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Immunogenetics Aug 2022Killer immunoglobulin-like receptors (KIR) regulate the function of natural killer cells through interactions with various ligands on the surface of cells, thereby... (Review)
Review
Killer immunoglobulin-like receptors (KIR) regulate the function of natural killer cells through interactions with various ligands on the surface of cells, thereby determining whether natural killer (NK) cells are to be activated or inhibited from killing the cell being interrogated. The genes encoding these proteins display extensive variation through variable gene content, copy number and allele polymorphism. The combination of KIR genes and their ligands is implicated in various clinical settings including haematopoietic stem cell and solid organ transplant and infectious disease progression. The determination of KIR genes has been used as a factor in the selection of optimal stem cell donors with haplotype variations in recipient and donor giving differential clinical outcomes. Methods to determine KIR genes have primarily involved ascertaining the presence or absence of genes in an individual. With the more recent introduction of massively parallel clonal next-generation sequencing and single molecule very long read length third-generation sequencing, high-resolution determination of KIR alleles has become feasible. Determining the extent and functional impact of allele variation has the potential to lead to further optimisation of clinical outcomes as well as a deeper understanding of the functional properties of the receptors and their interactions with ligands. This review summarizes recently published high-resolution KIR genotyping methods and considers the various advantages and disadvantages of the approaches taken. In addition the application of allele level genotyping in the setting of transplantation and infectious disease control is discussed.
Topics: Genotype; Haplotypes; Hematopoietic Stem Cell Transplantation; Humans; Killer Cells, Natural; Ligands; Receptors, KIR
PubMed: 35050404
DOI: 10.1007/s00251-021-01247-0 -
Bioinformatics (Oxford, England) Jan 2023Genotyping by sequencing is a powerful tool for investigating genetic variation in plants, but many economically important plants are allopolyploids, where homoeologous...
MOTIVATION
Genotyping by sequencing is a powerful tool for investigating genetic variation in plants, but many economically important plants are allopolyploids, where homoeologous similarity obscures the subgenomic origin of reads and confounds allelic and homoeologous SNPs. Recent polyploid genotyping methods use allelic frequencies, rate of heterozygosity, parental cross or other information to resolve read assignment, but good subgenomic references offer the most direct information. The typical strategy aligns reads to the joint reference, performs diploid genotyping within each subgenome, and filters the results, but persistent read misassignment results in an excess of false heterozygous calls.
RESULTS
We introduce the Comprehensive Allopolyploid Genotyper (CAPG), which formulates an explicit likelihood to weight read alignments against both subgenomic references and genotype individual allopolyploids from whole-genome resequencing data. We demonstrate CAPG in allotetraploids, where it performs better than Genome Analysis Toolkit's HaplotypeCaller applied to reads aligned to the combined subgenomic references.
AVAILABILITY AND IMPLEMENTATION
Code and tutorials are available at https://github.com/Kkulkarni1/CAPG.git.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
Topics: Genotype; Genotyping Techniques; Sequence Analysis, DNA; Heterozygote; Alleles; Software; High-Throughput Nucleotide Sequencing
PubMed: 36367243
DOI: 10.1093/bioinformatics/btac729 -
Heredity Mar 2021Sexually antagonistic coevolution is predicted to lead to the divergence of male and female genotypes related to the effects of substances transferred by males at mating...
Sexually antagonistic coevolution is predicted to lead to the divergence of male and female genotypes related to the effects of substances transferred by males at mating on female physiology. The outcome of mating should thus depend on the specific combination of mating genotypes. Although mating has been shown to influence female immunity in diverse insect taxa, a male-female genotype-by-genotype effect on female immunity post mating remains largely unexplored. Here, we investigate the effects of mating on female decorated cricket baseline immunity and the potential for a male-genotype-by-female-genotype interaction affecting this response. Females from three distinct genotypic backgrounds were left unmated or singly mated in a fully reciprocal design to males from the same three genotypic backgrounds. Hemocytes and hemocyte microaggregations were quantified for female cellular immunity, and phenoloxidase, involved in melanization, and antibacterial activity for humoral immunity. In this system, female cellular immunity was more reactive to mating, and mating effects were genotype-dependent. Specifically, for hemocytes, a genotype-by-mating status interaction mediated the effect of mating per se, and a significant male-female genotype-by-genotype interaction determined hemocyte depletion post mating. Microaggregations were influenced by the female's genotype or that of her mate. Female humoral immune measures were unaffected, indicating that the propensity for post-mating effects on females is dependent on the component of baseline immunity. The genotype-by-genotype effect on hemocytes supports a role of sexual conflict in post-mating immune suppression, suggesting divergence of male genotypes with respect to modification of female post-mating immunity, and divergence of female genotypes in resistance to these effects.
