Genetic Landscape of Robin Sequence: A Systematic Review.

The interpretation of genomic variants following whole exome sequencing (WES) can be aided using human phenotype ontology (HPO) terms to standardize clinical features and predict causative genes. We performed WES on 453 patients diagnosed prior to 18years of age and identified 114 pathogenic (P) or likely pathogenic (LP) variants in 112 patients. We utilized PhenoDB to extract HPO terms from provider notes and then used Phen2Gene to generate a gene score and gene ranking from each list of HPO terms. We assigned Phen2Gene gene rankings to 6 rank classes, with class 1 covering raw gene rankings of 1 to 10 and class 2 covering rankings from 11 to 50 out of a total of 17,126 possible gene rankings. Phen2Gene ranked causative genes into rank class 1 or 2 in 27.7% of cases and the genes in rank class 1 were all associated with well-characterized phenotypes. We found significant associations between the gene score and the number of years, since the gene was first published, the number of HPO terms with an hierarchical depth greater or equal to 11, and the number of Online Mendelian Inheritance in Man terms associated with the phenotype and gene. We conclude that genes associated with recognizable phenotypes and terms deep in the HPO hierarchy have the best chance of producing a high gene score and ranking in class 1 to 2 using Phen2Gene software with HPO terms. Clinicians and laboratory staff should consider these results when HPO terms are employed to prioritize candidate genes.

The phenotypic spectrum of individuals with SLC16A2 variants in MCT8 deficiency

Prenatal exome sequencing for fetuses with structural abnormalities: the next step.

Background and aimsBetween July 2016 and September 2018, NHS Genomic Medicine Centres (GMCs) recruited families with specified rare diseases to the 100,000 Genomes Project for whole genome sequencing (WGS), and...

The objective of this study was to evaluate the implementation of NGS within the French mitochondrial network, MitoDiag, from targeted gene panels to whole exome sequencing (WES) or whole genome sequencing (WGS) focusing on mitochondrial nuclear-encoded genes. Over 2000 patients suspected of Primary Mitochondrial Diseases (PMD) were sequenced by either targeted gene panels, WES or WGS within MitoDiag. We described the clinical, biochemical, and molecular data of 397 genetically confirmed patients, comprising 294 children and 103 adults, carrying pathogenic or likely pathogenic variants in nuclear-encoded genes. The cohort exhibited a large genetic heterogeneity, with the identification of 172 distinct genes and 253 novel variants. Among children, a notable prevalence of pathogenic variants in genes associated with oxidative phosphorylation (OXPHOS) functions and mitochondrial translation was observed. In adults, pathogenic variants were primarily identified in genes linked to mtDNA maintenance. Additionally, a substantial proportion of patients (54% (42/78) and 48% (13/27) in children and adults, respectively), undergoing WES or WGS testing displayed PMD mimics, representing pathologies that clinically resemble mitochondrial diseases. We reported the largest French cohort of patients suspected of PMD with pathogenic variants in nuclear genes. We have emphasized the clinical complexity of PMD and the challenges associated with recognizing and distinguishing them from other pathologies, particularly neuromuscular disorders. We confirmed that WES/WGS, instead of panel approach, was more valuable to identify the genetic basis in patients with "possible" PMD and we provided a genetic testing flowchart to guide physicians in their diagnostic strategy.

Treatment of Upper Airway Obstruction and Feeding Problems in Robin-Like Phenotype

The use of fetal exome sequencing in prenatal diagnosis: a points to consider document of the American College of Medical Genetics and Genomics (ACMG)

