ObjectiveTo observe and analyze the clinical phenotype and genetic characteristics of COL2A1 and COL11A1 de novo mutation (DNM) related Stickler syndrome type Ⅰ and Ⅱ patients. MethodsA family-based cohort study. From December 2023 to November 2024, 4 patients (all probands) with Stickler syndrome diagnosed by clinical and genetic testing in Department of Ophthalmology of People's Hospital of Ningxia Hui Autonomous Region and their parents (8 cases) were included in the study. The patients came from 4 unrelated families. A detailed medical history was taken, and the patients underwent best-corrected visual acuity (BCVA), refraction, and fundus color photography examinations. Systemic examinations included the oral and facial regions, skeletal, joints, and hearing. Peripheral venous blood samples were collected from the patients and their parents, and genomic DNA was extracted. Whole-exome sequencing was used to screen for pathogenic genes and their loci, which were then validated by Sanger sequencing and combined with segregation analysis in the families to identify candidate gene mutation sites. The candidate variants were assessed for pathogenicity according to the American College of Medical Genetics and Genomics (ACMG) criteria and guidelines for the classification of genetic variants. Additionally, cross-species conservation analysis was performed to determine the evolutionary conservation of wild-type amino acids, and protein three-dimensional modeling techniques were used to characterize the spatial conformational changes of the variant proteins and the alterations in their local hydrogen bond networks. ResultsAmong the 4 patients, there were 2 males and 2 females; their ages ranged from 3 to 12 years. There were 2 cases of Stickler syndrome type Ⅰ (proband of families 1 and 2) and 2 cases of type Ⅱ (proband of families 3 and 4). The diopters ranged from −8.00 to−18.00 D. BCVA ranged from no light perception to 0.6-. There were 2 cases each of vitreous membrane-like and “bead-like” opacity. Three cases showed peripapillary atrophy arcs and leopard pattern changes in the retina; one case had bilateral retinal detachment with a large macular hole in the left eye, which had previously been treated with vitrectomy surgery. One case had bilateral sensorineural hearing loss. There were 3 cases of simple micrognathia; one case had a flat nasal bridge, short nose, midface depression, and micrognathia. Two cases had excessive elbow joint extension. The phenotypes of the parents of the 4 patients were normal. Genetic testing results revealed that the probands of families 1 and 2 carried COL2A1 gene c.85+1G>C (M1) splice site variant and c.3950_3951insA (p.M1317Ifs*48) (M2) frameshift variant, respectively; the probands of families 3 and 4 carried COL11A1 gene (NM_001854.4) c.2549 G>T (p.G850V) (M3) missense variant and c.3816+6T>C (M4) splice site variant, respectively. The parents did not carry the related gene variants. Among them, M2, M3, and M4 are newly reported DNM. According to the ACMG guidelines, they were all considered likely pathogenic. The cross-species conservation analysis results showed that the wild-type amino acid of the COL11A1 gene M3 missense variant was highly conserved across multiple different species. Protein local structure modeling analysis revealed that the COL2A1 gene M2 frameshift variant and the COL11A1 gene M3 missense variant significantly altered the tertiary structure conformation of the protein, leading to abnormal spatial arrangement and hydrogen bond network in the key functional domains ConclusionThe COL2A1 gene M1 splice site variant, M2 frameshift variant, and the COL11A1 gene M3 missense variant, M4 splice site variant are respectively the potential pathogenic genes for families 1, 2, and families 3, 4; leading to the onset of Stickler syndrome type Ⅰ in families 1 and 2, and type Ⅱ in families 3 and 4.
