Characterization and Comparison of Genetic Variation in Cotesia flavipes (Hymenoptera: Braconidae) Mass Reared for Biological Pest Control Using Microsatellite Markers

The larval parasitoid Cotesia flavipes (Cameron) (Hymenoptera: Braconidae) is an important biological control agent of the sugarcane borer, Diatraea saccharalis (Fabricius) (Lepidoptera: Crambidae). This exotic parasitoid has been mass reared for field release since its introduction in the 1970s. Insects are exchanged between labs or introduced from the field, but without basic studies or criteria. Thus, the objective of this study was to evaluate the genetic variability of insects from six Brazilian States (São Paulo, Minas Gerais, Paraná, Goiás, Maranhão, and Alagoas) using microsatellites. Analysis of five loci using at least 22 females from each location was performed. The molecular analysis made possible to verify that four out of the five loci analyzed were polymorphic. The allele frequencies of three loci were in agreement with the Hardy-Weinberg Equilibrium for all insects of all regions. It was also observed that five alleles were exclusively presented in only two loci. The variation among and within populations was 24.65 and 75.34%, respectively. The estimated shared genotypes between the C. flavipes individuals showed that K = 2 was the most likely number of genetic groups causing the current variation, as well as high shared genotypes from these groups of the individuals. Considering all the analyzed loci, the genetic differentiation was at a moderate level. We suggest a possible mixture of biological materials based on genetic distances and the degree of structuring displayed.

Genomic polymorphism in tribal population of Tripura: Signifying their closer affinity with the Nepalese and Tibetan populations

BACKGROUND

India is the second most populous country in the world, which is aligned into various community segments.

AIM

To evaluate the genetic diversity of the tribal population of Tripura, we carried out this study.

SUBJECTS AND METHODS

15 autosomal STR markers were used for investigation of genomic diversity, inter- and intra- population relationships among the studied population, and other reported neighbouring tribal and caste populations.

RESULTS

Results indicated that the tribals of Tripura share their closer genetic affinity with the Trans-Himalayan (Nepalese, Bhutanese and Tibetan) populations. Locus D18S51 was found as the most discriminatory among all the studied loci with uppermost discrimination power (PD = 0.964) and lowest matching probability (Pm = 0.036) in the study. All the evaluated loci herein are useful, having the maximum value of combined power of discrimination (CPD = 1), combined power of exclusion (CPE = 0.99999746), combined paternity index (CPI = 3 × 10⁵) and combined matching probability (CPm = 2.12 × 1 0 ^-7).

CONCLUSION

Population genetic analysis showed that the studied population has genetic relatedness with the compared Nepalese and Tibetan populations i.e., Kathmandu, Tibet, Newar, and Gorkhas, followed by eastern and central Indian populations.

Association between Interleukin-1β Polymorphism at Rs16944 and Glucose Metabolism: A Cohort Study

Background: This study explored the correlation between the interleukin-1β gene rs16944 polymorphism and diabetes through epidemiological and follow-up investigations.Methods: The study was conducted on 600 subjects with normal glucose metabolism recruited from participants of the Risk Evaluation of cAncers in Chinese type 2 diabeTic Individuals: A lONgitudinal (REACTION) study in Luzhou, China in 2011. All subjects received a unified standardized questionnaire, physical examination, laboratory examination, and follow-up in 2016. Subjects were divided into normal glucose metabolism (NC), pre-diabetes (PDM), and type 2 diabetes mellitus (T2DM) groups according to their glucose metabolism after follow-up. The IL-1β gene rs16944 polymorphism was analyzed using the polymerase chain reaction-restriction fragment length polymorphism(PCR-RFLP) technique.Results: After follow-up, 386, 156, and 58 cases were observed in the NC, PDM, and T2DM groups, respectively. Serum IL-1β levels were compared to baselines at follow-up in the 3 groups; the difference in the T2DM group was statistically significant. The frequency distributions of the IL-1β gene rs16944 genotypes, i.e., CC, CT, and TT, were significantly different in the 3 groups, and the distributions in the T2DM and NC groups were significantly different. The frequency distributions of the C and T alleles of IL-1β rs16944 were not significantly different. Logistic regression analysis identified the CC+CT genotype as an independent risk factor for the development of diabetes in patients with normal glucose metabolism (OR = 2.457, 95% CI: 1.238-4.877).Conclusions: The IL-1β gene rs16944 C/T polymorphism may cause genetic susceptibility to T2DM in the Luzhou population. The CC+CT genotypes may increase T2DM risk.

