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1.
Leg Med (Tokyo) ; 54: 102008, 2022 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-34974234

RESUMEN

Although silent alleles in D19S433 typing using the GlobalFiler PCR Amplification Kit have been reported, the exact frequency of the D19S433 silent alleles in population data of 1501 Japanese individuals, which are widely used for the assessment of Japanese STR typing results, is unclear. In this study, we examined the exact D19S433 silent allele frequency in this population data. We newly observed the G32A variant causing silent alleles at D19S433 in five samples. Combining them with data including 30 samples with the variant reported previously, we determined that the total frequency of the silent alleles (i.e. the frequency of the G32A variant) in the 1501 Japanese samples was 0.0117 (35/3002). Using the D19S433 allele frequency data, we evaluated the effect of presence/absence information for the D19S433 silent allele on kinship tests. Likelihood ratios (LRs) were calculated for both simulated parent-child and full sibling cases, revealing that the LR may change by approximately 10-2 to 103 fold when the presence/absence of the D19S433 silent allele is revealed in a kinship test. Therefore, if a sufficiently large or small LR is obtained, there is little need to determine the presence/absence of the D19S433 silent allele in Japanese kinship tests using GlobalFiler. This study will be beneficial for the assessment of Japanese human identification and kinship test results using GlobalFiler.


Asunto(s)
Dermatoglifia del ADN , Antropología Forense , Alelos , Frecuencia de los Genes , Humanos , Japón , Repeticiones de Microsatélite , Reacción en Cadena de la Polimerasa
2.
BMC Genomics ; 23(1): 10, 2022 Jan 07.
Artículo en Inglés | MEDLINE | ID: mdl-34991484

RESUMEN

Extreme complexity in the Human Leukocyte Antigens (HLA) system and its nomenclature makes it difficult to interpret and integrate relevant information for HLA associations with diseases, Adverse Drug Reactions (ADR) and Transplantation. PubMed search displays ~ 146,000 studies on HLA reported from diverse locations. Currently, IPD-IMGT/HLA (Robinson et al., Nucleic Acids Research 48:D948-D955, 2019) database houses data on 28,320 HLA alleles. We developed an automated pipeline with a unified graphical user interface HLA-SPREAD that provides a structured information on SNPs, Populations, REsources, ADRs and Diseases information. Information on HLA was extracted from ~ 28 million PubMed abstracts extracted using Natural Language Processing (NLP). Python scripts were used to mine and curate information on diseases, filter false positives and categorize to 24 tree hierarchical groups and named Entity Recognition (NER) algorithms followed by semantic analysis to infer HLA association(s). This resource from 109 countries and 40 ethnic groups provides interesting insights on: markers associated with allelic/haplotypic association in autoimmune, cancer, viral and skin diseases, transplantation outcome and ADRs for hypersensitivity. Summary information on clinically relevant biomarkers related to HLA disease associations with mapped susceptible/risk alleles are readily retrievable from HLASPREAD. The resource is available at URL http://hla-spread.igib.res.in/ . This resource is first of its kind that can help uncover novel patterns in HLA gene-disease associations.


Asunto(s)
Antígenos HLA , Procesamiento de Lenguaje Natural , Alelos , Bases de Datos Factuales , Antígenos HLA/genética , Humanos , PubMed
3.
Trop Anim Health Prod ; 54(1): 50, 2022 Jan 12.
Artículo en Inglés | MEDLINE | ID: mdl-35022894

RESUMEN

The Bos indicus zebu cattle Butana is the most commonly used indigenous dairy cattle breed in Sudan. In the last years, high-yielding Holstein dairy cattle were introgressed into Butana cattle to improve their milk yield and simultaneously keep their good adaption to extreme environmental conditions. With the focus on the improvement of milk production, other problems arose such as an increased susceptibility to mastitis. Thus, genetic selection for mastitis resistance should be considered to maintain healthy and productive cows. In this study, we tested 10 single nucleotide polymorphisms (SNPs) which had been associated with somatic cell score (SCS) in Holstein cattle for association with SCS in 37 purebred Butana and 203 Butana × Holstein crossbred cattle from Sudan. Animals were genotyped by competitive allele-specific PCR assays and association analysis was performed using a linear mixed model. All 10 SNPs were segregating in the crossbred Butana × Holstein populations, but only 8 SNPs in Sudanese purebred Butana cattle. The SNP on chromosome 13 was suggestively associated with SCS in the Butana × Holstein crossbred population (rs109441194, 13:79,365,467, PBF = 0.054) and the SNP on chromosome 19 was significantly associated with SCS in both populations (rs41257403, 19:50,027,458, Butana: PBF = 0.003, Butana × Holstein: PBF = 6.2 × 10-16). The minor allele of both SNPs showed an increase in SCS. Therefore, selection against the disadvantageous minor allele could be used for genetic improvement of mastitis resistance in the studied populations. However, investigations in a bigger population and across the whole genome are needed to identify additional genomic loci.


