis was undertaken to define genotype-phenotype relationships using a Monte Carlo algorithm. 67 audiograms and 25 DPOAEs from 49 unique individuals positive for OTOF-related ANSD were collected. 51 unique OTOF pathogenic variants were identified of which 21 were missense and 30 were loss of function (LoF; nonsense, splice-site, copy number variants, and indels). There was a statistically significant difference in low, middle, and high frequency hearing thresholds between missense/missense and LoF/missense genotypes as compared to LoF/LoF genotypes (average hearing threshold for low, middle and high frequencies 70.9, 76.0, and 73.4 dB vs 88.5, 95.6, and 94.7 dB) via Tukey's test with age as a co-variate (P = 0.0180, 0.0327, and 0.0347, respectively). Hearing declined during adolescence with missense/missense and LoF/missense genotypes, with an annual mid-frequency threshold deterioration of 0.87 dB/year and 1.87 dB/year, respectively. 8.5% of frequencies measured via DPOAE were lost per year in individuals with serial tests. Audioprofiling of OTOF-related ANSD suggests significantly worse hearing with LoF/LoF genotypes. The unique pattern of variably progressive OTOF-related autosomal recessive ANSD may be amenable to gene therapy in selected clinical scenarios.

Interpretation and reporting of large regions of homozygosity and suspected consanguinity/uniparental disomy, 2021 revision: A technical standard of the American College of Medical Genetics and Genomics (ACMG).

Genomic testing, including single-nucleotide variation (formerly single-nucleotide polymorphism)-based chromosomal microarray and exome and genome sequencing, can detect long regions of homozygosity (ROH) within the genome. Genomic testing can also detect possible uniparental disomy (UPD). Platforms that can detect ROH and possible UPD have matured since the initial American College of Medical Genetics and Genomics (ACMG) standard was published in 2013, and the detection of ROH and UPD by these platforms has shown utility in diagnosis of patients with genetic/genomic disorders. The presence of these segments, when distributed across multiple chromosomes, may indicate a familial relationship between the proband's parents. This technical standard describes the detection of possible consanguinity and UPD by genomic testing, as well as the factors confounding the inference of a specific parental relationship or UPD. Current bioethical and legal issues regarding detection and reporting of consanguinity are also discussed.

The relationship between performance on the medical genetics and genomics in-training and certifying examinations.

PURPOSE: The American Board of Medical Genetics and Genomics (ABMGG) certifying examinations (CEs) are designed to assess relevant basic knowledge, clinical knowledge, and diagnostic skills of board-eligible candidates in primary specialty areas. The ABMGG in-training examinations (ITEs) provide formative feedback regarding knowledge and learning over time and assess readiness to attempt board certification. This study addresses the validity of the ABMGG ITE by evaluating its relationship with performance on CE utilizing established psychometric approaches. METHODS: Statistical analysis included bivariate Pearson correlation coefficients and linear regression to evaluate the strength of associations between ITE scores and CE scores. Logistic regression was used to assess the association between ITE scores and the probability of passing each CE. RESULTS: Logistic regression results indicated that ITE scores accounted for 22% to 44% of the variability in CE outcomes. Across 3 certification cycles, for every 1-point increase in ITE scores, the odds ratio for earning a passing score increased by a factor of 1.12 to 1.20 for the general CE, 1.14 to 1.25 for the clinical CE, and 1.12 to 1.20 for the laboratory CEs. CONCLUSION: The findings show a positive correlation between performance on the ITE examination and performance on and passing the ABMGG CE.

Occam's razor dulled: the occurrence of multiple genetic diagnoses.