Multi-dimensional diffusion process of allele frequencies in population genetics

One of the ultimate goals of population genetics is to theoretically describe the behavior of allele frequency. Diffusion theory has been commonly used for this purpose mainly in one-locus one-population models, although it is not easy to handle diffusion theory in models with multiple loci or with multiple populations. This review introduces several successful cases, where multi-dimensional diffusion equations contributed to addressing evolutionary questions, thereby demonstrating its strong potential in population genetics.

Genome Aggregation Database Version 4-Allele Frequency Changes and Impact on Variant Interpretation in Dystonia

BACKGROUND

Population-scale databases majorly contribute to variant interpretation. The recently released Genome Aggregation Database (gnomAD) v4 offers a >5-fold increased sample size compared to v2.1.1. Pathogenic variants absent from v2.1.1 are now registered in v4 at a considerable rate. The implications on variant interpretation in dystonia are unknown.

METHODS

All curated variants linked to the most common dominant forms of isolated dystonia were extracted from the International Parkinson's Disease and Movement Disorder Society Gene database. We compared variant population-frequencies and gene constraint metrics between gnomAD v2.1.1 and v4.

RESULTS

The majority of dystonia-causing variants (192/247, 77.7%) remained absent from the newer gnomAD version. Of 219 variants absent from v2.1.1, 27 (12.3%) appeared for the first time in v4.1, including well-established pathogenic alleles. Gene constraints for GNAL and KMT2B significantly decreased in v4.

CONCLUSIONS

A growing number of dystonia-linked alleles are seen in gnomAD v4. The presence in population-scale data does not preclude pathogenicity. © 2024 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

Prevalence and Reclassification of Genetic Variants in South African Populations with Breast Cancer

Concurrent testing of numerous genes for hereditary breast cancer (BC) is available but can result in management difficulties. We evaluated use of an expanded BC gene panel in women of diverse South African ancestries and assessed use of African genomic data to reclassify variants of uncertain significance (VUS). A total of 331 women of White, Black African, or Mixed Ancestry with BC had a 9-gene panel test, with an additional 75 genes tested in those without a pathogenic/likely pathogenic (P/LP) variant. The proportion of VUS reclassified using ClinGen gene-specific allele frequency (AF) thresholds or an AF > 0.001 in nonguidelines genes in African genomic data was determined. The 9-gene panel identified 58 P/LP variants, but only two of the P/LP variants detected using the 75-gene panel were in confirmed BC genes, resulting in a total of 60 (18.1%) in all participants. P/LP variant prevalence was similar across ancestry groups, but VUS prevalence was higher in Black African and Mixed Ancestry than in White participants. In total, 611 VUS were detected, representing 324 distinct variants. 10.8% (9/83) of VUS met ClinGen AF thresholds in genomic data while 10.8% (26/240) in nonguideline genes had an AF > 0.001. Overall, 27.0% of VUS occurrences could potentially be reclassified using African genomic data. Thus, expanding the gene panel yielded few clinically actionable variants but many VUS, particularly in participants of Black African and Mixed Ancestry. However, use of African genomic data has the potential to reclassify a significant proportion of VUS.

A Systematic Review and Meta-Analysis of Human Leukocyte Antigen-DR (HLA-DR) in Onychomycosis: HLA-DR8 Confers Susceptibility