Asunto(s)
Leche , Polimorfismo de Nucleótido Simple , Alelos , Animales , Bovinos/genética , Femenino , Genómica , Genotipo
4.
Methods Mol Biol ; 2392: 35-51, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-34773613

RESUMEN

Single-nucleotide variations have been associated to various genetic diseases, variations on drug efficiency, and differences in cancer prognostics. The detection of these changes in nucleic acid sequences from patient samples is particularly useful for accurate diagnosis, therapeutics, and disease management. A reliable allele-specific amplification is still an important challenge for molecular-based diagnostic technologies. In the last years, allele-specific primers have been designed for promoting the enrichment of certain variants, based on a higher stability of primer/template duplexes. Also, several methods are based on the addition of a blocking oligonucleotide that prevent the amplification of a specific variant, enabling that other DNA variants can be observed. In this context, genotyping methods based on isothermal amplification techniques are increasing, especially those assays aimed to be deployed at point-of-care applications. The correct selection of target sequences is crucial for reaching the required analytical performances, in terms of reaction time, amplification yield, and selectivity. The present chapter describes the design criteria for the selection of primers and blockers for relevant PCR approaches and novel isothermal strategies. Several successful examples are provided in order to highlight the main design restrictions and the potential to be extended to other applications.


Asunto(s)
Reacción en Cadena de la Polimerasa , Alelos , ADN , Humanos , Oligonucleótidos/genética
5.
Ann Lab Med ; 42(1): 54-62, 2022 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-34374349

RESUMEN

Background: Associations between IgA nephropathy (IgAN) and HLA-DRB1 and -DQB1 alleles have been reported in several ethnic groups. We investigated the association of HLA-DRB1 and -DQB1 alleles with the predisposition for IgAN and disease progression to end-stage kidney disease (ESKD) in Korean patients. Methods: We analyzed HLA-DRB1 and -DQB1 genotypes in 399 IgAN patients between January 2000 and January 2019 using a LIFECODES sequence-specific oligonucleotide (SSO) typing kit (Immucor, Stamford, CT, USA) or a LABType SSO Typing Test (One Lambda, Canoga Park, CA, USA). Alleles with a significant difference in two-digit resolution were further analyzed using in-house sequence-based typing and sequence-specific primer PCR. As controls, 613 healthy hematopoietic stem cell donors were included. Kidney survival was analyzed in 281 IgAN patients with available clinical and laboratory data using Cox regression analysis. Where needed, P-values were adjusted using Bonferroni correction. Results: The allele frequencies of HLA-DRB1*04:05 (corrected P [Pc]<0.001), -DQB1 *04:01 (Pc=0.048), and -DQB1*03:02 (Pc=0.021) were significantly higher in IgAN patients than in controls, whereas those of HLA-DRB1*07:01, -DRB1*15:01, -DQB1*02:02, and -DQB1*06:02 (Pc<0.001 for all) were significantly lower in IgAN patients than in controls. The allele frequency of HLA-DQB1*05:03 (Pc=0.016) was significantly lower in the ESKD group than in the non-ESKD group; however, there was no significant difference for ESKD progression between these groups. Conclusions: We report novel associations of HLA-DRB1*15:01, DQB1*02:02, -DQB1*03:02, and -DQB1*04:01 with IgAN. Further studies of HLA alleles associated with IgAN progression in a larger cohort and in various ethnic groups are needed.


