Abstract Disclosure: G. Ortiz: Speaker; Self; Rhythm Pharmaceuticals, Inc. S.B. Ten: Advisory Board Member; Self; Rhythm Pharmaceuticals, Inc. Speaker; Self; Rhythm Pharmaceuticals, Inc. W. Herring: Advisory Board Member; Self; Rhythm Pharmaceuticals, Inc, Novo Nordisk. O. Pinhas-Hamiel: None. E.A. Oral: Consulting Fee; Self; Rhythm Pharmaceuticals, Inc., Akcea Therapeutics, Ionis Pharmaceuticals Inc., Morphic Medical, Fractyl Laboratories, Regeneron Pharmaceuticals, Amryt Pharmaceuticals (now Chiesi), Third Rock Ventures, Rejuvenate Bio, NIDDK. Other; Self; Has patents for use of metreleptin in lipodystrophy and recombinant leptin or analogues in NASH. N. Rosano: Consulting Fee; Self; Novo Nordisk. Speaker; Self; Rhythm Pharmaceuticals, Inc. D. Koren: Employee; Self; Rhythm Pharmaceuticals, Inc.. Stock Owner; Self; Rhythm Pharmaceuticals, Inc. H. Lee: Employee; Self; Rhythm Pharmaceuticals, Inc.. Stock Owner; Self; Rhythm Pharmaceuticals, Inc. J. Garrison: Employee; Self; Rhythm Pharmaceuticals, Inc.. Stock Owner; Self; Rhythm Pharmaceuticals, Inc. O. Ohayon: Employee; Self; Rhythm Pharmaceuticals, Inc.. Stock Owner; Self; Rhythm Pharmaceuticals, Inc. P. Sleiman: Employee; Self; Rhythm Pharmaceuticals, Inc.. Stock Owner; Self; Rhythm Pharmaceuticals, Inc. M. Wabitsch: Consulting Fee; Self; Rhythm Pharmaceuticals, Inc.. Speaker; Self; Rhythm Pharmaceuticals, Inc.. Other; Self; Rhythm Pharmaceuticals, Inc. E. van den Akker: Speaker; Self; Federatie Medisch Specialisten, Stichting Kwaliteitsgelden Medisch Specialisten, Medialane TV, Pfizer, Inc.. Other; Self; Nederlandse Hartstichting/ZonMW, Stichting Erasmus Trustfonds, Rhythm Pharmaceuticals, Inc. J. Argente: Advisory Board Member; Self; Rhythm Pharmaceuticals, Inc. Speaker; Self; Rhythm Pharmaceuticals, Inc.. I. Farooqi: None. Background: DAYBREAK (NCT04963231) was designed to evaluate setmelanotide in individuals who carried a confirmed variant in ≥1 of 31 genes with strong or very strong relevance to the melanocortin-4 receptor (MC4R) pathway, which regulates energy balance and satiety. Methods: DAYBREAK is a 2-stage, double-blind, placebo-controlled trial conducted at 37 sites across 8 countries. Individuals aged 6 to 65 years with body mass index (BMI) ≥40 kg/m2 (aged ≥18 years) or ≥97th percentile (aged ≥6 to <18 years) and hyperphagia who carried variants classified as uncertain significance (VUS), likely pathogenic, or pathogenic according to the American College of Medical Genetics (ACMG) criteria in ≥1 of the 31 genes were eligible. Individuals with ≥5% BMI reduction from baseline (ie, responders) at the end of the 16-week, open-label run-in period (Stage 1) were eligible to enter a 24-week, double-blind, randomized, placebo-controlled period (Stage 2). The primary endpoint of Stage 1 was the proportion of responders per gene cohort at the end of the Stage. Results: A total of 164 individuals were enrolled; 100 patients who completed Stage 1 and 12 who discontinued treatment within a prespecified 2 weeks before the end of Stage 1 were included in the completers analysis. Participants were divided into 15 gene cohorts; of 7 cohorts with ≥5 patients, 6 (SEMA3[A-G], PLXNA[1-4], PHIP, TBX3, MAGEL2, and SIM1) showed potential setmelanotide efficacy (KSR2 did not). Response rates across cohorts (range, 25.0%-56.3%), intracohort response magnitudes (percent BMI change from baseline to Week 16; range, −6.4% to −4.0%), and intracohort variant types varied. While response rate was highest in the PHIP cohort (56.3% of the full cohort and 69.2% of completers), ≥1 patient per cohort achieved ≥10% BMI reduction. Because ∼80% of VUS are eventually reclassified to benign or likely benign, the inclusion of VUS may have contributed to response variability. An ad hoc analysis showed an increased response rate with updated versus starting ACMG variant classification. Overall, 49 responders across 6 gene cohorts were randomized into Stage 2. Setmelanotide was well tolerated with no new safety concerns. Conclusions: DAYBREAK Stage 1 identified 6 additional genes or gene families in the MC4R pathway that respond to setmelanotide. Response was associated with predicted variant pathogenicity, allowing for further refinement of patient selection. Stage 2 results will further elucidate Stage 1 findings. Presentation: 6/3/2024