Onychomycosis (OM) is a nail infection from various fungal species, representing a worldwide dermatologic health concern. The toenails are most often affected. Comorbid chronic health conditions and environmental and genetic factors play a role in the development of OM. It has been observed that certain populations have an increased risk of developing OM, suggesting an inherited component to its etiology. Recent studies have observed the impact of the human leukocyte antigen-DR (HLA-DR) profile on the likelihood of developing OM; however, none have aggregated these studies for a meta-analysis to determine a statistical effect. The literature was systematically reviewed following Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines to determine the effect of the HLA-DR profile on OM susceptibility. Studies that contained HLA-DR allele frequency data on patients with OM were included. Studies that contained too much allele frequency data, did not contain HLA-DR allele frequency data, or were written in a non-English language were excluded. Google Scholar, PubMed, and Scientific Direct databases were searched. The risk of bias was assessed by using the National Institutes of Health (NIH) quality assessment case-control study tool. The results were generated using Review Manager version 5.4 by extracting and inputting HLA-DR allele frequency data into the program. The program created aggregated odds ratios that were visually represented in forest plots. A total of five articles were included in the analysis. One hundred fifty-six patients with OM were used in this analysis. Mexican mestizos and United States Caucasian populations were represented in this study. Overall, the NIH risk of bias tool revealed that most studies included did not justify their sample size, or the assessors were not blinded. Of all the HLA-DR alleles analyzed, only HLA-DR8 revealed a statistically significant result with an odds ratio of 1.70 with a 95% CI (1.05-2.76). This suggests that HLA-DR8 confers a 70% higher risk of susceptibility to OM. This finding can help identify these target populations and serve as the basis for personalized treatment solutions.

Clonal dynamics of chronic myelomonocytic leukemia progression: paired-sample comparison

This study investigated the clonal evolution of chronic myelomonocytic leukemia (CMML) progression to secondary acute myeloid leukemia (sAML) by next-generation sequencing and pyrosequencing for variant allele frequency (VAF) of gene mutations and SNP microarray for copy neutral loss of heterozygosity (CN-LOH) in 38 paired samples from CMML/sAML patients of Taiwanese origin. The median interval between CMML and sAML samples collection was 14.9 months (1.0-89.6). RUNX1 (57%), TET2 (46%), SRSF2 (37%), and ASXL1 (28%) mutations were frequent at CMML diagnosis. Baseline VAF in epigenetic regulator genes was high (>35%) in 83% of mutational events at the CMML phase, remained stable in 78% (VAF changes <10%), and increased in 20% (increased VAF > 10%) during progression to sAML. Transcription factor genes showed high VAF (>35%) in 51% at the CMML phase, and stable VAF in 60% during progression. VAF of spliceosome genes was high (>35%) in 70% at CMML phase, and stable in 61% during progression. Activated signaling genes exhibited acquisition or loss during progression. TET2 mutations were often founding clones, and SRSF2, ASXL1, DNMT3A, EZH2, or spliceosome genes also acted as ancestral mutations. RUNX1 mutations were typically later events and occasionally ancestral hits or germline mutations. Acquisition of cytogenetic changes, signaling pathways genes (PTPN11, FLT3, NRAS, CBL), or AML-defined genes (NPM1, CEBPA, CBFB::MYH11) by linear or branching evolution occurred during sAML progression. CN-LOH was noted in EZH2, CBL, TET2, and DNMT3A genes. CEBPA mutation and concurrent biallelic TET2 with NRAS mutations at CMML diagnosis were risk factors for time to AML progression and overall survival. A characteristic ASXL1MT/RUNX1MT/SpliceosomeMT/signalingWT genetic profile was associated with monocyte counts of 0.5-1.0 × 109/l. This study highlights the complexity and heterogeneity of dynamic changes in clonal architecture during CMML progression, emphasizing its importance in pathogenesis, phenotype, risk stratification, and therapeutic strategy. © 2025 The Pathological Society of Great Britain and Ireland.

Frequencies of HFE gene mutations associated with haemochromatosis in the population of Libya living in Benghazi

THE STUDIES OF THE HFE MUTATIONS: H63D and C282Y in North African populations have revealed the extreme rarity or even the absence of the C282Y mutation. We have examined 200 chromosomes (100 Libyan people live in Benghazi) for the presence of the two HFE mutations by PCR-RFLP analysis by using PCR conditions used to amplify both Autosomal and Y chromosomal STRs. We have found that the allele frequencies are, respectively, 17% for the H63D and 0% for the C282Y. These results are consistent with the worldwide spread of the H63D mutation and the north European restriction of the C282Y.

Ethnic Differences in Genetic Ion Channelopathies Associated with Sudden Cardiac Death: A Systematic Review and Meta-Analysis

BACKGROUND AND AIMS

Reports of allele frequencies encoding ion channel, or their interacting proteins associated with sudden cardiac death among different ethnic groups have been inconsistent. Here, we aimed to characterize the distribution of these genes and their alleles among various ethnicities through meta-analysis.