Whole genome sequencing (WGS) improves Mendelian disorder diagnosis over whole exome sequencing (WES); however, additional diagnostic yields and costs remain undefined. We investigated differences between diagnostic and cost outcomes of WGS and WES in a cohort with suspected Mendelian disorders. WGS was performed in 38 WES-negative families derived from a 64 family Mendelian cohort that previously underwent WES. For new WGS diagnoses, contemporary WES reanalysis determined whether variants were diagnosable by original WES or unique to WGS. Diagnostic rates were estimated for WES and WGS to simulate outcomes if both had been applied to the 64 families. Diagnostic costs were calculated for various genomic testing scenarios. WGS diagnosed 34% (13/38) of WES-negative families. However, contemporary WES reanalysis on average 2 years later would have diagnosed 18% (7/38 families) resulting in a WGS-specific diagnostic yield of 19% (6/31 remaining families). In WES-negative families, the incremental cost per additional diagnosis using WGS following WES reanalysis was AU$36,710 (£19,407;US$23,727) and WGS alone was AU$41,916 (£22,159;US$27,093) compared to WES-reanalysis. When we simulated the use of WGS alone as an initial genomic test, the incremental cost for each additional diagnosis was AU$29,708 (£15,705;US$19,201) whereas contemporary WES followed by WGS was AU$36,710 (£19,407;US$23,727) compared to contemporary WES. Our findings confirm that WGS is the optimal genomic test choice for maximal diagnosis in Mendelian disorders. However, accepting a small reduction in diagnostic yield, WES with subsequent reanalysis confers the lowest costs. Whether WES or WGS is utilised will depend on clinical scenario and local resourcing and availability.

Aspirin-exacerbated respiratory disease is associated with variants in filaggrin, epithelial integrity, and cellular interactions

ACMG SF v3.0 list for reporting of secondary findings in clinical exome and genome sequencing: a policy statement of the American College of Medical Genetics and Genomics (ACMG)

BackgroundIdentifying Human Phenotype Ontology (HPO) terms is crucial for diagnosing and managing rare diseases. However, clinicians, especially junior physicians, often face challenges due to the complexity of describing patient phenotypes accurately. Traditional manual search methods using HPO databases are time-consuming and prone to errors.ObjectiveThe aim of the study is to investigate whether the use of multimodal large language models (MLLMs) can improve the accuracy of junior physicians in identifying HPO terms from patient images related to rare diseases.MethodsIn total, 20 junior physicians from 10 specialties participated. Each physician evaluated 27 patient images sourced from publicly available literature, with phenotypes relevant to rare diseases listed in the Chinese Rare Disease Catalogue. The study was divided into 2 groups: the manual search group relied on the Chinese Human Phenotype Ontology website, while the MLLM-assisted group used an electronic questionnaire that included HPO terms preidentified by ChatGPT-4o as prompts, followed by a search using the Chinese Human Phenotype Ontology. The primary outcome was the accuracy of HPO identification, defined as the proportion of correctly identified HPO terms compared to a standard set determined by an expert panel. Additionally, the accuracy of outputs from ChatGPT-4o and 2 open-source MLLMs (Llama3.2:11b and Llama3.2:90b) was evaluated using the same criteria, with hallucinations for each model documented separately. Furthermore, participating physicians completed an additional electronic questionnaire regarding their rare disease background to identify factors affecting their ability to accurately describe patient images using standardized HPO terms.ResultsA total of 270 descriptions were evaluated per group. The MLLM-assisted group achieved a significantly higher accuracy rate of 67.4% (182/270) compared to 20.4% (55/270) in the manual group (relative risk 3.31, 95% CI 2.58‐4.25; P<.001). The MLLM-assisted group demonstrated consistent performance across departments, whereas the manual group exhibited greater variability. Among standalone MLLMs, ChatGPT-4o achieved an accuracy of 48% (13/27), while the open-source models Llama3.2:11b and Llama3.2:90b achieved 15% (4/27) and 18% (5/27), respectively. However, MLLMs exhibited a high hallucination rate, frequently generating HPO terms with incorrect IDs or entirely fabricated content. Specifically, ChatGPT-4o, Llama3.2:11b, and Llama3.2:90b generated incorrect IDs in 57.3% (67/117), 98% (62/63), and 82% (46/56) of cases, respectively, and fabricated terms in 34.2% (40/117), 41% (26/63), and 32% (18/56) of cases, respectively. Additionally, a survey on the rare disease knowledge of junior physicians suggests that participation in rare disease and genetic disease training may enhance the performance of some physicians.ConclusionsThe integration of MLLMs into clinical workflows significantly enhances the accuracy of HPO identification by junior physicians, offering promising potential to improve the diagnosis of rare diseases and standardize phenotype descriptions in medical research. However, the notable hallucination rate observed in MLLMs underscores the necessity for further refinement and rigorous validation before widespread adoption in clinical practice.

