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Background Objective Methods Results Conclusions Commercial genome‐wide genotyping arrays have historically neglected coverage of genetic variation across populations.We aimed to create a multi‐ancestry genome‐wide array that would include a wide range of neuro‐specific genetic content to facilitate genetic research in neurological disorders across multiple ancestral groups, fostering diversity and inclusivity in research studies.We developed the Illumina NeuroBooster Array (NBA), a custom high‐throughput and cost‐effective platform on a backbone of 1,914,934 variants from the Infinium Global Diversity Array and added custom content comprising 95,273 variants associated with more than 70 neurological conditions or traits, and we further tested its performance on more than 2000 patient samples. This novel platform includes approximately 10,000 tagging variants to facilitate imputation and analyses of neurodegenerative disease–related genome‐wide association study loci across diverse populations.In this article, we describe NBA's potential as an efficient means for researchers to assess known and novel disease genetic associations in a multi‐ancestry framework. The NBA can identify rare genetic variants and accurately impute more than 15 million common variants across populations. Apart from enabling sample prioritization for further whole‐genome sequencing studies, we envisage that NBA will play a pivotal role in recruitment for interventional studies in the precision medicine space.From a broader perspective, the NBA serves as a promising means to foster collaborative research endeavors in the field of neurological disorders worldwide. Ultimately, this carefully designed tool is poised to make a substantial contribution to uncovering the genetic etiology underlying these debilitating conditions. © 2024 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA. [ABSTRACT FROM AUTHOR]

Genomic selection is widely implemented in livestock breeding programmes across species. Its potential is also evident for sheep breeding; however, it has several limitations, particularly because of the high genetic diversity across and within sheep breeds. In Germany, the predominant sheep breed is the Merino sheep. Until now, there has been no use of genomic selection in the German Merino sheep breeding programme. In this simulation study, different genomic selection strategies were compared with a reference scenario with a breeding value estimation based on pedigree BLUP. A simplified version of the German Merino sheep breeding programme, including a health and a production trait in the breeding goal, was simulated via the R package Modular Breeding Program Simulator (MoBPS). Real genotype data were used to create a population specific simulation. The reference scenario was compared with several alternative scenarios in which selection was based on single‐step GBLUP (ssGBLUP) breeding value estimation with varying genotyping strategies. In addition to scenarios in which all male and all male plus all female lambs were genotyped, scenarios with a preselection of lambs, that is only a certain proportion (top 25%, top 50%) genotyped, were simulated. The results revealed that genetic gain increased with increasing numbers of available genotypes. However, marginal gains decreased with increasing numbers of genotypes. Compared with the reference scenario, genotyping the top 25% of male lambs increased the genetic gain for the breeding ram population by 13% for both traits whereas genotyping the top 50% of male lambs or all male lambs led to increases of 18% (17%) or 26% (21%) for the health (production) trait, respectively. The potential of genotyping females in addition to male lambs was less evident on the male side with no significant differences between the scenarios with different proportions of genotyped females. The results have shown that genomic selection can be a valuable tool to increase genetic gain in the German Merino sheep population and that the genotyping of a certain proportion of animals might lead to substantial improvement over pedigree‐based breeding value estimation. Nevertheless, further studies, especially economic evaluations, are needed before practical implementation. [ABSTRACT FROM AUTHOR]

Introduction: The first small scale cultivation of potatoes in the Nordic countries began roughly 300 years ago, and later became an important staple food in the region. Organized conservation efforts began in the 1980s, and today, potato landraces, improved varieties, and breeding lines are conserved in genebanks at the Nordic Genetic Resource Center (NordGen), Sweden, and the Norwegian Genetic Resource Centre (NGS), Norway, as well as at potato breeding companies across Nordic countries. All these collections house a diverse array of genotypes with local names and local growing histories from the whole region. However, the presence of duplicates, and inconsistent naming has led to confusion. Methods: In this study, 198 accessions of cultivated potato (Solanum tuberosum L.) have been genotyped with 62 microsatellite (SSR) markers. The analyzed accessions came from three collections: 43 accessions from the Danish Potato Breeding Foundation in Vandel (LKF-Vandel), 90 from NordGen and 65 from NGS. Results and discussion: The genetic analysis revealed 140 unique potato genotypes and 31 groups/clusters of duplicates, most of which contained duplicate pairs and the others three to ten accessions. Several accessions with distinct names were genetically identical or very similar, suggesting historical sharing, and regional distribution of seed potatoes, leading to the emergence of diverse local names. Moreover, many improved varieties from early potato breeding were revealed to have duplicates that have been considered Nordic landraces. Furthermore, potato accessions with identical names but originating from different collections were confirmed to be duplicates. These findings have already influenced management decisions and will further improve management practices for Nordic potato collections. Additionally, this new knowledge will benefit Nordic potato breeding efforts and allow for the dissemination of more accurate information to other users of potato diversity. [ABSTRACT FROM AUTHOR]

Background & Objectives: Genotypic identification of the etiologic agents of vaginal candidiasis (VC) is of significance in epidemiologic studies and in the establishment of adequate treatment protocol. The aim of this study was to determine the antifungal susceptibility and gene diversity of C. albicans isolated from a group of Jordanian women with VC. Methods: A total of 312 isolates of candida species, recovered from women with vaginal candidiasis who attended gynecology clinics affiliated to three major private hospitals in Amman over a period of five months (July 2020 to December 2020) were included in this study. The isolated Candida were characterized by phenotypic and genotypic means. Genotypic studies were performed using specific PCR primers of the rDNA and RPS genes. Susceptibility testing of all C. albicans isolates was conducted following the National Committee for Clinical Laboratory Standards and E-test strips. Results: Candida albicans was the most dominant Candida spp. that caused VC among the studied population. C. albicans isolates were found to be of three different subtypes at the 25S rDNA gene. All isolates belonged to genotypes A, B and C while genotypes D and E were not detected. The diversity of C. albicans was higher on the basis of RPS region where the use of two markers (P-I and P-II) resulted in the identification of nine distinct C. albicans subtypes. The sensitivity testing revealed variations in the susceptibility of various genotypes to different antifungal drugs. Genotype A isolates were more susceptible to fluconazole, flucytosine and ketoconazole than genotypes B and C. Conclusion: Candida albicans incriminated as etiologic agents of vaginitis among Jordanian women exhibited relationship between various genotypes and antifungal drugs. [ABSTRACT FROM AUTHOR]

IVF laboratories routinely adopt morphological pronuclear assessment at the zygote stage to identify abnormally fertilized embryos deemed unsuitable for clinical use. In essence, this is a pseudo-genetic test for ploidy motivated by the notion that biparental diploidy is required for normal human life and abnormal ploidy will lead to either failed implantation, miscarriage, or significant pregnancy complications, including molar pregnancy and chorionic carcinoma. Here, we review the literature associated with ploidy assessment of human embryos derived from zygotes displaying a pronuclear configuration other than the canonical two, and the related pregnancy outcome following transfer. We highlight that pronuclear assessment, although associated with aberrant ploidy outcomes, has a low specificity in the prediction of abnormal ploidy status in the developing embryo, while embryos deemed abnormally fertilized can yield healthy pregnancies. Therefore, this universal strategy of pronuclear assessment invariably leads to incorrect classification of over 50% of blastocysts derived from atypically pronucleated zygotes, and the systematic disposal of potentially viable embryos in IVF. To overcome this limitation of current practice, we discuss the new preimplantation genetic testing technologies that enable accurate identification of the ploidy status of preimplantation embryos and suggest a progress from morphology-based checks to molecular fertilization check as the new gold standard. This alternative molecular fertilization checking represents a possible non-incremental and controversy-free improvement to live birth rates in IVF as it adds to the pool of viable embryos available for transfer. This is especially important for the purposes of 'family building' or for poor-prognosis IVF patients where embryo numbers are often limited. [ABSTRACT FROM AUTHOR]

BackgroundObjectiveMethodResultsConclusionNigeria remains one of the countries with a high hepatitis B virus (HBV) burden in Africa. Reports have indicated the presence of mixed HBV genotypes in Nigeria; however, there is still paucity of data regarding mixed genotype infections particularly in the Southern part of the country.Our aim is to determine the HBV genotype distribution among HBsAg-positive gastroenterology patients at the University College Hospital Ibadan, Nigeria.Serum samples were screened for HBsAg by ELISA, and positive samples were genotyped by semi-nested multiplex PCR for HBV genotypes A, B, C, D, E and F.Data generated were analyzed in R-studio. A total of 81/90 (90%) of HBsAg-positive samples were successfully genotyped, and genotype A was most prevalent with 15.7%, while genotypes B and E were the least with 1.2% each. Genotypes A/C infection was the highest among mixed infections with 40% prevalence, while genotypes A/D were the least prevalent mixed infection with 4.8%.We advocate for a comprehensive genotype analysis in larger cohorts across Nigeria, to give a more comprehensive understanding of the distribution and prevalence of different HBV genotypes population wide. [ABSTRACT FROM AUTHOR]

