Journal of Genetics最新文献

{"title":"Expanding the genetic and phenotypic spectrum of Baker–Gordon syndrome: a new de novo SYT1 variant","authors":"Francisco Javier Cotrina-Vinagre, María Elena Rodríguez-García, Lucía Del Pozo-Filíu, Pilar Quijada-Fraile, Francisco Martínez-Azorín","doi":"10.1007/s12041-024-01476-8","DOIUrl":"https://doi.org/10.1007/s12041-024-01476-8","url":null,"abstract":"<p>We report the case of a Spanish pediatric patient with developmental delay, hypotonia, feeding difficulties, visual problems, and hyperkinetic movements. Whole-exome sequencing uncovered a new heterozygous <i>de novo</i> Synaptotagmin 1 (<i>SYT1</i>) missense variant, NM_005639.3:c.930T&gt;A (p.Asp310Glu), in a female proband. This gene encodes the synaptotagmin-1 (SYT1) protein, which is a component of a protein complex involved in the fusion of synaptic vesicles with the presynaptic membrane. Pathogenic <i>SYT1</i> variants have been associated with Baker–Gordon syndrome (BAGOS), an autosomal dominant neurodevelopmental disorder. Although up to 30 cases have been identified worldwide, to the best of our knowledge, this is the first patient described with mitochondrial respiratory chain deficiencies and rod–cone dysfunction. In conclusion, our data expand both the genetic and phenotypic spectrum associated with <i>SYT1</i> variants.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"4 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141546691","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}

{"title":"Detection of caudal type homeobox 1 (CDX1) gene methylated DNA, as a stool-based diagnostic biomarker in colorectal cancer","authors":"Sarina Almasi, Lida Haghnazari, Seyedeh Ozra Hosseini, Nayebali Rezvani","doi":"10.1007/s12041-024-01473-x","DOIUrl":"https://doi.org/10.1007/s12041-024-01473-x","url":null,"abstract":"<p>Colorectal cancer (CRC) is known to develop due to the accumulation of both genetic and epigenetic alterations, resulting in the conversion of intestinal epithelial cells to malignant adenocarcinoma cells. Caudal type homeobox 1 (<i>CDX1</i>) gene is a homeobox transcription factor and a selective tumour suppressor gene that is an important factor for the development of intestinal cells. This gene plays a role in the differentiation of intestinal epithelial cells, and its expression decreases in a number of cell lines derived from CRC, which suggests that a lack of <i>CDX1</i> expression is a risk factor for the development of colorectal carcinoma. Therefore, the methylated DNA amounts of <i>CDX1</i> gene in stool samples were investigated as a noninvasive method for the detection of CRC. In the present study, the methylation of <i>CDX1</i> gene promoter region was assessed in stool samples of 50 CRC patients and 50 healthy individuals by MethyLight PCR using two primers and a Taq Man probe, which was completely specifically designed for fully methylated DNA of the gene promoter region. The percentage of methylated reference (PMR) of the studied gene in all samples was calculated similarly to previous studies. Statistical analysis was performed using SPSS 16. The PMR medians were 3.25 (95% CI: 0.1–100) and 0.1 (95% CI: 0.07–1) in the stool samples of CRC patients and healthy individuals, respectively. The results showed a significant difference in <i>CDX1</i> gene PMR between stool samples of CRC patients and controls (<i>P</i>-value &lt;0.001). According to the results of this study, it can be argued that measurement of <i>CDX1</i> gene DNA in stool samples using the MethyLight PCR has acceptable sensitivity and specificity, and is adequately potential to be used as a noninvasive complementary method for the diagnosis of CRC, along with colonoscopy as the gold standard to this end. This study is the first report on <i>CDX1</i> methylation in stool samples of CRC patients. Therefore, further research should be carried out with a larger sample size to evaluate its efficacy as a diagnostic biomarker in clinical laboratories.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"31 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141511349","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}

