Journal of Genetics最新文献_第10页

Diagnosis of prenatal 22q11.2 duplication syndrome: a two-case study. 产前22q11.2重复综合征的诊断:两例研究

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2023-01-01

Hening Li, Yanfei Gong, Jingyi Chen, Liyun Xie, Bojie Li, Yanghai Xiang, Meihua Xie

{"title":"Diagnosis of prenatal 22q11.2 duplication syndrome: a two-case study.","authors":"Hening Li, Yanfei Gong, Jingyi Chen, Liyun Xie, Bojie Li, Yanghai Xiang, Meihua Xie","doi":"","DOIUrl":"","url":null,"abstract":"The objective of the study was to perform the prenatal diagnosis of two foetuses with 22q11.2 duplication for 2.5 Mb after noninvasive prenatal testing (NIPT), and to explore the prenatal diagnosis and genetic characteristics of these foetuses. After amniocentesis, each foetus was diagnosed through karyotype analysis and single-nucleotide polymorphism array (SNP-array), and copy number variation using shotgun sequencing (CNV-seq) was carried out on each mother's peripheral blood for comparative analysis. Both pregnant woman 1 and pregnant woman 2 had foetal amniotic fluid chromosomal karyotypes of 46, XN. The SNP-array result for foetus 1 was arr[hg19] 22q11.21(18,648,856-21,800,471) x3; namely, 22q11.2 had a 3.1 Mb repeat, and the SNP-array result of foetus 2 was arr[hg19]22q11.2(18,648,855-21,464,764) x3; there was a 2.4 Mb repeat of 22q11.2. The CNV-Seq result of the peripheral blood of pregnant woman 1 was seq[hg19]22q11.2(18,953,139-21,449,967) x3; namely, in this mother's 22q11.2 region, there was ~2.5 Mb of duplicate fragment that was pathogenic to CNV. We confirmed that case 1 was inherited from the mother by CNV-seq. In both cases, however, there were key region deletions, including 41 OMIM genes such as CLTCL1, HIRA and TBX1. Both SNP-array and CNV-seq can effectively diagnose 22q11.2 duplication syndrome and clarify its fracture site and involved genes, which may facilitate understanding of the genotype and phenotype correlations.","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"102 ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10636918","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Mysteries in our genome. 我们基因组中的奥秘。

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2023-01-01

Durgadas P Kasbekar

引用次数: 0

A homozygous missense variant in PTPN2 with early-onset Crohn's disease, growth failure and dysmorphic features in an infant: a case report. PTPN2纯合错义变异伴婴儿早发性克罗恩病、生长衰竭和畸形特征:1例报告

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2023-01-01

Johnny Awwad, Mirna Souaid, Tony Yammine, Alain Chebly, Nabiha Salem, Rita Esber, Chantal Farra

{"title":"A homozygous missense variant in PTPN2 with early-onset Crohn's disease, growth failure and dysmorphic features in an infant: a case report.","authors":"Johnny Awwad, Mirna Souaid, Tony Yammine, Alain Chebly, Nabiha Salem, Rita Esber, Chantal Farra","doi":"","DOIUrl":"","url":null,"abstract":"Crohn's disease (CD) is a chronic idiopathic inflammatory bowel condition that can affect any part of the gastrointestinal tract. Several hundred candidate loci or genes including PTPN2 have been reportedly associated with CD. A whole-exome sequencing (WES) was conducted in a 9-year-old Lebanese girl with a CD onset at 13 months and in both her asymptomatic parents. The analysis detected an extremely rare homozygous variant in PTPN2: c.359C>T, p.(Ser120Leu) in the patient, while both her parents were heterozygous. This variant, located in the protein tyrosine phosphatase (PTP) domain within a highly conserved amino acid, is classified as VUS according to the American College of Medical Genetics (ACMG) criteria. To evaluate the hypothetical functional consequences of the identified variant, a quantitative expression analysis of PTPN2 was performed in blood tissues of the patient, her parents, and two healthy controls. PTPN2 expression was not noted in the patient compared to her parents and the normal controls, suggesting a functional PTPN2 impairment caused by c.359C>T. This variant c.359C>T, p.(Ser120Leu) in PTPN2 has never been previously described in the literature. Our report suggests an association of PTPN2: c.359C>T with early-onset CD.","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"102 ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9999559","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A novel missense variant in EIF2B5 identified in a consanguineous Iranian family with vanishing white matter disease and a brief review of the literature. 一种新的EIF2B5错义变异，在一个近亲伊朗家庭中发现，白质疾病消失，并简要回顾文献。