Asunto(s)
Glomerulonefritis por IGA , Alelos , Predisposición Genética a la Enfermedad , Glomerulonefritis por IGA/diagnóstico , Glomerulonefritis por IGA/genética , Cadenas HLA-DRB1/genética , Prueba de Histocompatibilidad , Humanos , República de Corea
6.
Anal Biochem ; 637: 114476, 2022 01 15.
Artículo en Inglés | MEDLINE | ID: mdl-34800430

RESUMEN

T790 M point mutations in EGFR exon 20 are regarded as the most common cause of resistance to epidermal growth factor receptor tyrosine kinase inhibitor treatment. In this study, a PCR-based lateral flow assay (PCR-LFA) was developed to detect T790 M mutations in human genomic DNA. Detection sensitivity was determined using DNA at different mutant to wild-type ratios. The limit of detection of mutant alleles was 15 copies per reaction. The sensitivity of detection of these mutations in 40 formalin-fixed paraffin-embedded tissue biopsies from non-small cell lung cancer patients was analyzed using PCR-LFA and amplification refractory mutation system (ARMS) PCR. Our assay provided the same information as ARMS PCR for 95% (38/40) of the samples. T790 M mutations were detected in 15 (37.5%) and 13 samples using our assay and ARMS PCR, respectively. Droplet digital PCR confirmed the presence of T790 M mutations in the two discordant samples. These results indicate that PCR-LFA is more sensitive than ARMS PCR for clinical screening of these mutations.


Asunto(s)
Carcinoma de Pulmón de Células no Pequeñas/genética , Receptores ErbB/genética , Neoplasias Pulmonares/genética , Mutación Puntual , Reacción en Cadena de la Polimerasa/métodos , Alelos , Biopsia/métodos , Carcinoma de Pulmón de Células no Pequeñas/patología , ADN de Neoplasias/genética , Resistencia a Antineoplásicos/efectos de los fármacos , Exones/genética , Humanos , Límite de Detección , Neoplasias Pulmonares/patología , Inhibidores de Proteínas Quinasas/farmacología , Sensibilidad y Especificidad
7.
Methods Mol Biol ; 2403: 91-106, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-34913119

RESUMEN

Danio rerio (zebrafish), traditionally used in forward genetic screens, has in the last decade become a popular model for reverse genetic studies with the introduction of TALENS, zinc finger nucleases, and CRISPR/Cas9. Unexpectedly, homozygous frameshift mutations generated by these tools frequently result in phenotypes that are less penetrant than those seen in embryos injected with antisense morpholino oligonucleotides targeting the same gene. One explanation for the difference is that some frameshift mutations result in nonsense-mediated decay of the gene transcript, a process which can induce expression of homologous genes. This form of genetic compensation, called transcriptional adaptation, does not occur when the mutant allele results in no RNA transcripts being produced from the targeted gene. Such RNA-less mutants can be generated by deleting a gene's promoter using a pair of guide RNAs and Cas9 protein. Here, we present a protocol and use it to generate alleles of arhgap29b and slc41a1 that lack detectable zygotic transcription. In the case of the arhgap29b mutant, an emerging phenotype did not segregate with the promoter deletion mutation, highlighting the potential for off-target mutagenesis with these tools. In summary, this chapter describes a method to generate zebrafish mutants that avoid a form of genetic compensation that occurs in many frameshift mutants.


Asunto(s)
Pez Cebra , Alelos , Animales , Sistemas CRISPR-Cas/genética , Proteínas de Transporte de Catión , ARN , ARN Guia/genética , Pez Cebra/genética , Proteínas de Pez Cebra/genética
8.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 39(1): 89-93, 2022 Jan 10.
Artículo en Chino | MEDLINE | ID: mdl-34964976

RESUMEN

OBJECTIVE: To explore the genetic basis for an individual with a para-Bombay phenotype. METHODS: A proband with mismatched forward and reverse serotypes for the ABO blood group was identified. Weakly expressed ABH blood type antigen on the surface of red blood cells was verified by absorption and release test, and the blood group substances in saliva was detected by sialic acid test. Exons 6 and 7 of the ABO gene and exons of the FUT1 and FUT2 genes were subjected to direct sequencing. RESULTS: The proband was found to be of O type by forward ABO serotyping and AB type by reverse ABO serotyping, though H and substance A and B were detected in her saliva. DNA sequencing revealed that she has harbored c.35C/T, c.328G/A, and c.504delC compound heterozygous variants of the FUT1 gene. Haploid analysis showed that her FUT1 genotype was h328A/h35T+504delC, which has been uploaded to the NCBI website (No. MW323551). CONCLUSION: The para-Bombay phenotype of the proband may be attributed to the novel compound heterozygous variants including c.504delC of the FUT1 gene, which may affect its function by altering the activity of FUT1 glycotransferase.


