Genetic and Clinical Spectrum of Osteogenesis Imperfecta in an Egyptian Cohort With a High Rate of Lethal Phenotypes.

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)

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

DNA-based screening and population health: a points to consider statement for programs and sponsoring organizations from the American College of Medical Genetics and Genomics (ACMG)

Osteogenesis imperfecta (OI) is a heritable disorder characterized by bone fragility and marked genetic and phenotypic heterogeneity. This study explores the molecular and clinical spectrum of OI, with a focus on autosomal recessive (AR) forms, therapeutic outcomes, and bone mineral density (BMD) in carriers of AR OI-associated gene variants from the Indian population. A total of 78 clinically suspected OI patients were analyzed, yielding a high diagnostic rate of 92.3%. Exome sequencing was performed in all cases, with whole-genome sequencing in selected exome-negative cases. Autosomal dominant (AD) and AR OI accounted for 66% and 34% of cases, respectively. P3H1 (n = 11) was the most frequently implicated AR gene causing OI, followed by SERPINF1 (n = 5) and WNT1 (n = 4), with 79% of AR variants being novel. Phenotypic evaluation (n = 67) revealed fractures, short stature (87%), and bony deformities (84%) as predominant features. A rare homozygous COL1A1 variant was identified in one patient, while another patient harbored additional variants in AD OI genes, suggesting a potential digenic or modifier effect. Phenotypic severity followed the order from most to least severe: AR genes > COL1A2 (substitution and non-substitution) > COL1A1 (substitution > non-substitution). A self-designed, preliminary clinical severity scoring system ranked CRTAP followed by P3H1, as the AR genes associated with the most severe phenotypes. Therapeutic assessment showed a significant reduction in fracture incidence following zoledronate therapy only in the COL1A1 group, with no notable improvements in the COL1A2 or AR groups. Additionally, BMD evaluation in carrier parents of AR gene causing OI indicated a higher predisposition to low BMD among WNT1 gene carriers. However, these findings are preliminary and limited by small sample size. This study provides an extensive genotypic and phenotypic characterization of OI in the Indian population, with a focus on AR OI. It documents differential therapeutic responses among genetic subgroups and provides preliminary observations on BMD in carrier parents of AR OI-an aspect that has been less explored previously and suggest the need for tailored management strategies. The findings in this study also raise the possibility of genetic modifiers contributing to phenotypic variability, warranting further investigation.

Dominant inheritance of osteogenesis imperfecta (OI) is caused by mutations in COL1A1 or COL1A2, the genes that encode type I collagen, and CRTAP, LEPRE1, PPIB, FKBP10, SERPINH1, and SP7 mutations were recently detected in a minority of patients with autosomal recessive OI. However, these findings have been mostly restricted to Western populations. The proportion of mutations and the correlations between genotype and phenotype in Chinese patients with OI are completely unknown. In this study, mutation analyses were performed for COL1A1, COL1A2, CRTAP, and LEPRE1 in a cohort of 58 unrelated Chinese patients with OI; the relationship between collagen type I mutations and clinical features was examined. A total of 56 heterozygous mutations were identified in COL1A1 and COL1A2, including 43 mutations in COL1A1 and 13 mutations in COL1A2. Among the 56 causative COL1A1 and COL1A2 mutations, 24 novel mutations were found, and 25 (44.6%) resulted in the substitution of a glycine within the Gly-X-Y triplet domain of the triple helix. Compared with COL1A1 haploinsufficiency (n=23), patients with mutations affecting glycine residues had a severe skeletal phenotype. In patients 18years of age or older, on average patients with COL1A1 haploinsufficiency were taller and had higher femoral neck bone mineral density than with patients with helical mutations. Interestingly, we found two novel compound heterozygous mutations in the LEPRE1 gene in two unrelated families with autosomal recessive OI. Although the genotype-phenotype correlation is still unclear, our findings are useful to understand the genetic basis of Chinese patients with OI.

Using Molecular Diagnostics for Inherited Retinal Dystrophies: The 6 "I"s That Are Necessary to Diagnose 2 Eyes Genetically.