Topics: Animals; Female; Genotype; Gryllidae; Immunity, Humoral; Male; Reproduction; Sexual Behavior, Animal
PubMed: 33219366
DOI: 10.1038/s41437-020-00384-8 -
Journal of Clinical Microbiology Sep 2021Mycobacterium leprae is the predominant cause of leprosy worldwide, and its genotypes can be classified into four single-nucleotide polymorphism (SNP) types and 16...
Mycobacterium leprae is the predominant cause of leprosy worldwide, and its genotypes can be classified into four single-nucleotide polymorphism (SNP) types and 16 subtypes. Determining M. leprae drug resistance and genotype is typically done by PCR and Sanger DNA sequencing, which require substantial effort. Here, we describe a rapid method involving multiplex PCR in combination with nested amplification and next-generation sequence analysis that allows simultaneous determination of M. leprae drug resistance and SNP genotype directly from clinical specimens. We used this method to analyze clinical samples from two paucibacillary, nine multibacillary, and six type-undetermined leprosy patients. Regions in , , , and that determine drug resistance and those for 84 SNP-InDels in the M. leprae genome were amplified from clinical samples and their sequences determined. The results showed that seven samples were subtype 1A, three were 1D, and seven were 3K. Three samples of the subtype 3K had mutation. The method may allow more rapid genetic analyses of M. leprae in clinical samples.
Topics: Humans; DNA, Bacterial; Drug Resistance, Bacterial; Genotype; Multiplex Polymerase Chain Reaction; Mycobacterium leprae; Sequence Analysis, DNA; Polymorphism, Single Nucleotide
PubMed: 34319800
DOI: 10.1128/JCM.00814-21 -
The Israel Medical Association Journal... Dec 2022APOE genotype strongly affects plasma lipid levels and risk for cardiovascular disease and cognitive decline. Studies of apo-e allelic and APOE genotype frequencies...
BACKGROUND
APOE genotype strongly affects plasma lipid levels and risk for cardiovascular disease and cognitive decline. Studies of apo-e allelic and APOE genotype frequencies among several populations have revealed interesting ethnic variations that might affect cardiovascular morbidity and cognition deterioration.
OBJECTIVES
To evaluate apo-e allelic frequency among Israeli newborns based on known variances in apo-e allelic frequencies in different countries.
METHODS
We examined 498 consecutive neonates born at Tel Aviv Sourasky Medical Center. Umbilical cord blood was sampled for genotyping and lipids. Birth weights were recorded. Demographics and parental risk factors for atherosclerosis were obtained from the mothers.
RESULTS
Most parents were native-born Israelis. Other countries of origin of grandparents were Morocco, Russia, and Iraq. The prevalence of APOE genotypes in Israel is APOE 2/2: 1.4%, APOE 2/3: 8.2%, APOE 3/3: 77.7%, and APOE 4/4: 11.8%. There were no associations of APOE genotype with parental country of origin. However, there was a tendency for APOE 3/4 to be more frequent in newborns of parents of Asian and African origin. Genotype 3/3 was more frequent in newborns whose parents came from Europe and America (78%) compared to those from Asia or Africa (69%).
CONCLUSIONS
It is important to determine risk factors such as APOE genotype for evaluation of premature atherosclerosis. Determining genetic and environmental risk factors may facilitate earlier treatment and prevent heart and brain atherosclerosis. APOE genotypes did not appear to affect total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, or triglyceride levels in newborns.
Topics: Humans; Infant, Newborn; Israel; Lipids; Apolipoproteins E; Genotype; Cholesterol, LDL; Atherosclerosis
PubMed: 36573773
DOI: No ID Found -
Genome Biology Oct 2022Genotyping is a core application of high-throughput sequencing. We present KAGE, a genotyper for SNPs and short indels that is inspired by recent developments within...