PURPOSE OF REVIEW: A single genetic diagnosis, especially from the analysis of a limited number of genes, may not signal the end of a diagnostic odyssey. When a patient with a genetic syndrome presents with symptoms that are not usually associated with their disease phenotype, additional genetic testing is warranted. RECENT FINDINGS: Although multiple co-existing genetic diagnoses may sound unlikely, many recent studies and case reports have demonstrated that this scenario is more common than expected. Studies involving whole exome and genome sequencing have identified a frequency of multiple genetic diagnoses and have identified clinical findings that make a second diagnosis more likely, which we have seen reflected in recent cases from our own clinic and consult service. These include multisystem disease, consanguinity, well described aneuploidies with rare or new symptoms, and complex structural chromosomal anomalies which may include multiple chromosomes and breakpoints that disrupt gene function. SUMMARY: Identifying a second diagnosis can have vast implications for patient management and counseling. Patients can be followed with appropriate medical screening and early interventions to support optimal child development. Furthermore, the patient's family can be impacted by ending the diagnostic odyssey, providing testing for other at-risk family members, and offering prenatal options.

The first post-natal clinical description of true mosaic complete tetrasomy 21: A case report.

Tetrasomy 21 is a rare occurrence. Only 14 cases have been reported in the literature, 8 of which are partial tetrasomy cases and 6 which are complete tetrasomy cases. Of the incidences, no proband with true complete tetrasomy 21 has survived the neonatal period. We report complete mosaic tetrasomy 21 in a female infant with the typical Down syndrome phenotype, including Hirschsprung's disease and atrioventricular (AV) canal defect. This is in contrast to cases of partial tetrasomy 21, which often have an atypical trisomy 21 presentation and multiple nonspecific traits, including short stature, microcephaly, and developmental delays. This case demonstrates the difference in clinical presentation between the partial and complete subtype of tetrasomy 21 and provides the first postnatal clinical picture of an infant with true mosaic complete tetrasomy 21.

Genetic testing hearing loss: The challenge of non syndromic mimics.

Congenital hearing loss is a common cause of morbidity in early childhood. There are multiple reasons for congenital hearing impairment, with genetic contribution becoming increasingly recognized. Sensorineural hearing loss has classically been viewed as either syndromic or non-syndromic. With the advent of DNA sequencing technology such as NextGen sequencing, a subcategory has arisen, that of non-syndromic mimics (NSM)s. NSMs present initially as isolated hearing loss but as the patient ages other phenotypes become evident. Early diagnosis of these conditions is imperative as patients may suffer significant morbidity and mortality from complications from their hearing loss syndrome. An example is QT prolongation in Jervell and Lange-Nielsen Syndrome. The need for genetic testing and proper genetic counseling is necessary for patients with hearing loss and testing should be done as early in life as possible.

Mandibular Distraction Osteogenesis as a Primary Intervention in Infants With Pierre Robin Sequence.

BACKGROUND: Pierre Robin sequence (PRS) is a triad of congenital facial abnormalities that can present as a syndrome (syndromic PRS [sPRS]) or an isolated entity (isolated PRS [iPRS]). Patients with PRS can develop airway and feeding problems that may result in failure to thrive. Mandibular distraction osteogenesis (MDO) is a method for improving the functional issues associated with breathing and feeding. There is a Paucity of literature evaluating the outcomes of MDO between sPRS and iPRS patients. METHODS: An institutional review board-approved retrospective review of PRS patients managed by a single surgeon and treated with MDO between January 2015 and December 2019 at a tertiary referral hospital was performed. The patients were stratified into iPRS or sPRS based on gene testing. Airway outcome measures included avoidance of tracheostomy, relief of sleep apnea, and oxygen saturation improvement. Primary feeding measures included achievement of full oral feeds and growth/weight gain. Statistical analysis included t tests and χ2 tests where appropriate using SPSS. RESULTS: Over the study period, of the 29 infants with PRS, 55% identified as iPRS and 45% as sPRS. There were no significant differences in the patient characteristics, apnea-hypoxia index (22.27 ± 12.27) and laryngeal view (3 ± 0.79) pre-MDO. After MDO, 83% of the subjects achieved a positive feeding outcome and 86% achieved a positive airway outcome with no statistical significance between sPRS and iPRS (P = 0.4369). There was a statistically significant change post-MDO in apnea-hypoxia index (5.24 ± 4.50, P = 0.02) and laryngeal view (1.59 ± 1.00, P = 0.01). CONCLUSIONS: Our recent experience would lead us to believe that sPRS patients have greater morbidities and challenging clinical developments that, when properly evaluated, can be managed by MDO. There is a potential role for MDO in reducing the need for traditional surgical interventions for respiratory and feeding problems in both iPRS and sPRS patients.