ObjectiveTo observe and analyze the genotype and clinical phenotype in 34 families of familial exudative vitreoretinopathy associated with (FEVR) gene variation.MethodsCohort study. Thirty-four FEVR families, in which the patients and both of their parents were all found to have FEVR-related gene mutations (proband 34 cases, 67 eyes; parents 68 cases, 136 eyes), were included in the study. These patients were identifIed from 722 FEVR patients through genetic screening, which diagnosed in Department of Ophtalmology of Xinhua Hospital and Tianjin Medical University Eye Hospital from January 2010 to December 2018. The probands and their parents underwent a comprehensive ophthalmological examination appropriate to their age, including BCVA, intraocular pressure, axial length, slit lamp examination, indirect ophthalmoscopy, FFA or color fundus photography or wide field color fundus photography. According to the severity of the disease, the clinical manifestations were divided into severe phenotype and mild phenotype. Thirty-four normal healthy people over 40 years old were included as the control group. The peripheral blood samples of FEVR family members and control group members were collected, and the genes known to be involved in FEVR, such as FZD4, LRP5, NDP, TSPAN12, ZNF408 and KIF11, were analyzed by next generation sequencing molecular genetics. The data were statistically analyzed by SPSS. The counting data was expressed in numbers or rates, and tested by Kruskal-Wallis test and χ2 test to find out the existence of significant difference.ResultsIn 67 eyes of the 34 probands, 48 eyes (71.64%) were classified into severe phenotype and 19 eyes (28.36%) were mild phenotype. In 136 eyes of 68 parents of the proband patients, 76 eyes (55.88%) were normal, 60 eyes (44.12%) were classified into mild phenotype, and no severe phenotype was found. A total of 65 variants of FEVR-related genes were detected in the 34 probands, of which LRP5 mutation was the most common (64.61%), followed by FZD4 (12.31%), NDP (10.77%), TSPAN12 (6.15%), ZNF408 (4.62%) and KIF11 (1.54%). Missense mutations were the most common variant in FEVR-related genes. However, the results of correlation analysis indicated that there was no significant correlation between the type of mutation and the severity of clinical phenotype (H=1.775, P=0.620). Among the 65 mutation types, 21 types have been previously identified and 44 were novel in this study. Thirty-nine eyes of 20 cases had only one single pathogenic mutation gene but with multiple mutation sites, 26 eyes of 13 cases carried 2 relevant pathogenic mutation genes, and 2 eyes in one case had 3 pathogenic mutation genes. The mutation frequencies of LRP5, NDP, ZNF408, FZD4, TSPAN12 and KIF11 genes in probands were significantly higher than those in control group, and the difference was statistically significant. The total mutation frequencies of LRP5, NDP, ZNF408, FZD4, TSPAN12 and KIF11 genes in proband group were significantly higher than those in control group (χ2=64.702, P＜0.001).ConclusionsIn the FEVR families, the most frequent mutations were those in LRP5, followed by FZD4, NDP, TSPAN12,ZNF408 and KIF11. Missense mutation is the most common type of FEVR-related gene mutation, but there is no significant correlation between the clinical phenotype and gene variation type. Most of the probands were with severe clinical phenotype, while most of the parents with FEVR pathogenic gene mutation showed normal or mild manifestations.
ObjectiveTo recognize the convulsion caused by hypoglycemia, and to analyze its genotype and clinical phenotype, so as to deepen the understanding of hyperinsulinemia.MethodFull exon detection were performed on 2 children with hypoglycemia and convulsions, who had been treated with antiepileptic drugs for 1 year in pediatric neurology department, Henan Provincial People’s Hospital in 2012 and 2014 respectively, but with poor curative effect.ResultABCC8 gene mutations were found in a child. The mutations located in Chromosome 11, with the nucleic acid changes of c.4607C>T (exon38) and the amino acid change of p.A1536V, rs745918247. The inheritancemode of ABCC8 gene could be autosomal dominant or autosomal recessive inheritance. Both of the parents were wild type on this genelocus. The gene mutation is associated with type 1 familial hyperinsulinemic hypoglycemia/nesidioblastosis. The other child was carrying GLUD1 gene mutation, witch is located in chromosome 10, with the nucleic acid changes of c.1498G>A (exon12) and the amino acid change of p.A500T. The inheritance mode of GLUD1 gene is autosomal dominant andthe child’s parents were both wild type. This gene mutationis associated with type 6 familial hyperinsulinemic hypoglycemia/nesidioblastosis. The 2 mutations have not been reported, which are new mutations.ConclusionMutations in these 2 gene loci may be the underlying cause of hypoglycemic convulsions, and are the best explanation for the poor convulsionscontrol of antiepileptic drugs.