Disclosure: R.C. Williams: None. S.S. Dahir: None. C.R. Lichtenfeld: None. L.T. Drake: None. L.R. Rehm: None. K.M. Dahir: Alexion Pharmaceuticals, Inc., Ultragenyx, Kyowa Kirin.Background: Osteogenesis Imperfecta (OI) is a group of rare inherited connective tissue disorders with low bone mass and fragility. In most cases, there is a reduction in the production or synthesis of normal type I collagen most commonly due to mutations in the COL1A1/COL1A2 genes. OI type VII is an autosomal recessive form of severe or lethal OI characterized by fractures at birth, bluish sclerae, early deformity of lower extremities, coxa vara, and osteopenia. Clinical manifestations of OI type VII include recurrent fractures that decrease after puberty and increased bone turnover. Affected individuals commonly exhibit below-average height and shortened upper arm and thigh bones. OI Type VII is caused by a homozygous or compound heterozygous mutation in the CRTAP gene on chromosome 3p22. Case Description: A 24-year-old Hispanic male presented for consultation of transition of care from pediatrics for a diagnosis of OI established at 8 days of age. The patient had no family history of the condition. Genetic screening for COL1A1 and COL1A2 gene mutations revealed no OI-associated abnormalities. At birth, he had bilateral femur fractures in both legs and broke his humerus and femur at ages 1 and 5 months, respectively. In his first 8 years of life, he had repeated breaks to both femurs as well as a left humerus and vertebral fracture. All fractures have been without trauma, such as reaching for an object. His last fracture was at age 14 which resulted in intermedullary rod placed. Prior medical management was IV Pamidronate initiated at the age of 7 and continued until the age of 16. Evaluation at age 24 was remarkable for marked joint laxity, opalescent dentin with brownish discoloration of malformed teeth, short stature with shortened upper arms, normal hearing and DXA scan normal. Genetic testing results revealed homozygous likely pathogenic variants in CRTAP c.471+4A>G and a variant of uncertain significance in the ANO5 c.1606A>C9. Conclusions: The diagnosis of osteogenesis imperfecta (OI) type VII was confirmed through a combination of genetic testing for CRTAP mutations and clinical history. While most OI cases (approximately 90%) result from COL1A1/COL1A2 mutations, distinguishing OI type VII relies on identifying pathogenic variants in CRTAP, a gene critical for collagen type I biosynthesis. A homozygous CRTAP mutation leads to OI due to a deficiency in cartilage-associated protein (CRTAP), impairing collagen modification. Expanded genetic testing panels play a crucial role in facilitating earlier diagnosis and intervention, particularly for individuals presenting with OI-consistent features but lacking COL1A1 and COL1A2 mutations. Incorporating CRTAP and other rare OI-related genes into routine diagnostic workflows enhances the detection of atypical OI subtypes, allowing for timely management and tailored treatment strategies that can improve patient outcomes.Presentation: Sunday, July 13, 2025

Rapid advances in DNA sequencing technologies have made it increasingly cost-effective to obtain accurate and timely large-scale genomic sequence data on individuals (short read massively parallel or next generation [next-gen]). A next-gen molecular diagnostic approach that has seen rapid deployment in the clinic over the last year is exome sequencing. Whole exome sequencing covers all protein-coding genes in the genome (≈1.1% of genome), and an exome test for a single patient generates ≈6 gigabases (109 bp) of DNA sequence data. A key challenge facing routine use of next-gen data in patient diagnosis and management is data interpretation. What sequence variant findings are relevant to diagnosis (pathogenic mutations)? What sequence variant findings are relevant to clinical care but not necessarily to patient diagnosis (clinically actionable incidental data)? What sequence information should be stored, and where can it be stored? This review provides a tutorial on current approaches to answering these questions. A recent landmark study showed that application of next-gen sequencing to a large cohort of idiopathic dilated cardiomyopathy patients found ≈27% of patients to show mutations of the titin gene, the most complex gene in the genome (363 exons). We use titin in cardiomyopathy as an exemplar for explaining next-gen sequencing approaches and data interpretation. Decreasing sequencing costs and broad dissemination of next-generation (next-gen) equipment and expertise are increasing availability of massively parallel sequencing of patient DNA samples (short read massively parallel or next-gen sequencing).1,2 Most rapidly expanding is exome sequencing, where all protein-coding sequences (exons) are selected from total genomic DNA and selectively sequenced.3 Alternative approaches to next-gen sequencing include targeted sequencing (TS) and whole genome (complete genome) sequencing. Currently, marketed targeted Sanger sequencing panels using traditional individual exon-by-exon sequencing remain expensive and time consuming, and massively parallel next-gen approaches are beginning to supplant …