METHODS

We conducted a systematic review and meta-analysis to assess the mean allele frequencies of channelopathy genes SCN5A, NOS1AP, KCNH2, KCNE1, and KCNQ1 among the Black, Caucasian, Asian, and Hispanic ethnicities. Searches in PubMed, Google Scholar, and Web of Science resulted in 18 reports published before July 2015 that met the eligible criteria. Allele frequencies were averaged by weight, and pooled values were calculated by inverse variance. Fixed-effects and random-effects models were used to pool effect sizes within each study and across different studies, respectively. Moreover, to extend our findings, we used sequenced genomic data from the Exome Aggregation Consortium to compare allele frequencies between different ethnicities.

RESULTS

Meta-analysis of published studies supports that Asians had the highest overall mean allele frequencies of NOS1AP (0.36%, 95% CI: 0.30, 0.43; P<0.001), and SCN5A frequencies (0.17%, 95% CI: 0.07, 0.27, P=0.001), and whereas Caucasians had the highest KCNH2 frequency (0.21%, 95% CI: 0.16, 0.25; P<0.001), and Hispanics the highest KCNQ1 frequency (0.16%). Analysis of the Exome Aggregation Consortium also provided consistent data in agreement the meta-analysis.

CONCLUSION

Overall, Asians carried the most alleles of genes associated with sudden cardiac death. The meta-analysis reveals significant differences in allele distribution of channelopathy-associated genes among different ethnic groups.

Frequencies of Cytochrome P450 2B6 and 2C8 Allelic Variants in the Mozambican Population

BACKGROUND

The cytochrome P450 enzymes (CYP) play an important role in the metabolism of many therapeutic agents. The activities of different enzymes exhibit variability in different populations, which causes variations in drug response or toxicity. The CYP2B6 and CYP2C8 enzymes are encoded by polymorphic genes characterised by different single nucleotide polymorphisms (SNPs). Several of these CYP variants are often associated with slow metabolism phenotypes. This study aimed to analyse the frequencies of allelic variants of CYP2B6 and CYP2C8 in the Mozambican population.

METHODS

Using a polymerase chain reaction and restriction fragment length polymorphism assay (PCR-RFLP), the frequencies of the allelic variants of CYP2B6 (c.64C>T, c.516G>T, c.777C>A, c.785A>G, c.1459C>T) and CYP2C8 (c.805A>T, c.416G>A, c.1196A>G, c.792C>G) were determined in 360 Mozambican blood donors.

RESULTS

The frequencies of the allelic variants of the CYP2B6 gene were 0.057, 0.426, 0.0, 0.410, and 0.004. For the CYP2C8 gene, the frequencies of the allelic variants were 0.160, 0.048, 0.0, and 0.005. No significant differences were observed between the gender and geographic distribution of volunteers around the country.

CONCLUSION

The frequencies of the allelic variants of the CYP2B6 and CYP2C8 genes were found to be homogeneously distributed in the Mozambican population and were comparable to other African populations. Further studies are required to explore the impact of these variants on the clinical response (efficacy and toxicity) of drugs, including antimalarials.

Genetic landscape of human neutrophil antigen variants in India from population-scale genomes

Antibodies against human neutrophil antigens (HNAs) play a significant role in various clinical conditions such as neonatal alloimmune neutropenia, transfusion-related acute lung injury, and other nonhemolytic transfusion reactions. This study aims to identify the genotype and allele frequencies of HNAs in the healthy Indian population. Ten genetic variants in four human genes encoding alleles of HNAs class I-V approved by the International Society of Blood Transfusion-Granulocyte Immunobiology Working Party were used in the analysis. Genetic variants from whole genome sequences of 1029 healthy Indian individuals corresponding to HNA alleles were analyzed. The frequencies of the variants were compared with global population datasets using an in-house computational pipeline. In HNA class I, allele frequencies of FCGR3B*01, FCGR3B*02, and FCGR3B*03 encoding HNA-1a, HNA-1b, and HNA-1c were 0.07, 0.8, and 0.13, respectively. HNA class 3 alleles namely SLC44A2*01 (encoding HNA-3a) and SLC44A2*02 (encoding HNA-3b) were found at allele frequencies of 0.78 and 0.22, respectively. The frequencies of ITGAM*01 encoding HNA-4a and ITGAM*02 encoding HNA-4a were 0.95 and 0.05, respectively. Furthermore, allele frequencies of HNA class 5 alleles were 0.32 for ITGAL*01 (encoding HNA-5a) and 0.68 for ITGAL*02 (encoding HNA-5b). Interestingly, it was also found that rs2230433 variant deciding the HNA class 5 alleles, was highly prevalent (78.2%) in the Indian population compared with other global populations. This study presents the first comprehensive report of HNA allele and genotype frequencies in the Indian population using population genome datasets of 1029 individuals. Significant difference was observed in the prevalence of HNA5a and HNA5b in India in comparison to other global populations.

