Objective To detect the single nucleotide polymorphisms ( SNPs) in the upstream promoter region of chemokine like factor ( CKLF) gene and analyze their possible associations with asthma and asthma-related phenotypes. Methods Direct Sequence of the 1553bp upstream promoter region of CKLF gene was performed in 245 Chinese Han human genomic DNAs ( 119 asthmatics and 126 controls) .The frequencies of alleles, genotypes, and haplotypes were determined and the association of these SNPs with asthma were further analyzed. Results Four novel SNPs, SNP88 ( T gt; C) , SNP196 ( T gt; C) , SNP568 ( C gt;G) , and SNP1047 ( C gt; G) were found in the promoter region of CKLF. The frequency of rare allele was 0. 168 ( SNP88C) , 0. 168 ( SNP196C) , 0. 352 ( SNP568G) and 0. 167 ( SNP1047G) , respectively.Haplotypes, their frequencies and the linkage disequilibrium coefficients between SNPs were constructed.Complete linkage disequilibrium( LDs) were observed between SNP88 and SNP196, SNP88 and SNP1047,as well as SNP196 and SNP1047, respectively ( D′=1. 000, r2 = 1. 000) . SNP568 was in partial LD with the other three SNPs ( r2 = 0. 366) . No association between asthma and the SNPs was observed. Conclusions Four SNPs in the regulatory region of CKLF in Chinese Han population were firstly identified. Although no significant correlation with asthma was revealed, the SNP and haplotype information is useful for other disease association studies in the future.
【Abstract】 Objective To analyze the correlations between the mt5351G and mt6680C genotypes in mitochondrial DNA ( mtDNA) haplogroup M and susceptibility to high altitude pulmonary edema ( HAPE)among the Hans. Methods Specimens from206 Hans cases of HAPE and 144 matched Hans controls were collected. Then PCR-RFLP method was used to determine haplogroup M and N of mtDNA, and PCR-LDR was used to genotype mt5351G and mt6680C in the haplogroup M in these samples. Results The frequencies of haplogroup Mand N were 49. 0% and 51.0% in the HAPE patients, and 47. 2% and 52. 8% in the controls, respectively, with no significant difference between the HAPE patients and the controls. In the haplogroup M, the genotype of mt6680C and mt5351G frequencies in the HAPE patients were both significantly higher than the controls ( both 12. 0% vs. 1. 5% , P = 0. 016) . Conclusion The existence of mt5351G and mt6680C genotypes in the haplogroup Mis a risk factor for HAPE among the Hans.
Objective To investigate the genotype and phenotype in patients with leber congenital amaurosis (LCA), and offer accurate genetic counseling and prenatal diagnosis for those families. Methods Three LCA patients and their parents were recruited for this study and received detailed collection of medical history and family history from March to August 2016. The three patients received fundus fluorescein angiography examination and their parents received slit-lamp microscope and indirect ophthalmoscopy examinations. DNA was extracted from the patients and their family members. Whole-exome sequencing method was used for genetic diagnosis and typing of the three LCA patients and their parents. Results The three patients with different clinical features had a definite clinical diagnosis of LCA. Patient 1 showed pale disc, attenuated vessels aroud the optic disc and the salt-and-pepper appearance of the retina, had the homozygous c.744.745insT (p.249, L>Ffs4) mutation inSPATA7. Patient 2 showed optic disc pallor and attenuated retinal vessels, had the heterozygous c.535G>A, p.A179T mutation inWFS1. Patient 3 showed pale disc, atrophic macular and retinal and choroidal degeneration, had the heterozygous mutation in CRB1, RPGRIP1, SPATA7. Conclusion LCA has characteristics of genetic heterogeneity and clinical and phenotypic diversity.