Background: The Jra antigen is a high-prevalence red blood cell (RBC) antigen. Reports on cases of fatal hemolytic disease of the fetus and newborn and acute hemolytic transfusion reactions suggest that antibodies against Jra (anti-Jra) have potential clinical significance. Identifying anti-Jra is challenging owing to a lack of commercially available antisera. We developed an alternative approach to rapidly predict the presence of anti-Jra using the Taq-Man single-nucleotide polymorphism (SNP)-genotyping method. Methods: Residual peripheral blood samples from 10 patients suspected of having the anti-Jra were collected. Two samples with confirmed Jr(a-) RBCs and anti-Jra were used to validate the TaqMan genotyping assay by comparing the genotyping results with direct sequencing. The accuracy of the assay in predicting the presence of anti-Jra was verified through crossmatching with in-house Jr(a-) O+ RBCs. Results: The TaqMan-genotyping method was validated with two Jr(a-) RBC- and anti-Jraconfirmed samples that showed concordant Jra genotyping and direct sequencing results. Jra genotyping for the remaining samples and crossmatching the serum samples with inhouse Jr(a-) O+ RBCs showed consistent results. Conclusions: We validated a rapid, simple, accurate, and cost-effective method for predicting the presence of anti-Jra using a TaqMan-based SNP-genotyping assay. Implementing this method in routine practice in clinical laboratories will assist in solving difficult problems regarding alloantibodies to high-prevalence RBC antigens and ultimately aid in providing safe and timely transfusions and proper patient care. [ABSTRACT FROM AUTHOR]

Background: Cannabis sativa is seeing a global resurgence as a food, fiber and medicinal crop for industrial hemp and medicinal Cannabis industries respectively. However, a widespread moratorium on the use and research of C. sativa throughout most of the 20th century has seen the development of improved cultivars for specific end uses lag behind that of conventional crops. While C. sativa research and development has seen significant investments in the recent past, resulting in a suite of publicly available genomic resources and tools, a versatile and cost-effective mid-density genotyping platform for applied purposes in breeding and pre-breeding is lacking. Here we report on a first mid-density fixed-target SNP platform for C. sativa. Results: The High-throughput Amplicon-based SNP-platform for medicinal Cannabis and industrial Hemp (HASCH) was designed using a combination of filtering and Integer Linear Programming on publicly available whole-genome sequencing and RNA sequencing data, supplemented with in-house generated genotyping-by-sequencing (GBS) data. HASCH contains 1,504 genome-wide targets of high call rate (97% mean) and even distribution across the genome, designed to be highly informative (> 0.3 minor allele frequency) across both medicinal cannabis and industrial hemp gene pools. Average numbers of mismatch SNP between any two accessions were 251 for medicinal cannabis (N = 116) and 272 for industrial hemp (N = 87). Comparing HASCH data with corresponding GBS data on a collection of diverse C. sativa accessions demonstrated high concordance and resulted in comparable phylogenies and genetic distance matrices. Using HASCH on a segregating F2 population derived from a cross between a tetrahydrocannabinol (THC)-dominant and a cannabidiol (CBD)-dominant accession resulted in a genetic map consisting of 310 markers, comprising 10 linkage groups and a total size of 582.7 cM. Quantitative Trait Locus (QTL) mapping identified a major QTL for CBD content on chromosome 7, consistent with previous findings. Conclusion: HASCH constitutes a versatile, easy to use and cost-effective genotyping solution for the rapidly growing Cannabis research community. It provides consistent genetic fingerprints of 1504 SNPs with wide applicability genetic resource management, quantitative genetics and breeding. [ABSTRACT FROM AUTHOR]

Objective: The aim of this study was to replicate associations of GWAS-significant loci with severe COVID-19 in the population of Central Russia, to investigate associations of the SNPs with thromboinflammation parameters, to analyze gene-gene and gene-environmental interactions. Materials and Methods: DNA samples from 798 unrelated Caucasian subjects from Central Russia (199 hospitalized COVID-19 patients and 599 controls with a mild or asymptomatic course of COVID-19) were genotyped using probe-based polymerase chain reaction for 10 GWAS-significant SNPs: rs143334143 CCHCR1, rs111837807 CCHCR1, rs17078346 SLC6A20-LLZTFL1, rs17713054 SLC6A20-LLZTFL1, rs7949972 ELF5, rs61882275 ELF5, rs12585036 ATP11A, rs67579710 THBS3, THBS3-AS1, rs12610495 DPP9, rs9636867 IFNAR2. Results: SNP rs17713054 SLC6A20-LZTFL1 was associated with increased risk of severe COVID-19 in the entire group (risk allele A, OR = 1.78, 95% CI = 1.22-2.6, p = 0.003), obese individuals (OR = 2.31, 95% CI = 1.52-3.5, p = 0.0002, (pbonf = 0.0004)), patients with low fruit and vegetable intake (OR = 1.72, 95% CI = 1.15-2.58, p = 0.01, (pbonf = 0.02)), low physical activity (OR = 1.93, 95% CI = 1.26-2.94, p = 0.0035, (pbonf = 0.007)), and nonsmokers (OR = 1.65, 95% CI = 1.11-2.46, p = 0.02). This SNP correlated with increased BMI (p = 0.006) and worsened thrombodynamic parameters (maximum optical density of the formed clot, D (p = 0.02), delayed appearance of spontaneous clots, Tsp (p = 0.02), clot size 30 min after coagulation activation, CS (p = 0.036)). SNP rs17078346 SLC6A20-LZTFL1 was linked with increased BMI (p = 0.01) and severe COVID-19 in obese individuals (risk allele C, OR = 1.72, 95% CI = 1.15-2.58, p = 0.01, (pbonf = 0.02)). SNP rs12610495 DPP9 was associated with increased BMI (p = 0.01), severe COVID-19 in obese patients (risk allele G, OR = 1.48, 95% CI = 1.09-2.01, p = 0.01, (pbonf = 0.02)), and worsened thrombodynamic parameters (time to the start of clot growth, Tlag (p = 0.01)). For rs7949972 ELF5, a protective effect against severe COVID-19 was observed in non-obese patients (effect allele T, OR = 0.67, 95% CI = 0.47-0.95, p = 0.02, (pbonf = 0.04)), improving thrombodynamic parameters (CS (p = 0.02), stationary spatial clot growth rates, Vst (p = 0.02)). Finally, rs12585036 ATP11A exhibited a protective effect against severe COVID-19 in males (protective allele A, OR = 0.51, 95% CI = 0.32-0.83, p = 0.004). SNPs rs67579710 THBS3, THBS3-AS1, rs17713054 SLC6A20-LZTFL1, rs7949972 ELF5, rs9636867 IFNAR2--were involved in two or more of the most significant G×G interactions (pperm = 0.01). The pairwise combination rs67579710 THBS3, THBS3-AS1 × rs17713054 SLC6A20-LZTFL1 was a priority in determining susceptibility to severe COVID-19 (it was included in four of the top five most significant SNP-SNP interaction models). Conclusion: Overall, this study represents a comprehensive molecular-genetic and bioinformatics analysis of the involvement of GWAS-significant loci in the molecular mechanisms of severe COVID-19, gene-gene and geneenvironmental interactions, and provides evidence of their relationship with thromboinflammation parameters in patients hospitalized in intensive care units. [ABSTRACT FROM AUTHOR]

Background: Alzheimer's disease (AD) exhibits considerable phenotypic heterogeneity, suggesting the potential existence of subtypes. AD is under substantial genetic influence, thus identifying systematic variation in genetic risk may provide insights into disease origins. Objective: We investigated genetic heterogeneity in AD risk through a multi-step analysis. Methods: We performed principal component analysis (PCA) on AD-associated variants in the UK Biobank (AD cases = 2,739, controls = 5,478) to assess structured genetic heterogeneity. Subsequently, a biclustering algorithm searched for distinct disease-specific genetic signatures among subsets of cases. Replication tests were conducted using the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset (AD cases = 500, controls = 470). We categorized a separate set of ADNI individuals with mild cognitive impairment (MCI; n = 399) into genetic subtypes and examined cognitive, amyloid, and tau trajectories. Results: PCA revealed three distinct clusters ("constellations") driven primarily by different correlation patterns in a region of strong LD surrounding the MAPT locus. Constellations contained a mixture of cases and controls, reflecting disease-relevant but not disease-specific structure. We found two disease-specific biclusters among AD cases. Pathway analysis linked bicluster-associated variants to neuron morphogenesis and outgrowth. Disease-relevant and disease-specific structure replicated in ADNI, and bicluster 2 exhibited increased cerebrospinal fluid p-tau and cognitive decline over time. Conclusions: This study unveils a hierarchical structure of AD genetic risk. Disease-relevant constellations may represent haplotype structure that does not increase risk directly but may alter the relative importance of other genetic risk factors. Biclusters may represent distinct AD genetic subtypes. This structure is replicable and relates to differential pathological accumulation and cognitive decline over time. [ABSTRACT FROM AUTHOR]

Genetic variation in the FCGR3B gene is responsible for different variants of human neutrophil antigen 1 (HNA-1). Laboratory techniques currently utilized for routine HNA-1 genotyping, predominantly PCR-sequence-specific primer (PCR-SSP) and PCR-sequence-based typing (PCR-SBT), lack specificity for FCGR3B. This study compares the capabilities and limitations of existing technologies including an in-house TaqMan PCR, a commercial PCR-SSP test, PCR-SBT and multiplex ligation-dependent probe amplification (MLPA) with those of a long-read nanopore sequencing assay. Testing was performed with both related and unrelated Danish samples with different copy numbers and/or rare alleles. Long-read nanopore sequencing was validated by blind testing of ten English samples. The results showed that FCGR3B copy numbers correlate with a dose-dependent distribution of alleles that complicates genotyping by TaqMan PCR, PCR-SSP and PCR-SBT, due to co-amplification of the homologous FCGR3A gene. MLPA can correctly quantify the dose-dependent distribution but not detect novel variants. Long-read nanopore sequencing showed high specificity for FCGR3B and was able to detect dosage-dependent distribution, and rare and novel variants that were previously not described. Current HNA-1 genotyping methods cannot produce unambiguous allele-level results, whereas long-read nanopore sequencing has shown the potential to resolve observed ambiguities, identify new HNA-1 variants and allow definitive allele assignment. [ABSTRACT FROM AUTHOR]