{"title":"Association of polymorphisms of HSD11B1 and ACE genes with trachoma disease","authors":"LAURA L. VALDEZ-VELAZQUEZ, HÉCTOR OCHOA-DÍAZ-LÓPEZ, IVÁN DELGADO-ENCISO, HÉCTOR RANGEL-VILLALOBOS, IRÁM P. RODRÍGUEZ-SÁNCHEZ, ROSARIO GARCÍA-MIRANDA, DOIREYNER DANIEL VELÁZQUEZ-RAMÍREZ, NANCY A. REYES-MÉNDEZ, CARLOS EDUARDO BARAJAS-SAUCEDO, MARGARITA L. MARTÍNEZ-FIERRO","doi":"10.1007/s12041-024-01474-w","DOIUrl":"https://doi.org/10.1007/s12041-024-01474-w","url":null,"abstract":"<p>Trachoma, caused by <i>Chlamydia trachomatis</i>, is the most common infectious blindness in the world and is present in indigenous Mayan from Chiapas (Mexico). Inflammatory genes are activated when suffering from trachoma, thus some polymorphisms could increase the susceptibility to develop irreversible blindness. This study aimed to evaluate the genetic risk of developing late-stage trachoma in Mayan ethnic groups. In a case–control study (<i>n</i> = 51 vs <i>n</i> = 102, respectively), the following single-nucleotide polymorphisms (SNPs) in genes related to inflammation were analysed: <i>HSD11B1</i> (rs11807619), <i>HSD11B1</i> (rs932335), ABCG2 (rs2231142), SLCO1B1 (rs4149056), IL-10 (rs1800890), TNF (rs1800629), MMP2 (rs243865) and <i>ACE</i>. Three SNPs were associated with late-stage trachoma risk: (i) the T allele of rs11807619, (ii) the C allele of rs932335, which are linked to the <i>HSD11B1</i> gene (OR = 22.5–27.3), particularly in men when adjusts for gender (OR = 16–16.7); and (iii) D allele of rs4340 in the <i>ACE</i> gene (OR = 5.2–5.3). In fact, significant linkage disequilibrium demonstrated association between <i>ACE</i> gene and <i>HSD11B1</i> SNPs (r = 0.17–0.179; <i>P</i> = 0.0048–0.0073). Two SNPs <i>HSD11B1</i> gene (<i>P</i> = 0.013 vs 0.0039) and <i>HSD11B1</i>–<i>ACE</i> haplotypes showed association with late-stage trachoma in Mayan ethnic groups.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"42 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141530271","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}

{"title":"Special clinical entity with 15q26 deletion: a novel case report","authors":"Wei-Liang Liu, Fang Li, Lu Liu, Rong Ai","doi":"10.1007/s12041-024-01468-8","DOIUrl":"https://doi.org/10.1007/s12041-024-01468-8","url":null,"abstract":"<p>In the past, there were no easily distinct and recognizable features as a guide for precise clinical and genetic diagnosis of cases with chromosome microdeletions involving 15q26 including <i>CHD2</i>. The present study analysed the clinical data and collected venous blood samples from a pediatric patient and his healthy family members for DNA testing. The whole-exome sequencing was performed by the next-generation sequencing (NGS). Chromosomal copy-number variations were tested based on NGS. We present a review of all cases with chromosome microdeletions affecting <i>CHD2</i>. A novel <i>de novo</i> 5.82-Mb deletion at 15q25.3-15q26.1 including <i>CHD2</i> was identified in our patient who is an 11.6-year-old boy. We first found surprising efficacy of lamotrigine in controlling intractable drop seizures in the individual. These cases have development delay, behavioural problems, epilepsy, variable multiple anomalies, etc. Phenotypes of individuals with deletions involving 15q26 including <i>CHD2</i> are highly variable with regard to facial features and multiple developmental anomalies. We first found the special clinical entity of development delay, behavioural problems, epilepsy, variable skeletal and muscular anomalies, abnormalities of variable multiple systems and characteristic craniofacial phenotypes in patients with chromosome microdeletions involving <i>CHD2</i>. The larger deletions involving 15q26 including <i>CHD2</i> tend to cause the classical phenotype. A distinctive craniofacial appearance of the classical phenotype is midface hypoplasia and perifacial protrusion.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"21 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141166152","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}

{"title":"Extraction of genomic DNA for sequencing from snail Helix lucorum","authors":"Dmitry Panteleev, Anastasia Sadova, Galina Pavlova","doi":"10.1007/s12041-024-01472-y","DOIUrl":"https://doi.org/10.1007/s12041-024-01472-y","url":null,"abstract":"<p>Genomic studies make it possible to breakthrough in many fields such as biochemistry, physiology, phylogenetics, etc., though they are unworkable without sequences of genomic DNA of an organism. The terrestrial mollusks’ genomes would benefit gastropod biology investigations, that are unavailable so far due to problems in DNA integrity and quality after the isolation procedures. Here we describe a fast and handy protocol for genomic DNA extraction from the tissues of <i>Helix lucorum,</i> which allows to yield high-quality samples applicable for downstream analysis such as high-throughput DNA sequencing. Troubleshooting revealed the nuclease activity of snail tissue lysate, which may be avoided by heating the lysate and decreasing the incubation time.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"57 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141061784","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}