Study Objectives To identify genetic susceptibility variants in pediatric obstructive sleep apnea in European American and African American children. Methods A phenotyping algorithm using electronic medical records was developed to recruit cases with OSA and control subjects from the Center for Applied Genomics at Children’s Hospital of Philadelphia (CHOP). Genome-wide association studies (GWAS) were performed in pediatric OSA cases and control subjects with European American (EA) and African American (AA) ancestry followed by meta-analysis and sex stratification. Results The algorithm accrued 1486 subjects (46.3% European American, 53.7% African American). We identified genomic loci at 1p36.22 and 15q26.1 that associated with OSA risk in EA and AA, respectively. We also revealed a shared risk locus at 18p11.32 (rs114124196, p = 1.72 × 10-8) across EA and AA populations. Additionally, association at 1q43 (rs12754698) and 2p25.1 (rs72775219) was identified in the male-only analysis of EA children with OSA, while association at 8q21.11 (rs6472959), 11q24.3 (rs4370952) and 15q21.1 (rs149936782) was detected in the female-only analysis of EA children and association at 18p11.23 (rs9964029) was identified in the female-only analysis of African-American children. Moreover, the 18p11.32 locus was replicated in an EA cohort (rs114124196, p = 8.8 × 10-3). Conclusions We report the first GWAS for pediatric OSA in European Americans and African Americans. Our results provide novel insights to the genetic underpins of pediatric OSA.

Objective Data from DNA genotyping via a 96-SNP panel in a study of 25,015 clinical samples were utilized for quality control and tracking of sample identity in a clinical sequencing network. The study aimed to demonstrate the value of both the precise SNP tracking and the utility of the panel for predicting the sex-by-genotype of the participants, to identify possible sample mix-ups. Results Precise SNP tracking showed no sample swap errors within the clinical testing laboratories. In contrast, when comparing predicted sex-by-genotype to the provided sex on the test requisition, we identified 110 inconsistencies from 25,015 clinical samples (0.44%), that had occurred during sample collection or accessioning. The genetic sex predictions were confirmed using additional SNP sites in the sequencing data or high-density genotyping arrays. It was determined that discrepancies resulted from clerical errors (49.09%), samples from transgender participants (3.64%) and stem cell or bone marrow transplant patients (7.27%) along with undetermined sample mix-ups (40%) for which sample swaps occurred prior to arrival at genome centers, however the exact cause of the events at the sampling sites resulting in the mix-ups were not able to be determined.

Thoracic insufficiency syndromes are a genetically and phenotypically heterogeneous group of disorders characterized by congenital abnormalities or progressive deformation of the chest wall and/or vertebrae that result in restrictive lung disease and compromised respiratory capacity. We performed whole exome sequencing on a cohort of 42 children with thoracic insufficiency to elucidate the underlying molecular etiologies of syndromic and non-syndromic thoracic insufficiency and predict extra-skeletal manifestations and disease progression. Molecular diagnosis was established in 24/42 probands (57%), with 18/24 (75%) probands having definitive diagnoses as defined by laboratory and clinical criteria and 6/24 (25%) probands having strong candidate genes. Gene identified in cohort patients most commonly encoded components of the primary cilium, connective tissue, and extracellular matrix. A novel association between KIF7 and USP9X variants and thoracic insufficiency was identified. We report and expand the genetic and phenotypic spectrum of a cohort of children with thoracic insufficiency, reinforce the prevalence of extra-skeletal manifestations in thoracic insufficiency syndromes, and expand the phenotype of KIF7 and USP9X -related disease to include thoracic insufficiency.