Cultivated potato, Solanum tuberosum L., is considered an autotetraploid with 12 chromosomes with four homologous phases. However, recent evidence found that, due to frequent large phase deletions in the genome, gene ploidy is not constant across the genome. The elite cultivar "Otava" was found to have an average gene copy number of 3.2 across all loci. Breeding programs for elite potato cultivars rely increasingly on genomic prediction tools for selection breeding and elucidation of quantitative trait loci underpinning trait genetic variance. These are typically based on anonymous single nucleotide polymorphism (SNP) markers, which are usually called from, for example, SNP array or sequencing data using a tetraploid model. In this study, we analyzed the impact of using whole genome markers genotyped as either tetraploid or observed allele frequencies from genotype-by-sequencing data on single-trait additive genomic best linear unbiased prediction (GBLUP) genomic prediction (GP) models and single-marker regression genome-wide association studies of potato to evaluate the implications of capturing varying ploidy on the statistical models employed in genomic breeding. A panel of 762 offspring of a diallel cross of 18 parents of elite breeding material was used for modeling. These were genotyped by sequencing and phenotyped for five key performance traits: chipping quality, length/width ratio, senescence, dry matter content, and yield. We also estimated the read coverage required to confidently discriminate between a heterozygous triploid and tetraploid state from simulated data. It was found that using a tetraploid model neither impaired nor improved genomic predictions compared to using the observed allele frequencies that account for true marker ploidy. In genome-wide associations studies (GWAS), very minor variations of both signal amplitude and number of SNPs supporting both minor and major quantitative trait loci (QTLs) were observed between the two data sets. However, all major QTLs were reproducible using both data sets. [ABSTRACT FROM AUTHOR]

Summary The last decade has seen significant growth in the application of DNA‐based methods for extended antigen typing, and the use of gene sequencing to consider variation in blood group genes to guide clinical care. The challenge for the field now lies in educating professionals, expanding accessibility and standardizing the use of genotyping for routine patient care. Here we discuss applications of genotyping when transfusion is not straightforward including when compatibility cannot be demonstrated by routine methods, when Rh type is unclear, when allo‐ and auto‐antibodies are encountered in stem cell and organ transplantation, for prenatal testing to determine maternal and foetal risk for complications, and Group A subtyping for kidney and platelet donors. We summarize current commercial testing resources and new approaches to testing including high‐density arrays and targeted next‐generation sequencing (NGS). [ABSTRACT FROM AUTHOR]

The hepatitis delta virus (HDV) is a unique pathogen with significant global health implications, affecting individuals who are coinfected with the hepatitis B virus (HBV). HDV infection has profound clinical consequences, manifesting either as coinfection with HBV, resulting in acute hepatitis and potential liver failure, or as superinfection in chronic HBV cases, substantially increasing the risk of cirrhosis and hepatocellular carcinoma. Given the complex dynamics of HDV infection and the urgent need for advanced research tools, this article introduces vHDvDB 2.0, a comprehensive HDV full-length sequence database. This innovative platform integrates data preprocessing, secondary structure prediction, and epidemiological research tools. The primary goal of vHDvDB 2.0 is to consolidate HDV sequence data into a user-friendly repository, thereby facilitating access for researchers and enhancing the broader scientific understanding of HDV. The significance of this database lies in its potential to streamline HDV research by providing a centralized resource for analyzing viral sequences and exploring genotype-specific characteristics. It will also enable more in-depth research within the HDV sequence domains. [ABSTRACT FROM AUTHOR]

Summary: High‐throughput genotyping arrays have provided a cost‐effective, reliable and interoperable system for genotyping hexaploid wheat and its relatives. Existing, highly cited arrays including our 35K Wheat Breeder's array and the Illumina 90K array were designed based on a limited amount of varietal sequence diversity and with imperfect knowledge of SNP positions. Recent progress in wheat sequencing has given us access to a vast pool of SNP diversity, whilst technological improvements have allowed us to fit significantly more probes onto a 384‐well format Axiom array than previously possible. Here we describe a novel Axiom genotyping array, the 'Triticum aestivum Next Generation' array (TaNG), largely derived from whole genome skim sequencing of 204 elite wheat lines and 111 wheat landraces taken from the Watkins 'Core Collection'. We used a novel haplotype optimization approach to select SNPs with the highest combined varietal discrimination and a design iteration step to test and replace SNPs which failed to convert to reliable markers. The final design with 43 372 SNPs contains a combination of haplotype‐optimized novel SNPs and legacy cross‐platform markers. We show that this design has an improved distribution of SNPs compared to previous arrays and can be used to generate genetic maps with a significantly higher number of distinct bins than our previous array. We also demonstrate the improved performance of TaNGv1.1 for Genome‐wide association studies (GWAS) and its utility for Copy Number Variation (CNV) analysis. The array is commercially available with supporting marker annotations and initial genotyping results freely available. [ABSTRACT FROM AUTHOR]

Plenodomus lingam (Leptosphaeria maculans) and P. biglobosus (L. biglobosa) are fungi causing Phoma leaf spot/stem canker, an international damaging disease of oilseed rape (Brassica napus) and other brassicas. In Europe, fungicides used for disease management are mainly sterol 14α‐demethylase (CYP51) inhibitors (DMIs/azoles); quinone‐outside inhibitors (QoIs) and succinate dehydrogenase inhibitors (SDHIs) are also used. Decreased DMI sensitivity has emerged in Australian and eastern European P. lingam populations and is mediated by CYP51 promoter inserts resulting in target site overexpression. In this study using in vitro sensitivity testing, we report decreased DMI (prothioconazole‐desthio, mefentrifluconazole) sensitivity in modern western European P. lingam isolates (collected 2022–2023) compared to older baseline (1992–2005) isolates. Around 85% of modern western European P. lingam isolates collected, for which the CYP51 promoter region was sequenced, carried a promoter insert, but target site alterations were not detected. Six different CYP51 promoter inserts were identified, most commonly a 237 bp fragment of the Sahana transposable element. Inserts were associated with an approximately 3‐ to 10‐fold decrease in sensitivity to the DMIs tested. In contrast to P. lingam, PCR screening revealed CYP51 promoter inserts were absent in modern western European P. biglobosus isolates (2021–2023). Combined data indicate P. lingam isolates lacking an insert were similarly (or slightly more) sensitive to the DMIs tested for P. biglobosus, whereas those carrying an insert were slightly less sensitive than P. biglobosus. No evidence for substantive sensitivity shifts to the QoI (pyraclostrobin) or SDHI (boscalid) fungicides tested was obtained for either Plenodomus species. [ABSTRACT FROM AUTHOR]

Recombination is a key mechanism in breeding for promoting genetic variability. Multiparental populations (MPPs) constitute an excellent platform for precise genotype phasing, identification of genome-wide crossovers (COs), estimation of recombination frequencies, and construction of recombination maps. Here, we introduce haploMAGIC, a pipeline to detect COs in MPPs with single-nucleotide polymorphism (SNP) data by exploiting the pedigree relationships for accurate genotype phasing and inference of grandparental haplotypes. haploMAGIC applies filtering to prevent false-positive COs due to genotyping errors (GEs), a common problem in high-throughput SNP analysis of complex plant genomes. Hence, it discards haploblocks not reaching a specified minimum number of informative alleles. A performance analysis using populations simulated with AlphaSimR revealed that haploMAGIC improves upon existing methods of CO detection in terms of recall and precision, most notably when GE rates are high. Furthermore, we constructed recombination maps using haploMAGIC with high-resolution genotype data from 2 large multiparental populations of winter rapeseed (Brassica napus). The results demonstrate the applicability of the pipeline in real-world scenarios and showed good correlations in recombination frequency compared with alternative software. Therefore, we propose haploMAGIC as an accurate tool at CO detection with MPPs that shows robustness against GEs. [ABSTRACT FROM AUTHOR]

Background: Antibodies against blood group antigens play a key role in the pathophysiology of haemolytic transfusion reactions (HTRs) and haemolytic disease of the fetus and newborn (HDFN). This study aimed to determine the frequencies of alleles, genotypes, and risk of alloimmunisation of clinically significant blood group systems in ethnic northeastern Thais. Methods: In total, 345 unrelated, healthy, ethnic northeastern Thais were tested using the in‐house PCR‐sequence specific primers (PCR‐SSP) method for simultaneously genotyping of RHCE, Kell, Duffy, Kidd, Diego and MNS glycophorin hybrids and results confirmed by Sanger sequencing. Results: In this cohort, the alleles RHCE*C (81.0%) and RHCE*e (84.8%) were more prevalent than RHCE*c (19.0%) and RHCE*E (15.2%). The most common predicted haplotype combinations of the RHCE alleles were C+c‐E−e+(R1R1) (59.4%) followed by the C+c+E+e+ (R1R2) (20.6%) and C+c+E−e+ (R1r) (11.3%). The KEL*01 allele was not found in this study. The frequencies of FY*01 and FY*02 were 88.3% and 11.7%, respectively. The genotype FY*02/02 was found in four samples (1.2%). The frequencies of JK*01 and JK*02 were 52.5% and 47.5%, respectively. Homozygous JK*02/02 was found in 81 samples (23.5%). The frequencies of DI*01 and DI*02 were 0.6% and 99.4%, respectively. In total, 64 samples (18.6%) were found to carry the MNS glycophorin hybrids. Conclusions: Our results indicated a possible high risk of c, E, Fyb, Jka, Jkb and Mia alloimmunisation in these populations. Moreover, methods established for genotyping clinically significant blood groups in this study can now be utilised in routine clinical application. [ABSTRACT FROM AUTHOR]