Objective To investigate HPV infection, genotype distribution of HPV infection among 8 944 females of health examination in West China Hospital of Sichuan University. Methods We enrolled 8 944 females of health examination in West China Hospital of Sichuan University from January to September in 2016. HPV genotyping was performed by Luminex fluorescence technique. Excel 2007 and SPSS 17.0 softwares were used to analyze the infection and genotype distribution of HPV. Results The HPV infection rate of 8 944 health examination women was 14.4% (1 291/8 944). Among them, there were 1 025 cases of single infection, the infection rate was 11.5% (1 025/8 944); there were 266 cases of multiple infection, the infection rate was 3.0% (266/8 944). The infection rates of 20 to 25 years and ≥66 years groups in single and multiple infection were higher than other age groups. In the single and multiple infections, the most common genotypes were HPV52, 53, 16 and 58. Infection rate of HPV52 was the highest in single infection, which had two increased age groups including 31 to 35 years and 61 to 65 years old. Infection rate of HPV52 and HPV16 were increased in 20 to 25 years old group of multiple infections. Conclusion In view of the prevalence of HPV infection among health examination females and the genotype distribution, we recommend incorporating HPV52, 53 and 58 into future vaccine screening.
Objective To investigate the genetic polymorphism of methicillin resistant Staphylococcus aureus ( MRSA) isolated from hospital acquired pneumonia. Methods Seventy-four hospitalized patients were diagnosed as noscomial MRSA pneumonia from January 2007 to January 2008 in Xinhua Hospital, Shanghai Jiaotong Univesity. The genes of MRSA were amplified by random amplified polymorphic DNA typing ( RAPD) assay in 82 clinical isolates from these patients. Results Two to 15 amplified DNA fragments were observed in agarose gel and they were classified into 11 genotypes. Genotypes Ⅲ, Ⅵ and Ⅶ ( 32. 56% , 30. 23% and 13. 95% , respectively) were mainly isolated from the ICU. Both independent genotypes and overlapping genotpyes with those from ICU were identified in isolates from the departments of geriatrics, emergency and respiratory medicine. Outbreak or cluster cases ( 48. 65% ) were found in 36 of the 74 patients while all outbreak cases occurred in the ICU. Conclusions Noscomial MRSA pneumonia is easy to disseminate and small-scale outbreak may occur especially in ICU. RAPD is valuable for identification and prevention of the spread of MRSA in hospital.
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.
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 analyze hepatitis B virus (HBV) genotype distribution and drug-resistant mutations in West China Hospital of Sichuan University, providing basis for hepatitis B individualized treatment.MethodsA total of 786 chronic hepatitis B patients admitted to West China Hospital of Sichuan University from January 2016 to December 2018 were enrolled in the study. Genotype and drug-resistant mutations were analyzed by Sanger sequencing, and statistical analysis was conducted by χ2 test.ResultsThree genotypes (B, C and D) were identified in 786 samples, 489 (62.2%) in genotype B, 291 (37.0%) in genotype C , and 6 (0.8%) in genotype D. The distribution differences of B and C genotypes in age and ethnic groups were statistically significant (P<0.05). Among them, 627 cases had drug-resistant mutations, with a drug-resistant mutation rate of 79.8%. A total of 262 cases (33.3%) were resistant to lamivudine and tibivudine, 102 cases (13.0%) were resistant to lamivudine, tibivudine and entecavir; 83 cases (10.6%) were resistant to adefovir dipivoxil. No tenofovir resistant strains were detected in 786 samples. There were statistically significant differences in drug resistance between B and C genotypes (χ2=14.356, P<0.01). The most common single mutation was M204I [179 cases (22.8%)], followed by 46 cases (5.9%) of A181V/T associated with adefovir dipivoxil resistance. The most common mixed mutation was L180M+M204V/I in 83 cases (10.6%), and another 102 cases (13.0%) showed M250V and/or V173L and/or T184A/G/S/I and/or S202G/I with L180M+M204V/I.ConclusionsHBV genotypes in West China Hospital of Sichuan University are mainly B and C, and the situation of drug resistance is severe and the mutation pattern is complex. Therefore, detecting HBV genotype and drug resistance mutation is necessary, which may develop better clinical treatments.
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.
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.