Potential status of A1 and A2 variants of bovine beta-casein gene in milk samples of Indian cattle breeds

This study aimed to determine the polymorphism in 7th exon of beta-casein gene (CSN2) gene in seven domestic (Kosali, Tharparkar, Gangatiri, Sahiwal, Gir, Khariar, Motu) and two exotic cattle breeds (Jersey and Holstein-Friesian). Genomic DNA was extracted from 1000 milk samples, and the C > A polymorphism in CSN2 was determined using the tetra-primer amplification refractory mutation system-polymerase chain reaction method. In all Indigenous cattle breeds, the mean frequency of A1A2 and A2A2 genotypes was 0.19 and 0.80, respectively. The A1A1 genotype was absent in all seven domestic cattle breeds. The frequency of the A2A2 genotype was highest in the Gir breed (0.93). However, the Sahiwal, Tharparkar, and Motu breeds also had a higher frequency of A2A2 genotype compared to other breeds. In contrast, Gangatiri breed of India showed lowest frequency of A2A2 genotype. The mean A1 and A2 allele frequency was 0.09 and 0.91, respectively. In exotic breeds, the mean frequencies of the A1A1, A1A2, and A2A2 genotypes were 0.42, 0.55, and 0.03, respectively. Similarly, the mean A1 and A2 allele frequency was 0.69 and 0.31, respectively. This study suggests the high potential of Gir, Sahiwal, Tharparkar, and Motu cattle for A2 milk production since they carry a favorable A2 genotype.

Genotypic and Allelic Frequencies of Degenerative Myelopathy in an Italian Canine Population

Canine degenerative myelopathy is a fatal neurodegenerative disorder that affects the spinal cord. It is a late-onset disease, with symptoms becoming evident later in life at approximately 8 years of age. The principal aim of this study was to retrospectively evaluate allelic and genotypic frequencies of the c.118G > A and c.52A > T mutations located on the SOD1 gene in an Italian canine population to provide detailed information on the prevalence of the mutations in the country. The genetic data of different breeds were collected through DNA tests over a nine-year period in the Italian canine population. For each dog, the breed, sex, age, and DNA test results were recorded. Allelic and genotypic frequencies were calculated. A total of 1667 DNA tests for the c.118G > A and c.52A > T mutations were carried out on 84 breeds. For the analysis of prevalence, only breeds counting more than 20 subjects have been considered, for a total of 1410 DNA tests obtained from 13 different breeds. In the population tested for the c.118G > A mutation, 65.47% (n. 893) of the subjects were clear, 25.59% (n. 349) were heterozygous carriers, and 8.94% (n. 122) were homozygous for the mutated allele. The mutation showed the highest frequency in Pembroke Welsh Corgis (55.49%) and the lowest frequencies in Poodles (6.32%) and Australian Shepherds (7.14%). The allelic frequency of the c.52A > T mutation was 7.61% in the Bernese Mountain dog. Neither variant differed between females and males in genotypic frequencies. The present study provides insights into the allelic and genotypic frequencies of canine degenerative myelopathy in different dog breeds in Italy.