Background and Objectives: The RHCE gene plays an important role in the complex and polymorphic Rh blood group system. RHCE genotyping holds significant clinical and transfusion‐related implications. The objective of this study was to evaluate the accuracy of RHC/c genotyping in the Chinese Han population. Materials and Methods: Blood samples were obtained from 653 Chinese Han blood donors. The serological RhD and RhCcEe types were determined using monoclonal antibodies. Subsequently, multiplex real‐time polymerase chain reaction (PCR) analysis was performed for RHC and RHc genotyping. Additionally, exon 2 of RHCE and exon 1 of RHD were sequenced. Results: The analysis in this study found 443 RhD‐positive donors and 210 RhD‐negative donors. Among the 653 total donors, discrepancies between the RHC genotyping results and the serological results were found in 37 individuals. Specifically, 6 false‐positive RhC results in RhD‐positive donors and 28 false‐positive RhC results in RhD‐negative donors were identified based on c.48C in RHCE exon 1. Additionally, 3 false‐negative RhC results were observed in the RhD‐positive donors due to a 109 bp insertion in RHCE intron 2. RHc typing demonstrated complete consistency between the real‐time PCR and the serological results. Conclusion: In the Chinese Han population, RHC genotyping was reliable when consistent results were achieved by both c.48C‐based and 109 bp insertion‐based genotyping. Moreover, RHc genotyping based on c.203A and c.307C polymorphic loci demonstrated dependable performance. [ABSTRACT FROM AUTHOR]

Toxoplasma gondii, a common protozoan parasite, poses significant public health risks due to its potential to cause toxoplasmosis in humans and can be contracted from pigs, which are considered its critical intermediate host. The aim of this study is to evaluate the prevalence of T. gondii in slaughtered pigs for human consumption, emphasizing the zoonotic implications and the need for improved biosecurity and monitoring practices in pig farming. A total of 1,526 pig samples (1,051 whole blood samples and 384 lung tissue samples from the local slaughterhouse and 91 aborted fetus samples from local farms) were collected throughout the whole country of Korea in 2020. Among them, 6 (0.4%) were found to be infected with T. gondii by nested PCR. When compared by sample type, the prevalence of T. gondii was significantly higher in the aborted fetus samples (2.2%, 2/91) than in the blood (0.3%, 3/1,051) and lung tissue samples (0.3%, 1/384). The B1 gene sequence of T. gondii was similar (97.9–99.8%) to that of the other T. gondii isolates. This study represents the first molecular genotyping survey of T. gondii in the lung tissue of fattening pigs and aborted fetuses in Korea. Our findings indicated the importance of adopting preventive measures including the implementation of rigorous farm hygiene protocols and the promotion of public awareness about the risks of consuming undercooked pork. By addressing the gaps in current control strategies and encouraging the One Health approach, this study contributes to the development of more effective strategies to mitigate the transmission of T. gondii from pigs to humans, ultimately safeguarding public health. [ABSTRACT FROM AUTHOR]

Background and Aim: Methicillin-resistant Staphylococcus aureus (MRSA) causes infectious diseases that are clinically problematic. Methicillin resistance is encoded by the mecA gene on the mobile staphylococcal cassette chromosome mec (SCCmec), with SCCmec types I to V being the most prevalent. Staphylococcal protein A gene (spa) typing is a genotyping method designed for S. aureus. This study aimed to use SCCmec and spa genotyping-based methods to identify the genetic diversity of clinical MRSA isolates. Methods: Fifty MDR-MRSA isolates from tertiary hospitals in Egypt were subjected to molecular-based typing using multiplex PCR to identify SCCmec types I to V and detect spa types via spa DNA sequence analysis. Results: The predominant SCCmec types were SCCmec Ⅴ (34%) and SCCmec Ⅳ (32%). The spa sequence analysis revealed 13 definite spa types, with t084 (24.2%) being the most prevalent, followed by t688 (15.1%). Based on both genotyping methods, 20 diverse MRSA clones were identified, with the most predominant MRSA clones being CC15-SCCmecⅤ-t084 and CC15-SCCmecⅣ-t084 (12.1%). Conclusion: MRSA bacteria in Egyptian hospitals are genetically different, indicating that the strains have diverse origins. Thus, regular surveillance of MRSA diversity is required to detect emergent clones for precise epidemiological evaluation and improved procedures to prevent the spread of this superbug. [ABSTRACT FROM AUTHOR]

This study aimed to isolate and characterize Pseudomonas native strains from the rhizospheric soil of Minthostachys verticillata plants to evaluate their potential as plant growth-promoting rhizobacteria (PGPR). A total of 22 bacterial isolates were obtained and subjected to various biochemical tests, as well as assessments of plant growth-promoting traits such as phosphate solubilization, hydrogen cyanide production, biocontrol properties through antibiosis, and indole acetic production. Genotypic analysis via 16S rRNA gene sequencing and phylogenetic tree construction identified the strains, with one particular strain named SM 33 showing significant growth-promoting effects on M. verticillata seedlings. This strain, SM 33, showed high similarity to Stutzerimonas stutzeri based on 16S rRNA gene sequencing and notably increased both shoot fresh weight and root dry weight of the plants. These findings underscore the potential application of native Pseudomonas strains in enhancing plant growth and health, offering promising avenues for sustainable agricultural practices. [ABSTRACT FROM AUTHOR]

Barley is a major grain crop in Canada and is used for generating malt, in addition to being used as human food and animal feed. Differentiating barley varieties is important for malt quality assurance and grain handling. Here, we present a DNA-based testing method for the identification of Canadian barley varieties. The method uses 24 custom TaqMan genotyping assays, which are analyzed using the high-throughput SmartChip system (Takara Bio Inc.). Using this method, we are able to distinguish 124 barley varieties commonly grown in Canada. [ABSTRACT FROM AUTHOR]

Despite tea [Camellia sinensis (L.) O. Kuntze] is one of the top non-alcoholic beverages consumed around the world; its genetic and phenotypic diversity is less understood compared to other plantation crops. The study's aims were to undertake phenotypic and genotypic characterization of Sri Lankan and Indian tea germplasm and to identify diverse accessions to accelerate tea breeding programmes in both countries. A total of 171 tea accessions, comprising 94 Sri Lankan and 77 Indian accessions were used. All the accessions were subjected to phenotyping and genotyping using 28 polymorphic simple sequence repeat (SSR) markers. Based on 16 morphological characters, the first three principal components explained 57.61% and 58.43% of the total variability of Sri Lankan and Indian accessions, respectively. Young shoot pubescence, young shoot pigmentation, serration of leaf margin, and mature leaf colour contributed positively to the grouping of accessions. Based on Neighbor-joining analysis, all Sri Lankan accessions grouped in a single cluster, whereas Indian accessions grouped in two distinct clusters. The Gower's distance method was the most appropriate than other methods for developing core subsets. Among 21 Sri Lankan core accessions selected, 11 accessions belong to introductions, five TRI-developed cultivars and five estate selections. Among 18 Indian core accessions selected, 11 belong to China types, two Assam types and five Indian recommended cultivars. The current study is the first study to compare tea germplasm of both countries and the results are useful for tea crop improvement programme, conservation and utilization of tea germplasm in India and Sri Lanka in the future. [ABSTRACT FROM AUTHOR]

Maâmora is a cork oak forest in Morocco known for its production of sweet acorns. Genetic diversity and relationships were evaluated in 240 individuals from five Cantons. The nine inter simple sequence repeat (ISSR) primers used in this study generated 368 polymorphic fragments and showed 100% polymorphism. A moderate level of genetic diversity (I = 0.28, He = 0.173) was observed. The analysis of molecular variance (AMOVA) showed that the highest level of diversity occurred within the populations (75%). A genetic structure was obtained using unweighted pair group method with arithmetic mean (UPGMA) and principal coordinate analysis (PCoA) analyses. 39 alleles were generated with a mean of 557 alleles per locus using seven simple sequence repeats (SSR) markers to establish DNA-fingerprinting for genotyping of 47 "Plus" tree systematically characterized. The analysis of diversity revealed significant polymorphism (94%) and allelic richness with high observed heterozygosity, which was confirmed by the negative value of Fis (− 0319). Nm is equal to 10.23, and Gst and Fst are equal to 0.022 and 0.052, respectively, revealing low inter-population variability. Genetic typing of the entire collection of "Plus" trees has identify 47 different genotypes. Eight unique alleles and 16 genotypes with specific markers were identified in this study. These results could be used to select the genotypes of interest for the multiplication of seedlings for reforestation and breeding programs. [ABSTRACT FROM AUTHOR]