Asunto(s)
Sistema del Grupo Sanguíneo ABO , Fucosiltransferasas , Sistema del Grupo Sanguíneo ABO/genética , Alelos , China , Femenino , Fucosiltransferasas/genética , Genotipo , Humanos , Fenotipo
9.
Gene ; 808: 145965, 2022 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-34530083

RESUMEN

Bovine leukocyte antigen, class II, DO beta (BoLA-DOB) is related to antigen presentation, which can triggered by multicul factors. And the condition of immune function determines how much cattle load to heat stress. To evaluate the relationship between heat-resistance and single nucleotide polymorphisms (SNPs) in BoLA-DOB gene, our study has taken further analysis in Chinese indigenous cattle for the first time. A missense single nucleotide polymorphism (rs464874590) was detected in BoLA-DOB gene. We directly sequenced rs464874590 (NM_001013600.1 g.7122762 A > G) in BoLA-DOB gene of 522 individuals of 26 cattle breeds. The frequency of allele G gradually decreases from south to north with distinct climatic distribution characteristics. Further association analysis was carried out between different genotypes and environmental parameters, including annual mean temperature (T), relative humidity (RH), and temperature-humidity index (THI). The result showed that three genotypes were significantly correlated with T, H, and THI (P < 0.01), indicating that GG genotype was distributed in areas with hot and moist conditions. Therefore, our results suggested that the rs464874590 could be applied as a genetic marker to detect the heat-resistance of Chinese indigenous cattle.


Asunto(s)
Respuesta al Choque Térmico/genética , Antígenos de Histocompatibilidad Clase II/genética , Alelos , Animales , Bovinos , China , Frecuencia de los Genes/genética , Estudios de Asociación Genética , Genotipo , Respuesta al Choque Térmico/fisiología , Antígenos de Histocompatibilidad Clase II/inmunología , Humedad , Polimorfismo de Nucleótido Simple/genética , Temperatura
10.
Gene ; 808: 145967, 2022 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-34530085

RESUMEN

Glycogenosis type II (GSDII), or Pompe disease (MIM 232300), is an inherited autosomal recessive disorder caused by deficiency of the lysosomal acid-α-glucosidase. Mutations in the GAA gene alter normal enzyme production and lead to progressive buildup of intralysosomal glycogen, which plays an essential role in the severity and progression of the disease. We report here the study of 76 patients from Spain with either infantile or late onset form of Pompe disease. The analysis consisted in the molecular study of exons and intron flanking fragments of GAA gene. We have identified 55 different molecular pathogenic variants, 12 of them not previously described. In addition, we have determined a frequency of 84.37% for the c.-32-13T>G mutation in patients with the late-onset form of the disease. Functional characterization of some splice mutations showed deleterious mechanisms on the processing of mRNA.


Asunto(s)
Enfermedad del Almacenamiento de Glucógeno Tipo II/genética , alfa-Glucosidasas/genética , Alelos , Exones/genética , Femenino , Frecuencia de los Genes/genética , Predisposición Genética a la Enfermedad , Pruebas Genéticas , Genotipo , Glucógeno/metabolismo , Enfermedad del Almacenamiento de Glucógeno Tipo II/metabolismo , Humanos , Intrones/genética , Masculino , Mutación , Polimorfismo de Nucleótido Simple/genética , Empalme del ARN/genética , España/epidemiología , alfa-Glucosidasas/metabolismo
11.
Gene ; 808: 145970, 2022 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-34547372