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2023-01-01

Parisa Nourmohammadi, Mostafa Asadollahi, Arezou Karamzade, Yeganeh Eshaghkhani, Meisam Babaei, Zahra Golchehre, Seyedeh Roksana Taheri, Sepideh Hasani, Mahdieh Taghizadeh, Mohammad Keramatipour

{"title":"A novel missense variant in EIF2B5 identified in a consanguineous Iranian family with vanishing white matter disease and a brief review of the literature.","authors":"Parisa Nourmohammadi, Mostafa Asadollahi, Arezou Karamzade, Yeganeh Eshaghkhani, Meisam Babaei, Zahra Golchehre, Seyedeh Roksana Taheri, Sepideh Hasani, Mahdieh Taghizadeh, Mohammad Keramatipour","doi":"","DOIUrl":"","url":null,"abstract":"Vanishing of white matter (VWM) is a hereditary heterogeneous brain disorder that most often affects children. However, the onset of the disease varies from childhood to adulthood. VWM is caused by mutations in one of the five genes encoding subunits of the eukaryotic initiation factor eIF2B. In the current study, we aimed to determine the genetic cause of VWM in a large consanguineous Iranian family with three affected members. Next-generation sequencing was conducted on the proband to determine the underlying cause of VWM. The identified variant was validated by PCR-Sanger sequencing in the patient and was also segregated in his parents and two other affected members of the pedigree. The potential functional effects of this mutation within EIF2B5 were predicted by in silico analysis. We have also reviewed all EIF2B5 disease-causing variants and available clinical features of each patient reported in HGMD Professional 2022.2. A novel homozygous variant c.746T>G [p.Ile249Ser] was detected in EIF2B5 which was co-segregated with the disease in all affected family members in an autosomal recessive manner. All employed in silico prediction tools and 3D structure analysis for the novel mutation also supported the pathogenicity of this variant. Our study not only expanded the spectrum of the pathogenic variants in EIF2B5 but also presented a literature review on EIF2B5-related conditions that provide a comprehensive picture of the genetic nature of this gene and phenotypic variability in patients.","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"102 ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10179432","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identification of genetic polymorphism of the MBL2 gene and its association with clinical mastitis in Murrah buffaloes. 默拉水牛MBL2基因多态性的鉴定及其与临床乳腺炎的关系

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2023-01-01

Shahid Ahmad Shergojry, Archana Verma, Minerva Ghani, Ishwar Dayal Gupta, Nazir Ahmad Mir

{"title":"Identification of genetic polymorphism of the MBL2 gene and its association with clinical mastitis in Murrah buffaloes.","authors":"Shahid Ahmad Shergojry, Archana Verma, Minerva Ghani, Ishwar Dayal Gupta, Nazir Ahmad Mir","doi":"","DOIUrl":"","url":null,"abstract":"Mastitis is a serious bovine disease which causes significant commercial loss. Polymorphism of mannose-binding lectin genes in bovine may be regarded as a functional and positional candidate gene for mastitis resistance and complement activity. In the present study, single-nucleotide polymorphism (SNP) of MBL2 gene in 200 Murrah buffaloes was investigated using the polymerase chain reaction direct sequence (PCR direct sequence) technique, and four new SNPs at 1262G>A, 3382A>T, 4387C>T and 4511C>T loci of Mannose binding lectin 2 (MBL2) gene were found. Pair linkage disequilibrium analysis and haplotype construction of MBL2 gene were performed using SHEsis software. Two nonsynonymous types of changes were observed at 1262G>A (Gly40Asp) and 4387C>T (Thr166Met) of MBL2 protein. These amino acid changes were however predicted not to affect the protein function in any manner. An odds ratio analysis showed that the A allele of 1262G>A, A allele of 3382A>T, C allele of 4387C>T and C allele of 4511C>T had 3.7, 5.19, 7.82 and 3.7 fold increased risk for developing clinical mastitis in Murrah buffaloes, respectively, identifying that these alleles are 'at-risk' alleles and showed significant association with increased risk for clinical mastitis in Murrah buffaloes (P<0.01). Genotypic association analysis revealed that Murrah buffaloes with AG, AT, CT and TT genotypes at 1262G>A, 3382A>T, 4387C>T and 4511C>T loci of ,MBL2 gene, respectively were found significantly least susceptible to clinical mastitis compared to other genotypes. A total of seven haplotypes were constructed from four SNPs of MBL2 gene. Haplotypes association analysis showed that animals with allelic combination of haplotypes Hap6 (GTCT) and Hap7 (GTTT) were significantly least susceptible to clinical mastitis compared to other haplotypes in Murrah buffaloes (P<0.01).","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"102 ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9334121","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Mitochondrial markers differentiate two distinct phylogenetic groups in indigenous rice landraces of northeast India: an evolutionary insight. 线粒体标记区分两个不同的系统发育群体在印度东北部的本土水稻地方品种:一个进化的见解。

