Antiviral and Anti-Inflammatory Therapeutic Effect of RAGE-Ig Protein against Multiple SARS-CoV-2 Variants of Concern Demonstrated in K18-hACE2 Mouse and Syrian Golden Hamster Models.

SARS-CoV-2 variants of concern (VOCs) continue to evolve and reemerge with chronic inflammatory long COVID sequelae, necessitating the development of anti-inflammatory therapeutic molecules. Therapeutic effects of the receptor for advanced glycation end products (RAGE) were reported in many inflammatory diseases. However, a therapeutic effect of RAGE in COVID-19 has not been reported. In the present study, we investigated whether and how the RAGE-Ig fusion protein would have an antiviral and anti-inflammatory therapeutic effect in the COVID-19 system. The protective therapeutic effect of RAGE-Ig was determined in vivo in K18-hACE2 transgenic mice and Syrian golden hamsters infected with six VOCs of SARS-CoV-2. The underlying antiviral mechanism of RAGE-Ig was determined in vitro in SARS-CoV-2-infected human lung epithelial cells (BEAS-2B). Following treatment of K18-hACE2 mice and hamsters infected with various SARS-CoV-2 VOCs with RAGE-Ig, we demonstrated (1) significant dose-dependent protection (i.e., greater survival, less weight loss, lower virus replication in the lungs); (2) a reduction of inflammatory macrophages (F4/80+/Ly6C+) and neutrophils (CD11b+/Ly6G+) infiltrating the infected lungs; (3) a RAGE-Ig dose-dependent increase in the expression of type I IFNs (IFN-α and IFN-ß) and type III IFN (IFNλ2) and a decrease in the inflammatory cytokines (IL-6 and IL-8) in SARS-CoV-2-infected human lung epithelial cells; and (4) a dose-dependent decrease in the expression of CD64 (FcgR1) on monocytes and lung epithelial cells from symptomatic COVID-19 patients. Our preclinical findings revealed type I and III IFN-mediated antiviral and anti-inflammatory therapeutic effects of RAGE-Ig protein against COVID-19 caused by multiple SARS-CoV-2 VOCs.

Experiences of hereditary cancer care among transgender and gender diverse people: "It's gender. It's cancer risk it's everything".

Transgender and gender diverse (TGD) individuals are a significant yet underrepresented population within genetic counseling research and broader LGBTQI+ health studies. This underrepresentation perpetuates a cycle of exclusion from the production of medical knowledge, impacting the quality and equity of care received by TGD individuals. This issue is particularly poignant in cancer genetic counseling, where TGD individuals with elevated cancer risk receive risk assessment, counseling, and referral to support based on risk figures and standards of care developed for cisgender individuals. The experiences of TGD individuals navigating inherited cancer syndromes remain largely undocumented in medical literature, posing challenges to the provision of inclusive care by genetics providers. To bridge this knowledge gap, we conducted a cross-sectional qualitative study. Nineteen semi-structured interviews were held with gender diverse adults having hereditary cancer syndromes, family histories of such syndromes, or personal histories of chest cancer. Our study employed thematic analysis using combined inductive and deductive methods to illuminate how hereditary cancer care intersects with participants' gender identities, gender expression, and gender-affirming care experiences. Participants reflected on care experiences that felt affirming or triggered gender dysphoria. Participants also discussed the interplay between risk-reducing mastectomy and top surgery, exploring co-emergent dynamics between cancer risk management and gender expression. Significantly, participants identified actionable strategies for healthcare providers to enhance support for gender diverse patients, including the mindful use of gendered language, collaborative decision-making, and conveying allyship. These findings offer valuable insights into tailoring genetic counseling to meet the unique needs of TGD individuals, advancing the path toward inclusive and appropriate care for LGBTQI+ individuals with hereditary cancer syndromes.

Beyond multiple choice: Clinical simulation as a rigorous and inclusive method for assessing genetic counseling competencies.

