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1.
Sci Justice ; 64(2): 232-242, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38431380

RESUMO

Items of worn clothing are routinely examined for DNA in forensic casework, commonly with the expectation that at least some of the DNA will come from a wearer of the item, so-called 'wearer DNA'. This study investigated DNA recovered from hooded jumpers that were regularly worn and laundered for four weeks and then subsequently worn by a different individual for four hours. This study also systematically investigated whether using different recovery methods or sampling locations on the jumpers might distinguish between DNA deposited by the regular and most recent wearers of clothing. Four volunteers each wore a new hooded jumper regularly (6 h/day, 2 days/week, washed at weekends) during two 4-week periods. At the end of each month, DNA was first recovered by cutting out and mini-taping the inside left cuff, half-collar, pocket and underarm fabric. The jumpers were then worn by a different individual for four hours, and DNA was again recovered by cutting out and mini-taping, but this time from the inside right cuff, half-collar, pocket and underarm fabric. All DNA samples (n = 128) were quantified and profiled. DNA quantities ranged from 0 to âˆ¼40 ng with an outlier of âˆ¼150 ng, and no significant differences were observed among recovery methods and sampling locations, nor whether one or two wearers had worn the jumpers. However, one volunteer consistently deposited significantly more DNA to their jumpers than two other volunteers, confirming the impact of 'shedder status' on DNA deposition during wearing of clothing. When jumpers were regularly worn by one wearer, the majority (72.7-83.3 %) of the samples for all wearers across both months comprised a major profile of the wearer with a minor profile of non-wearer alleles. When jumpers were then worn by a second wearer, the composition of the profiles obtained were generally reproducible across the recovery methods used, the sampling locations and the two replicates of the experiment for each pairing of wearers. However, profile compositions differed between wearer pairings. Overall, ∼60 % of profiles obtained gave a major profile of the regular wearer, whereas âˆ¼30 % gave a major profile of the second wearer. The remaining profiles comprised other much less frequent observations of single-source profiles of each wearer and equal proportions of DNA from both wearers. Non-wearer DNA was also observed in the majority of samples, both before and after jumpers were worn by a second wearer. For one volunteer's jumpers, a recurring non-wearer DNA profile was observed that could be attributed to their romantic partner, and this DNA persisted on the jumpers even after being worn by the second wearer. This study provides insight on the impact of shedder status, multiple wearers, different recovery methods and sampling locations on the quantities of DNA and compositions of DNA profiles recovered from authentically regularly-worn hooded jumpers. The findings also provide a preliminary dataset that can be used to infer activity level probabilities in casework.


Assuntos
Impressões Digitais de DNA , Manejo de Espécimes , Humanos , Probabilidade , DNA/genética , Alelos
2.
HLA ; 103(3): e15381, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38433615

Assuntos
Alelos , Humanos
3.
HLA ; 103(3): e15378, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38433661

RESUMO

HLA-B*58:01:40 differs from HLA-B*58:01:01 by a single nucleotide change in exon 3, 507 C- > T (codon 145.3 CGC- > CGT).


Assuntos
Povo Asiático , Genes MHC Classe I , Humanos , Alelos , Povo Asiático/genética , Antígenos HLA-B/genética , China
5.
HLA ; 103(3): e15422, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38433656

RESUMO

Characterization of HLA-DQB1*02:02:01:18, -DQB1*02:02:01:19, -DQB1*03:02:01:20 and -DQB1*05:03:01:10 alleles in Spanish individuals.


Assuntos
Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Alelos , Cadeias beta de HLA-DQ/genética , Mutação
6.
HLA ; 103(3): e15425, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38433683

RESUMO

HLA-B*41:02:01:11 and -C*08:266 were detected in a solid organ recipient during the HLA typing process.


Assuntos
Genes MHC Classe I , Genômica , Humanos , Alelos , Antígenos HLA-B/genética , Teste de Histocompatibilidade
7.
HLA ; 103(3): e15423, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38433704

RESUMO

Nucleotide substitutions in codons -1 and 84 of HLA-B*40:01:01 result in a novel allele, HLA-B*40:01:35.