Genotyping is a core application of high-throughput sequencing. We present KAGE, a genotyper for SNPs and short indels that is inspired by recent developments within graph-based genome representations and alignment-free methods. KAGE uses a pan-genome representation of the population to efficiently and accurately predict genotypes. Two novel ideas improve both the speed and accuracy: a Bayesian model incorporates genotypes from thousands of individuals to improve prediction accuracy, and a computationally efficient method leverages correlation between variants. We show that the accuracy of KAGE is at par with the best existing alignment-free genotypers, while being an order of magnitude faster.
Topics: Algorithms; Bayes Theorem; Genome, Human; Genotype; Genotyping Techniques; High-Throughput Nucleotide Sequencing; Humans; INDEL Mutation; Polymorphism, Single Nucleotide; Sequence Analysis, DNA
PubMed: 36195962
DOI: 10.1186/s13059-022-02771-2 -
PLoS Computational Biology Aug 2021The killer-cell immunoglobulin-like receptor (KIR) complex on chromosome 19 encodes receptors that modulate the activity of natural killer cells, and variation in these...
The killer-cell immunoglobulin-like receptor (KIR) complex on chromosome 19 encodes receptors that modulate the activity of natural killer cells, and variation in these genes has been linked to infectious and autoimmune disease, as well as having bearing on pregnancy and transplant outcomes. The medical relevance and high variability of KIR genes makes short-read sequencing an attractive technology for interrogating the region, providing a high-throughput, high-fidelity sequencing method that is cost-effective. However, because this gene complex is characterized by extensive nucleotide polymorphism, structural variation including gene fusions and deletions, and a high level of homology between genes, its interrogation at high resolution has been thwarted by bioinformatic challenges, with most studies limited to examining presence or absence of specific genes. Here, we present the PING (Pushing Immunogenetics to the Next Generation) pipeline, which incorporates empirical data, novel alignment strategies and a custom alignment processing workflow to enable high-throughput KIR sequence analysis from short-read data. PING provides KIR gene copy number classification functionality for all KIR genes through use of a comprehensive alignment reference. The gene copy number determined per individual enables an innovative genotype determination workflow using genotype-matched references. Together, these methods address the challenges imposed by the structural complexity and overall homology of the KIR complex. To determine copy number and genotype determination accuracy, we applied PING to European and African validation cohorts and a synthetic dataset. PING demonstrated exceptional copy number determination performance across all datasets and robust genotype determination performance. Finally, an investigation into discordant genotypes for the synthetic dataset provides insight into misaligned reads, advancing our understanding in interpretation of short-read sequencing data in complex genomic regions. PING promises to support a new era of studies of KIR polymorphism, delivering high-resolution KIR genotypes that are highly accurate, enabling high-quality, high-throughput KIR genotyping for disease and population studies.
Topics: Africa, Southern; Alleles; Computational Biology; Computer Simulation; Databases, Nucleic Acid; Europe; Gene Dosage; Genetics, Population; Genotype; High-Throughput Nucleotide Sequencing; Humans; Immunogenetics; Polymorphism, Genetic; Receptors, KIR; Sequence Alignment; Software Design
PubMed: 34339413
DOI: 10.1371/journal.pcbi.1008904 -
PloS One 2018The knowledge of circulating HCV genotypes and subtypes in a country is crucial to guide antiviral therapy and to understand local epidemiology. Studies investigating...
BACKGROUND
The knowledge of circulating HCV genotypes and subtypes in a country is crucial to guide antiviral therapy and to understand local epidemiology. Studies investigating circulating HCV genotypes and their trends have been conducted in Belgium. However they are outdated, lack nationwide representativeness or were not conducted in the general population.
METHODS
In order to determine the distribution of different circulating HCV genotypes in Belgium, we conducted a multicentre study with all the 19 Belgian laboratories performing reimbursed HCV genotyping assays. Available genotype and subtype data were collected for the period from 2008 till 2015. Furthermore, a limited number of other variables were collected: some demographic characteristics from the patients and the laboratory technique used for the determination of the HCV genotype.
RESULTS
For the study period, 11,033 unique records collected by the participating laboratories were used for further investigation. HCV genotype 1 was the most prevalent (53.6%) genotype in Belgium, with G1a and G1b representing 19.7% and 31.6%, respectively. Genotype 3 was the next most prevalent (22.0%). Further, genotype 4, 2, and 5 were responsible for respectively 16.1%, 6.2%, and 1.9% of HCV infections. Genotype 6 and 7 comprise the remaining <1%. Throughout the years, a stable distribution was observed for most genotypes. Only for genotype 5, a decrease as a function of the year of analysis was observed, with respectively 3.6% for 2008, 2.3% for 2009 and 1.6% for the remaining years. The overall M:F ratio was 1.59 and was mainly driven by the high M:F ratio of 3.03 for patients infected with genotype 3. Patients infected with genotype 3 are also younger (mean age 41.7 years) than patients infected with other genotypes (mean age above 50 years for all genotypes). The patients for whom a genotyping assay was performed in 2008 were younger than those from 2015. Geographical distribution demonstrates that an important number of genotyped HCV patients live outside the Belgian metropolitan cities.
