Osteogenesis imperfecta Vietnamis

Väitekirja elektrooniline versioon ei sisalda publikatsiooneOsteogenesis imperfecta (OI) on haruldane geneetiline haigus, mida iseloomustab madal luude mass, sagedased luumurrud ja skeleti deformatsioonid. Haigus on tuntud ka kui "habraste luude haigus". Haiguse raskus varieerub kerge vormist kuni letaalseni. Lisaks luude haprusele ja deformatsioonidele võivad esineda sinised skleerad, lühike kasv, hammaste dentiini kahjustus ja kuulmislangus. Umbes 90% OI juhtudest tekib haigus kollageeni geenide mutatsioonist. OI patogenees ja geneetika ei ole aga siiski veel täielikult teada. Samuti pole leitud ka seoseid OI geneetiliste mutatsioonide ja haiguse raskusastme, soo või etniliste rühmadega. Varem OI-d Vietnamis uuritud ei ole. Selle uurimuse eesmärgiks oli kirjeldada haiguse esinemist, kliinilised tunnused ning uurida kollageeni geenide mutatsioone Vietnami patsientidel. Patsientide leidmiseks kontakteerusid uurijad kõigi haiglate, tervisekeskuste ja patsientide ühendustega. Uuringusse kaasati 146 OI patsienti 120-st perekonnast. Nendest 99-s peres ei olnud haigust varem esinenud ja 21 perekonnas oli OI teada. Kõikidel patsiendid olid skeleti deformatsioonid, 34 patsiendil oli luumurrud esinenud juba enne sündi. Kokku oli 18 patsienti (12,33%), kellel oli esinenud elu jooksul üle 30 luumurru. Keskmine luumurdude arv oli 13,23. Skeletivälistest tunnustest sinised skleerad esinesid 117 ja kuulmislangus 26 OI patsiendil. Dentinogeneesi häire esines 60,96% OI patsientidest. Geneetilise analüüsi tulemuste hindamisel leiti tugev korrelatsioon DI ja I tüüpi kollageeni häire esinemise vahel. DI patsientidel esines mitmeid hambumuse häireid ning puuduvate hammaste hulk oli oluliselt suurem võrreldes kontrollgrupiga. Kollageeni COL1A1 mutatsioone esines 36,3%-l ja COL1A2 mutatsioone 23,1%-l patsientidest, mis on madalam võrreldes teiste populatsioonidega. Samuti avastasime mitmeid uudsed patogeenseid variante, mis erineb varasematest uuringutest. Leitud OI patsientide hulk ja raske fenotüübiga patsientide ülekaal näitab, et haigus on Vietnamis suure tõenäosusega jäänud diagnoosimata. Uuringu tulemused näitasid ka väiksemat kollageeni mutatsioonide arvu Vietnami patsientidel võrreldes teistes s.h. Aasia populatsioonidega. Uuring näitas, et Vietnami OI on unikaalne nii fenotüübilt kui genotüübilt.Osteogenesis Imperfecta (OI), known also as “brittle bone disease”, is a rare genetic disorder of bones. OI is characterized by low bone mass, bone fragility, and skeletal deformity. The variability of the OI ranges from mild to lethal forms. In addition to bone fragility and skeletal deformities, patients may develop a short stature, dentinogenesis imperfecta, blue eye sclerae and progressive hearing loss. At present, about 90% of OI cases arise due to mutations in the collagen genes. Some OI cases remain genetically undiagnosed and pathogenesis and genetics are not completely known. There is still no evidence of an association between OI with gender, race, or ethnic group. OI was not been studied in a Vietnamese population before. The aims of this study were to describe the epidemiology, clinical features, and mutations in the collagen genes among Vietnamese OI patients. A totally 146 OI patients from 120 OI families were included in the study. There was 99 families without previous OI history and 21 families had two or more generations of OI history. All patients had skeletal deformations. 34 OI patients had a history of intrauterine fractures. There were 18 patients (12.33%) who had suffered over 30 fractures. The mean number of lifetime fractures for was 13.23. There was 117 OI patients with blue sclera, 89 dentinogenesis imperfecta and 26 hearing loss. DI was indentifed in 60.96% patients with OI. Genetic analysis suggests presence of correlation between DI and abnormality of collagen type I. The occlusal features were common in OI patients. We identified COL1A1 mutations in 36.3% and COL1A2 mutations in 23.1% of patients, which is lower compared to other populations. Also, the amount of discovered novel pathogenic variants is different from previous studies. The number of found affected individuals and severe phenotypes indicates that the disease is underdiagnosed in Vietnam. The results will find practical use in educating of physicians about the signs of OI in order to improve diagnosis and prevention of complications of this rare disorder. Our data also showed a lower number of collagen OI pathogenic variants in studied Vietnamese patients compared to reported rates for other OI populations. Current study showed that Vietnamese OI population is unique for investigation of OI phenotype and genotype