ObjectivesTo compare different formula calculated dosages with the actual doses of warfarin from patients in Beijing Hospital so as to investigate suitable warfarin dosing models for Chinese patients.MethodsOne hundred and three Chinese patients with long-term prescription of warfarin were randomly selected from Beijing Hospital from July 2012 to May 2013. The CYP2C9 and VKROC1 genotypes and basic statistical information were collected. SPSS 18.0 software was used to compare the differences between different formula calculated dosages and the actual dosages of warfarin.ResultsFive genotypes were found in 103 patients, including: CYP2C9 AA genotype + VKORC1 AA genotype (n=72, 69.9%), CYP2C9 AA genotype + VKORC1 AG genotype (n=17, 16.5%), CYP2C9 AC genotype + VKORC1 AA genotype (n=10, 9.7%), CYP2C9 AC genotype + VKORC1 AG genotype (n=3, 2.9%) and CYP2C9 AA genotype + VKORC1 GG genotype (n=1, 1%). Compared with the actual dosages of warfarin, the degree of coincidence was highest for dosages calculated by Jeffrey’s formula.Conclusions Using Jeffrey’s formula to calculate warfarin dosages may be more suitable for Chinese patients with using long-term warfarin. Due to limited sample size, prospective and large sample size studies are required to verify the above conclusion.
ObjectiveTo identify the causative gene and observe the phenotypic characteristics of a family with isolated microphthalmia-anophthalmia-coloboma (MAC). MethodsA retrospective clinical study. One patient (proband) and 3 family members of a family with MAC visited the Henan Eye Hospital from May 2019 to May 2022 were included in the study. The patient's medical history and family history were inquired in detail, and the best corrected visual acuity (BCVA), slit lamp microscope, fundus photography, optical coherence tomography (OCT), ophthalmological B mode ultrasound and axial length (AL) measurement were performed. The peripheral venous blood of the proband, his parents and brother was collected for Trio whole-exome sequencing and pathogenic gene screening. Fluorescence quantitative Polymerase chain reaction was used to verify the suspicious variations. The clinical features of the patient's ocular and systemic also were observed. ResultsThe proband, male, was 3 years old at the first visit. The horizontal pendular nystagmus was detected in both eyes. Vertical elliptical microcornea and keyhole-shaped iris colobomas were detected in both eyes. The objective refraction at first visit (3 years old) was －4.00 DS/－0.50 DC×105° (OD) and －3.50 DS/－1.25 DC×80° (OS). Refraction and BCVA at 6 years old: －6.50 DS/－2.00 DC×110°→0.05 (OD) and －6.00 DS/－1.50 DC×80°→0.2 (OS). The AL at 4 years and 10 months old was 24.62 mm (OD) and 23.92 mm (OS), respectively. The AL at 5 years and 7 months old was 25.24 mm (OD) and 24.36 mm (OS), respectively. Ultrasonography shows tissue defects in both eyes. Fundus photography showed the inferior choroidal coloboma involving optic disc. OCT showed the optic disc in both eyes was abnormal with colobomas around, and the retinal neurosensory layer in colobomas area was disordered and thin; the retinoschisis was visible in the left eye. The proband's parents and siblings have normal phenotypes. Whole exome sequencing reveals a denovo heterozygous deletion of YAP1 gene: YAP1, chr11: 10280247-102100671, NM_ 001130145, loss 1 (EXON: 6-9). The results of bioinformatics analysis were pathogenic variants. Parents and siblings were of the wild type. ConclusionsLoss of heterozygosity in exons 6-9 of YAP1 gene is the pathogenic variation in this family. It can cause abnormal development of anterior segment, chorioretinal colobomas, deepening of axial myopia, even severe macular colobomas and retinoschisis.