RESUMEN

Small mother against decapentaplegic (SMAD) family member 3 (SMAD3) is well correlated with the inflammatory response of chronic obstructive pulmonary disease (COPD). A previous study indicated that the single nucleotide polymorphism (SNP) rs36221701 of SMAD3 was related to the risk of inflammatory disease. Hence, given the pathogenesis of COPD is intently associated with smoking and gene polymorphism, this study aims to analyze the relationship between SMAD3 rs36221701 and COPD susceptibility, and to explore whether the interaction is related to smoking status. We studied the association between the rs36221701 and rs34307601 of SMAD3 and COPD susceptibility, a total of 541 COPD patients and 534 controls of the Uyghur population were recruited at the First People's Hospital and the village of Kashi. The interrelation of the two SNPs with the risk of COPD was determined by calculating odds ratio (OR) and 95% confidence interval (95% CI). We found a significant association between the rs36221701 and COPD risk in the non-smoking population. TC genotype showed a significant decreased association with COPD risk (OR = 0.59, 95% CI = 0.41-0.83, P < 0.05), but CC genotype can increased the COPD risk (OR > 1, P < 0.05). In addition, COPD susceptibility was not related to the genetic variations in the rs34307601 (P > 0.05). In conclusion, we confirmed that the SMAD3 rs36221701 may be associated with COPD susceptibility in the Chinese Uyghur population, especially among non-smokers. Our data provide new light for the relationship between SMAD3 gene polymorphisms and COPD susceptibility in the Chinese Uyghur population.


Asunto(s)
Enfermedad Pulmonar Obstructiva Crónica/genética , Proteína smad3/genética , Anciano , Alelos , Estudios de Casos y Controles , China/epidemiología , Fumar Cigarrillos/efectos adversos , Fumar Cigarrillos/genética , Femenino , Frecuencia de los Genes/genética , Estudios de Asociación Genética , Predisposición Genética a la Enfermedad/genética , Genotipo , Humanos , Masculino , Persona de Mediana Edad , Oportunidad Relativa , Polimorfismo de Nucleótido Simple/genética , Enfermedad Pulmonar Obstructiva Crónica/fisiopatología , Proteína smad3/metabolismo
12.
Gene ; 808: 145989, 2022 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-34624458

RESUMEN

SERPINB5 is a mammary serine protease inhibitor, which is involved in various cellular functions. The aberrant expression of SERPINB5 is reported in many cancers along with GBC but limited information is available about its role in genetic predisposition for GBC. We carried out case-control study in 206 cases and 219 controls. Promoter SNPs were genotyped by Sanger's sequencing. In-silico promoter analysis and luciferase reporter assay were done to elucidate the role of promoter variants in regulation of SERPINB5 expression. Out of four SNPs, three SERPINB5 promoter variants showed association with GBC in different models. The 'C' allele of variant rs17071138 was found to be significantly associated with GBC (p = 0.017). The 'T' allele of rs3744940 significantly increased the risk for GBC in dominant (p = 0.035) and additive models (p = 0.005). Also, rs3744941 'T' allele increased the risk for GBC by dominant (p = 0.042) as well as additive models (p = 0.016). In-silico promoter analysis and luciferase reporter assay revealed the probable regulatory role of the SERPINB5 promoter variant rs17071138 on the expression. Overall, our study reveals the genetic association of SERPINB5 promoter variants with GBC and possible role of rs17071138 in the regulation of expression.


Asunto(s)
Neoplasias de la Vesícula Biliar/genética , Regulación de la Expresión Génica/genética , Serpinas/genética , Adulto , Alelos , Estudios de Casos y Controles , Femenino , Neoplasias de la Vesícula Biliar/metabolismo , Neoplasias de la Vesícula Biliar/fisiopatología , Expresión Génica/genética , Frecuencia de los Genes/genética , Predisposición Genética a la Enfermedad/genética , Genotipo , Haplotipos/genética , Humanos , India , Desequilibrio de Ligamiento , Masculino , Persona de Mediana Edad , Polimorfismo de Nucleótido Simple/genética , Regiones Promotoras Genéticas/genética , Secuencias Reguladoras de Ácidos Nucleicos/genética , Serpinas/fisiología
13.
J Theor Biol ; 533: 110956, 2022 01 21.
Artículo en Inglés | MEDLINE | ID: mdl-34736949

RESUMEN

Frequencies of deleterious mutations are higher than expected in many plants. Here, by developing a two-locus two-allele model, I examine the effects of differential timing of the expression of deleterious mutations (two-stage effects) on the maintenance of mutations. I assume early- and late-acting loci to distinguish whether maintenance of mutations in populations with high selfing rates is explained better by two-stage effects of single mutations, or by separate mutations in both early- and late-acting loci. I found that, when ovules are overproduced, the stable frequency of early-acting mutations is higher if mutations also occur in a late-acting locus than if a late-acting mutation is lacking. The stable frequency of late-acting mutations is higher if mutations also occur in an early-acting locus than if an early-acting mutation is lacking. Selective interference does not account for these results because analyses in which the number of loci subject to mutations is equalized are included. Overproduction of ovules has little effect on maintenance if either early- or late-acting mutations are lacking, whereas when ovules are not overproduced, the two-stage effect does not enhance the maintenance of mutations. Hence, mutations occurring in both loci coupled with overproduction of ovules enhances the maintenance of mutations in populations with high selfing rates. The detailed mechanisms underlying the two-stage effect were also analyzed.


