Journal of Genetics最新文献_第3页

A novel partial mRNA-derived duplication of the DMD gene identified in NGS carrier screening. 在NGS携带者筛选中发现的一种新的部分mrna衍生的DMD基因复制。

IF 1.2 4区生物学

Journal of Genetics Pub Date : 2025-01-01

Xue Zhang, Gang Wang, Yuan Wan, Yanling Dong, Daru Lu, Bo Tan

引用次数: 0

Analysis of tandem repeats in seven telomere-to-telomere primate genomes. 7个端粒-端粒灵长类基因组串联重复序列分析。

IF 2.9 4区生物学

Journal of Genetics Pub Date : 2025-01-01

Anukrati Sharma, Divya Tej Sowpati

{"title":"Analysis of tandem repeats in seven telomere-to-telomere primate genomes.","authors":"Anukrati Sharma, Divya Tej Sowpati","doi":"","DOIUrl":"","url":null,"abstract":"Tandem repeats (TRs) are highly polymorphic low complexity regions present in all the genomes. The length variation in TRs, particularly that of short TRs (STRs), is associated with several cellular functions such as gene expression and genome organization. In humans, an abnormal expansion of a few STR loci is linked to neurodegenerative diseases. Despite their importance, limitations and gaps in reference genomes prohibit the comprehensive analysis of TRs. Recent advances in high-throughput sequencing technologies have enabled the generation of gapless, telomere-to-telomere (T2T) genomes of humans and other ape species. Here, we report the TR landscape of seven primate T2T genomes, including humans. Our analysis indicates that TRs of 1-100 nucleotide (nt) motifs cover 3.5-6.9% of large primate genomes, with the highest density observed in gorilla (69 kb per Mbp). Large motif size TRs are prevalent and contribute abundantly to higher-order repeats. As an example, we describe a species-specific 32 nt A/T rich motif that contributes to subtelomeric repeats. Finally, we present the motif decomposition and substructure of pentameric repeats in Y chromosomes of six ape species. Our work illutrates the dynamics of TRs in large genomes, and showcases the utility of complete genomes for better understanding the role of low complexity sequences.","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"104 ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144333254","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

Deletion of RAI1 noncoding exons 1-2 causes Smith-Magenis syndrome. RAI1非编码外显子1-2的缺失导致Smith-Magenis综合征。

IF 2.9 4区生物学

Journal of Genetics Pub Date : 2025-01-01

Uri Hamiel, Alina Kurolap, Chofit Chai Gadot, Adi Mory, Anat Bar Shira, Hagit Baris Feldman, Daphna Marom

{"title":"Deletion of RAI1 noncoding exons 1-2 causes Smith-Magenis syndrome.","authors":"Uri Hamiel, Alina Kurolap, Chofit Chai Gadot, Adi Mory, Anat Bar Shira, Hagit Baris Feldman, Daphna Marom","doi":"","DOIUrl":"","url":null,"abstract":"Smith-Magenis syndrome (SMS) is a complex genetic disorder characterized by developmental delay and a typical behavioral phenotype. Interstitial 17p11.2 deletions, which include the RAI1 gene are detected in >90% of patients, while single nucleotide variants (SNVs) are detected in the rest. The RAI1 gene is encoded from exons 3 onwards, while exons 1-2 are noncoding. It is unclear whether genetic variants preceding exon 3 cause SMS. We evaluated a 15-month-old infant for developmental delay and infantile spasms who was found to carry a deletion encompassing exons 1-2 of RAI. To determine whether the deletion of the noncoding exons 1-2 of the RAI1 gene is associated with SMS and to elucidate the underlying mechanism of this association. A singleton exome-based gene panel was performed, followed by chromosomal-microarray (CMA) to confirm the results. Real time quantitative PCR (RT-qPCR) analysis was conducted to evaluate RAI1 mRNA expression. CMA confirmed a de novo 737.8 kbp deletion on 17p11.2, which includes exons 1-2 of RAI1 but spares exons 3 onwards. RT-qPCR analysis on RNA extracted from the patient, father and three unrelated controls revealed that the patient has RAI1 haploinsufficiency. We show that deletion of the RAI1 noncoding exons 1-2, which spares the gene's coding region, causes RAI1 haploinsufficiency by eliminating regulatory elements, including the gene promoter, thus causing SMS and expanding the mutational spectrum of SMS.","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"104 ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144093894","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

NGLY1-CDDG: report of two cases from India and brief review of literature. NGLY1-CDDG：印度2例病例报告及文献综述。