Expanding the Russian allele frequency reference via cross-laboratory data integration: insights from 7452 exome samples

Population allele frequency is crucially important for accurate interpretation of known and novel variants in medical genetics. Recently, several large allele frequency databases, such as the Genome Aggregation Database (gnomAD), have been created to serve as a global reference for such studies. However, frequencies of many rare alleles vary dramatically between populations, and population-specific allele frequency is often more informative than the global one. Many countries and regions, including Russia, remain poorly studied from the genetic perspective. Here, we report the first successful attempt to integrate genetic information between major medical genetic laboratories in Russia. We construct RUSeq, an open, large-scale reference set of genetic variants by analyzing 7452 exome samples collected in two major Russian cities-Moscow and St. Petersburg. An ∼10-fold increase in sample size compared to previous studies allowed us to characterize extensive genetic diversity within the admixed Russian population with contributions from several major ancestral groups. We highlight 51 known pathogenic variants that are overrepresented in Russia compared to other European countries. We also identify several dozen high-impact variants that are present in healthy donors despite being annotated as pathogenic in ClinVar and falling within genes associated with autosomal dominant disorders. The constructed database of genetic variant frequencies in Russia has been made available to the medical genetics community through a variant browser available at http://ruseq.ru.

Putative adaptive loci show parallel clinal variation in a California-endemic wildflower

As the global climate crisis continues, predictions concerning how wild populations will respond to changing climate conditions are informed by an understanding of how populations have responded and/or adapted to climate variables in the past. Changes in the local biotic and abiotic environment can drive differences in phenology, physiology, morphology and demography between populations leading to local adaptation, yet the molecular basis of adaptive evolution in wild non-model organisms is poorly understood. We leverage comparisons between two lineages of Calochortus venustus occurring along parallel transects that allow us to identify loci under selection and measure clinal variation in allele frequencies as evidence of population-specific responses to selection along climatic gradients. We identify targets of selection by distinguishing loci that are outliers to population structure and by using genotype-environment associations across transects to detect loci under selection from each of nine climatic variables. Despite gene flow between individuals of different floral phenotypes and between populations, we find evidence of ecological specialization at the molecular level, including genes associated with key plant functions linked to plant adaptation to California's Mediterranean climate. Single-nucleotide polymorphisms (SNPs) present in both transects show similar trends in allelic similarity across latitudes indicating parallel adaptation to northern climates. Comparisons between eastern and western populations across latitudes indicate divergent genetic evolution between transects, suggesting local adaptation to either coastal or inland habitats. Our study is among the first to show repeated allelic variation across climatic clines in a non-model organism.

Very low frequency of the lactase persistence allele LCT-13910T in the Armenian population

Primary lactose malabsorption is characterised by a down-regulation of lactase activity after weaning and inability to digest lactose in adulthood. It has been suggested that the historical introduction of dairying led to a positive selection for lactase persistence variants in a regulatory region upstream of the LCT gene. Here, we genotyped 202 Armenian subjects for LCT-13910T, a lactase persistence variant which is widespread in Europeans. The homozygous C/C genotype associated with primary hypolactasia, the heterozygous C/T and the homozygous T/T lactase persistence genotypes were found in 191 (94.6%), 11 (5.4%), and 0 (0.0%) samples, respectively. The frequency for the LCT-13910*T allele was 2.7%. The observed allele frequency of 2.7% for LCT-13910T is even lower than previously reported and supports current phenotypic data about lactose malabsorption in Armenia.

Determination of Carrier Frequency of Actionable Pathogenic Variants in Autosomal Recessive Genetic Diseases in the Turkish Cypriot Population

Whole-exome DNA sequencing is a rich source of clinically useful information for specialists, patients, and their families, as well as elucidating the genetic basis of monogenic and complex diseases in clinical diagnosis. However, interpreting and reporting variants encompassing exome and genome sequence analysis outcome data are one of the greatest challenges of the genomic era. In this study, we aimed to investigate the frequency and allele frequency spectrum of single nucleotide variants accepted as recessive disease carrier status in Turkish Cypriot exomes. The same sequencing platform and data processing line were used for the analysis of data from 100 Turkish Cypriot whole-exome sequence analysis. Identified variants were classified according to ACMG guidelines, and pathogenic variants were confirmed in other databases such as ClinVar, HGMD, Varsome, etc. Pathogenic variants were detected in 68 genes out of 100 whole-exome sequence data. The carriage rate was the highest in the CYP21A2 gene, causing 21-hydroxylase deficiency (14.70%), 11.76% in the HBB gene causing β-thalassemia, 10.29% in the BTD gene causing biotinidase deficiency, 8.82% in the CFTR gene causing cystic fibrosis, 8.82% in the RBM8A gene causing thrombocytopenia-absent radius syndrome, which is an ultra-rare disease, and 5.88% in the GAA gene causing glycogen storage disease II. The carriage of pathogenic variants in other genes causing the disease (GJB2, PAH, GALC, CYP11B2, COL4A3, HBA1, etc.) was determined as less than 5.00%. Also, the identified variations in the mentioned gene within the examined population were reported. The most prevalent mutation in North Cyprus was a missense variant (c.1360 C>T, p.Pro454Ser) detected in the CYP21A2 gene (rs6445), and the most frequently seen variant in the HBB gene was c.93-21G>A (rs35004220). We investigated reported pathogenic variants by estimating the lower and upper limits of carrier and population frequencies for autosomal recessive diseases, for which exome sequencing may reveal additional medically relevant information. Determining the lower and upper limits of these frequencies will shed light on preventive medicine practices and governmental actions.