CONCLUSION
This national monitoring study allowed a clear and objective view of the circulating HCV genotypes in Belgium and will help health authorities in the establishment of cost effectiveness determinations before implementation of new treatment strategies. This baseline characterization of the circulating genotypes is indispensable for a continuous surveillance, especially for the investigation of the possible impact of migration from endemic regions and prior to the increasing use of highly potent direct-acting antiviral (DAA) agents.
Topics: Adult; Aged; Belgium; Female; Genotype; Hepacivirus; Hepatitis C; Hepatitis C, Chronic; Humans; Male; Middle Aged; Prevalence
PubMed: 30517127
DOI: 10.1371/journal.pone.0207584 -
Journal of Genetics 2022gene, which encodes a-actinin-3 and actin-binding protein, has been found to be associated with strong athletic performance, especially among track and field athletes....
gene, which encodes a-actinin-3 and actin-binding protein, has been found to be associated with strong athletic performance, especially among track and field athletes. Therefore, in this study, our aim was to compare the allelic and genotype frequencies of the ACTN3 R577X variant among elite athletes specialized in different branches, and nonathletic controls in Turkey. In the present study, 316 subjects, including 168 athletes and 148 sedentary controls were genotyped for the R577X variant. Genotyping was conducted by polymerase chain reaction (PCR) method. Additionally, we evaluated the groups by dividing them as females and males. There were 48 females and 120 males in the athletes group, and 43 females and 105 males in the control group. Genetic associations were evaluated by chi-squire test or Fisher's exact test. There was a significant difference between the athletes and controls in terms of the R577X variant. RR and XX genotypes increased in the controls compared to the athletes, while RX genotype was higher in the athletes than the controls ( = 0.030). Then we evaluated the groups by separating them as females and males. Genotype distribution of the R577X differed between the male athletes and the male controls ( = 0.046). R577X RX genotype increased in the male athletes compared to the male control ( = 0.046). But R577X genotype and allele distribution was not significant between female athletes and female control group (>0.05). As far as we know, this study is the largest series examining the R577X variant in Turkish athletes. Our results support that the R577X variant has a heterozygous advantage in athletic performance in the Turkish population. However, epigenetic, gene-gene and gene-environment interactions affects athlete performance should not be forgotten.
Topics: Actinin; Athletes; Athletic Performance; Female; Genotype; Humans; Male; Turkey
PubMed: 35652203
DOI: No ID Found -
Japanese Journal of Infectious Diseases Jan 2022This study assessed the biofilm production ability (BPA) and other microbiological features of Streptococcus canis strains. Forty strains of companion-animal origin,...
This study assessed the biofilm production ability (BPA) and other microbiological features of Streptococcus canis strains. Forty strains of companion-animal origin, including the host information, from 2015 and 2017 were randomly selected, and three strains of blood-origin from two humans and one dog were included. We measured BPA using crystal violet staining, along with S. canis M-like protein (SCM) allele typing, sequence type (ST) determination, antimicrobial resistance (AMR) phenotyping/genotyping, and virulence-associated gene profiling (gbp, ap1, fp1, and brp). BPA measurements revealed 35 strains with BPA and 48 strains without BPA. There was an association between the producer and the isolation year (2017). Moreover, we observed an association between the non-producer and SCM allele 1 and ST9, and between the producer and SCM allele 10 and ST21. Furthermore, we observed a correlation between the producer and the presence of AMR genotypes. Specifically, there was an association between the producer and ap1 detection, and between non-producer and gbp detection. Our results suggest a correlation between biofilm producers and other microbiological features (i.e. isolation year, SCM allele type 10, ST21, presence of AMR genotypes, and ap1 detection).
Topics: Animals; Biofilms; Dogs; Genotype; Streptococcal Infections; Streptococcus
PubMed: 34193659
DOI: 10.7883/yoken.JJID.2020.1086