Mutation analysis of the <i>COL1A1</i> and <i>COL1A2</i> genes in Vietnamese patients with osteogenesis imperfecta

BackgroundThe genetics of osteogenesis imperfecta (OI) have not been studied in a Vietnamese population before. We performed mutational analysis of the COL1A1 and COL1A2 genes in 91 unrelated OI patients of Vietnamese origin. We then systematically characterized the mutation profiles of these two genes which are most commonly related to OI.MethodsGenomic DNA was extracted from EDTA-preserved blood according to standard high-salt extraction methods. Sequence analysis and pathogenic variant identification was performed with Mutation Surveyor DNA variant analysis software. Prediction of the pathogenicity of mutations was conducted using Alamut Visual software. The presence of variants was checked against Dalgleish's osteogenesis imperfecta mutation database.ResultsThe sample consisted of 91 unrelated osteogenesis imperfecta patients. We identified 54 patients with COL1A1/2 pathogenic variants; 33 with COL1A1 and 21 with COL1A2. Two patients had multiple pathogenic variants. Seventeen novel COL1A1 and 10 novel COL1A2 variants were identified. The majority of identified COL1A1/2 pathogenic variants occurred in a glycine substitution (36/56, 64.3 %), usually serine (23/36, 63.9 %). We found two pathogenic variants of the COL1A1 gene c.2461G > A (p.Gly821Ser) in four unrelated patients and one, c.2005G > A (p.Ala669Thr), in two unrelated patients.ConclusionOur data showed a lower number of collagen OI pathogenic variants in Vietnamese patients compared to reported rates for Asian populations. The OI mutational profile of the Vietnamese population is unique and related to the presence of a high number of recessive mutations in non-collagenous OI genes. Further analysis of OI patients negative for collagen mutations, is required

On the Out of Distribution Robustness of Foundation Models in Medical Image Segmentation

Constructing a robust model that can effectively generalize to test samples under distribution shifts remains a significant challenge in the field of medical imaging. The foundational models for vision and language, pre-trained on extensive sets of natural image and text data, have emerged as a promising approach. It showcases impressive learning abilities across different tasks with the need for only a limited amount of annotated samples. While numerous techniques have focused on developing better fine-tuning strategies to adapt these models for specific domains, we instead examine their robustness to domain shifts in the medical image segmentation task. To this end, we compare the generalization performance to unseen domains of various pre-trained models after being fine-tuned on the same in-distribution dataset and show that foundation-based models enjoy better robustness than other architectures. From here, we further developed a new Bayesian uncertainty estimation for frozen models and used them as an indicator to characterize the model's performance on out-of-distribution (OOD) data, proving particularly beneficial for real-world applications. Our experiments not only reveal the limitations of current indicators like accuracy on the line or agreement on the line commonly used in natural image applications but also emphasize the promise of the introduced Bayesian uncertainty. Specifically, lower uncertainty predictions usually tend to higher out-of-distribution (OOD) performance.Comment: Advances in Neural Information Processing Systems (NeurIPS) 2023, Workshop on robustness of zero/few-shot learning in foundation model