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More than 100 laboratories in the World Health Organization Global Measles and Rubella Laboratory Network (GMRLN) perform nucleic acid-based methods for case confirmation of measles or rubella infections and/or strain surveillance (genotyping). The quality of laboratory data is critical to ensure that diagnostic results and country reports to regional verification committees are based on accurate data. A molecular External Quality Assurance (mEQA) program was initiated by the US-CDC in 2014 to evaluate the performance of laboratories in the network. The inclusion of testing for measles and rubella viruses, with a focus on detection and genotyping, plus the diversity of assays and platforms employed required a flexible and comprehensive proficiency testing program. A stepwise introduction of new evaluation criteria gradually increased the stringency of the proficiency testing program, while giving laboratories time to implement the required changes. The mEQA program plays an important role in many processes in the GMRLN, including informing plans for the training of laboratory staff, access to reagents, and the submission of sequence data to global databases. The EQA program for Local Public Health Institutes in Japan is described as an example for national mEQA programs. As more laboratories initiate molecular testing, the mEQA will need to continue to expand and to adapt to the changing landscape for molecular testing. [ABSTRACT FROM AUTHOR]

Leishmania infantum is considered the predominant Leishmania species responsible for visceral leishmaniasis (VL) in Greece but limited molecular-typing-based studies have been performed so far. We retrospectively analyzed data and serum samples collected from 3661 individuals suspected for VL in a sixteen-year period, from 2005 to 2020, to study the seasonality and demographic characteristics of VL cases and to define the L. infantum genotypes circulating in the country. Serum samples were tested with immunofluorescence assay and/or molecular assay. qPCR Leishmania-positive samples were subjected to genotypic analysis based on polymorphisms in 12 microsatellite regions of the internal transcribed spacers (ITSs) 1 and 2. We diagnosed 219 definite (6%, sample with a positive molecular assay and/or antibody titer ≥ 1:400) and 230 probable (6.3%, sample with antibody titer between 1:100 and 1:200) VL cases. Data analysis revealed that amongst VL-definite cases, the age group (≥65) constitutes the most affected factor, since 36.9% of the VL cases belonged to this age group. Amongst the VL definite cases, the most frequently reported symptoms were fever (83%), splenomegaly (49%), and hepatomegaly (40%), but this was not the case for immunocompromised patients that developed non-typical symptoms of leishmaniasis. Although no statistically significant differences in the overall seasonality of VL cases were observed, February and June showed a significantly higher proportion of VL cases compared to August and December. Genotyping of ITS1 and ITS2 regions revealed that all VL cases belong to ITS type A of L. infantum. Our study provides epidemiological information on VL and demonstrates for the first time, providing genotypic data, the circulation of ITS type A L. infantum in Greece. [ABSTRACT FROM AUTHOR]

Micronutrient deficiencies (MNDs) particularly zinc (Zn) and iron (Fe) remain widespread in sub-Saharan Africa (SSA) due to low dietary intake. Wheat is an important source of energy globally, although cultivated wheat is inherently low in grain micronutrient concentrations. Malawian wheat/Am. muticum and Malawian wheat/T. urartu BC1F3 introgression lines, developed by crossing three Malawian wheat varieties (Kenya nyati, Nduna and Kadzibonga) with DH-348 (wheat/Am. muticum) and DH-254 (wheat/T. urartu), were phenotyped for grain Zn and Fe, and associated agronomic traits in Zn-deficient soils, in Malawi. 98% (47) of the BC1F3 introgression lines showed higher Zn above the checks Paragon, Chinese Spring, Kadzibonga, Kenya Nyati and Nduna. 23% (11) of the introgression lines showed a combination of high yields and an increase in grain Zn by 16-30 mg kg-1 above Nduna and Kadzibonga, and 11-25 mg kg-1 above Kenya nyati, Paragon and Chinese Spring. Among the 23%, 64% (7) also showed 8-12 mg kg-1 improvement in grain Fe compared to Nduna and Kenya nyati. Grain Zn concentrations showed a significant positive correlation with grain Fe, whilst grain Zn and Fe negatively and significantly correlated with TKW and grain yield. This work will contribute to the efforts of increasing mineral nutrient density in wheat, specifically targeting countries in the SSA. [ABSTRACT FROM AUTHOR]

Antibiotic resistance in the treatment of H. pylori infection is the principal reason for the failure of eradication regimens using the triple therapy. We reviewed the mechanisms of H. pylori antibiotic resistance and assessed the molecular tools commonly used to detect antibiotic resistance in Latin America. Most commonly reported molecular techniques were PCR and sequencing, as well as its variants PCR-RFLP and qPCR to detect the genes and mutations involved in the resistance to clarithromycin (CLR), amoxicillin (AMX), levofloxacin (LVX), tetracycline (TET), and metronidazole (MTZ). The mutation-associated resistance rates varied from 2.2% to 83.3% for CLA and 12% to 100% for LVX in 7 and 4 countries, respectively, whereas for MTZ the resistance frequency was between 50% to 100% in 4 countries. For TET and AMX, frequency of the resistance was in the range of 0% to 27% (5 and 3 countries, respectively). Molecular tools can be used for the rapid detection of resistance to CLR, LVX, and TET, whereas genotypic analysis is not appropriate to detect resistance to AMX and MTZ due to genomic changes found in the rdxA and pbp1A genes. The revision of the different molecular methods showed that qPCR and RFLP are the best tools to detect the resistance of H. pylori. Few molecular tools have been developed in Latin America to detect H. pylori resistance to antibiotics. More studies would be needed to understand better efficient strategies to prevent further emergence of antimicrobial resistance. [ABSTRACT FROM AUTHOR]

Cryptococcosis is an opportunistic systemic mycosis caused by Cryptococcus neoformans and C. gattii species complexes and is of increasing global importance. Maintaining continued surveillance of the antifungal susceptibility of environmental C. neoformans and C. gattii isolates is desirable for better managing cryptococcosis by identifying resistant isolates and revealing the emergence of intrinsically resistant species. Relevant research data from Egypt are scarce. Thus, this study aimed to report the genetic diversity of C. neoformans and C. gattii species complexes originating from different environmental sources in Egypt, antifungal susceptibility profiles, antifungal combinations, and correlations of susceptibility with genotypes. A total of 400 environmental samples were collected, 220 from birds and 180 from trees. Cryptococcus spp. were found in 58 (14.5%) of the samples, 44 (75.9%) of the isolates were recovered from birds and 14 (24.1%) from trees. These isolates were genotyped using M13 polymerase chain reaction-fingerprinting and URA5 gene restriction fragment length polymorphism analysis. Of the 31 C. neoformans isolates, 24 (77.4%), 6 (19.4%) and one (4.4%) belonged to VNI, VNII, and VNIII genotypes, respectively. The 27 C. gattii isolates belonged to VGI (70.4%), VGII (18.5%), and VGIII (11.1%) genotypes. Non-wild type C. neoformans and C. gattii isolates that may have acquired resistance to azoles, amphotericin B (AMB), and terbinafine (TRB) were observed. C. gattii VGIII was less susceptible to fluconazole (FCZ) and itraconazole (ITZ) than VGI and VGII. C. neoformans isolates showed higher minimum inhibitory concentrations (MICs) to FCZ, ITZ, and voriconazole (VRZ) than those of C. gattii VGI and VGII. Significant (P < 0.001) correlations were found between the MICs of VRZ and ITZ (r = 0.64) in both C. neoformans and C. gattii isolates, FCZ and TRB in C. neoformans isolates, and FCZ and TRB (r = 0.52) in C. gattii isolates. There is no significant differences in the MICs of TRB in combination with FCZ (P = 0.064) or in combination with AMB (P = 0.543) and that of TRB alone against C. gattii genotypes. By calculating the fractional inhibitory concentration (FIC) index, the combination of FCZ + AMB was synergistic against all tested genotypes. These findings expand our knowledge of ecological niches, genetic diversity, and resistance traits of C. neoformans and C. gattii genotypes in Egypt. Further investigations into how they are related to clinical isolates in the region are warranted. [ABSTRACT FROM AUTHOR]

Introduction: Genotyping large-scale gene bank collections requires an appropriate sampling strategy to represent the diversity within and between accessions. Methods: A panel of 44 common bean (Phaseolus vulgaris L.) landraces from the Alliance Bioversity and The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT) gene bank was genotyped with DArTseq using three sampling strategies: a single plant per accession, 25 individual plants per accession jointly analyzed after genotyping (in silico-pool), and by pooling tissue from 25 individual plants per accession (seq-pool). Sampling strategies were compared to assess the technical aspects of the samples, the marker information content, and the genetic composition of the panel. Results: The seq-pool strategy resulted inmore consistent DNA libraries for quality and call rate, although with fewer polymorphic markers (6,142 single-nucleotide polymorphisms) than the in silico-pool (14,074) or the single plant sets (6,555). Estimates of allele frequencies by seq-pool and in silico-pool genotyping were consistent, but the results suggest that the difference between pools depends on population heterogeneity. Principal coordinate analysis, hierarchical clustering, and the estimation of admixture coefficients derived froma single plant, in silico-pool, and seq-pool successfully identified the well-known structure of Andean and Mesoamerican gene pools of P. vulgaris across all datasets. Conclusion: In conclusion, seq-pool proved to be a viable approach for characterizing common bean germplasm compared to genotyping individual plants separately by balancing genotyping effort and costs. This study provides insights and serves as a valuable guide for gene bank researchers embarking on genotyping initiatives to characterize their collections. It aids curators in effectively managing the collections and facilitates marker-trait association studies, enabling the identification of candidate markers for key traits. [ABSTRACT FROM AUTHOR]