Assuntos
Povo Asiático , Genes MHC Classe I , Humanos , Alelos , Povo Asiático/genética , Antígenos HLA-B/genética , Nucleotídeos
8.
HLA ; 103(3): e15426, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38433707

RESUMO

HLA-A*01:01:01:112 differs from the HLA-A*01:01:01:01 allele by one nucleotide substitution in the 5'UTR.


Assuntos
Medula Óssea , Antígenos HLA-A , Humanos , Alelos , Grécia , Regiões 5' não Traduzidas , Antígenos HLA-A/genética
9.
HLA ; 103(3): e15421, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38433722

RESUMO

Few data exist on the role of genetic factors involving the HLA system on response to Covid-19 vaccines. Moving from suggestions of a previous study investigating the association of some HLA alleles with humoral response to BNT162b2, we here compared the HLA allele frequencies among weak (n = 111) and strong (n = 123) responders, defined as those healthcare workers with the lowest and the highest anti-Spike antibody levels after vaccination. Individuals with clinical history of Covid-19 or positive anti-nucleocapside antibodies were excluded. We found the common HLA-A*03:01 allele as an independent predictor of strong humoral response (OR = 12.46, 95% CI: 4.41-35.21, p < 0.0001), together with younger age of vaccines (p = 0.004). Correlation between antibody levels and protection from breakthrough infection has been observed, with a 2-year cumulative incidence of 42% and 63% among strong and weak responders, respectively (p = 0.03). Due to the high frequency of HLA-A*03:01 and the need for seasonal vaccinations against SARS-CoV-2 mutants, our findings provide useful information about the inter-individual differences observed in humoral response after Covid-19 vaccine and might support further studies on the next seasonal vaccines.


Assuntos
Vacinas contra COVID-19 , COVID-19 , Humanos , Infecções Irruptivas , Alelos , Vacina BNT162 , COVID-19/prevenção & controle , SARS-CoV-2 , Vacinação , Antígenos HLA-A
10.
Sci Adv ; 10(9): eadj9797, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38427739

RESUMO

We used N-ethyl-N-nitrosurea-induced germline mutagenesis combined with automated meiotic mapping to identify specific systolic blood pressure (SBP) and heart rate (HR) determinant loci. We analyzed 43,627 third-generation (G3) mice from 841 pedigrees to assess the effects of 45,378 variant alleles within 15,760 genes, in both heterozygous and homozygous states. We comprehensively tested 23% of all protein-encoding autosomal genes and found 87 SBP and 144 HR (with 7 affecting both) candidates exhibiting detectable hypomorphic characteristics. Unexpectedly, only 18 of the 87 SBP genes were previously known, while 26 of the 144 genes linked to HR were previously identified. Furthermore, we confirmed the influence of two genes on SBP regulation and three genes on HR control through reverse genetics. This underscores the importance of our research in uncovering genes associated with these critical cardiovascular risk factors and illustrate the effectiveness of germline mutagenesis for defining key determinants of polygenic phenotypes that must be studied in an intact organism.


Assuntos
Etilnitrosoureia , Camundongos , Animais , Pressão Sanguínea/genética , Frequência Cardíaca/genética , Mutagênese , Etilnitrosoureia/toxicidade , Alelos
11.
BMC Bioinformatics ; 25(1): 91, 2024 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-38429654

RESUMO

BACKGROUND: Uncovering functional genetic variants from an allele-specific perspective is of paramount importance in advancing our understanding of gene regulation and genetic diseases. Recently, various allele-specific events, such as allele-specific gene expression, allele-specific methylation, and allele-specific binding, have been explored on a genome-wide scale due to the development of high-throughput sequencing methods. RNA secondary structure, which plays a crucial role in multiple RNA-associated processes like RNA modification, translation and splicing, has emerged as an essential focus of relevant research. However, tools to identify genetic variants associated with allele-specific RNA secondary structures are still lacking. RESULTS: Here, we develop a computational tool called 'AStruct' that enables us to detect allele-specific RNA secondary structure (ASRS) from RT-stop based structuromic probing data. AStruct shows robust performance in both simulated datasets and public icSHAPE datasets. We reveal that single nucleotide polymorphisms (SNPs) with higher AStruct scores are enriched in coding regions and tend to be functional. These SNPs are highly conservative, have the potential to disrupt sites involved in m6A modification or protein binding, and are frequently associated with disease. CONCLUSIONS: AStruct is a tool dedicated to invoke allele-specific RNA secondary structure events at heterozygous SNPs in RT-stop based structuromic probing data. It utilizes allelic variants, base pairing and RT-stop information under different cell conditions to detect dynamic and functional ASRS. Compared to sequence-based tools, AStruct considers dynamic cell conditions and outperforms in detecting functional variants. AStruct is implemented in JAVA and is freely accessible at: https://github.com/canceromics/AStruct .