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2023-01-01

Madhuchhanda Parida, Gayatri Gouda, Parameswaran Chidambaranathan, Ngangkham Umakanta, Jawahar Lal Katara, Cayalvizhi Balasubramania Sai, Sanghamitra Samantaray, Bhaskar Chandra Patra, Trilochan Mohapatra

{"title":"Mitochondrial markers differentiate two distinct phylogenetic groups in indigenous rice landraces of northeast India: an evolutionary insight.","authors":"Madhuchhanda Parida, Gayatri Gouda, Parameswaran Chidambaranathan, Ngangkham Umakanta, Jawahar Lal Katara, Cayalvizhi Balasubramania Sai, Sanghamitra Samantaray, Bhaskar Chandra Patra, Trilochan Mohapatra","doi":"","DOIUrl":"","url":null,"abstract":"The inheritance of the mitochondria genome and its diversity is unique for genetic and evolutionary studies relative to nuclear genomes. Northeast India and Himalayan regions are considered as one of the centres of indica rice origin. Also, rice diversity in northeast India is very distinct and highly suited for evolutionary studies. Although reports are available on the genetic diversity of indigenous northeast rice landraces, its relationship with the wild relatives is not yet properly explored and understood. In an attempt, mitochondrial markers were used to study the evolutionary relationship between the 68 landraces of northeast India and wild relatives (O. rufipogon and O. nivara) along with IR64 (indica) and Nipponbare (japonica) were taken as reference cultivars. Phylogenetically, the findings include two distinct clusters in the indigenous northeast India landraces representing indica and japonica groups. Further, the wild relatives and ~60% of northeast India landraces were identified to be closely related to the Nipponbare cluster. Besides, landraces of northeast India grouping with the indica group (IR64) are characterized by the absence of wild relatives. This indicates that there are two distinct evolutionary paths in the origin of northeast Indian rice landraces based on mitochondrial markers diversity and it is proposed that the inheritance of mitochondria, mitonuclear genome interactions, and bottleneck events could have genetically separated these two phylogenetically unique groups of northeast rice landraces.","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"102 ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9253213","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Exome sequencing and microarray identified a novel large exonic deletion in SYT2 gene in an ultra-rare case with recessive CMS type 7. 外显子组测序和微阵列技术在一个罕见的隐性7型CMS病例中发现了SYT2基因的一个新的大外显子缺失。

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2023-01-01

C P Ravi Kumar, Parag M Tamhankar, Radhika Manohar, Sheetal Sharda, G K Madhavilatha, S G Thenral, Sandhya Nair, A K Bojamma

引用次数: 0

A time-calibrated mitogenomic phylogeny suggests that Korean Hyalessa fuscata is a bridge between Chinese and Japanese H.maculaticollis. 一项时间校准的有丝分裂基因组系统发育研究表明，韩国的褐斑玻璃是中国和日本斑点玻璃之间的桥梁。

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2023-01-01

Hoa Quynh Nguyen, Phuong-Thao Ho, Sungsik Kong, Yoonhyuk Bae, Thai Hong Pham, Huyen Thi La, Yikweon Jang

{"title":"A time-calibrated mitogenomic phylogeny suggests that Korean Hyalessa fuscata is a bridge between Chinese and Japanese H.maculaticollis.","authors":"Hoa Quynh Nguyen, Phuong-Thao Ho, Sungsik Kong, Yoonhyuk Bae, Thai Hong Pham, Huyen Thi La, Yikweon Jang","doi":"","DOIUrl":"","url":null,"abstract":"The cicada species, Hyalessa fuscata and H. maculaticollis(Hemiptera: Cicadidae), share numerous morphological characters, and their status as distinct species remains controversial. We reconstructed a phylogeny based on two new mitogenomes of H. fuscata from Korea and H. maculaticollis from Japan, in combination with GenBank sequences of H. maculaticollis from China and Japan, and other closely related cicada species. Maximum likelihood and Bayesian inference phylogenies showed that H. fuscata from Korea is more closely related to H. maculaticollis from China than either is to H. maculaticollis from Japan. The time-calibrated Bayesian evolutionary analysis by sampling trees (BEAST) phylogeny indicated that the mainland and insular forms diverged approximately 1.7-2.6 million years ago. This coincides with the formation of the East China Sea land bridge between East Asia and the Japanese archipelago, which would provide a dispersal corridor for Hyalessa from the mainland via the Korean peninsula southeastward to Japan. East Asian H. fuscata is a geographic variant that may be considered synonymous with H. maculaticollis.","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"102 ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10643049","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Overexpression of microRNA-130a-3p suppresses glucose lipid levels and oxidative damage in diabetic retinopathy mice via modulating cell division cycle 42. microRNA-130a-3p的过表达通过调节细胞分裂周期42抑制糖尿病视网膜病变小鼠的糖脂水平和氧化损伤。