ObjectiveTo clarify the relationship between the G/C polymorphism of inflammatory gene matrix metalloproteinase-2 (MMP2) and warfarin therapy after cardiac valve replacement (CVR). MethodsWe finally identified 96 patients who received additional warfarin therapy after CVR as a trial group and 78 patients without the warfarin therapy as a control group. Gene sequencing techniques were adopted to determine single nucleotide polymorphism allele. We analyzed genotype and clinical features of the two groups and explored the relationship between the different MMP2 geno-types and warfarin therapy after CVR. Logistic regression was used to analyze the correlation between genotypes and risk factors after CVR and Kaplan-Meier survival curves were performed to analyze the survival time and efficacy of patients carrying MMP2 GC and GG genotypes. ResultsThe distribution of MMP2 genotype in patients receiving warfarin therapy after surgery was different from that in patients without warfarin therapy. The results of multivariate logistic regression analysis showed that GC and GG genotypes were risk factors of complications of CVR. The proportion of GG genotype was higher in the patients with postoperative complications compared with those without. The survival time of patients carrying genotype MMP2 GG was shorter than those carrying GC genotype (P < 0.05), which reveals that the level of MMP2 GG genotype was associated with the prognosis. ConclusionG allele of MMP2 is a risk factor of complications following CVR. GG genotype is relevant to CVR and prognosis, which can be regarded as a risk factor post CVR.
Online Mendelian Inheritance in Man (OMIM) is a knowledge source and data base for human genetic diseases and related genes. Each OMIM entry includes clinical synopsis, linkage analysis for candidate genes, chromosomal localization and animal models, which has become an authoritative source of information for the study of the relationship between genes and diseases. As overlap of disease symptoms may reflect interactions at the molecular level, comparison of phenotypic similarity may indicate candidate genes and help to discover functional connections between genes and proteins. However, the OMIM has used free text to describe disease phenotypes, which does not suit computer analysis. Standardization of OMIM data therefore has important implications for large-scale comparison of disease phenotypes and prediction of phenotype-genotype correlations. Recently, standard medical language systems, term frequency-inverse document frequency and the law of cosines for document classification have been introduced for mining of OMIM data. Combined with Gene Ontology and various comparison methods, this has achieved substantial successes. In this article, we have reviewed various methods for standardization and similarity comparison of OMIM data. We also predicted the trend for research in this direction.
Objective To explore the clinical characteristics of patients who were infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) of different genotypes. Methods A retrospective study was conducted on 111 SARS-CoV-2 infected cases at home and abroad admitted to Chengdu Public Health Clinical Medical Center between January and September 2020. The basic information, gene sequencing results (Pangolin typing method), clinical typing, first laboratory examinations 24 hours after admission, and whether repositive after discharge were collected. According to Pangolin typing, patients were divided into five groups: A, B, B.X, B.1.X and B.1.1.X. The basic information (age, sex, and origin), laboratory test results (lymphocyte count, C-reactive protein, serum amyloid A, CD3+ T lymphocytes, CD4+ T lymphocytes, and CD8+ T lymphocytes), clinical classification and whether repositive were compared among different genotype infected patients. Results Among the 111 infected patients, 54 (48.6%) were males and 57 (51.4%) were females. Their ages ranged from 16 to 87 years, with a median age of 49 years. In terms of clinical classification, there were 10 asymptomatic cases (9.0%), 10 mild cases (9.0%), 64 ordinary cases (57.7%), 13 severe cases (11.7%), and 14 critical cases (12.6%). There were 75 domestic cases (67.6%) and 36 imported cases (32.4%). Eighty cases (72.1%) did not return to positive, and 31 cases (27.9%) returned to positive. There were 8 cases infected by type A virus, 18 cases infected by type B virus, 26 cases infected by type B.X virus, 5 cases infected by type B.1.X virus, and 54 cases infected by type B.1.1.X virus. Among patients infected by different genotype viruses, no statistically significant difference was found in sex, age, clinical type, laboratory examination, or whether repositive (P>0.05), but there was statistically significant difference in the distribution of domestic and imported cases (P=0.016). Type B virus infected patients were mostly domestic cases, while type B.X virus infected patients were mostly imported cases. Conclusion The distribution of domestic and imported cases is different among SARS-CoV-2 of different genotypes.