Genetic Interaction Between Two VNTRs in the SLC6A4 Gene Regulates Nicotine Dependence in Vietnamese Men

Nicotine dependence is an addiction to tobacco products and a global public health concern. Association between the SLC6A4 polymorphisms and nicotine dependence is controversial. Two variable number tandem repeat (VNTR) domains, termed HTTLPR and STin2, in the SLC6A4 gene are well characterized transcriptional regulatory elements. Their polymorphism in the copy number of the repeat correlates with the particular personality and psychiatric traits. We analyzed nicotine dependence in 1,804 participants from Central Vietnam. The Fagerström Test (FTND) was used to evaluate the nicotine dependence and PCR was used to determine the SLC6A4 HTTLPR and STin2 VNTRs. The HTTLPR VNTR was associated with difficulties to refrain from smoking in a prohibiting environment. The STIn2 10/10 genotype was associated with (1) years of smoking, (2) difficulties to quit the first cigarette, and (3) higher number of cigarettes smoked per day (CPD). Stratification analysis was used to find the genetic interaction between these two VNTRs in nicotine dependence as they may synergistically regulate the SLC6A4 expression. Smokers with the S/S HTTLPR genotypes showed a much stronger association between STin2 10/10 variant and CPD. This finding is consistent with the molecular evidence for the functional interaction between HTTLPR and STin2 in cell line models, where STin2 has described as a stronger expressional regulator. Similarly, we found that STin2 is a much stronger modifier of smoking with 10/10 genotype related to higher nicotine dependence. The present study supports genetic interaction between HTTLPR and STin2 VNTRs in the regulation of nicotine dependence with the dominance of the STin2 effects. This finding could be explained by their differential effect on the SLC6A4 expression

IFITM5 pathogenic variant causes osteogenesis imperfecta V with various phenotype severity in Ukrainian and Vietnamese patients

Background Osteogenesis imperfecta (OI) covers a spectrum of bone fragility disorders. OI is classified into five types; however, the genetic causes of OI might hide in pathogenic variants of 20 different genes. Often clinical OI types mimic each other. This sometimes makes it impossible to identify the OI type clinically, which can be a risk for patients. Up to 90% of OI types I–IV are caused by pathogenic variants in the COL1A1/2 genes. OI type V is caused by the c.-14C > T pathogenic variant in the 5′UTR of the IFITM5 gene and is characterized by hyperplastic callus formation and the ossification of interosseous membranes. Results In the current study, we performed IFITM5 5′UTR region mutational analysis using Sanger sequencing on 90 patients who were negative for COL1A1/2 pathogenic variants. We also investigated the phenotypes of five patients with genetically confirmed OI type V. The proportion of OI type V patients in our cohort of all OI patients was 1.48%. In one family, there was a history of OI in at least three generations. Phenotype severity differed from mild to extremely severe among patients, but all patients harbored the same typical pathogenic variant. One patient had no visible symptoms of OI type V and was suspected to have had OI type IV previously. We also identified a case of extremely severe hyperplastic callus in a 15-year-old male, who has hearing loss and brittleness of teeth. Conclusions OI type V is underlined with some unique clinical features; however, not all patients develop them. The phenotype spectrum might be even broader than previously suspected, including typical OI features: teeth brittleness, bluish sclera, hearing loss, long bones deformities, and joint laxity. We suggest that all patients negative for COL1A1/2 pathogenic variants be tested for the presence of an IFITM5 pathogenic variant, even if they are not expressing typical OI type V symptoms. Further studies on the pathological nature and hyperplastic callus formation mechanisms of OI type V are necessary

LVM-Med: Learning Large-Scale Self-Supervised Vision Models for Medical Imaging via Second-order Graph Matching