Asunto(s)
Endogamia , Selección Genética , Alelos , Modelos Genéticos , Mutación
14.
Methods Mol Biol ; 2392: 17-33, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-34773612

RESUMEN

Classical restriction fragment length polymorphism (RFLP) and sequencing are labor-intensive and expensive methods to study single base changes, whereas polymerase chain reaction amplification of specific alleles (PASA) or allele-specific polymerase chain reaction (ASPCR) is a PCR-based application that allows direct detection of any point mutation by analyzing the PCR products in an ethidium bromide-stained agarose or polyacrylamide gel. PASA is based on oligonucleotide primers containing one or more 3' mismatch with the target DNA making it refractory to primer extension by Thermus aquaticus DNA polymerase lacking the 3' to 5' exonuclease proofreading activity because of which it is also called amplification refractory mutation system-PCR (ARMS-PCR). This technique has found application in detection of allele, mutation, single-nucleotide polymorphisms (SNPs) causing genetic and infectious diseases. This chapter describes an approach of cohort PASA in context of genotyping single and double mutant worms generated to study the process of cell migration and axon outgrowth in C. elegans. Single worm-based cohort PASA allows genotyping for identification of single base mutations; particularly it is convenient method to detect mutations without a visible phenotype.


Asunto(s)
Caenorhabditis elegans , Polimorfismo de Nucleótido Simple , Alelos , Animales , Caenorhabditis elegans/genética , Genotipo , Reacción en Cadena de la Polimerasa , Polimorfismo de Longitud del Fragmento de Restricción , Polimerasa Taq , Thermus
15.
Ann Lab Med ; 42(2): 274-277, 2022 Mar 01.
Artículo en Inglés | MEDLINE | ID: mdl-34635619

RESUMEN

Spinocerebellar ataxia type 1 (SCA1) is an autosomal dominant disease caused by abnormal CAG repeat expansion in the ataxin 1 gene (ATXN1). The presence of CAT interruption(s) is important for diagnosing SCA1 in patients with 39-44 repeat alleles, as only uninterrupted alleles are considered abnormal. Determining the CAT interruption status might also be important for patients with >44 repeats, as the length of the longest uninterrupted CAG repeat stretch has been correlated with age at SCA1 onset. We detected CAT interruption(s) in the archived samples of Korean SCA1 patients using a traditional restriction enzyme method and validated the usefulness of a fluorescence-based tethering PCR procedure. Among the 2,312 alleles analyzed from 1,156 patients, we found 17 expanded alleles with ≥39 repeats, 71% of which harbored 39-44 repeats. Restriction enzyme method of six samples (four with 39-44 repeats and two with >44 repeats) revealed that none of the expanded alleles had CAT interruption(s). Tethering PCR showed the characteristic electropherogram pattern expected without CAT interruption(s). Along with the enzyme restriction method, tethering PCR can be applied to determine the number of allele repeats and provide information on CAT interruption(s) in clinical laboratories.


Asunto(s)
Ataxina-1 , Ataxias Espinocerebelosas , Degeneraciones Espinocerebelosas , Alelos , Ataxina-1/genética , Humanos , Reacción en Cadena de la Polimerasa , República de Corea , Ataxias Espinocerebelosas/diagnóstico , Ataxias Espinocerebelosas/genética , Degeneraciones Espinocerebelosas/genética
16.
Food Chem ; 369: 130887, 2022 Feb 01.
Artículo en Inglés | MEDLINE | ID: mdl-34461519

RESUMEN

Rapid deterioration of rice bran due to the LOX3 enzyme catalysed oxidation of PUFA is the major bottleneck for its utilization in various downstream applications. In the present study, we have identified a set of nine novel LOX3-null rice accessions carrying a deletion of C residue in the exon2 causing a frameshift mutation resulting in a truncated non-functional LOX3 protein. Our study, further manifested the predominance of C deletion based LOX3-null allele, named lox3-b, in the aromatic rice germplasm particularly in the Indian Basmati rice group. The LOX3-null genotypes exhibited significantly reduced rancidity, after six months of storage. They also showed significantly lower percentage reduction of linoleic acid (LA), higher γ-oryzanol content and lower hexanal content. A functional dCAPS marker designed based on the deletion polymorphism clearly differentiated LOX3 and lox3-b alleles, and has the potential application in marker assisted rice breeding programmes to develop cultivars with better bran storability.