Educational use of clinical simulation is a way for students to immerse themselves within a realistic yet safe and structured environment as they practice clinical skills. It is widely used in healthcare training and evaluation, and there are best practices for design, implementation, debriefing, and assessment. An increasing number of genetic counseling graduate programs use simulation in various ways, ranging from role-plays to working with professional simulated/standardized patient (SP) actors. At this time, there is very little consistency across programs, research on the approaches, and standards by which simulation is incorporated into training. Simulation is an understudied but promising approach for genetic counselor (GC) education and assessment. After graduation, GCs demonstrate their competence as entry-level providers through American Board of Genetic Counseling (ABGC) multiple-choice examination (MCE), along with their participatory clinical encounters from graduate training. Data from genetic counseling and other professions highlight the limitations and biases of MCEs, suggesting they not only fail to accurately capture competency, but also that they disadvantage underrepresented individuals from entering the field. In addition, MCEs are limited as a tool for assessing nuanced counseling and communication skills, as compared to more quantitative scientific knowledge. We propose that innovative, evidence-based approaches such as simulation have the potential to not only enhance learning, but also to allow GCs to better demonstrate competency during training and in relation to the board examination. Collaborative approaches, research, and funding are needed to further explore the viability of routinely incorporating simulation into GC training and assessment.

Antiviral CD19+CD27+ Memory B Cells Are Associated with Protection from Recurrent Asymptomatic Ocular Herpesvirus Infection.

Reactivation of herpes simplex virus 1 (HSV-1) from latently infected neurons of the trigeminal ganglia (TG) leads to blinding recurrent herpetic disease in symptomatic (SYMP) individuals. Although the role of T cells in herpes immunity seen in asymptomatic (ASYMP) individuals is heavily explored, the role of B cells is less investigated. In the present study, we evaluated whether B cells are associated with protective immunity against recurrent ocular herpes. The frequencies of circulating HSV-specific memory B cells and of memory follicular helper T cells (CD4+ Tfh cells), which help B cells produce antibodies, were compared between HSV-1-infected SYMP and ASYMP individuals. The levels of IgG/IgA and neutralizing antibodies were compared in SYMP and ASYMP individuals. We found that (i) the ASYMP individuals had increased frequencies of HSV-specific CD19+CD27+ memory B cells, and (ii) high frequencies of HSV-specific switched IgG+CD19+CD27+ memory B cells detected in ASYMP individuals were directly proportional to high frequencies of CD45R0+CXCR5+CD4+ memory Tfh cells. However, no differences were detected in the level of HSV-specific IgG/IgA antibodies in SYMP and ASYMP individuals. Using the UV-B-induced HSV-1 reactivation mouse model, we found increased frequencies of HSV-specific antibody-secreting plasma HSV-1 gD+CD138+ B cells within the TG and circulation of ASYMP mice compared to those of SYMP mice. In contrast, no significant differences in the frequencies of B cells were found in the cornea, spleen, and bone-marrow. Our findings suggest that circulating antibody-producing HSV-specific memory B cells recruited locally to the TG may contribute to protection from symptomatic recurrent ocular herpes. IMPORTANCE Reactivation of herpes simplex virus 1 (HSV-1) from latently infected neurons of the trigeminal ganglia (TG) leads to blinding recurrent herpetic disease in symptomatic (SYMP) individuals. Although the role of T cells in herpes immunity against blinding recurrent herpetic disease is heavily explored, the role of B cells is less investigated. In the present study, we found that in both asymptomatic (ASYMP) individuals and ASYMP mice, there were increased frequencies of HSV-specific memory B cells that were directly proportional to high frequencies of memory Tfh cells. Moreover, following UV-B-induced reactivation, we found increased frequencies of HSV-specific antibody-secreting plasma B cells within the TG and circulation of ASYMP mice compared to those of SYMP mice. Our findings suggest that circulating antibody-producing HSV-specific memory B cells recruited locally to the TG may contribute to protection from recurrent ocular herpes.

Research participants' perspectives about the return of uninformative genomic test results in a clinical research setting.