Background and Aims We aim to derive and validate a score estimating the probability of identifying a variant explicative of the renal phenotype using Exome Sequencing (ES) in adults with CKD of uncertain origin. Method Participants: prospective cohort study including all consecutive index patients with a CKD from uncertain origin in three French nephrology units (metropolitan: Sorbonne University Hospitals, Paris, and Conception Hospital, Marseille; overseas: La Réunion University Hospital, Réunion island) who underwent ES between October 11th, 2017 and May 31st, 2023. Outcome measure: identification of a causal variant using ES data, according to the American College of Medical Genetics and Genomics diagnostic criteria. Candiate variables and feature engineering: raw data regarding patients’ phenotypes was prospectively entered in a collection form at the time of ES by the prescribing physician. Structured data (yes/no questions and lists) was mapped to Human Phenotype Ontology (HPO) terms. Unstructured data (free text) was manually translated into HPO terms by the same investigator (nephrologist), which was blinded to ES results. First, second and third-order ancestor HPO terms were included in the analysis. Score's derivation: an optimal weighted average of multiple models (“ensemble model”) was specified, following guidelines provided in a recently published article (PMID:36905602). Score's validation: internal validation using 10-fold cross validation, followed by internal-external validation (data from 2/3 centers was used to develop a model which was then tested using data from the remaining center; this process was repeated in each center). Results We included 2,490 patients, 560/2,490 (22.5%) of whom had a causal variant identified by ES. We collected 1,028 distinct HPO terms describing the patients’ phenotypes. The most common term was “Hypertension”, occurring in 2,079/2,490 (83.5%) patients. In internal validation, the score showed accurate calibration and discrimination (area under the receiver operating characteristics curve (AUC): 0.71, 95% CI 0.68 to 0.73; index of precision accuracy (IPA): 0.11, 95% CI 0.09 to 0.13). Performances were moderately diminished in internal-external validation but remained satisfactory (Tenon: AUC 0.64, IPA 0.04; Marseille: AUC 0.67, IPA 0.04; La Réunion: 0.68, IPA 0.09). Conclusion We derived, internally and internally-externally validated a clinical score which accurately predicts the probability of obtaining a genetic diagnosis using Exome Sequencing. Feature engineering could further increase the score's performances. Automatic computation by clinicians using an interactive tool is achievable and could be of clinical utility, especially to guide resource allocation in case of a low pretest probability.