Asunto(s)
Oryza , Alelos , Genotipo , Lipooxigenasas , Oryza/genética , Fitomejoramiento , Proteínas de Plantas , Polimorfismo Genético
17.
Gene ; 807: 145933, 2022 Jan 10.
Artículo en Inglés | MEDLINE | ID: mdl-34464678

RESUMEN

BACKGROUND: Cervical-cancer is among the most commonly diagnosed cancers in women, and infection with human papillomavirus (HPV) is associated with an increased risk of cervical cancer and altered serum concentrations of inflammatory cytokines. We have explored the association between a genetic variation in the Interleukin-10 (IL-10) gene (rs1800896) and cervical cancer risk and its relationship with tissue Interferon gamma (IFN-γ), Transforming growth factor beta (TGF-ß), Tumor necrosis factor alpha (TNF-α) concentrations in women with cervical cancer. METHODS: A total of 315 women with, or without cervical cancer, were recruited into the study. DNA was extracted from cervical cells, and genotyping was undertaken using Taq-man real-time PCR. The genotype frequency and allele distribution were analyzed together with their association with pathological data. The association of the rs1800896 gene variation with tissue levels of the inflammatory cytokines was also investigated. RESULTS: Our data showed a significant association between the A allele of the rs1800896 gene variant and the presence of cervical cancer. In particular, patients with AG/AA genotypes had an increased risk of cervical cancer with an odds ratio of 1.929 (95% confidence interval [CI]: 0.879-4.23, P < 0.001) in a recessive model, compared with the GG genotype. Also, the tissue concentrations of IFN-γ, TGF-ß, and TNF-α in cervical tissues were significantly higher in women with cervical cancer (P < 0.001) and were associated with the AA genotype. CONCLUSION: We have found an association between the polymorphism rs1800896 in the IL-10 gene and an increased risk of cervical cancer as well as a higher level of tissue inflammatory cytokines. Further investigations are necessary on the value of emerging biomarkers for the risk stratification for the management of cervical cancer patients.


Asunto(s)
Interleucina-10/genética , Neoplasias del Cuello Uterino/genética , Adulto , Alelos , Alphapapillomavirus/genética , Alphapapillomavirus/patogenicidad , Citocinas , Femenino , Frecuencia de los Genes/genética , Genotipo , Humanos , Inflamación , Interferón gamma , Interleucina-10/metabolismo , Persona de Mediana Edad , Oportunidad Relativa , Papillomaviridae/genética , Papillomaviridae/patogenicidad , Polimorfismo de Nucleótido Simple/genética , Reacción en Cadena en Tiempo Real de la Polimerasa , Factores de Riesgo , Factor de Crecimiento Transformador beta/metabolismo , Factor de Necrosis Tumoral alfa/metabolismo
18.
Gene ; 807: 145950, 2022 Jan 10.
Artículo en Inglés | MEDLINE | ID: mdl-34481003

RESUMEN

This population-based longitudinal study is the first investigation that assesses the association of common MC4R SNPs with the obesity-related parameters over time and determines the effect of risk alleles during the three adulthood life periods (early, middle, and late) in a large Iranian cohort, a population with a unique genetic make-up that has been understudied and relatively unexplored. We obtained the genotype of 5370 unrelated adults who participated in the ongoing Tehran Cardiometabolic Genetic Study (TCGS) cohort project for the common MC4R SNPs. Linear regression and linear mixed model analyses were performed to examine the effect of MC4R polymorphisms on maximum BMI and other obesity-related factors over time. We recognized that several SNPs associated with the maximum BMI and the increased BMI, waist circumference, and waist-hip ratio across Iranian adults over a lifetime. Interestingly, we found that rs9954571-A has a yet unreported protective role against obesity-related factors, including BMI, waist circumference, waist-hip ratio, and triglyceride level. Additionally, a survey of the impact of the MC4R risk score throughout the adulthood life periods indicated that the MC4R risk score is influenced both the elevated BMI and waist circumference only during the early adulthood period. Our findings can expand our knowledge about the MC4R genetic variant's contributions to adulthood obesity and highlight the importance of evaluating the genetic components affecting obesity over a lifetime, which could be considered for obesity clinical screening and treatment.