CD21 deficiency in 2 siblings and frequency of the associated mutation in the Danish population

The clinical presentation of CD21 deficiency in 2 siblings caused by a novel mutation in the CD21 gene is reported, and the frequency of this mutation in the Danish population is explored. Successful treatment with IgG replacement in both patients with CD21 deficiency is also reported.

ALFRED: an allele frequency database for microevolutionary studies

Many kinds of microevolutionary studies require data on multiple polymorphisms in multiple populations. Increasingly, and especially for human populations, multiple research groups collect relevant data and those data are dispersed widely in the literature. ALFRED has been designed to hold data from many sources and make them available over the web. Data are assembled from multiple sources, curated, and entered into the database. Multiple links to other resources are also established by the curators. A variety of search options are available and additional geographic based interfaces are being developed. The database can serve the human anthropologic genetic community by identifying what loci are already typed on many populations thereby helping to focus efforts on a common set of markers. The database can also serve as a model for databases handling similar DNA polymorphism data for other species.

HLA class II antigens in Croatian patients with pemphigus vulgaris and their correlation with anti-desmoglein antibodies

Pemphigus vulgaris (PV) is an acquired autoimmune blistering disease characterized by the production of autoantibodies targeting desmosomal cadherins, primarily desmoglein 1 and desmoglein 3, leading to acantholysis. The etiology of PV is multifactorial, including genetic susceptibility. This retrospective study aimed to evaluate the association of HLA class II alleles and PV and to examine the impact of PV-associated HLA class II alleles on the concentration of anti-desmoglein antibodies. The study group included 30 patients in whom the diagnosis of PV was confirmed by histopathological analysis, immunofluorescence findings, and ELISA testing for detecting antibodies against desmoglein 1 and desmoglein 3. HLA class II alleles were typed by polymerase chain reaction with sequence-specific primers (PCR-SSP). The control group consisted of 190 healthy volunteer blood donors. Data analysis revealed a significantly higher frequency of HLA class II alleles in our population of patients with PV, including HLA-DRB1*04:02, HLA-DRB1*14:54, HLA-DQB1*03:02, HLA-DQB1*05:03, HLA- DQA1*03:01, and HLA-DQA1*01:04, as well as a significantly lower frequency of HLA-DQA1*05:01 compared to the control group. We have also investigated the influence of risk alleles for PV, recognized in almost all study populations, HLA-DRB1*04:02 and HLA-DQB1*05:03, on the concentration of antibodies against desmogleins 1 and 3 in relation to the presence of these alleles. The results showed significantly higher levels of antibodies directed against desmoglein 3 among patients with DRB1*04:02 compared to patients without this allele. No difference was found for anti-desmoglein 1 antibodies. Regarding DQB1*05:03 allele, statistical analysis showed no differences in the concentration of anti-desmoglein antibodies in patients carrying this allele versus those without it.