The majority of genomic sequencing and microarray results are clinically uninformative, meaning that they do not suggest a need for any behavioral action or medical intervention. Prior studies have shown that recipients of uninformative genomic testing results ("uninformative results" hereafter) may incorrectly interpret them to imply a lowered risk of disease or false reassurance about future health risks. Few studies have examined how patients understand uninformative results when they are returned in a research setting, where there is wide variation in analytical specifications of testing, interpretation and reporting practices, and resources to support the return of results. We conducted cross-sectional interviews (N = 17) to explore how a subset of research participants in one genomics study at the National Institutes of Health reacted to and understood their uninformative test results, which were returned to them via a patient portal without genetic counseling. We found that most participants did not remember the details of the informed consent process, including the distinction between "primary" and "secondary" findings. Participants had questions about what genes were tested for and, in most cases, requested a list of the genes covered. Several participants incorrectly assumed that autosomal recessive carrier results would have been reported to them if detected. Some participants interpreted their uninformative results to mean that they could forgo prenatal testing, and participants had mixed expectations about whether their results might be reinterpreted in the future. These themes suggest that there are specific challenges to returning uninformative results in research settings. Educational supplements to uninformative test reports may be most useful if they contextualize results in relation to other types of clinical genetic or genomic testing that may be made available to research participants in their lifetimes.

Clinical exome sequencing of 1000 families with complex immune phenotypes: Toward comprehensive genomic evaluations.

BACKGROUND: Prospective genetic evaluation of patients at this referral research hospital presents clinical research challenges. OBJECTIVES: This study sought not only a single-gene explanation for participants' immune-related presentations, but viewed each participant holistically, with the potential to have multiple genetic contributions to their immune phenotype and other heritable comorbidities relevant to their presentation and health. METHODS: This study developed a program integrating exome sequencing, chromosomal microarray, phenotyping, results return with genetic counseling, and reanalysis in 1505 individuals from 1000 families with suspected or known inborn errors of immunity. RESULTS: Probands were 50.8% female, 71.5% were ≥18 years, and had diverse immune presentations. Overall, 327 of 1000 probands (32.7%) received 361 molecular diagnoses. These included 17 probands with diagnostic copy number variants, 32 probands with secondary findings, and 31 probands with multiple molecular diagnoses. Reanalysis added 22 molecular diagnoses, predominantly due to new disease-gene associations (9 of 22, 40.9%). One-quarter of the molecular diagnoses (92 of 361) did not involve immune-associated genes. Molecular diagnosis was correlated with younger age, male sex, and a higher number of organ systems involved. This program also facilitated the discovery of new gene-disease associations such as SASH3-related immunodeficiency. A review of treatment options and ClinGen actionability curations suggest that at least 251 of 361 of these molecular diagnoses (69.5%) could translate into ≥1 management option. CONCLUSIONS: This program contributes to our understanding of the diagnostic and clinical utility whole exome analysis on a large scale.

The Responsibility to Recontact Research Participants after Reinterpretation of Genetic and Genomic Research Results.

The evidence base supporting genetic and genomic sequence-variant interpretations is continuously evolving. An inherent consequence is that a variant's clinical significance might be reinterpreted over time as new evidence emerges regarding its pathogenicity or lack thereof. This raises ethical, legal, and financial issues as to whether there is a responsibility to recontact research participants to provide updates on reinterpretations of variants after the initial analysis. There has been discussion concerning the extent of this obligation in the context of both research and clinical care. Although clinical recommendations have begun to emerge, guidance is lacking on the responsibilities of researchers to inform participants of reinterpreted results. To respond, an American Society of Human Genetics (ASHG) workgroup developed this position statement, which was approved by the ASHG Board in November 2018. The workgroup included representatives from the National Society of Genetic Counselors, the Canadian College of Medical Genetics, and the Canadian Association of Genetic Counsellors. The final statement includes twelve position statements that were endorsed or supported by the following organizations: Genetic Alliance, European Society of Human Genetics, Canadian Association of Genetic Counsellors, American Association of Anthropological Genetics, Executive Committee of the American Association of Physical Anthropologists, Canadian College of Medical Genetics, Human Genetics Society of Australasia, and National Society of Genetic Counselors.