BackgroundOsteogenesis imperfecta (OI), a rare autosomal inheritable disorder characterized by bone fragility and skeletal deformity, is caused by pathogenic variants in genes impairing the synthesis and processing of extracellular matrix protein collagen type I. With the use of next‐generation sequencing and panels approaches, an increasing number of OI patients can be confirmed and new pathogenic variants can be discovered. This study sought to identify pathogenic gene variants in a Chinese family with OI I.MethodsWhole‐exome sequencing was used to identify pathogenic variants in the proband, which is confirmed by Sanger sequencing and cosegregation analysis; MES, HSF, and Spliceman were used to analyze this splicing variant；qRT‐PCR was performed to identify the mRNA expression level of COL1A1 in patient peripheral blood samples; Minigene splicing assay was performed to mimic the splicing process of COL1A1 variants in vitro; Analysis of evolutionary conservation of amino acid residues and structure prediction of the mutant protein.ResultsA novel splicing pathogenic variant (c.3814+1G>T) was identified in this OI family by using whole‐exome sequencing, Sanger sequencing, and cosegregation analysis. Sequencing of RT‐PCR products from the COL1A1 minigene variant reveals a 132‐nucleotide (nt) insertion exists at the junction between exons 48 and exon 49 of the COL1A1 cDNA. Splicing assay indicates that the mutated minigene produces an alternatively spliced transcript which may cause a frameshift resulting in early termination of protein expression. The molecular analysis suggested that the altered amino acid is located at the C‐terminus of type I procollagen.ConclusionOur study reveals the pathogenesis of a novel COL1A1 splicing pathogenic variant c.3814+1G>T in a Chinese family with OI I.

Whole Exome Sequencing and Extended Thrombophilia Testing in Patients with Venous Thromboembolism

P3-09-05: Clinical outcome of patients with advanced triple negative breast cancer with germline and somatic variants in homologous recombination gene

Introduction: Left ventricular non-compaction (LVNC) represents a genetically heterogeneous cardiomyopathy which occurs in both children and adults. Its genetic spectrum overlaps with other types of cardiomyopathy. However, LVNC phenotypes in different age groups can have distinct genetic aetiologies. The aim of the study was to decipher the genetic spectrum of LVNC presented in childhood. Patient Group and Methods: Twenty patients under the age of 18 years diagnosed with LVNC were enrolled in the study. Target sequencing and whole-exome sequencing were performed using a panel of 108 cardiomyopathy-associated genes. Pathogenic, likely pathogenic, and variants of unknown significance found in genes highly expressed in cardiomyocytes were considered as variants of interest for further analysis. Results: The median age at presentation was 8.0 (0.1–17) years, with 6 patients presenting before 1 year of age. Twelve (60%) patients demonstrated reduced ejection fraction. Right ventricular (RV) dilation was registered in 6 (30%), often in combination with reduced RV contractility (25%). Almost half (45%) of the patients demonstrated biventricular involvement already at disease presentation. For pathogenic and likely pathogenic variants, the positive genotyping rate was 45%, and these variants were found mainly in non-contractile structural sarcomeric genes (ACTN2, MYPN, and TTN) or in metabolic and signal transduction genes (BRAF and TAZ). Likely pathogenic TAZ variants were detected in all 5 patients suspected of having Barth syndrome. No pathogenic or likely pathogenic variants were found in genes encoding for sarcomeric contractile proteins, but variants of unknown significance were detected in 3 out of 20 patients (MYH6, MYH7, and MYLK2). In 4 patients, variants of unknown significance in ion-channel genes were detected. Conclusion: We detected a low burden of contractile sarcomeric variants in LVNC patients presenting below the age of 18 years, with the major number of variants residing in non-contractile structural sarcomeric genes. The identification of the variants in ion-channel and related genes not previously associated with LVNC in paediatric patients requires further examination of their functional role.

eP296: Familial MECP2 variants: a report of 4 affected families highlighting the variable phenotypic spectrum and implications for genetic counseling