Simple Summary: VaIN after hysterectomy is a rare intraepithelial neoplasia strongly associated with HR-HPV infection. It is hypothesized that the laparoscopic hysterectomy procedure may cause a higher incidence of VaIN in hysterectomized women. In a retrospective study of 170 women hysterectomized due to CIN3 or due to benign uterine pathology, all cases of high-grade VaIN occurred in women with persistent HPV. The most frequent genotype was 16. All these elements suggest that it is a history of HPV-related disease of the lower genital tract and viral persistence, rather than hysterectomy itself, that should be considered risk factors for the development of high-grade VaIN. A vaginal wall biopsy under colposcopy is recommended to be routinely performed before surgery for patients undergoing hysterectomy due to CIN3 or stage IA cervical cancer, which will help determine the necessary extent of vaginal resection during the procedure. The data from the literature show that women undergoing a LEEP due to CIN3 have a greater risk of having subsequent high-grade anogenital intraepithelial neoplasia or cancer, and the risk is greater for vaginal cancer than for anal and vulvar cancers. It is hypothesized that the laparoscopic hysterectomy procedure may cause a higher incidence of VaIN in hysterectomized women. There are few studies addressing this issue, and they show mixed results. This study aimed to investigate the incidence of high-grade or severe VaIN in the population of women undergoing hysterectomy for CIN3 or benign uterine disease and illustrate the treatment options and follow-up. Methods: This retrospective study was conducted on 170 women who underwent a laparoscopic hysterectomy due to high-grade cervical intraepithelial neoplasia (CIN3) or benign gynecological disease. The follow-up strategy included performing a cotest and colposcopy with biopsy if necessary. The median time between primary treatment and a diagnosis of high-grade VaIN was 18 months. Results: High-grade or severe VaIN was found in eight patients after hysterectomy (4.7%). All cases of high-grade VaIN occurred in women with persistent HPV infection. The most frequent genotype was 16. Women hysterectomized due to CIN3 showed an eight-fold greater risk than women hysterectomized due to benign disease of developing high-grade VaIN. The risk of VaIN is low in women hysterectomized due to benign disease. The risk of developing VaIN is greater in women with viral persistence. Conclusion: All these elements suggest that it is a history of HPV-related disease of the lower genital tract and viral persistence, rather than hysterectomy itself, that should be considered risk factors for the development of high-grade VaIN. After hysterectomy, patients with a history of CIN should undergo annual screening with vaginal dome cytology and HPV testing. [ABSTRACT FROM AUTHOR]

Introduction: McLeod syndrome (MLS) is a rare X-linked recessive disorder affecting multiple systems. Herein, we present the clinical symptoms, laboratory diagnostic results, and genetic characteristics of a patient with MLS caused by a novel c.459_460insC variation in the XK gene. Case Presentation: A 58-year-old male Chinese patient presented with neurological symptoms, seeking belated medical attention at the hospital. Numerous laboratory tests indicated a high likelihood of MLS, featuring chronic granulomatosis and neuroacanthocytosis. The patient’s blood samples were sent to the Blood Center of Zhejiang Province, China, for further analysis. Sequencing analysis revealed a novel hemizygous c.459_460insC variation in exon 2 of the XK gene. Therefore, we identified a patient with MLS possessing a novel genetic variation (GenBank Accession No. OQ473658). Conclusion: Our findings elucidate a novel c.459_460insC variation associated with MLS, resulting in a frameshift and premature stop codon (p.Leu154Profs*45). The clinical manifestations, laboratory examination, and XK gene analysis in this case will aid in diagnosing MLS in future patients. [ABSTRACT FROM AUTHOR]

Background: Genotyping of individuals plays a pivotal role in various biological analyses, with technology choice influenced by multiple factors including genomic constraints, number of targeted loci and individuals, cost considerations, and the ease of sample preparation and data processing. Target enrichment capture of specific polymorphic regions has emerged as a flexible and cost-effective genomic reduction method for genotyping, especially adapted to the case of very large genomes. However, this approach necessitates complex bioinformatics treatment to extract genotyping data from raw reads. Existing workflows predominantly cater to phylogenetic inference, leaving a gap in user-friendly tools for genotyping analysis based on capture methods. In response to these challenges, we have developed GeCKO (Genotyping Complexity Knocked-Out). To assess the effectiveness of combining target enrichment capture with GeCKO, we conducted a case study on durum wheat domestication history, involving sequencing, processing, and analyzing variants in four relevant durum wheat groups. Results: GeCKO encompasses four distinct workflows, each designed for specific steps of genomic data processing: (i) read demultiplexing and trimming for data cleaning, (ii) read mapping to align sequences to a reference genome, (iii) variant calling to identify genetic variants, and (iv) variant filtering. Each workflow in GeCKO can be easily configured and is executable across diverse computational environments. The workflows generate comprehensive HTML reports including key summary statistics and illustrative graphs, ensuring traceable, reproducible results and facilitating straightforward quality assessment. A specific innovation within GeCKO is its 'targeted remapping' feature, specifically designed for efficient treatment of targeted enrichment capture data. This process consists of extracting reads mapped to the targeted regions, constructing a smaller sub-reference genome, and remapping the reads to this sub-reference, thereby enhancing the efficiency of subsequent steps. Conclusions: The case study results showed the expected intra-group diversity and inter-group differentiation levels, confirming the method's effectiveness for genotyping and analyzing genetic diversity in species with complex genomes. GeCKO streamlined the data processing, significantly improving computational performance and efficiency. The targeted remapping enabled straightforward SNP calling in durum wheat, a task otherwise complicated by the species' large genome size. This illustrates its potential applications in various biological research contexts. [ABSTRACT FROM AUTHOR]

Chronic obstructive pulmonary disease (COPD) is a common respiratory disease globally, characterized by obstructive ventilatory disorder under pulmonary function tests. Recent years have witnessed a yearly increase in the prevalence of COPD. To investigate the impact of respiratory virus infections on patients with acute exacerbation of chronic obstructive pulmonary disease (AECOPD), and to perform sequencing typing and mutation analysis of viruses with high detection rate. A total of 1523 inpatients with AECOPD admitted to our hospital from April 1,2020 to March 30,2022 were collected and divided into two groups: the infected group (n= 532) and the non-infected group (n= 991). The related indexes between the two groups were collected and compared (including clinical characteristics and laboratory tests that blood cell count, PCT, CRP, adenovirus, respiratory syncytial virus, rhinovirus, influenza A virus, influenza B virus, etc.). In the infected group, the proportion of patients with palpitations (49.44% VS 8.07%, P< 0.001), lipid metabolism abnormalities (18.42% VS 39.96%, P< 0.001), heart failure (39.85% VS 29.87%, P< 0.001), disease duration (17.48 ± 7.47 VS 12.45 ± 11.43 d, P< 0.001), and poor prognosis (69.55% VS 17.15%, P< 0.001) were higher than those in the non-infected group; Adenovirus (ADV) accounted for 75.94% (404/532) of all infected viruses. 31 virus strains could be categorized into 16 ADV-C1, one ADV-C5, two ADV-B3, three ADV-B7, two ADV-D17, two ADV-D19, and five ADV-D27, which were similar to the serotypes reported in severe pneumonia. Furthermore, three strains of C1 adenovirus were found to be highly homologous to the original strain AF534906 by sequencing, and the phylogenetic trees of the three main structural genes were all on the same branch as the original strain. Base mutations and amino acid variants were found in each structural gene segment. In clinical data, it’s found that patients with mutations are worse than those without mutations. Respiratory viruses are common in patients with poor prognosis of AECOPD, especially adenovirus, respiratory syncytial virus. Respiratory virus infections will lead to the deterioration of patients with AECOPD, accompanied by longer treatment cycles and poor prognosis. [ABSTRACT FROM AUTHOR]

Background and Objectives Materials and Methods Results Conclusion To investigate the prevalence, genotype and haematological characteristics of glucose‐6‐phosphate dehydrogenase (G6PD) deficiency in the blood donor population of Wuxi area (Jiangsu Province, China) and to assess the impact of their red blood cell (RBC) units on clinical transfusion.We conducted genotyping and large‐scale screening for G6PD enzyme activity in the blood donors of Wuxi City. In addition, we assessed the haematological parameters of G6PD‐deficient and non‐deficient blood donors, and investigated the adverse transfusion reactions in patients transfused with G6PD‐deficient blood.We investigated 17,113 blood donors, among whom 44 (0.26%) were tested positive for G6PD deficiency. We identified 40 G6PD gene variants, among which c.1388G>A, c.1376G>T, c.1024C>T and c.95A>G were common. In addition, we identified two novel G6PD gene variants, c.1312G>A and c.1316G>A. The G6PD‐deficient and non‐deficient blood samples showed a significant difference in the RBC, mean corpuscular volume (MCV), mean corpuscular Hb (MCH), RBC distribution width, total bilirubin (TBIL), direct bilirubin (DBIL) and indirect bilirubin (IBIL) values. However, the two samples showed no significant difference in the haemolysis rate at the end of the storage period. Finally, transfusion with G6PD‐deficient RBC units did not lead to any adverse transfusion reactions.The positive rate of G6PD deficiency in the blood donor population of Wuxi City is 0.26%, and the genetic variants identified in this population are consistent with the common genetic variants observed in the Chinese population. Blood centres can establish a database on G6PD‐deficient blood donors and mark their RBC units to avoid their use for special clinical patients. [ABSTRACT FROM AUTHOR]