BackgroundAs a collaboration model between the International HundredK+ Cohorts Consortium (IHCC) and the Davos Alzheimer's Collaborative (DAC), our aim was to develop a trans-ethnic genomic informed risk assessment (GIRA) algorithm for Alzheimer's disease (AD). MethodsThe GIRA model was created to include polygenic risk score calculated from the AD genome-wide association study loci, the apolipoprotein E haplotypes, and non-genetic covariates including age, sex, and the first three principal components of population substructure. ResultsWe validated the performance of the GIRA model in different populations. The proteomic study in the participant sites identified proteins related to female infertility and autoimmune thyroiditis and associated with the risk scores of AD. ConclusionsAs the initial effort by the IHCC to leverage existing large-scale datasets in a collaborative setting with DAC, we developed a trans-ethnic GIRA for AD with the potential of identifying individuals at high risk of developing AD for future clinical applications.

Objective:Data from DNA genotyping via a 96-SNP panel in a study of 25,015 clinical samples were utilized for quality control and tracking of sample identity in a clinical sequencing network. The study aimed to demonstrate the value of both the precise SNP tracking and the utility of the panel for predicting the sex-by-genotype of the participants, to identify possible sample mix-ups.Results:Precise SNP tracking showed no sample swap errors within the clinical testing laboratories. In contrast, when comparing predicted sex-by-genotype to the provided sex on the test requisition, we identified 110 inconsistencies from 25,015 clinical samples (0.44%), that had occurred during sample collection or accessioning. The genetic sex predictions were confirmed using additional SNP sites in the sequencing data or high-density genotyping arrays. It was determined that discrepancies resulted from clerical errors, samples from transgender participants and stem cell or bone marrow transplant patients along with undetermined sample mix-ups.

ObjectiveHyperphagia and early-onset, severe obesity are clinical characteristics of rare melanocortin-4 receptor (MC4R) pathway diseases due to loss-of-function (LOF) variants in genes comprising the MC4R pathway. In vitro functional characterization of 12,879 possible exonic missense variants from single-nucleotide variants (SNVs) of LEPR, POMC, and PCSK1 was performed to determine the impact of these variants on protein function.MethodsSNVs of the three genes were transiently transfected into cell lines, and each variant was subsequently classified according to functional impact. We validated three assays by comparing classifications against functional characterization of 29 previously published variants.ResultsOur results significantly correlated with previously published pathogenic categories (r = 0.623; P = 3.03 x 10(-4)) of all potential missense variants arising from SNVs. Of all observed variants identified through available databases and a tested cohort of 16,061 patients with obesity, 8.6% of LEPR, 63.2% of PCSK1, and 10.6% of POMC variants exhibited LOF, including variants currently classified as a variant of uncertain significance (VUS).ConclusionsThe functional data provided here can assist in the reclassification of several VUS in LEPR, PCSK1, and POMC and highlight their impact in MC4R pathway diseases.

Background: Asthma is a chronic inflammatory disorder with a strong genetic inheritance. Although more than 100 loci were reported through the genome-wide association study of European populations, the genetic underpinning of asthma in African American individuals remains largely elusive.Objective: We aimed to identify genetic loci associated with asthma in African American individuals.Methods: Three cohorts were genotyped at the Children's Hospital of Philadelphia by using the Illumina single-nucleotide polymorphism array platform. Genotype imputation was performed by using the Trans-Omics for Precision Medicine (TOPMed) reference panel, which includes whole genome sequencing data from more than 100,000 individuals. A meta-analysis of 3 Children's Hospital of Philadelphia cohorts and 10 Consortium on Asthma among African Ancestry Populations in the Americas cohorts, totaling 19,628 subjects, was conducted to identify genetic loci associated with asthma in African American individuals.Results: Our study identified 12 loci surpassing the classical genome-wide significance threshold (5 x 10-8). Of those loci, 8 reached the stricter significance threshold (3 x 10-8). The 9p24.1 locus (rs10975467 [P = 1.63 x 10-8]) has previously been associated with asthma in European individuals. Six loci are associated with enhancer activities, 2 loci are in DNase I-hypersensitive regions, and all of them are associated with regulatory motifs. Moreover, the locus 11q13.4 (rs7480008) is an expression quantitative trait locus of XRRA1 in lung (P = 9.4 x 10-10), and the locus 13q14.3 (rs1543525) is a splicing quantitative trait locus of DHRS12 in lung (P = 1.1 x 10-13).Conclusions: Our findings provide candidate genetic loci for therapeutic target identification and prioritization for African populations. (J Allergy Clin Immunol 2023;151:1132-6.)