Approximately 5% of rhabdomyosarcoma (RMS) cases are due to known cancer predisposition syndromes (e.g., Li-Fraumeni syndrome, Neurofibromatosis-1), but these estimates have not been confirmed in large-scale studies. Furthermore, no recommended germline testing protocols exist for RMS. We tested the hypothesis that germline mutation burden is greater than previously reported and present several new predisposition genes as potential drivers of pediatric RMS. We sequenced 59 cancer susceptibility genes in 213 children with RMS enrolled on one clinical trial (COG ARST0531), unselected for family history of cancer. Validation was performed with Sanger sequencing. Our analysis included determining the incidence of pathogenic variants in known RMS predisposition genes, followed by other cancer predisposition genes on our panel but not previously associated with RMS. In our cohort, 3.9% of unselected RMS cases harbor a pathogenic variant in a known predisposition gene (Table 1). Using VAAST, we next identified the top 10 genes possibly associated with RMS. Variants of uncertain significance (VUS) were restricted to rare variants (<0.1%) with severe CADD and Polyphen2 scores, which added 16 additional patients (7.4%). To distinguish incidental findings from true correlations, we compared our allele frequencies to those in the GnomAD database (126,216 exome sequences and 15,136 whole-genome sequences). Including both pathogenic mutations and rare VUS, 10.8% of RMS cases carry a variant with potentially important clinical implications, suggesting that newly diagnosed RMS would benefit from multigene genetic testing. Future directions include linkage to clinical data such as family history, age at diagnosis, tumor stage/location/histology, and clinical outcome, as well as expanding both the RMS and control cohorts. Table 1.List of genes with numbers of carriers identified in 213 rhabdomyosarcoma casesGeneCarriers%% of carriers in GnomADSIR95% CIP=valueTruncating Variants and Known Pathogenic MissenseATM00.42%---BAP100.87%0.05%---BRCA220.87%0.85%1.01(0.12-3.66)1.1736DICER110.43%0.06%7.75(0.20-43.19)0.2421MSH210.43%0.15%2.93(0.07-16.30)0.5790NF120.87%0.88%0.98(0.12-3.54)1.2088PMS200.87%0.18%---PTCH100.15%---TP5331.30%0.13%10.10(2.08-29.51)0.0070WT101.30%0.02%---Total93.90%3.42%1.14(0.52-2.16)0.7882Combined Analysis of Pathogenic Variants plus Variants of Uncertain Significance (VUS)ATM20.87%0.78%1.11(0.13-4.02)1.0734BAP120.87%0.22%3.89(0.47-14.05)0.1891BRCA220.87%1.52%0.57(0.07-2.06)1.7286DICER173.03%0.86%3.52(1.41-7.24)0.0089MSH210.43%0.78%0.56(0.01-3.10)1.6690NF120.87%1.70%0.51(0.06-1.84)1.8062PMS210.43%0.64%0.68(0.02-3.78)1.5425PTCH131.30%0.86%1.52(0.31-4.43)0.6348TP5341.73%0.25%6.93(1.89-17.76)0.0058WT110.43%0.31%1.40(0.04-7.81)1.0197Total2510.82%9.94%1.09(0.70-1.61)0.7232 Citation Format: Erin L. Young, Luke Maese, Rosann Robinson, Lance Pflieger, Barry Moore, Shawn Rynearson, Trent Fowler, Sean V. Tavtigian, Mark Yandell, Clinton C. Mason, Douglas S. Hawkins, Philip J. Lupo, Joshua D. Schiffman. Pathogenic mutations and variants of unknown significance (VUS) in cancer predisposition genes are associated with over 10% of pediatric rhabdomyosarcoma: a report from the Children’s Oncology Group [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2704. doi:10.1158/1538-7445.AM2017-2704

Background: Acquired generalized lipodystrophy (AGL) is characterized by near-total fat loss that develops after birth. Although the molecular pathogenesis of AGL is unclear, there is a link to autoimmunity and inflammation. Notably, the panniculitis associated variety of AGL may present with subcutaneous inflammatory nodules that ultimately progress to generalized fat loss. Here, we report on a complex patient with AGL in whom whole-exome sequencing (WES) identified several pathogenic variants and variants of uncertain significance (VUS) that encourage us to think about AGL more broadly. Clinical Case: This is a 38-year-old male who was first diagnosed with juvenile rheumatoid arthritis at age 2, after being evaluated for delayed ability to ambulate. At that time, he was also diagnosed with Weber-Christian disease following a skin biopsy due to the suspicion of panniculitis. Over time, he progressively lost body fat throughout the body and developed hypertriglyceridemia, hypertension, and nephropathy leading to the diagnosis of AGL. At age 10, he was diagnosed with type 1 diabetes mellitus, and at age 14, with autoimmune hepatitis. Due to the tightening of his hands, calf pain, and increased CPK levels, a muscle biopsy was performed, suggesting polymyositis. He had been treated with azathioprine and steroids, which were discontinued at age 26, after a liver biopsy that showed grade 2 fibrosis. Further, he was diagnosed with non-ischemic dilated cardiomyopathy (DCM), evolving with atrial fibrillation with a rapid ventricular response and complicated with left atrial appendage thrombus. Of interest, his mother and two maternal aunts had been diagnosed with atrial fibrillation. One of his maternal uncles presented non-ischemic cardiomyopathy and an early sudden cardiac arrest. His mother also had mitochondrial myopathy, and his father had type 2 diabetes mellitus and IgG deficiency. WES identified three different variants: a maternally inherited pathogenic variant in TTN (c.88473_88477delAGCTT; p.W29493X) associated with DCM, a paternally inherited pathogenic variant in TNFRSF13B (c.310T>C; p.C104R) associated with CVID/IgA deficiency, and a maternally inherited variant of uncertain clinical significance in NLRP3 (c.1469G>A; p.R490K). Although the frequency of this variant was relatively high, several variants in the NLRP3 gene have been previously associated with inflammasomopathy. Conclusion: This case highlights challenging presentations of AGL and the complexity of the disease. As we are yet beginning to understand the molecular mechanisms behind the so-called “acquired fat loss” and its relation to inflammatory and complex immune system diseases, further efforts are critical to better recognize different AGL phenotypes and phenotype-genotype correlations. Additional efforts should be placed on WES for AGL patients and functional validation of identified VUSs.