ObjectiveTo analyze genotype frequencies of CYP2C19 in healthy Asian population, and to provide evidence-based data for further personalized drug therapy and pharmacogenomics research. MethodsLiterature was retrieved from digital databases of PubMed, EMbase, The Cochrane Library (Issue 2, 2013), CNKI, WanFang Data, VIP and CBM from their established dates to August, 2013. According to the inclusion and exclusion criteria, the data of the allele frequencies of the gene were extracted, pooled, and analyzed. ResultsA total of 36 articles were included, involving 15 countries and 9 693 healthy populations. Analysis was conducted on regional features, by regions as China, East Asia (China, Korea and Japan), Southeast Asia (Vietnam, Thailand, Malaysia, Singapore, Myanmar and Indonesia), South Asia (India) and West Asia (Palestine, Lebanon, Iran, Turkey and Jordan). The results showed that the genotype frequencies of *1/*1, *1/*2, *1/*3, *2/*2, *2/*3 and *3/*3 were 37.2%, 41.4%, 6.7%, 9.9%, 4.1% and 0.7% (Chinese, n=4 105); 36.4%, 39.1%, 8.8%, 9.5%, 4.9% and 1.3% (East Asian, n=6 198); 44.9%, 41.1%, 4.7%, 7.0%, 1.8% and 0.6% (Southeast Asian, n=1 933); 43.5%, 42.9%, 0.3%, 12.7%, 0.6% and 0.0% (South Asian, n=361); 77.8%, 18.9%, 0.3%, 2.6%, 0.1% and 0.3% (West Asia, n=1 201); and 43.5%, 37.1%, 6.6%, 8.3%, 3.5% and 1.0% (Asian, n=9 693). ConclusionThe present study suggests that there is a great difference on the genotype frequencies of CYP2C19 for different ethnic groups in China, and at different regions in Asia. Besides, genetic variation is impacted by geographical factors such as region and environment.
OBJECTIVE: Porcine stress syndrome (PSS) is one kind of molecular genetics defect diseases of pig which will cause malignant hyperthermia syndrome (MHS) and is the first index should be excluded in screening of a pig species for xenotransplantation. It was reported that mutation of pig rynodine receptor(RYR1) gene is the main reason for PSS. In this study, RYR1 genotypes of the Chinese Banna mini pig inbred line and inbreeding closed colony Wuzhishan pig were investigated with polymerase chain reaction-restriction endonuclease fragment length polymorphism (PCR-RFLP) technique. METHODS: Antevenocaval whole blood samples were collected from 50 Banna mini-pig inbred-line(BMI), 15 inbreeding Wuzhishan pig (WZSP) and 25 Neijiang pigs (NJP) as negative control, the primer were designed and synthesized, PCR reaction was conducted following the sequence of 94 degrees C (1 min), 58 degrees C (1 min) and 72 degrees C (1 min) for 30 cycles. The PCR products were digested with restriction endonuclease HhaI and then electrophoresis check. RESULTS: A 659 bp DNA fragment was amplified with these two primers, the HALNN sample fragment was cut into fragments as 493 bp and 166 bp individually after the digestion, indicates no point mutation at site 1,843 in RYR1 gene in all tested BMI pig and WZSP. Namely, the RYR1 genotype of 50 cases of BMI and 15 cases of WZSP were HALNN, therefore their phenotype is PSS negative. CONCLUSION: It indicates that the genotype of Banna mini pig inbred line and inbreeding Wuzhishan pig are HALNN therefore PSS absolutely negative, the group penetrance is 0. This is consistent with experimental observation. It suggests that Banna mini pig inbred line and inbreeding Wuzhishan pig may be the alternative donor for xenotransplantation.