Assuntos
Regulação da Expressão Gênica , RNA , RNA/genética , RNA/química , Alelos , Splicing de RNA , Sequenciamento de Nucleotídeos em Larga Escala/métodos
12.
Biochemistry (Mosc) ; 89(1): 84-96, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-38467547

RESUMO

The review discusses the mechanisms of monoallelic expression, such as genomic imprinting, in which gene transcription depends on the parental origin of the allele, and random monoallelic transcription. Data on the regulation of gene activity in the imprinted regions are summarized with a particular focus on the areas controlling imprinting and factors influencing the variability of the imprintome. The prospects of studies of the monoallelic expression are discussed.


Assuntos
Metilação de DNA , Impressão Genômica , Alelos
13.
Adv Exp Med Biol ; 1444: 237-258, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38467984

RESUMO

Highly polymorphic human leukocyte antigen (HLA) molecules (alleles) expressed by different classical HLA class I and class II genes have crucial roles in the regulation of innate and adaptive immune responses, transplant rejection and in the pathogenesis of numerous infectious and autoimmune diseases. To date, over 35,000 HLA alleles have been published from the IPD-IMGT/HLA database, and specific HLA alleles and HLA haplotypes have been reported to be associated with more than 100 different diseases and phenotypes. Next generation sequencing (NGS) technology developed in recent years has provided breakthroughs in various HLA genomic/gene studies and transplant medicine. In this chapter, we review the current information on the HLA genomic structure and polymorphisms, as well as the genetic context in which numerous disease associations have been identified in this region.


Assuntos
Antígenos HLA , Antígenos de Histocompatibilidade Classe I , Humanos , Antígenos de Histocompatibilidade Classe I/genética , Antígenos HLA/genética , Polimorfismo Genético , Antígenos de Histocompatibilidade Classe II/genética , Haplótipos , Alelos
14.
Clin Lab ; 70(3)2024 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-38469779

RESUMO

BACKGROUND: Rh(D) phenotype in a sample from a 19-year-old female patient showed weak positivity (1+). A follow-up sample was requested to further define the Rh(D) phenotype, her Rh(D) phenotype was tested by using another reagent, Rh(D) phenotype still showed weak reactivity (1+), RhCcEe phenotype was Ccee. METHODS: Seven samples from the family members of the proposita were received. The RhDCcEe phenotypes were typed by the microcolumn gel card and the unexpected antibodies were assayed by indirect anti-human globulin test (IAT). Genomic DNA was extracted from the blood sample and the novel RHD1058G>C allele was detected through an established sequence-specific primer PCR (PCR-SSP), RHD exons 1 - 10 were sequenced afterward by exon-specific amplification. The distribution of RHD1058G>C allele and RHD weak positive phenotype were investigated in the pedigrees. RESULTS: The unexpected antibodies all were negative in the family members. The novel RHD1058G>C allele was found in the proposita, her father, and grandfather. Five family members were detected serologically with the common Rh(D)-positive phenotypes either as homozygote of RHD/RHD or heterozygote of RHD/RHd. Two family members were detected as weak D phenotypes in accordance with the genotyping results by PCR-SSP, and both of them have a D1058Ce haplotype and a dce haplotype. One member, her father, was tested common Rh(D)-positive with D1058Ce haplotype and a Dce haplotype. CONCLUSIONS: These data allow us to describe the characteristics of the weak D phenotype with a novel c.RHD-1058G>C allele, which may be partial D and increase the risk of RHD alloantibody. The novel RHD1058G>C allele was inherited in three generations in a family rather than spontaneous mutation in an individual.