Background/Aims The introduction of targeted gene panel sequencing has revolutionised the approach to genetic testing in paediatric rheumatology, particularly for autoinflammatory diseases (AID). There has been progression from gene panels to genome-wide “agnostic” sequencing to keep pace with new disease-gene discovery, phenotypic variability, and an ever-increasing number of disease phenocopies. Thus, in 2022, we moved from gene panel sequencing to whole exome sequencing (WES) as our primary mode of genetic testing in our highly specialised autoinflammation centre (GOSH-ACE). We now summarise the clinical impact over 10 years of these genetic sequencing approaches. Methods Targeted-enrichment gene panel or WES were performed in-house or by Informed Genomics Limited. Variants were annotated with ANNOVAR and filtered with an R pipeline using standard population-frequency/predicted pathogenicity approaches, and bioinformatic tools including Exomiser and ExomeDepth. Clinical data were provided by the referring clinician and encoded using human phenotype ontology (https://hpo.jax.org/). Results Prior to 2022, 476 patients underwent targeted testing using either a neuroinflammation or broader inflammation and vasculitis panel, and a further 177 patients have since undergone WES. Median age at time of testing was 10.6 years (range = 0-68) and 48.7% were female. All patients had an inflammatory phenotype, including but not limited to recurrent fever, vasculitis/vasculopathy, neuroinflammation, Behçet’s disease, systemic lupus erythematosus, systemic sclerosis, systemic-onset juvenile idiopathic arthritis or juvenile dermatomyositis. Targeted panel testing provided a diagnostic genotype in 25.8% (n = 123/476); while 23.2% (n = 41/177) of cases who underwent WES had a diagnostic genotype. Despite these similar diagnostic yields, WES was considered overall superior to panel testing as it enabled regular updating of the virtual panel analysis pipeline; and real-time exome-wide reanalysis of “unsolved” cases following a change in clinical phenotype or a novel disease-gene association discovery in the field. WES also led to a clinically actionable incidental genotype finding in 28 cases (15.8%). Conclusion The diagnostic yield of contributory genotypes is surprisingly similar for gene panel testing and WES. However, WES offers the advantage of more robust in silico reanalysis over time for unsolved cases, and additional diagnostic yield by detection of clinically important incidental genotypes. Regarding this latter point, careful and explicit patient consent regarding return of incidental findings is imperative when using WES in routine practice. It is inevitable that whole genome sequencing (WGS) will replace WES in the future. However, the routine use of WGS is currently limited by our lack of understanding of non-coding regions of the genome, the higher cost of sequencing, and data storage requirements. Therefore, for the time-being, WES remains our first-line approach to genetic testing for patients with inflammatory phenotypes. Disclosure F. Price-Kuehne: None. A. Burleigh: None. E. Omoyinmi: None. D. McCreary: None. Y. Hong: None. K. McLellan: None. K. Nazmutdinova: None. D. Eleftheriou: Grants/research support; D.E. has received institutional grants from Lilly, Sobi, Roche and Pfizer. P. Brogan: Consultancies; P.B. has received consultancy fees from Roche, Novartis and SOBI and speaker fees from UCB. Grants/research support; P.B. has received institutional grants from: Novartis, SOBI, Roche, Chemocentryx and Novimmune.