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2023-01-01

Hui Wang, Xu Dong, Jing Zhou, Caoyu Sun

{"title":"Overexpression of microRNA-130a-3p suppresses glucose lipid levels and oxidative damage in diabetic retinopathy mice via modulating cell division cycle 42.","authors":"Hui Wang, Xu Dong, Jing Zhou, Caoyu Sun","doi":"","DOIUrl":"","url":null,"abstract":"MicroRNA (miR)-130a-3p has been unraveled to exert effects on diabetes. However, the research for probing its role in diabetic retinopathy (DR) is limited. Our study intends to unravel the regulatory effects of miR-130a-3p on DR development via cell division cycle 42 (CDC42). The DR mouse model was established and the serum sample of DR patients was collected. The levels of miR- 130a-3p and CDC42 in DR mice and patients were detected. The nucleic acids modified miR-130a-3p or CDC42 were injected into DR mice to examine the change of glucose lipid levels, visual acuity, oxidative response and the distribution and expression of CDC42 in retinal tissues in DR mice. The target relationship between miR-130a-3p and CDC42 was confirmed. MiR-130a-3p expression was reduced while CDC42 levels were elevated in DR (P<0.05). The upregulation of miR-130a-3p could hinder glucose lipid levels, improve the visual acuity, relieve the oxidative response and decrease CDC42 expression levels in DR mice (P<0.05). The CDC42 elevation reversed the positive effects of upregulated miR-130a-3p on DR progression (P<0.05). MiR-130a-3p targeted CDC42. The elevated miR-130a-3p relieves glucose lipid levels and oxidative damage in DR by modulating CDC42. The study provides novel therapeutic targets for DR treatment.","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"102 ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10670365","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Distinct gene expression patterns of SOX2 and SOX2OT variants in different types of brain tumours. SOX2和SOX2OT变异在不同类型脑肿瘤中的不同基因表达模式

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2023-01-01

Youssef Fouani, Akram Gholipour, Maziar Oveisee, Alireza Shahryari, Hooshang Saberi, Seyed Javad Mowla, Mahshid Malakootian

{"title":"Distinct gene expression patterns of SOX2 and SOX2OT variants in different types of brain tumours.","authors":"Youssef Fouani, Akram Gholipour, Maziar Oveisee, Alireza Shahryari, Hooshang Saberi, Seyed Javad Mowla, Mahshid Malakootian","doi":"","DOIUrl":"","url":null,"abstract":"Numerous investigations have been recently published on the dysregulated expression of long-noncoding RNAs (lncRNAs) in various cancer types, emphasizing that abnormal lncRNA expression is a major contributor to tumourigenesis. A broad spectrum of lncRNAs is expressed in the central nervous system, where these RNAs seem to play key roles in brain development and function. In addition to expressing SOX2, a master regulator of pluripotency that lies within its third intron, lncRNA SOX2OT has a proposed role in regulating neural development. Based on our previous studies, alternative splicing of SOX2OT generates two alternatively spliced variants (SOX2OT-S1 and SOX2OT-S2). The present study investigated the expression patterns of SOX2OT variants and SOX2 in three principal types of brain tumours (gliomas, meningiomas and pituitary adenomas) and in four brain tumour cell lines (U87-MG, 1321N1, A172 and DAOY). Total RNAwas extracted from 34 human brain tumour specimens, and the expression profile of target genes was measured using a real-time reverse transcription PCR approach. Our data revealed distinct expression patterns for SOX2OT variants and SOX2 in the brain tumour samples, indicating their potential involvement in brain tumourigenesis. Moreover, our results highlighted the potential usefulness of SOX2OT-S1, SOX2OT-S2, and SOX2 in molecular diagnosis and brain tumour classification.","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"102 ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9611588","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0