Background: There are ten genotypes of Echinococcus granulosus with different intermediate and final hosts affecting the parasite's life cycle and its transmission to humans. Therefore, this study was conducted to determine the genotype of isolated hydatid cysts using the simple and fast high-resolution melting point analysis (HRM) method. Methods: The paraffin tissue samples of patients who underwent surgery were obtained from the pathology sample bank of Vasei and Emdad Hospitals in Sabzevar, Iran during 2010-2020. The DNA content of the samples was extracted after collecting and determining the characteristics using the DNA extraction kit. PCR was performed on the samples and the presence of the hydatid cyst genome was confirmed using the special Master Kit. Mix PCR of Solis Biodyne Company and Real-Time device (Bio-Rad) were used, and the genetic identity of hydatid cysts were determined. Results: Out of 33 paraffin samples, 21 samples contained hydatid cyst DNA, two of which were from the brain and 19 from the liver tissues; 12 samples did not contain hydatid cyst DNAs. All liver samples were from sheep species (G1), and the brain samples were from buffalo species (G3). Therefore, 9.53% of the Echinococcus species collected were buffalo (G3), and 90.47% were sheep (G1) strain. Conclusion: Based on previous patterns, HRM methods can be used for easy and quick identification of Echinococcus strains. The G1 strain was the dominant strain causing hydatid cyst in different human organs, including the liver and brain. [ABSTRACT FROM AUTHOR]

• A great amount of CF-patients have faulty information regarding their CFTR genotype. • Whole-CFTR-locus sequencing greatly increases the diagnostic yield. • More than 40 novel CFTR variants described here for the first time. • Whole-CFTR-locus sequencing should be implemented into diagnostic workflows. In times of genotype guided therapy options, a total of 3.2 % of people with CF (pwCF) in the German CF Registry [1] only have one or no CFTR -variant detected after genetic analysis. Additionally, genetic data in the Registry can be documented as free text and can therefore be prone to error. In order to allow the greatest possible amount of pwCF access to modern therapies, we conducted a re-evaluation of free text entries and established a custom-whole- CFTR -locus NGS-approach for all pwCF who remained without genetic confirmation afterwards. To this end, we assembled 731 free text variants of 655 pwCF in the German CF Registry. All variants were evaluated using ClinVar, HGMD and CFTR1/2, corrected in the Registries' database and uploaded to ClinVar. PwCF whose diagnosis remained uncertain as well as additional pwCF or pwCFTR-RD that were assembled through a nationwide call for testing of unclear cases were offered genetic analysis. Samples were analysed using a target-capture based NGS-custom-design-panel covering the entire CFTR -locus. Evaluation of free text variants led to the discovery of 43 variants not formerly reported in the context of CF. The Registries' dropdown list was extended by 497 variants and over 500 pwCF were provided with their most up-to-date genotype. Samples of 47 pwCF/pwCFTR-RD were sequenced via NGS with an overall success rate of 61.7 %, resulting in implementation of entire CFTR -genotyping into routine diagnostics. Entire CFTR -genotyping can greatly increase the genetic diagnostic rate of pwCF/pwCFTR-RD and should be considered after inconspicuous CFTR screening panels in CFTR-diagnostics. [ABSTRACT FROM AUTHOR]

The study aimed to investigate molecularly the presence of flea-borne viruses in infested small ruminants with fleas. It was carried out in Egypt's Northern West Coast (NWC) and South Sinai Governorate (SSG). Three specific primers were used targeting genes, ORF103 (for Capripoxvirus and Lumpy skin disease virus), NS3 (for Bluetongue virus), and Rdrp (for Coronavirus), followed by gene sequencing and phylogenetic analyses. The results revealed that 78.94% of sheep and 65.63% of goats were infested in the NWC area, whereas 49.76% of sheep and 77.8% of goats were infested in the SSG region. Sheep were preferable hosts for flea infestations (58.9%) to goats (41.1%) in the two studied areas. Sex and age of the animals had no effects on the infestation rate (p > 0.05). The season and site of infestation on animals were significantly different between the two areas (p < 0.05). Ctenocephalides felis predominated in NWC and Ctenocephalides canis in SSG, and males of both flea species were more prevalent than females. Molecular analysis of flea DNA revealed the presence of Capripoxvirus in all tested samples, while other viral infections were absent. Gene sequencing identified three isolates as sheeppox viruses, and one as goatpox virus. The findings suggest that Capripoxvirus is adapted to fleas and may be transmitted to animals through infestation. This underscores the need for ongoing surveillance of other pathogens in different regions of Egypt. [ABSTRACT FROM AUTHOR]

Human noroviruses (HuNoVs) are highly contagious pathogens responsible of norovirus-associated acute gastroenteritis (AGE). GII.4 is the prevailing HuNoV genotype worldwide. Currently there are no studies on the molecular monitoring and phylogenetic analysis of HuNoVs in the territory of the Sverdlovsk region; therefore, it is not possible to objectively assess their genetic diversity. The aim of the study is to carry out genotyping and phylogenetic analysis of HuNoVs in the Sverdlovsk region from 2022 to 2023. Fecal samples (n = 510) were collected from children suffering from HuNoV-AGE in municipalities of the Sverdlovsk region and the capsid genotype was determined by amplifying the ORF1/ORF2 junction. Of the 196 HuNoVs typed, which represent 38% of the studied samples, the largest share of HuNoV genotypes belong to the GII genogroup—86%, followed by the GI genogroup—14%. Noroviruses GII.4 and GII.17 were the co-dominant capsid genotypes (33.2% each). Phylogenetic analysis demonstrates that the identified sequences on the territory of the Sverdlovsk region have the smallest genetic distance, which gives grounds for their unification into a common cluster. Routine monitoring and phylogenetic analysis of circulating norovirus pathogens spectrum will enable timely tracking of HuNoVs genetic diversity and evolutionary events. This will lead to the development of more effective anti-epidemic measures, ultimately reducing the burden of infectious diseases. [ABSTRACT FROM AUTHOR]

Candidemia is a major cause of morbidity and mortality in health care settings, and its epidemiology is changing. In the last two decades, the proportion of non-albicans Candida (NAC) yeasts in candidemia has increased. These yeasts more often display resistance to common antifungals. In many western countries, candidemia is mainly caused by susceptible C. albicans, while in resource-limited countries, including Iran, the candidemia species distribution is studied less often. Here, we investigated the species distribution, resistance levels, and characteristics of patients with candidemia in five hospitals in Mashhad (northeast Iran) for two years (2019–2021). Yeast isolates from blood were identified with MALDI-TOF MS and subjected to antifungal susceptibility testing (AFST) using the broth microdilution method, while molecular genotyping was applied to Candida parapsilosis isolates. In total, 160 yeast isolates were recovered from 160 patients, of which the majority were adults (60%). Candidemia was almost equally detected in men (48%) and women (52%). Almost half of patients (n = 67, 49%) were from intensive care units (ICUs). C. parapsilosis (n = 58, 36%) was the most common causative agent, surpassing C. albicans (n = 52, 33%). The all-cause mortality rate was 53%, with C. albicans candidemia displaying the lowest mortality with 39%, in contrast to a mortality rate of 59% for NAC candidemia. With microbroth AFST, nearly all tested isolates were found to be susceptible, except for one C. albicans isolate that was resistant to anidulafungin. By applying short tandem repeat (STR) genotyping to C. parapsilosis, multiple clusters were found. To summarize, candidemia in Mashhad, Iran, from 2019 to 2021, is characterized by common yeast species, in particular C. parapsilosis, for which STR typing indicates potential nosocomial transmission. The overall mortality is high, while resistance rates were found to be low, suggesting that the high mortality is linked to limited diagnostic options and insufficient medical care, including the restricted use of echinocandins as the first treatment option. [ABSTRACT FROM AUTHOR]

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Donor and recipient human cytomegalovirus (HCMV) seropositive (D+R+) lung transplant recipients (LTRs) often harbor multiple strains of HCMV, likely due to transmitted donor (D) strains and reactivated recipient (R) strains. To date, the extent and timely occurrence of each likely source in shaping the post‐transplantation (post‐Tx) strain population is unknown. Here, we deciphered the D and R origin of the post‐Tx HCMV strain composition in blood, bronchoalveolar lavage (BAL), and CD45+ BAL cell subsets. We investigated either D and/or R formalin‐fixed paraffin‐embedded blocks or fresh D lung tissue from four D+R+ LTRs obtained before transplantation. HCMV strains were characterized by short amplicon deep sequencing. In two LTRs, we show that the transplanted lung is reseeded by R strains within the first 6 months after transplantation, likely by infiltrating CD14+ CD163+/− alveolar macrophages. In three LTRs, we demonstrate both rapid D‐strain dissemination and persistence in the transplanted lung for >1 year post‐Tx. Broad inter‐host diversity contrasts with intra‐host genotype sequence stability upon transmission, during follow‐up and across compartments. In D+R+ LTRs, HCMV strains of both, D and R origin can emerge first and dominate long‐term in subsequent episodes of infection, indicating replication of both sources despite pre‐existing immunity. [ABSTRACT FROM AUTHOR]