IF 1.2 4区生物学

Journal of Genetics Pub Date : 2025-01-01

Mihika B Dave, Vrajesh P Udani, Anaita U Hegde, Tester F Ashavaid, Alpa J Dherai

{"title":"NGLY1-CDDG: report of two cases from India and brief review of literature.","authors":"Mihika B Dave, Vrajesh P Udani, Anaita U Hegde, Tester F Ashavaid, Alpa J Dherai","doi":"","DOIUrl":"","url":null,"abstract":"N-glycanase1 (NGLY1) deficiency, an autosomal recessive disorder identified a decade ago, is categorized as a congenital disorder of deglycosylation (CDDG). This disorder arises from bi-allelic variants in the NGLY1 gene, leading to impaired protein deglycosylation. Phenotypically, individuals with NGLY1 deficiency present with intellectual disability, movement disorders, liver dysfunction, muscular hypotonia, etc., termed as NGLY1-CDDG, its diagnosis relies primarily on next generation sequencing (NGS) and till date, it has been diagnosed in over 100 patients. However, there are no previous reports on this from India. We report the first two NGLY1 cases from India in this study. These patients presented with developmental delay, movement disorder, microcephaly, hypotonia and suspicion of congenital disorder of glycosylation (CDG) and were assessed for glycosylation defect using the high pressure liquid chromatography (HPLC) based transferrin isoform analysis and whole exome sequencing (WES). Both patients exhibited a normal transferrin isoform pattern and harboured variants in NGLY1 gene. The variants, NM_018297.4:c.571C[T; p.Gln191Ter and NM_018297.4:c.707G[A; p.Trp236Ter on exons 4 and 5, respectively, identified in our patients are bi-allelic loss of function homozygous variants that have not been previously reported. These variants are inferred as pathogenic in view of genotype-phenotype correlation, parental segregation analysis, in-silico analyses, and absence of other genetic disorders. We have also summarized literature reports on NGLY1-CDDG and compared the phenotype and variants of our patients with the reported cases. These cases contribute to the clinical, biochemical, and molecular understanding of NGLY1 deficiency among Indians, thereby elucidating the presence of NGLY1-CDDG in India.","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"104 ","pages":""},"PeriodicalIF":1.2,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144847117","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 intron variant in the prolactin gene associated with eggshell weight and thickness with putative alternative splicing patterns in chickens 催乳素基因中的一个新型内含子变异与鸡的蛋壳重量和厚度有关，并具有假定的替代剪接模式

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2024-09-14 DOI: 10.1007/s12041-024-01482-w

Dhafer A. Ali, Nihad Abdul-Lateef Ali, Thamer R. S. Aljubouri, Mohammed Baqur S. Al-Shuhaib

{"title":"A novel intron variant in the prolactin gene associated with eggshell weight and thickness with putative alternative splicing patterns in chickens","authors":"Dhafer A. Ali, Nihad Abdul-Lateef Ali, Thamer R. S. Aljubouri, Mohammed Baqur S. Al-Shuhaib","doi":"10.1007/s12041-024-01482-w","DOIUrl":"https://doi.org/10.1007/s12041-024-01482-w","url":null,"abstract":"Raising Iraqi indigenous chickens (IIC) is restricted by their thin and low eggshell weights. Due to the importance of the prolactin (Prl) gene in regulating a wide range of egg production traits, this study assessed the potential genetic polymorphisms associated with Prl that may influence these traits. The polymorphism was examined in three Prl loci of the IIC breed (n = 120) in comparison with the standard Hyline breed (n = 120). The polymorphism of both breeds was associated with eggshell weight and thickness indices for 16 weeks, starting from the 44th to the 59th week. After genotyping three loci within Prl by polymerase chain reaction-single-stranded conformation polymorphism (SSCP) method, only one novel SNP was identified in intron 4, namely 129G > A. The identified intron SNP exerted a significant association with both eggshell thickness and weight indices throughout the investigation period. Birds with GG genotype exhibited higher indices of eggshell thickness and weight than those with the GA and AA genotypes, respectively. The employed in silico tools predicted a remarkable ability for the identified SNP to alter the mRNA splicing pattern, which might be related to altered prolactin activity in birds having an alternative allele A. This study is the first to suggest the significance of this novel intron SNP in assessing eggshell traits in chickens.","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"86 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260527","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

Assessment of the contribution of VDR and VDBP/GC genes in the pathogenesis of celiac disease 评估 VDR 和 VDBP/GC 基因在乳糜泻发病机制中的作用

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2024-09-13 DOI: 10.1007/s12041-024-01480-y