SummaryBackgroundLynch syndrome is a rare familial cancer syndrome caused by pathogenic variants in the mismatch repair genes MLH1, MSH2, MSH6, or PMS2, that cause predisposition to various cancers, predominantly colorectal and endometrial cancer. Data are emerging that pathogenic variants in mismatch repair genes increase the risk of early-onset aggressive prostate cancer. The IMPACT study is prospectively assessing prostate-specific antigen (PSA) screening in men with germline mismatch repair pathogenic variants. Here, we report the usefulness of PSA screening, prostate cancer incidence, and tumour characteristics after the first screening round in men with and without these germline pathogenic variants.MethodsThe IMPACT study is an international, prospective study. Men aged 40–69 years without a previous prostate cancer diagnosis and with a known germline pathogenic variant in the MLH1, MSH2, or MSH6 gene, and age-matched male controls who tested negative for a familial pathogenic variant in these genes were recruited from 34 genetic and urology clinics in eight countries, and underwent a baseline PSA screening. Men who had a PSA level higher than 3·0 ng/mL were offered a transrectal, ultrasound-guided, prostate biopsy and a histopathological analysis was done. All participants are undergoing a minimum of 5 years' annual screening. The primary endpoint was to determine the incidence, stage, and pathology of screening-detected prostate cancer in carriers of pathogenic variants compared with non-carrier controls. We used Fisher's exact test to compare the number of cases, cancer incidence, and positive predictive values of the PSA cutoff and biopsy between carriers and non-carriers and the differences between disease types (ie, cancer vs no cancer, clinically significant cancer vs no cancer). We assessed screening outcomes and tumour characteristics by pathogenic variant status. Here we present results from the first round of PSA screening in the IMPACT study. This study is registered with ClinicalTrials.gov, NCT00261456, and is now closed to accrual.FindingsBetween Sept 28, 2012, and March 1, 2020, 828 men were recruited (644 carriers of mismatch repair pathogenic variants [204 carriers of MLH1, 305 carriers of MSH2, and 135 carriers of MSH6] and 184 non-carrier controls [65 non-carriers of MLH1, 76 non-carriers of MSH2, and 43 non-carriers of MSH6]), and in order to boost the sample size for the non-carrier control groups, we randomly selected 134 non-carriers from the BRCA1 and BRCA2 cohort of the IMPACT study, who were included in all three non-carrier cohorts. Men were predominantly of European ancestry (899 [93%] of 953 with available data), with a mean age of 52·8 years (SD 8·3). Within the first screening round, 56 (6%) men had a PSA concentration of more than 3·0 ng/mL and 35 (4%) biopsies were done. The overall incidence of prostate cancer was 1·9% (18 of 962; 95% CI 1·1–2·9). The incidence among MSH2 carriers was 4·3% (13 of 305; 95% CI 2·3–7·2), MSH2 non-carrier controls was 0·5% (one of 210; 0·0–2·6), MSH6 carriers was 3·0% (four of 135; 0·8–7·4), and none were detected among the MLH1 carriers, MLH1 non-carrier controls, and MSH6 non-carrier controls. Prostate cancer incidence, using a PSA threshold of higher than 3·0 ng/mL, was higher in MSH2 carriers than in MSH2 non-carrier controls (4·3% vs 0·5%; p=0·011) and MSH6 carriers than MSH6 non-carrier controls (3·0% vs 0%; p=0·034). The overall positive predictive value of biopsy using a PSA threshold of 3·0 ng/mL was 51·4% (95% CI 34·0–68·6), and the overall positive predictive value of a PSA threshold of 3·0 ng/mL was 32·1% (20·3–46·0).InterpretationAfter the first screening round, carriers of MSH2 and MSH6 pathogenic variants had a higher incidence of prostate cancer compared with age-matched non-carrier controls. These findings support the use of targeted PSA screening in these men to identify those with clinically significant prostate cancer. Further annual screening rounds will need to confirm these findings.FundingCancer Research UK, The Ronald and Rita McAulay Foundation, the National Institute for Health Research support to Biomedical Research Centres (The Institute of Cancer Research and Royal Marsden NHS Foundation Trust; Oxford; Manchester and the Cambridge Clinical Research Centre), Mr and Mrs Jack Baker, the Cancer Council of Tasmania, Cancer Australia, Prostate Cancer Foundation of Australia, Cancer Council of Victoria, Cancer Council of South Australia, the Victorian Cancer Agency, Cancer Australia, Prostate Cancer Foundation of Australia, Asociación Española Contra el Cáncer (AECC), the Instituto de Salud Carlos III, Fondo Europeo de Desarrollo Regional (FEDER), the Institut Català de la Salut, Autonomous Government of Catalonia, Fundação para a Ciência e a Tecnologia, National Institutes of Health National Cancer Institute, Swedish Cancer Society, General Hospital in Malmö Foundation for Combating Cancer.

ObjectiveAdenomatous polyposis syndrome (APS) is a rare hereditary disease characterized by the development of multiple (more than 20) adenomas of the colon with a high-risk of malignant transformation without surgical treatment. The most aggressive form of APS, with >100 polyps before the age of 45 years, is mostly caused by germline pathogenic variants in the APC gene but patients with germline variants in the MUTYH and, very rarely, in the SMAD4 and BMPR1A genes were also reported. Routine molecular testing methods, such as Sanger sequencing, multiplex ligation-dependent probe amplification (MLPA) or multigene NGS panels, may fail to detect pathogenic variants in non-coding regions.Patients and methodsDNA from blood samples of 10 patients (with age of APS manifestation between 15 and 45 years) with over 100 adenomatous colonic polyps identified by endoscopic examination was subjected to whole genome sequencing (WGS). Prior genetic testing did not detect any germline pathogenic variants in the APC and MUTYH coding exons in these patients.ResultsPathogenic and likely pathogenic germline variants in non-coding regions of genes were identified in 3 patients. Two unrelated patients had the same c.-190G>A (rs879253785) in the 1B promoter of the APC gene (NM_001127511.3), while the third patient had a c.-152-2A>G variant in the BMPR1A gene (NM_004329.3). Using standard NGS panels or whole exome sequencing (WES) would not have detected these variants.ConclusionOur results demonstrate that WGS is a useful genetic testing method for young patients with over 100 adenomatous colonic polyps, when routine DNA diagnostic methods fail to establish the genetic cause of the disease.