Assuntos
Povo Asiático , Antígenos de Grupos Sanguíneos , Humanos , Feminino , Adulto Jovem , Adulto , Alelos , Genótipo , Fenótipo , Povo Asiático/genética , China , Sistema do Grupo Sanguíneo Rh-Hr/genética
15.
Clin Lab ; 70(3)2024 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-38469785

RESUMO

BACKGROUND: The aim was to analyze the serological and molecular genetic characteristics of a rare B(A) subtype pedigree, explore its pathogenesis, and discuss transfusion strategies. METHODS: ABO blood typing serological tests were conducted on a female subject and her family member using standard serological methods. Sequencing analysis of the ABO gene exons 6 and 7 was performed using PCR technique for the female subject and her family member to examine the blood types of the participants. RESULTS: The serological test results showed a discrepancy between the forward and reverse typings of the female subject. The forward typing was similar to that of AB subtype serological forward typing, while the reverse typing indicated AB blood type. Based on the sequencing results, it is inferred that the female subject and her son have 8 mutations on one BA.02 chain: 297A>G, 526C>G, 657C>T, 700C>G, 703G>A, 796C>A, 803G>C, and 930G>A. Comparing these eight mutation sites with the Blood Group Antigen Gene Mutation Database (BGMUT), it was found that the female subject had a heterozygous mutation at c.700C>G in the 7th exon of the B.01 gene, consistent with the characteristics of the BA.02 allele. The genotype of the female subject was determined as A1.02/ BA.02, while the genotype of her son was determined as O.01.01/BA.02. CONCLUSIONS: The serological presentation of the B(A) subtype for the female subject reported in this study was unique. It differed from previously reported cases, indicating that the determination of B(A) subtypes cannot solely rely on serological testing. It requires a comprehensive analysis combining the results of genetic testing and pedigree investigation.


Assuntos
Sistema ABO de Grupos Sanguíneos , Transfusão de Sangue , Humanos , Feminino , Sistema ABO de Grupos Sanguíneos/genética , Genótipo , Heterozigoto , Mutação , Alelos , Fenótipo
16.
HLA ; 103(3): e15432, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38470345

RESUMO

HLA-C*06:372 differs from HLA-C*06:02:01:01 by a single substitution in exon 4.


Assuntos
Etnicidade , Antígenos HLA-C , Humanos , Antígenos HLA-C/genética , Alelos , Genes MHC Classe I , Células-Tronco
17.
HLA ; 103(3): e15436, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38470352

RESUMO

HLA-B*40:06:01:18 differs from HLA-B*40:06:01:02 by one nucleotide change in the 5'UTR (T > C).


Assuntos
Povo Asiático , Genes MHC Classe I , Humanos , Alelos , Regiões 5' não Traduzidas , Antígenos HLA-B/genética
18.
Proc Biol Sci ; 291(2018): 20232816, 2024 Mar 13.
Artigo em Inglês | MEDLINE | ID: mdl-38471544

RESUMO

Beneficial reversals of dominance reduce the costs of genetic trade-offs and can enable selection to maintain genetic variation for fitness. Beneficial dominance reversals are characterized by the beneficial allele for a given context (e.g. habitat, developmental stage, trait or sex) being dominant in that context but recessive where deleterious. This context dependence at least partially mitigates the fitness consequence of heterozygotes carrying one non-beneficial allele for their context and can result in balancing selection that maintains alternative alleles. Dominance reversals are theoretically plausible and are supported by mounting empirical evidence. Here, we highlight the importance of beneficial dominance reversals as a mechanism for the mitigation of genetic conflict and review the theory and empirical evidence for them. We identify some areas in need of further research and development and outline three methods that could facilitate the identification of antagonistic genetic variation (dominance ordination, allele-specific expression and allele-specific ATAC-Seq (assay for transposase-accessible chromatin with sequencing)). There is ample scope for the development of new empirical methods as well as reanalysis of existing data through the lens of dominance reversals. A greater focus on this topic will expand our understanding of the mechanisms that resolve genetic conflict and whether they maintain genetic variation.