{"title":"Mitogenome features and phylogenetic analysis of red algae, Grateloupia cornea (Rhodophyta, Halymeniales)","authors":"Maheshkumar Prakash Patil, Young-Ryun Kim, Shinya Nakashita, Jong-Oh Kim, Kyunghoi Kim","doi":"10.1007/s12041-024-01471-z","DOIUrl":"https://doi.org/10.1007/s12041-024-01471-z","url":null,"abstract":"<p>The mitogenome is an important tool for taxonomic and evolutionary investigation. Here, a few complete mitogenomes of red algae have been reported. We have reported the complete mitogenome sequences of <i>Grateloupia cornea</i> Okamura, 1913 (Rhodophyta, Halymeniales). The genome is 30,595 bp in circumference, and has a strongly biased [AT] = 66.9%. Like most other <i>Grateloupia</i> species, it has a group II intron in the <i>cox1</i> gene. Maximum likelihood and maximum parsimony analyses showed that <i>G. cornea</i> is more closely related to <i>G. asiatica</i>. This shows that the group II intron in the <i>cox1</i> ORF present in most species of <i>Grateloupia</i> was present in their common ancestor, and uniquely lost in <i>G. asiatica</i>. The seven <i>Grateloupia</i> species with known mitogenome sequences remain monophyletic, with the genus <i>Polyopes</i> as sister taxon. The complete mitochondrial genome data will be valuable for future research on comparative mitochondrial genome analysis, an extensive understanding of gene content and organization, evolution of the <i>cox1</i> intron in Rhodophyta as well as phylogenetic analysis.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"29 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141061738","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}

{"title":"The first complete mitochondrial genome of the critically endangered Malaysian giant turtle, Orlitia borneensis (Testudines: Geoemydidae)","authors":"Mohd Hairul Mohd Salleh, Yuzine Esa","doi":"10.1007/s12041-024-01469-7","DOIUrl":"https://doi.org/10.1007/s12041-024-01469-7","url":null,"abstract":"<p>We present here the complete mitochondrial sequence of the critically endangered Malaysian giant turtle, <i>Orlitia borneensis</i>. The assembled mitochondrial genome includes 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes (rRNAs), and one control region. This mitochondrial genome has been archived in the NCBI GenBank with accession number OQ808845. The <i>Batagur</i> control region is relatively smaller than <i>O. borneensis</i> and closer to <i>Aldabrachelys gigantea</i>, which suggests potentially that <i>O. borneensis</i> has undergone an expansion in the control region.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"162 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140889897","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}

{"title":"Genetic characterization and linkage analysis of spotted leaf 6, liguleless and lax panicle traits in mutant rice","authors":"Mohammad Nurul Matin, Kyung Eun Lee, Sang Gu Kang","doi":"10.1007/s12041-024-01466-w","DOIUrl":"https://doi.org/10.1007/s12041-024-01466-w","url":null,"abstract":"<p>Phenotypic mutants are valuable resources for elucidating the function of genes responsible for their expression. This study examined mutant rice strains expressing three traits: spotted leaf 6 (<i>spl6</i>), lax panicle (<i>lax</i>), and liguleless (<i>lg</i>). In the mutant, the <i>spl6</i> phenotype was a genetically programmed lesion-mimicking mutation (LMM) that displayed spontaneously scattered spots across the leaf surface. In the <i>lg</i> trait, the plant lacked a collar region, and there were no auricles and ligules at the junction of the leaf blade and leaf sheath. The <i>lax</i> panicle trait manifested as sparely arranged spikelets resulting from the terminal spikelet with no lateral spikelets, which caused a drastic reduction of the total seed number in the mutant. All three mutant genes were genetically recessive and had nuclear gene regulation. The dihybrid segregation of the <i>lg</i> gene was classified independently according to the Mendelian 9:3:3:1 dihybrid segregation ratio in the F₂ generation, suggesting that the <i>lg</i> gene is not linked to the same chromosome as the <i>lax</i> and <i>spl6</i> genes. On the other hand, <i>spl6</i> and <i>lax</i> were not assorted independently, indicating that they are closely linked on chromosome 1 in rice. Additional linkage analysis from the recombination of <i>spl6</i> and <i>lax</i> genes reconfirmed that the two genes were ~9.4 cM away from each other. The individual single-gene mutant plant from one plant with a three-gene mutation (<i>spl6, lax</i>, and <i>lg</i>) was isolated and characterized, which will be a crucial resource for the gene cloning and molecular characterization of these genes.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"12 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140608763","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}