Genomic tools for health: Secondary findings as findings to be shared.

PURPOSE: Whether and how to disclose secondary finding (SF) information to children is ethically debated. Some argue that genetic testing of minors should be limited to preserve the child's future autonomy. Others suggest that disclosure of SFs can occur if it is in the best interests of the child. However, the ways that parents conceptualize and weigh their child's future autonomy against the interests of their child and other family members are unknown. METHODS: To explore how parents understand SF disclosure in the context of their child and other family members' lives, we conducted semistructured interviews with 30 families (40 parents in total). All parents had children who were enrolled in a genetic sequencing protocol that returned results by default. RESULTS: We found that parents did not routinely conceptualize SFs as distinctive health information. Rather parents saw this information as part of their child's overall health. To make decisions about disclosure, parents weighed their child's ability to understand the SF information and their other family member's need to know. CONCLUSION: Because most families desired SF information, we argue that disclosure of SF be reconceptualized to reflect the lived experiences of those who may receive this information.

Reason-Based Abortion Bans, Disability Rights, and the Future of Prenatal Genetic Testing.

Recent advances in prenatal genetic testing have made testing for congenital disorders more accessible, with emerging technologies promising further expansion of available testing options. In particular, non-invasive prenatal testing ("NIPT") has allowed women to identify more fetal disorders earlier in pregnancy than was possible only a decade ago. In addition to allowing women to prepare for the birth of a child with a disability, prenatal diagnoses give women the ability to terminate a pregnancy to avoid raising a child with a disability, a choice driven by myriad factors.

Exome sequencing study in a clinical research setting finds general acceptance of study returning secondary genomic findings with little decisional conflict.

The most appropriate strategies for managing secondary genomic findings (SF) in clinical research are being developed and evaluated. We surveyed patients at the National Institute of Allergy and Infectious Diseases (NIAID) to evaluate decisional conflict regarding enrolling in a study that returns SF. Responses were collected using a cross-sectional survey after informed consent but before return of SF. Sixty-six adults of 116 eligible participants responded. No participant explicitly declined because they did not want to possibly receive a SF. Sixty-five of 66 (98%) participants thought it was appropriate to return SFs in research; one participant was unsure. Decisional conflict regarding enrolling in a study returning SF was low overall with 68% of participants reporting a score of less than 10 on a 100-point decisional conflict scale, implying that they felt informed, clear on what they wanted, and supported. Lower genetic literacy was weakly associated with higher decisional conflict (Spearman's rho = -0.297, p = .015). Six participants reported confusion related to the choices about SFs. Our data suggest that participants in our study feel it is appropriate to receive SF and have little decisional conflict about potentially receiving such information; however, some participants may need further education and counseling.

An ethical framework for genetic counseling in the genomic era.

The field of genetic counseling has grown and diversified since the profession emerged in the early 1970s. In the same period, genomic testing has become more complex, profitable, and widespread. With these developments, the scope of ethical considerations relevant to genetic counseling has expanded. In light of this, we find it helpful to revisit how ethical and relational variables are used to inform genetic counseling practice. Our specific focus is on whether, and to what extent, it is ethically acceptable for genetic counselors to make normative recommendations to patients. This article builds on prior literature that has critiqued nondirectiveness, a concept that has influenced and constrained the modern profession of genetic counseling since its origin. In it, we review scholarly efforts to move beyond nondirectiveness, which we believe privilege patient autonomy at the expense of other important values. We then argue that genetic counselors should favor a more explicit commitment to the principles of beneficence and non-maleficence, as well as a broader understanding of autonomy and the relational variables that impact genetic counseling. Finally, to translate our arguments into practice, we present a framework of six considerations that genetic counselors should take into account when deciding whether it is ethically acceptable, or even desirable, to make recommendations to patients in certain areas of their work.

Caregivers' perception of and experience with variants of uncertain significance from whole exome sequencing for children with undiagnosed conditions.