Stickler Syndrome (SS): Laser Prophylaxis for Retinal Detachment (Modified Ora Secunda Cerclage, OSC/SS).

PURPOSE: To introduce a novel technique of encircling laser prophylaxis (ora secunda cerclage Stickler syndrome, OSC/SS) to prevent rhegmatogenous retinal detachment (RRD) in Stickler syndrome eyes. PATIENTS AND METHODS: After first eye RRD at age 50 and at age 18, respectively, a 53-year-old father and his 22-year-old son with type 2 SS (STL2) gave informed consent and underwent OSC/SS prophylaxis, performed in each fellow eye. A 26-year-old STL2 daughter then suffered first eye retinal detachment and similarly chose fellow eye OSC/SS prophylaxis. A second son, 28 years of age with STL2, chose OSC/SS prophylaxis in both eyes. RESULTS: The three OSC/SS treated fellow eyes have gone 12 years, 11 years, and 8 years without RRD. STL1 and less common STL2 eyes are known to have a similar rate of RRD, and 80% of STL1 fellow eyes develop RRD at a median of 4 years in the absence of prophylaxis. Moreover, five of six (83%) known STL2 family members suffered RRD, only the STL2 son with bilateral OSC/SS remaining bilaterally attached. All five OSC/SS treated eyes (average 8.7 years post-prophylaxis) retained preoperative visual acuity of 20/20 to 20/30, with an average, asymptomatic reduction of meridional field in each eye to 50 degrees. In contrast, in the three eyes having suffered RRD prior to presentation, visual acuity ranged from 20/125 to 8/200 and average meridional field was 29 degrees. CONCLUSION: Encircling grid laser (OSC) modified in Stickler eyes to encompass the ora serrata and extend posteriorly to and between the vortex vein ampullae (OSC/SS) is a reasonable RRD prophylaxis option to offer STL1 and STL2 patients as an alternative to no treatment or less effective prophylaxis. Because of rarity and severity, the ultimate proof of safety and efficacy will likely come not from randomized trials, but from a non-randomized, prospective, cohort comparison study of such individual efforts.

JARID2 haploinsufficiency is associated with a clinically distinct neurodevelopmental syndrome.

PURPOSE: JARID2, located on chromosome 6p22.3, is a regulator of histone methyltransferase complexes that is expressed in human neurons. So far, 13 individuals sharing clinical features including intellectual disability (ID) were reported with de novo heterozygous deletions in 6p22-p24 encompassing the full length JARID2 gene (OMIM 601594). However, all published individuals to date have a deletion of at least one other adjoining gene, making it difficult to determine if JARID2 is the critical gene responsible for the shared features. We aim to confirm JARID2 as a human disease gene and further elucidate the associated clinical phenotype. METHODS: Chromosome microarray analysis, exome sequencing, and an online matching platform (GeneMatcher) were used to identify individuals with single-nucleotide variants or deletions involving JARID2. RESULTS: We report 16 individuals in 15 families with a deletion or single-nucleotide variant in JARID2. Several of these variants are likely to result in haploinsufficiency due to nonsense-mediated messenger RNA (mRNA) decay. All individuals have developmental delay and/or ID and share some overlapping clinical characteristics such as facial features with those who have larger deletions involving JARID2. CONCLUSION: We report that JARID2 haploinsufficiency leads to a clinically distinct neurodevelopmental syndrome, thus establishing gene-disease validity for the purpose of diagnostic reporting.