Assuntos
Variação Genética , Seleção Genética , Fenótipo , Heterozigoto , Alelos , Modelos Genéticos , Aptidão Genética
19.
Theor Appl Genet ; 137(3): 64, 2024 Mar 02.
Artigo em Inglês | MEDLINE | ID: mdl-38430392

RESUMO

KEY MESSAGE: An improved estimator of genomic relatedness using low-depth high-throughput sequencing data for autopolyploids is developed. Its outputs strongly correlate with SNP array-based estimates and are available in the package GUSrelate. High-throughput sequencing (HTS) methods have reduced sequencing costs and resources compared to array-based tools, facilitating the investigation of many non-model polyploid species. One important quantity that can be computed from HTS data is the genetic relatedness between all individuals in a population. However, HTS data are often messy, with multiple sources of errors (i.e. sequencing errors or missing parental alleles) which, if not accounted for, can lead to bias in genomic relatedness estimates. We derive a new estimator for constructing a genomic relationship matrix (GRM) from HTS data for autopolyploid species that accounts for errors associated with low sequencing depths, implemented in the R package GUSrelate. Simulations revealed that GUSrelate performed similarly to existing GRM methods at high depth but reduced bias in self-relatedness estimates when the sequencing depth was low. Using a panel consisting of 351 tetraploid potato genotypes, we found that GUSrelate produced GRMs from genotyping-by-sequencing (GBS) data that were highly correlated with a GRM computed from SNP array data, and less biased than existing methods when benchmarking against the array-based GRM estimates. GUSrelate provides researchers with a tool to reliably construct GRMs from low-depth HTS data.


Assuntos
Técnicas de Genotipagem , Polimorfismo de Nucleotídeo Único , Humanos , Técnicas de Genotipagem/métodos , Análise de Sequência de DNA/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Alelos
20.
Theor Appl Genet ; 137(4): 81, 2024 Mar 13.
Artigo em Inglês | MEDLINE | ID: mdl-38478168

RESUMO

KEY MESSAGE: Six QTLs of resistance to sugarcane orange rust were identified in modern interspecific hybrids by GWAS. For five of them, the resistance alleles originated from S. spontaneum. Altogether, they efficiently predict disease resistance. Sugarcane orange rust (SOR) is a threatening emerging disease in many sugarcane industries worldwide. Improving the genetic resistance of commercial cultivars remains the most promising solution to control this disease. In this study, an association panel of 568 modern interspecific sugarcane hybrids (Saccharum officinarum x S. spontaneum) from Réunion's breeding program was evaluated for its resistance to SOR under natural conditions of infection. Two genome-wide association studies (GWAS) were conducted between disease reactions and 183,842 single nucleotide polymorphism (SNP) markers obtained by targeted genotyping-by-sequencing. Five resistance quantitative trait loci (QTLs), named Oru1, Oru2, Oru3, Oru4 and Oru5, were identified using a single-locus GWAS (SL-GWAS). These five QTLs all originated from the species S. spontaneum. A multi-locus GWAS (ML-GWAS) uncovered an additional but less significant resistance QTL named Oru6, which originated from S. officinarum. All six QTLs had a moderate to major phenotypic effect on disease resistance. Prediction accuracy estimated with linear regression models based on each of the five QTLs identified by SL-GWAS was between 0.16-0.41. Altogether, these five QTLs provided a relatively high prediction accuracy of 0.60. In comparison, accuracies obtained with six genome-wide prediction models (i.e., GBLUP, Bayes-A, Bayes-B, Bayes-C, Bayesian Lasso and RKHS) reached only 0.65. The good prediction accuracy of disease resistance provided by the QTLs and the predominant S. spontaneum origin of their resistance alleles pave the way for effective marker-assisted breeding strategies.


Assuntos
Saccharum , Saccharum/genética , Estudo de Associação Genômica Ampla , Teorema de Bayes , Alelos , Resistência à Doença/genética , Melhoramento Vegetal
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