Despite its promising diagnostic yield, whole exome sequencing (WES) frequently introduces variant(s) of uncertain significance (VUS), which have been speculated to cause parental stress and anxiety. This study aimed to explore the psychosocial impact of receiving a VUS from pediatric WES on caregivers and to identify implications for clinical practice. Fourteen telephone interviews were conducted with parents or legal guardians who received VUS results from their child's WES to assess their understanding of the result, affective responses, perceived impact, and adaptation. Our content analysis showed that most participants had a good understanding of the purpose of the test and the majority of them recalled the result category. Most participants deemed the result had no impact thus far on their perception of their child's condition. However, one participant reported feelings of fear related to the VUS. Most participants experienced a range of emotions from receiving the result. The majority of participants reported that this result did not significantly alter their child's care or their ability to take care of their child, and three participants reported empowerment. Additionally, several participants expressed an interest in research studies and peer support groups dedicated to families with a VUS identified on WES. Our study elicited new information about the psychosocial impact of receiving a VUS from WES. This insight may help to guide pre- and post-WES counseling in the future.

Clinical whole exome sequencing in child neurology practice.

OBJECTIVE: Whole exome sequencing (WES) represents a significant breakthrough in clinical genetics as a powerful tool for etiological discovery in neurodevelopmental disorders. To better characterize the genetic landscape of neurodevelopmental disorders, we analyzed patients in our pediatric neurogenetics clinic who underwent WES. METHODS: We performed a retrospective cohort study on 78 patients with various neurodevelopmental disabilities and unrevealing workup prior to WES. We characterized their molecular diagnoses, clinical features, and whether their previous treatment plan changed due to WES results. RESULTS: The overall presumptive diagnostic rate for our cohort was 41% (n = 32 of 78 patients). Nineteen patients had a single autosomal dominant (AD) disorder, 11 had a single autosomal recessive (AR) disorder, 1 had an X-linked dominant disorder, and 1 had both an AD and an AR disorder. The 32 patients with pathogenic or likely pathogenic variants exhibited various neurobehavioral and neuroimaging abnormalities, including intellectual disability/developmental delay (n = 28), cerebral palsy-like encephalopathy (n = 11), autism spectrum disorder (n = 5), delayed/hypomyelination (n = 7), and cerebellar abnormalities (n = 9). The results of WES affected management for all patients with a presumptive diagnosis, triggering reproductive planning (n = 27), disease monitoring initiation (n = 4), investigation of systemic involvement of the disorder(s) (n = 6), alteration of presumed disease inheritance pattern (n = 7), changing of prognosis (n = 10), medication discontinuation (n = 5) or initiation (n = 2), and clinical trial education (n = 3). INTERPRETATION: The high diagnostic yield of WES supports its use in pediatric neurology practices. It may also lead to earlier diagnosis, impacting medical management, prognostication, and family planning. WES therefore serves as a critical tool for the child neurologist.

Novel KIF7 missense substitutions in two patients presenting with multiple malformations and features of acrocallosal syndrome.

We present two children who both had two missense mutations in the Kinesin Family Member 7 (KIF7) gene. A seven year old female with severe developmental delays, failure to thrive and growth retardation, infantile spasms, a cardiac vascular ring and right-sided aortic arch, imperforate anus, hydronephrosis with a right renal cyst, syndactyly and abnormal white matter was a compound heterozygote for c.3365C > G, predicting p.(Ser1122Trp) that was maternally inherited and c.2482G > A, predicting p.(Val828Met) that was paternally inherited. An eight year old female with severe developmental delays, epilepsy, left postaxial polydactyly of the hand and abnormalities of brain development including hydrocephalus, pachygyria and absence of the body and splenium of the corpus callous was a compound heterozygote for c.461G > A, predicting p.(Arg154Gln) and c.2959 G > A, predicting p.(Glu987Lys) that was maternally inherited and her father was unavailable for testing. The presentations in these children include features of acrocallosal syndrome, such as hypoplasia of the corpus callosum, enlarged ventricles, facial dysmorphism with a prominent forehead and broad halluces in the first child, but included atypical findings for individuals previously reported to have truncating mutations in KIF7, including imperforate anus, infantile spasms and severe growth retardation. We conclude that these phenotypes may result from the KIF7 sequence variants and abnormal hedgehog signaling, but that the full spectrum of KIF7-associated features remains to be determined.