Background Neurodevelopmental disorders (NDDs), such as attention deficit hyperactivity disorder (ADHD) and autism spectrum disorder (ASD), are examples of complex and partially overlapping phenotypes that often lack definitive corroborating genetic information. ADHD and ASD have complex genetic associations implicated by rare recurrent copy number variations (CNVs). Both of these NDDs have been shown to share similar biological etiologies as well as genetic pleiotropy. Methods Platforms aimed at investigating genetic-based associations, such as high-density microarray technologies, have been groundbreaking techniques in the field of complex diseases, aimed at elucidating the underlying disease biology. Previous studies have uncovered CNVs associated with genes within shared candidate genomic networks, including glutamate receptor genes, across multiple different NDDs. To examine shared biological pathways across two of the most common NDDs, we investigated CNVs across 15,689 individuals with ADHD ( n = 7920), ASD ( n = 4318), or both ( n = 3,416), as well as 19,993 controls. Cases and controls were matched by genotype array (i.e., Illumina array versions). Three case–control association studies each calculated and compared the observed vs. expected frequency of CNVs across individual genes, loci, pathways, and gene networks. Quality control measures of confidence in CNV-calling, prior to association analyses, included visual inspection of genotype and hybridization intensity. Results Here, we report results from CNV analysis in search for individual genes, loci, pathways, and gene networks. To extend our previous observations implicating a key role of the metabotropic glutamate receptor (mGluR) network in both ADHD and autism, we exhaustively queried patients with ASD and/or ADHD for CNVs associated with the 273 genomic regions of interest within the mGluR gene network (genes with one or two degrees protein–protein interaction with mGluR 1–8 genes). Among CNVs in mGluR network genes, we uncovered CNTN4 deletions enriched in NDD cases ( P = 3.22E − 26, OR = 2.49). Additionally, we uncovered PRLHR deletions in 40 ADHD cases and 12 controls ( P = 5.26E − 13, OR = 8.45) as well as clinically diagnostic relevant 22q11.2 duplications and 16p11.2 duplications in 23 ADHD + ASD cases and 9 controls ( P = 4.08E − 13, OR = 15.05) and 22q11.2 duplications in 34 ADHD + ASD cases and 51 controls ( P = 9.21E − 9, OR = 3.93); those control samples were not with previous 22qDS diagnosis in their EHR records. Conclusion Together, these results suggest that disruption in neuronal cell-adhesion pathways confers significant risk to NDDs and showcase that rare recurrent CNVs in CNTN4 , 22q11.2, and 16p11.2 are overrepresented in NDDs that constitute patients predominantly suffering from ADHD and ASD. Trial registration ClinicalTrials.gov Identifier: NCT02286817 First Posted: 10 November 14, ClinicalTrials.gov Identifier: NCT02777931 first posted: 19 May 2016, ClinicalTrials.gov Identifier: NCT03006367 first posted: 30 December 2016, ClinicalTrials.gov Identifier: NCT02895906 first posted: 12 September 2016.

Atopic dermatitis (AD) is a common inflammatory skin condition and prior genome-wide association studies (GWAS) have identified 71 associated loci. In the current study we conducted the largest AD GWAS to date (discovery N = 1,086,394, replication N = 3,604,027), combining previously reported cohorts with additional available data. We identified 81 loci (29 novel) in the European-only analysis (which all replicated in a separate European analysis) and 10 additional loci in the multi-ancestry analysis (3 novel). Eight variants from the multi-ancestry analysis replicated in at least one of the populations tested (European, Latino or African), while two may be specific to individuals of Japanese ancestry. AD loci showed enrichment for DNAse I hypersensitivity and eQTL associations in blood. At each locus we prioritised candidate genes by integrating multi-omic data. The implicated genes are predominantly in immune pathways of relevance to atopic inflammation and some offer drug repurposing opportunities.