Obtaining large pre-trained models that can be fine-tuned to new tasks with limited annotated samples has remained an open challenge for medical imaging data. While pre-trained deep networks on ImageNet and vision-language foundation models trained on web-scale data are prevailing approaches, their effectiveness on medical tasks is limited due to the significant domain shift between natural and medical images. To bridge this gap, we introduce LVM-Med, the first family of deep networks trained on large-scale medical datasets. We have collected approximately 1.3 million medical images from 55 publicly available datasets, covering a large number of organs and modalities such as CT, MRI, X-ray, and Ultrasound. We benchmark several state-of-the-art self-supervised algorithms on this dataset and propose a novel self-supervised contrastive learning algorithm using a graph-matching formulation. The proposed approach makes three contributions: (i) it integrates prior pair-wise image similarity metrics based on local and global information; (ii) it captures the structural constraints of feature embeddings through a loss function constructed via a combinatorial graph-matching objective; and (iii) it can be trained efficiently end-to-end using modern gradient-estimation techniques for black-box solvers. We thoroughly evaluate the proposed LVM-Med on 15 downstream medical tasks ranging from segmentation and classification to object detection, and both for the in and out-of-distribution settings. LVM-Med empirically outperforms a number of state-of-the-art supervised, self-supervised, and foundation models. For challenging tasks such as Brain Tumor Classification or Diabetic Retinopathy Grading, LVM-Med improves previous vision-language models trained on 1 billion masks by 6-7% while using only a ResNet-50.Comment: Update Appendi

Genetic interaction between two VNTRs in the MAOA gene is associated with the nicotine dependence

Nicotine dependence is an addiction to tobacco products and a global public health concern that in part would be influenced by our genetics. Smokers are reported to have reduced MAOA activity, but the results from genetic associations with this gene have been inconclusive. Two functionally relevant variable number tandem repeat (VNTR) domains, termed uVNTR and dVNTR, in the MAOA gene are well characterized transcriptional regulatory elements. In the present study, we analyzed uVNTR and dVNTR polymorphisms in the MAOA gene in the Vietnamese male population of smokers and non-smokers in order to assess the association of MAOA with the nicotine dependence measured by the Fagerström Test for Nicotine Dependence (FTND). Individual analysis of VNTRs separately identified uVNTR to be associated with the F6 question of the FTND indicating the stronger addiction to nicotine. No associations were found between the dVNTR and smoking behavior. The combination of dVNTR and uVNTR, that predicts low expression of MAOA (10–3 haplotypes), was significantly associated with the higher nicotine dependence (FTND score), longer smoking duration, and more persistent smoking behavior (fewer quit attempts). In conclusion, our study confirms that low MAOA expression is genetically predictive to the higher nicotine dependence

The clinical features of osteogenesis imperfecta in Vietnam

Purpose Osteogenesis imperfecta (OI) has not been studied in a Vietnamese population before. The aim of this study was to systematically collect epidemiological information, investigate clinical features and create a clinical database of OI patients in Vietnam for future research and treatment strategy development. Method Participants underwent clinical and physical examinations; also medical records were reviewed. Genealogical information was collected and family members’ phenotypical manifestations recorded. Cases were classified according to the Sillence classification. Results In total, 146 OI patients from 120 families were studied: 46 with OI Type I, 46 with Type III and 54 with Type IV. Almost patients had skeletal deformations. One hundred and forty-two had a history of fractures, 117 blue sclera, 89 dentinogenesis imperfecta and 26 hearing loss. The total number of fractures was 1,932. Thirty-four patients had intra-uterine fractures and nine had perinatal fractures. Surgery was performed 163 times in 58 patients; 100 osteosyntheses and 63 osteotomies. Bisphosphonate treatment was used in 37 patients. The number of affected individuals and predominance of severe forms of OI indicate that the disease is under diagnosed in Vietnam, especially in cases without a family history or with mild form of OI. Deformities appeared in all patients with different severity and localisation, affecting mostly the lower limbs. OI medical and surgical treatment rates are low and in most cases surgery was performed due to fractures. Conclusions Compared to previous studies, our results indicate a lower OI prevalence and greater severity of symptoms in the Vietnamese population when compared with other areas. Further investigation, improved diagnosis and treatment are needed to increase the patients’ quality of life

The genetic legacy of continental scale admixture in Indian Austroasiatic speakers (vol 9, 3818, 2019)

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