'Out of hours' adult CT head interpretation by senior emergency department staff following an intensive teaching session: a prospective blinded pilot study of 405 patients.

AIM: Cranial CT is the gold standard for the investigation of intracranial emergencies. The aim of this pilot study was to audit whether senior emergency physicians were able to report CT head scans accurately and reliably having attended structured teaching. MATERIALS AND METHODS: Senior emergency physicians attended a 3 h teaching session. Following this, they independently reported adult CT head scans between 22:00 and 08:00 using a pro forma. CT head examinations performed in this 'out of hours' period were formally reported by a consultant radiologist on the following morning. Data were collected in a blinded fashion over an 8-month period. RESULTS: 405 adult CT head examinations were performed. 360 pro formas were available for analysis, and the rest were excluded either because a consultant radiologist had been rung to discuss the results (five patients) or because the pro forma was not completed (40 patients). Concordance between consultant radiologists and emergency physicians was found in 339 (94%) of the cases (κ coefficient 0.78). None of the discordant cases was managed inappropriately or had an adverse clinical outcome. All cases of extradural, subdural and subarachnoid haemorrhage were detected by emergency physicians. CONCLUSIONS: In conclusion, we feel that this model can be employed as a safe and long-term alternative provided that the radiology department are committed to providing ongoing teaching and that a database is maintained to highlight problem areas. Emergency physicians need to remember that the clinical status of the patient must never be ignored, irrespective of their CT head findings.

Queering genomics: How cisnormativity undermines genomic science.

Over the past century, genetics and genomics ("genomics") have contributed significantly to our knowledge of human biology and disease. Genomics has also bolstered inaccurate and harmful arguments about "essential" differences between socially defined groups. These purported differences have reinforced class hierarchies and justified the mistreatment of groups such as Black people, Indigenous people, and other people of color and/or people with disabilities. With this history in mind, we explore how genomics is used to reinforce scientifically unsound understandings of the relationship between two fundamental aspects of the human experience: sex and gender. We argue that imprecise, inaccurate practices for collecting data and conducting genomic research have adversely influenced genomic science and can contribute to the stigmatization of people whose sex and/or gender challenge binary expectations. The results have been to preclude transgender and intersex people from accessing high-quality, evidence-based healthcare and to hinder their participation in scientifically sound research. In this perspective, we use the lens of queer theory to render this situation more visible. First, we highlight the theoretical contributions queer theory can make to genomic science. Second, we examine practices in research and clinical genomics that exclude and stigmatize transgender and intersex people. Third, we highlight the ways that many current genomic research practices generate false conclusions that are used to support unjust public policies. We conclude by recommending ways that clinicians and researchers can-and should-harness the scientific, social, and cultural power of genomics to advance knowledge and improve lives across the spectra of sex and gender.

Characterizing Decision-Making Surrounding Exercise in ARVC: Analysis of Decisional Conflict, Decisional Regret, and Shared Decision-Making.