{"title":"Foetal haemoglobin elevation, unfavourable prognosis, and protective role of genetic variants HBG2 rs7482144, HBS1L-MYB rs9399137 and BCL11A rs4671393 in children with ALL","authors":"FRANCISCO JAVIER BORRAYO-LÓPEZ, BERTHA IBARRA-CORTÉS, FRANCISCO JAVIER PEREA-DÍAZ, ABRIL IXCHEL MUÑOZ-ZÚÑIGA, HÉCTOR MONTOYA-FUENTES, JANETH MARGARITA SOTO-PADILLA, LOURDES DEL CARMEN RIZO-DE LA TORRE","doi":"10.1007/s12041-024-01470-0","DOIUrl":"https://doi.org/10.1007/s12041-024-01470-0","url":null,"abstract":"<p>In acute lymphoblastic leukaemia (ALL), elevated foetal haemoglobin (HbF) levels have been associated with the prognosis of patients. Genetic variants in HbF regulatory genes: BAF chromatin remodelling complex subunit (<i>BCL11A</i>), HBS1L-MYB transcriptional GTPase intergenic region (<i>HBS1L-MYB</i>), Krüppel-like factor 1 (<i>KLF1</i>), haemoglobin gamma subunit 2 (<i>HBG2</i>), haemoglobin gamma subunit 1 (<i>HBG1</i>), and haemoglobin subunit beta pseudogene 1 (<i>HBBP1</i>) are often associated with elevated HbF concentration. This study investigated the association of genetic variants in HbF regulatory genes with HbF concentration, unfavourable prognosis, and outcome in children with ALL. We quantified HbF concentration and genotyped 17 genetic variants in 48 patients with ALL and 64 children without ALL as a reference group. HbF concentration was higher in patients than in the reference group (4.4% vs 1.4%), and 75% (<i>n</i> = 36) of the patients had HbF &gt; 2.5%. Unfavourable prognosis ALL was established in 68.8% (<i>n</i> = 33) of the patients. Variant <i>HBG2</i> rs7482144 was associated with high HbF concentration (<i>P</i> = 0.015); while <i>HBS1L</i>-<i>MYB</i> rs9399137 (<i>P</i> = 0.001), <i>HBG2</i> rs7482144 (<i>P</i> = 0.001) and the β-globin genes <i>HBG2</i>, <i>HBG1</i>, and <i>HBPP1</i> haplotype TGC (<i>P</i> = 0.017) with unfavourable prognosis ALL. Additionally, variant <i>BCL11A</i> rs4671393 showed a protective role (<i>P</i> = 0.0001). In conclusion, variants <i>HBG2</i> rs7482144, <i>HBS1L</i>-<i>MYB</i> rs9399137 and <i>BCL11A</i> rs4671393 may play a significant role in ALL.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"29 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140608701","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}

{"title":"Reflections on assortative mating, social stratification, and genetics","authors":"Oliver Mayo, Vidyanand Nanjundiah","doi":"10.1007/s12041-024-01467-9","DOIUrl":"https://doi.org/10.1007/s12041-024-01467-9","url":null,"abstract":"<p>A recent report by G. Clark points to a sustained persistence of social status in England that extends vertically across several generations and horizontally across many levels of kinship. We seek to put his findings in historical perspective. We do so by relating them to two lines of thinking related to biological inheritance. One predated the rediscovery of Mendel’s work and led to the field of quantitative genetics, which dealt on the whole with quasi-continuously varying traits. The other is based on the rediscovery itself and led to a reconciliation between quantitative genetics and discrete Mendelian elements of heredity. Both were enmeshed with the supposed need for, and societal consequences of, eugenics and assortative mating. Also on both issues, the significant ideas can be traced to R. A. Fisher, inspired in one case by F. Galton and in the other by J. A. Cobb, with strong support for Galton and Cobb coming from Karl Pearson. Clark’s findings point to societal stratification, and assortative mating for wealth is a straightforward hypothesis to account for it. However, it should be noted that the findings support, but do not prove, the hypothesis.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"2 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140563334","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}