Asunto(s)
Obesidad/genética , Receptor de Melanocortina Tipo 4/genética , Adulto , Alelos , Índice de Masa Corporal , Estudios de Cohortes , Femenino , Frecuencia de los Genes/genética , Predisposición Genética a la Enfermedad/genética , Genotipo , Humanos , Irán/epidemiología , Estudios Longitudinales , Masculino , Tamizaje Masivo/métodos , Persona de Mediana Edad , Obesidad/metabolismo , Fenotipo , Polimorfismo de Nucleótido Simple/genética , Receptor de Melanocortina Tipo 4/metabolismo , Factores de Riesgo , Circunferencia de la Cintura/genética , Relación Cintura-Cadera/métodos
19.
Gene ; 807: 145951, 2022 Jan 10.
Artículo en Inglés | MEDLINE | ID: mdl-34500051

RESUMEN

AIMS: The purpose of the present study was to analyze the role of selected polymorphisms of SIRT3 and SIRT5 in gastric carcinogenesis. METHODS: For this study, 500 blood samples of GC patients and 500 blood samples of healthy individuals were collected. Six selected polymorphisms of mitochondrial sirtuins were analyzed for analysis using Tetra-Arms PCR followed by DNA sequencing. RESULTS: Mutant allele frequencies of selected polymorphisms [rs3782116 (p < 0.0001), rs6598072 (p < 0.0001) and rs11246020 (p < 0.0001), rs938222 (p = 0.0136), rs3757261 (p = 0.0005) and rs2841511 (p = 0.0015)] were observed significant higher in GC patients vs controls. Haplotype analysis was performed, and 51 haplotypes were generated using haploview software. Among these haplotypes, eleven haplotypes were found associated with a significantly increased risk of GC. Furthermore, SNP-SNP interaction showed a significant correlation between studied SNPs and GC risk. Kaplan Meier analysis showed that mutant allele frequencies of selected polymorphisms are linked with a significant decrease in survival of GC patients CONCLUSIONS: It can be concluded that selected SNPs may be associated with enhanced risk of GC and hence can be potential prognostic markers for prognosis and predisposition of GC.


Asunto(s)
Sirtuina 3/genética , Sirtuinas/genética , Neoplasias Gástricas/genética , Alelos , Estudios de Casos y Controles , China/epidemiología , Femenino , Frecuencia de los Genes/genética , Predisposición Genética a la Enfermedad/genética , Variación Genética/genética , Genotipo , Haplotipos , Humanos , Masculino , Persona de Mediana Edad , Mitocondrias/genética , Polimorfismo de Nucleótido Simple/genética , Pronóstico , Estudios Retrospectivos , Factores de Riesgo , Sirtuina 3/sangre , Sirtuina 3/metabolismo , Sirtuinas/sangre , Sirtuinas/metabolismo
20.
Food Chem ; 371: 131205, 2022 Mar 01.
Artículo en Inglés | MEDLINE | ID: mdl-34598118

RESUMEN

Near-isogenic lines Nip(Wxb/SSIj), Nip(Wxb/SSIi), Nip(wx/SSIj) and Nip(wx/SSIi) in the japonica rice Nipponbare (Nip) background containing allelic variation in the starch synthase gene SSI and Wx were investigated for cooked rice grain quality, starch morphology, pasting profiles, fine structure and crystallinity characteristics. Rice grains carrying the SSIi allele had poor cooked rice taste in the Wxb background. The introduction of SSIi caused reduced cooked rice grain elongation, especially in the wx background. Starch granule size was reduced in SSIi rice and the viscosity of flour and starch prepared from SSIi rice was markedly increased. Moreover, analysis of the starch molecular structure revealed a remarkable increase in the short amylopectin chains and reduced starch relative crystallinity compared with SSIj rice, which resulted in decreased gelatinization characteristics. These results suggest that SSI allelic variation has multiple effects on rice grain quality, as well as starch fine structure.


Asunto(s)
Oryza , Almidón Sintasa , Alelos , Oryza/genética , Proteínas de Plantas/genética , Almidón , Almidón Sintasa/genética
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