BACKGROUND: Limiting high-intensity exercise is recommended for patients with arrhythmogenic right ventricular cardiomyopathy (ARVC) due to its association with penetrance, arrhythmias, and structural progression. Guidelines recommend shared decision-making (SDM) for exercise level, but there is little evidence regarding its impact. Therefore, we sought to evaluate the extent and implications of SDM for exercise, decisional conflict, and decisional regret in patients with ARVC and at-risk relatives. METHODS: Adults diagnosed with ARVC or with positive genetic testing enrolled in the Johns Hopkins ARVC Registry were invited to complete a questionnaire that included exercise history and current exercise, SDM (SDM-Q-9), decisional conflict, and decisional regret. RESULTS: The response rate was 64.8%. Two-thirds of participants (68.0%, n=121) reported clinically significant decisional conflict regarding exercise at diagnosis/genetic testing (DCS [decisional conflict scale]≥25), and half (55.1%, n=98) in the past year. Prevalence of decisional regret was also high with 55.3% (n=99) reporting moderate to severe decisional regret (DRS [decisional regret scale]≥25). The extent of SDM was highly variable ranging from no (0) to perfect (100) SDM (mean, 59.6±25.0). Those diagnosed in adolescence (≤age 21) reported significantly more SDM (P=0.013). Importantly, SDM was associated with less decisional conflict (ß=-0.66, R2=0.567, P<0.01) and decisional regret (ß=-0.37, R2=0.180, P<0.001) and no difference in vigorous intensity aerobic exercise in the 6 months after diagnosis/genetic testing or the past year (P=0.56; P=0.34, respectively). CONCLUSIONS: SDM is associated with lower decisional conflict and decisional regret; and no difference in postdiagnosis exercise. Our data thus support SDM as the preferred model for exercise discussions for ARVC.

Chromosomal microarray analysis supplements exome sequencing to diagnose children with suspected inborn errors of immunity.

Purpose: Though copy number variants (CNVs) have been suggested to play a significant role in inborn errors of immunity (IEI), the precise nature of this role remains largely unexplored. We sought to determine the diagnostic contribution of CNVs using genome-wide chromosomal microarray analysis (CMA) in children with IEI. Methods: We performed exome sequencing (ES) and CMA for 332 unrelated pediatric probands referred for evaluation of IEI. The analysis included primary, secondary, and incidental findings. Results: Of the 332 probands, 134 (40.4%) received molecular diagnoses. Of these, 116/134 (86.6%) were diagnosed by ES alone. An additional 15/134 (11.2%) were diagnosed by CMA alone, including two likely de novo changes. Three (2.2%) participants had diagnostic molecular findings from both ES and CMA, including two compound heterozygotes and one participant with two distinct diagnoses. Half of the participants with CMA contribution to diagnosis had CNVs in at least one non-immune gene, highlighting the clinical complexity of these cases. Overall, CMA contributed to 18/134 diagnoses (13.4%), increasing the overall diagnostic yield by 15.5% beyond ES alone. Conclusion: Pairing ES and CMA can provide a comprehensive evaluation to clarify the complex factors that contribute to both immune and non-immune phenotypes. Such a combined approach to genetic testing helps untangle complex phenotypes, not only by clarifying the differential diagnosis, but in some cases by identifying multiple diagnoses contributing to the overall clinical presentation.

The contribution of rare copy number variants in FAS toward pathogenesis of autoimmune lymphoproliferative syndrome.

Autoimmune lymphoproliferative syndrome (ALPS) is characterized by chronic nonmalignant lymphadenopathy, splenomegaly, cytopenias, and other autoimmune manifestations. ALPS is caused by lymphocyte accumulation from defects in FAS-mediated apoptosis. Heterozygous germline or somatic pathogenic single nucleotide variants in FAS are the most common molecular etiology of ALPS. Through the Centralized Sequencing Program at the National Institute of Allergy and Infectious Diseases, we performed exome sequencing on subjects with a clinical diagnosis of ALPS, with a subset receiving copy number variant (CNV) analysis. In this cohort, we identified 3 subjects from unrelated families with CNVs at the FAS locus. One subject had a de novo ∼0.828 Mb copy number loss encompassing all of FAS. The second subject had a maternally inherited ∼1.004 Mb copy number loss encompassing all of FAS. The third subject had a paternally inherited ∼0.044 Mb copy number loss encompassing exons 7 through 9 of FAS. Subjects with deletions in FAS had clinical presentations and biomarker profiles similar to those with ALPS and with germline and somatic FAS variants. We demonstrate that CNV analysis should be pursued if there is clinical and biomarker evidence of ALPS because it can lead to a molecular diagnosis and appropriate treatment when FAS sequencing is inconclusive.