Pratibha Banerjee, Harinder Singh, Priyanka Tiwari, Ajit Sood, Vandana Midha, Gursewak Singh, B K Thelma, Sabyasachi Senapati

{"title":"Assessment of the contribution of VDR and VDBP/GC genes in the pathogenesis of celiac disease","authors":"Pratibha Banerjee, Harinder Singh, Priyanka Tiwari, Ajit Sood, Vandana Midha, Gursewak Singh, B K Thelma, Sabyasachi Senapati","doi":"10.1007/s12041-024-01480-y","DOIUrl":"https://doi.org/10.1007/s12041-024-01480-y","url":null,"abstract":"Vitamin-D deficiency (VDD) is a global health concern. It is known to play a critical role in the immunomodulation, and thus, its metabolism could be investigated to unravel its contribution in common immune-mediated diseases, e.g., celiac disease (CD). Genotyping of SNPs from vitamin D receptor (VDR) gene, such as rs11568820 (Cdx2) and rs2228570 (Fok1) using allele specific multiplex polymerase chain reaction (ASM-PCR) and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) respectively; and rs7041 and rs4588 of vitamin D binding protein (VDBP/GC) using PCR-RFLP were done in 969 subjects including CD cases (n=506) and controls (n=463). Genotype data for 86 CD and 712 controls for rs11568820 and rs7041 were retrieved from already published Immunochip genotype data. Serum concentration of vitamin-D and vitamin D binding protein (VDBP) were measured for 283 participants (98 CD and 185 controls). rs4588-A allele was identified as protective allele [OR=0.6(0.4–0.7), P<0.0001]. Significantly reduced serum level of vitamin-D was observed in CD patients [median=16.25 ng/mL, IQR (8.94–23.60)] than in controls [median=19.94 ng/mL, IQR (13.91–28.46)] with P=0.001. Notably, rs7041-GG, rs4588-CC, and 1F (GC) haplotype of VDBP/GC showed significant association (P<0.05) with reduced serum vitamin D level. We did not find any significant association with VDBP serum concentration. Significant vitamin D and VDBP level correlations were observed in controls (spearman r = 0.3, P=0.005). The present study highlights the significance of reduced vitamin-D serum level in CD. 1F variant of VDBP and lower vitamin-D levels contribute to CD. No correlation between vitamin-D and VDBP levels suggests that vitamin-D supplementation may improve vitamin-D levels but might not affect VDBP levels in CD subjects.","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"42 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142196522","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 PNLDC1 associated with nonobstructive azoospermia 与非梗阻性无精子症相关的 PNLDC1 新型错义变体

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2024-08-20 DOI: 10.1007/s12041-024-01478-6

Mouness Rahimian, Masomeh Askari, Najmeh Salehi, Mojtaba Jaafarinia, Mohsen Forouzanfar, Navid Almadani, Andrea Riccio, Mehdi Totonchi

{"title":"A novel missense variant in PNLDC1 associated with nonobstructive azoospermia","authors":"Mouness Rahimian, Masomeh Askari, Najmeh Salehi, Mojtaba Jaafarinia, Mohsen Forouzanfar, Navid Almadani, Andrea Riccio, Mehdi Totonchi","doi":"10.1007/s12041-024-01478-6","DOIUrl":"https://doi.org/10.1007/s12041-024-01478-6","url":null,"abstract":"The most severe type of male infertility is nonobstructive azoospermia (NOA), where there is no sperm in the ejaculate due to failure of spermatogenesis. The predictable frequency of NOA in the general population is one in 100 men. Genetic studies have recognized dozens of NOA genes. Most NOA aetiologies remain idiopathic. Monogenic mutations can be a reason for a part of idiopathic NOA cases. To address this, we studied the pedigree of a consanguineous family with three NOAs by a family-based exome sequencing. Our goal was to pinpoint the genetic variants responsible for idiopathic NOA to aid future clinical genetic diagnostics and treatment strategies. Bioinformatics analysis followed by Sanger sequencing revealed that NOA patients were homozygous for a rare novel missense variant in PNLDC1 (NM_173516:exon9:c.710G>A;p.Gly237Asp). In silico, single-cell RNA sequencing data analysis and protein modelling demonstrated that PNLDC1, Gly237Asp resided in the conserved region of the CAF1 domain which could lead to local instability in the structure and alteration of protein phosphorylation site. We conclude that the novel missense PNLDC1 variant may affect meiosis and spermatogenesis, leading to NOA and the genetic cause of this idiopathic NOA family. Our result helps genetic counselling for idiopathic NOA cases and provides the occasion for more efficient diagnosis in the clinical setting.","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"25 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142196505","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

miR-7160 inhibits gastric cancer cell proliferation and metastasis by silencing SIX1 miR-7160 通过沉默 SIX1 抑制胃癌细胞增殖和转移