Methylation markers have shown potential for triaging high‐risk HPV‐positive (hrHPV+) women to identify those at increased risk of invasive cervical cancer (ICC). Our aim was to assess the performance of the S5 DNA methylation classifier for predicting incident high‐grade cervical intraepithelial neoplasia (CIN) and ICC among hrHPV+ women in the ARTISTIC screening trial cohort. The S5 classifier, comprising target regions of tumour suppressor gene EPB41L3 and L1 and L2 regions of HPV16, HPV18, HPV31, and HPV33, was assayed by pyrosequencing in archived hrHPV+ liquid‐based samples from 343 women with high‐grade disease (139 CIN2, 186 CIN3, and 18 ICC) compared to 800 hrHPV+ controls. S5 DNA methylation correlated directly with increasing severity of disease and inversely with lead time to diagnosis. S5 could discriminate between hrHPV+ women who developed CIN3 or ICC and hrHPV+ controls (p <.0001) using samples taken on average 5 years before diagnosis. This relationship was independent of cytology at baseline. The S5 test showed much higher sensitivity than HPV16/18 genotyping for identifying prevalent CIN3 (93% vs. 61%, p =.01) but lower specificity (50% vs. 66%, p <.0001). The S5 classifier identified most women at high risk of developing precancer and missed very few prevalent advanced lesions thus appearing to be an objective test for triage of hrHPV+ women. The combination of methylation of host and HPV genes enables S5 to combine the predictive power of methylation with HPV genotyping to identify hrHPV‐positive women who are at highest risk of developing CIN3 and ICC in the future. [ABSTRACT FROM AUTHOR]

Molecular surveillance of circulating measles variants serves as a line of evidence for the absence of endemic circulation and provides a means to track chains of transmission. Molecular surveillance for measles (genotyping) is based on the sequence of 450 nucleotides at the end of the nucleoprotein coding region (N450) of the measles genome. Genotyping was established in 1998 and, with over 50,000 sequence submissions to the Measles Nucleotide Surveillance database, has proven to be an effective resource for countries attempting to trace pathways of transmission. This review summarizes the tools used for the molecular surveillance of measles and describes the challenge posed by the decreased number of circulating measles genotypes. The Global Measles and Rubella Laboratory Network addressed this challenge through the development of new tools such as named strains and distinct sequence identifiers that analyze the diversity within the currently circulating genotypes. The advantages and limitations of these approaches are discussed, together with the need to generate additional sequence data including whole genome sequences to ensure the continued utility of strain surveillance for measles. [ABSTRACT FROM AUTHOR]

Tularemia is an acute febrile disease caused by the Gram-negative bacillus Francisella tularensis. Based on genetic and phenotypic characteristics, three subspecies are distinguished: tularensis, holarctica, and mediasiatica. F. tularensis subsp. mediasiatica remains the least studied subspecies. Over the past decade, new foci of distribution of F. tularensis subsp. mediasiatica have been discovered in Russia (Siberia), expanding the possible distribution area by thousands of kilometers. This article provides whole genome single nucleotide polymorphism (wgSNP) and polymorphic tandem repeats (MLVA) analyses of 28 mediasiatica strains isolated between 1965 and 2004 in Kazakhstan. Despite high genetic homogeneity, MLVA with eleven loci (MLVA11) demonstrates a high discriminatory ability (diversity index, 0.9497). The topological structure of the trees based on wgSNP and MLVA is not comparable; however, clustering remains congruent for most outbreaks, with the exception of two strains from one outbreak that are identical in terms of wgSNP but differ at three tandem repeat loci. Based on wgSNP, the strains are assigned to one of the three currently known mediasiatica sublineages, lineage M.I, together with other historical strains maintained in collections in Russia and Sweden. wgSNP shows limited previously unknown genetic diversity, with the M.I lineage size being only 118 SNPs. The wgSNP genotype is not strongly correlated with year and place of isolation. [ABSTRACT FROM AUTHOR]

Objective To study the RHD genotyping of primary screening RhD negative population in Beijing, and analyze the serological characteristics of different genotypes and the distribution of Rh phenotypes. Methods From August 2022 to January 2024, 204 RhD negative samples in our hospital were initially screened by microplate or microcolumn agglutination method. RhD antigen phenotype was identified by saline tube method, and RhD negative confirmation test was performed by microcolumn gel-indirect antiglobulin technology.RHD genotyping was performed by polymerasing chain reaction-sequence specific primmer (PCR-SSP) method and sequencing technology, and the phenotypic frequency and gene frequency were calculated. Results The distribution of Rh serologic phenotypes in 204 RhD negative samples were 112 cases of ccee (54.90%) > 73 cases of Ccee (35.78%) > 9 cases of CCee (4.41%) > 6 cases of ccEe (2.94%) > 4 cases of CcEe (1.96%). A total of 7 RHD genotypes were detected in this study, including 129 cases of RHD* 01N.01 (63.24%), 44 cases of RHD* 01EL.01 (21.57%), 26 cases of RHD* 01N.03 (12.75%), 2 cases of RHD* 01N.16 (0.98%), 1 case of RHD* 06.03.01 (0.49%), 1 case of weak RHD* 15 (0.49%) and 1 case of RHD* 13.01/RHD* 01N.01 (0.49%). The frequency and phenotype distribution of Rh blood group antigen gene were consistent with Hardy-Weinberg equilibrium (P>0.05). Conclusion The RHD gene is polymorphic in the primary screening RhD negative population in Beijing, and the most common RhD negative genotype is RHD* 01N.01, and the RHD variant is RHD* 01EL.01.This study may provide data to support the clinical implementation of genotype-matched blood transfusions.

In modern breeding work, considerable attention is paid to genetic resources of cattle, genetic assessment of which, with proper crossbreeding and selection, can increase efficiency of the entire industry. One way to realize the genetic resources of animals is to use information about polymorphism of milk productivity genes. The aim of the study was to determine polymorphism of -lactoglobulin gene in in Kholmogorsky cows and to identify its effect on economically valuable milk indicators. The experiments were carried out on the breeding stock of Kholmogorsky breed in Kholmogorsky Plemzavod. The genotype of the studied animals for LGB gene was determined by PCR RFLP using Hae III restriction endonuclease. It was established that the allele B of the -lactoglobulin gene was dominant in the genome of the studied sample of cows and its frequency of occurrence was 68%, while the most common genotype was AB (47.4%). To assess the effect of different LGB genotypes on milk productivity and milk quality of Kholmogorsky cows, productivity indicators for the last completed lactation were combined into subgroups depending on the genotypes and compared with each other. Most likely, the uniqueness of the Kholmogorsky breed, expressed not only in terms of milk productivity, exterior and constitution, but also in the gene pool, influenced the discrepancy between the obtained results and general patterns. Firstly, in our case, B allele has a positive effect both on qualitative and technological characteristics of milk, and on quantitative indicators of milk productivity. Secondly, the largest value of milk yield and the mass fraction of dry matter belongs to animals with the AB genotype. We recommended to include the procedure for assessing polymorphism of LGB gene in a set of breeding and production work activities to increase the economic efficiency of the enterprise. Such a step will also contribute to the further comprehensive study of this gene as a breeding marker.

Abstract Background Cannabis sativa is seeing a global resurgence as a food, fiber and medicinal crop for industrial hemp and medicinal Cannabis industries respectively. However, a widespread moratorium on the use and research of C. sativa throughout most of the 20th century has seen the development of improved cultivars for specific end uses lag behind that of conventional crops. While C. sativa research and development has seen significant investments in the recent past, resulting in a suite of publicly available genomic resources and tools, a versatile and cost-effective mid-density genotyping platform for applied purposes in breeding and pre-breeding is lacking. Here we report on a first mid-density fixed-target SNP platform for C. sativa. Results The High-throughput Amplicon-based SNP-platform for medicinal Cannabis and industrial Hemp (HASCH) was designed using a combination of filtering and Integer Linear Programming on publicly available whole-genome sequencing and RNA sequencing data, supplemented with in-house generated genotyping-by-sequencing (GBS) data. HASCH contains 1,504 genome-wide targets of high call rate (97% mean) and even distribution across the genome, designed to be highly informative (> 0.3 minor allele frequency) across both medicinal cannabis and industrial hemp gene pools. Average numbers of mismatch SNP between any two accessions were 251 for medicinal cannabis (N = 116) and 272 for industrial hemp (N = 87). Comparing HASCH data with corresponding GBS data on a collection of diverse C. sativa accessions demonstrated high concordance and resulted in comparable phylogenies and genetic distance matrices. Using HASCH on a segregating F2 population derived from a cross between a tetrahydrocannabinol (THC)-dominant and a cannabidiol (CBD)-dominant accession resulted in a genetic map consisting of 310 markers, comprising 10 linkage groups and a total size of 582.7 cM. Quantitative Trait Locus (QTL) mapping identified a major QTL for CBD content on chromosome 7, consistent with previous findings. Conclusion HASCH constitutes a versatile, easy to use and cost-effective genotyping solution for the rapidly growing Cannabis research community. It provides consistent genetic fingerprints of 1504 SNPs with wide applicability genetic resource management, quantitative genetics and breeding.