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2024-08-19 DOI: 10.1007/s12041-024-01479-5

Meng Meng, Guoxin Guan, Xingming Liu, Wei Sun, Xinye Cui, Saiya Fu, Fuwen Luo

{"title":"miR-7160 inhibits gastric cancer cell proliferation and metastasis by silencing SIX1","authors":"Meng Meng, Guoxin Guan, Xingming Liu, Wei Sun, Xinye Cui, Saiya Fu, Fuwen Luo","doi":"10.1007/s12041-024-01479-5","DOIUrl":"https://doi.org/10.1007/s12041-024-01479-5","url":null,"abstract":"Upregulation of homeoprotein SIX1 in gastric cancer (GC) is related to tumour proliferation and invasion. MicroRNA-7160 (miR-7160) is a homeoprotein SIX1-targeting miRNA that downregulates miR-7160, leading to cancer development. Total gastric cancer samples were collected from six patients, and relative expression levels of SIX1 mRNA and miRNAs were analysed by qRT-PCR. To evaluate the regulation of SIX1 by miR-7160, pGL3-SIX1-mut, pGL3-SIX1, and miR-7160 mimics transfected into cells using lipofectamine 2000. After transfection, proliferation and apoptosis in cultured cells were assessed using the nuclear TUNEL staining and CCK8 reagent, respectively. We demonstrated that the downregulation of miR-7160 in human gastric cancer cells is related to the upregulation of SIX1 mRNA. In gastric cancer cell lines, miR-7160 overexpression could downregulate the expression and inhibit cancer cell proliferation and growth in vitro. However, overexpression of miR-7160 did not increase gastric cancer cell apoptosis. In vitro downregulation of SIX1 decreased vimentin, N-cadherin, and other EMT-related gene expression and increased E-cadherin expression. In brief, miR-7160, by targeting SIX1, inhibits gastric cancer proliferation and cell growth in vitro, which provides an idea for introducing a new treatment option for gastric cancer.","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"42 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142196506","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

COQ7 splice site variant causing a spastic paraparesis phenotype in siblings COQ7 剪接位点变异导致同胞出现痉挛性截瘫表型

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2024-07-10 DOI: 10.1007/s12041-024-01477-7

Haseena Sait, Manmohan Pandey, Shubha R. Phadke

{"title":"COQ7 splice site variant causing a spastic paraparesis phenotype in siblings","authors":"Haseena Sait, Manmohan Pandey, Shubha R. Phadke","doi":"10.1007/s12041-024-01477-7","DOIUrl":"https://doi.org/10.1007/s12041-024-01477-7","url":null,"abstract":"The COQ7 gene is one of the causative genes for primary COQ10 deficiency-related disorders. OMIM-related phenotypes include severe encephalo-myo-nephrocardiopathy and distal hereditary motor neuronopathy. In the present study, we performed the exome sequencing analysis on the proband of a single family with two siblings affected by hereditary spastic paraparesis (HSP). Segregation analysis was conducted on the affected siblings and parents using the Sanger sequencing. In silico secondary and tertiary pre-mRNA structure analysis and protein modelling were carried out. Exome sequencing identified a homozygous splice site variant in the COQ7 gene (NM_016138.5: c.367+5G>A) in the proband. Sanger sequencing confirmed the homozygous status in the affected sibling and heterozygous status in both parents, consistent with autosomal recessive inheritance. In silico secondary and tertiary premRNA structure analysis and protein modelling predicted the deleterious nature of the variant. This case highlights a distinct intermediate phenotype of COQ7 related disorders comprising early-onset spastic paraparesis due to a novel splice site variant in the COQ7 gene. This expands the spectrum of clinical manifestations associated with COQ7 deficiency and underscores the importance of considering COQ7 gene mutations in the differential diagnosis of HSP.","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"153 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141587456","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

Expanding the genetic and phenotypic spectrum of Baker–Gordon syndrome: a new de novo SYT1 variant 扩展贝克-戈登综合征的遗传和表型谱：一个新的SYT1基因变异体

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2024-07-05 DOI: 10.1007/s12041-024-01476-8

Francisco Javier Cotrina-Vinagre, María Elena Rodríguez-García, Lucía Del Pozo-Filíu, Pilar Quijada-Fraile, Francisco Martínez-Azorín

引用次数: 0