Additional evidence supports GRM6 p.Thr178Met as a cause of congenital stationary night blindness in three horse breeds

Congenital stationary night blindness (CSNB) is an ocular disorder characterized by nyctalopia. An autosomal recessive missense mutation in glutamate metabotropic receptor 6 (GRM6 c.533C>T, p.(Thr178Met)), called CSNB2, was previously identified in one Tennessee Walking Horse and predicted to reduce binding affinity of the neurotransmitter glutamate, impacting the retinal rod ON-bipolar cell signaling pathway. Thus, the first aim was to identify the allele frequency (AF) of CSNB2 in breeds with reported cases of CSNB and breeds closely related to the Tennessee Walking Horse. The second aim was to perform ocular examinations in multiple breeds to confirm the link between genotype and CSNB phenotype. In evaluating 3518 horses from 14 breeds, the CSNB2 allele was identified in nine previously unreported breeds. The estimated AF was highest in pacing Standardbreds (0.17) and lowest in American Quarter Horses (0.0010). Complete ophthalmic examinations and electroretinograms (ERG) were performed on 19 horses from three breeds, including one CSNB2 homozygote from each breed. All three CSNB2/CSNB2 horses had an electronegative ERG waveform under scotopic light conditions consistent with CSNB. The remaining 16 horses (seven CSNB2/N and nine N/N) had normal scotopic ERG results. All horses had normal photopic ERGs. This study provides additional evidence that GRM6 c.533C>T homozygosity is likely causal to CSNB in Tennessee Walking Horses, Standardbreds, and Missouri Fox Trotting Horses. Genetic testing is recommended for breeds with the CSNB2 allele to limit the production of affected horses. This study represents the largest across-breed identification of CSNB in the horse and suggests that this disorder is likely underdiagnosed.

Changes in genomic inbreeding and diversity over half a century in Swedish Red and Swedish Holstein dairy cattle

Swedish Red (SR) and Swedish Holstein (SH) are the dominating commercial dairy cattle breeds in Sweden. Both breeds have undergone substantial changes during the last half century due to intensive selection for breeding goal traits, but also resulting from increased international exchange of breeding animals and genetic drift. The aim of this study was to learn more about changes in genomic diversity and inbreeding in these two breeds over time. Therefore, semen samples from old bulls were genotyped using the 150K Genomic Profiler SNP array and combined with 50K SNP array genotype data, obtained for more recent bulls from the Nordic Cattle Genetic Evaluation. Different measures of level of homozygosity, genomic inbreeding, relatedness and changes in allele frequency were estimated for bulls born during different time periods from the 1950s until 2020. In total, more than 33,000 SNPs for 9737 SR and 5041 SH bulls were included in the analysis using PLINK v1.9. The results showed higher average homozygosity for SR than for SH bulls up to around 2000, but the difference was very small after that. The average inbreeding coefficients based on deviation from expected homozygosity as well as on runs of homozygosity decreased until the early 1980s in both breeds, whereafter they started to increase again for SH, but stayed more stable for SR. From the 1990s onwards, SH displayed higher average inbreeding coefficients than SR. In the last studied birth year group (2015-2020), the mean inbreeding coefficient based on runs of homozygosity was 5.9% for SH and 3.7% for SR. A principal component analysis showed a pattern of genetic relationships related to the birth year period of the bulls, illustrating the gradual change of the genetic material within each breed. The change in allele frequency over time was generally larger for SH than for SR. The results show that the inbreeding level was higher half a century ago than at present, and the inbreeding levels were lower than in some other studied populations. Still, the increase seen for inbreeding coefficients and homozygosity, especially in SH during recent years, should be considered in future breeding strategies.

Common, Intermediate and Well-Documented HLA Alleles in the Brazilian Population: An Analysis of the Brazilian Bone Marrow Donor Registry (REDOME)

This study investigates the HLA allele diversity in Brazil, a reflection of the country's unique history of population admixture. The international comparison of findings emphasises the importance of incorporating underrepresented populations into global HLA databases. We present a comprehensive analysis of HLA alleles within the Brazilian population, utilising high-resolution sequencing data from 298,000 unrelated haematopoietic stem cell volunteer donors registered with the Brazilian Bone Marrow Donor Registry (REDOME). Our research encompasses donors from all regions of Brazil, identifying HLA alleles that are catalogued as common, intermediate or well-documented (CIWD Version 3.0). We evaluated the alleles of HLA-A, HLA-B, HLA-C, HLA-DRB1, HLA-DQA1, HLA-DQB1, HLA-DPA1 and HLA-DPB1. At a two-field resolution, we identified 1969 alleles: 418 were classified as common, 358 as intermediate and 1193 as non-CIWD in Brazil. Notably, we report HLA alleles that, while not classified as common or intermediate in the CIWD 3.0 catalogue, are prevalent within the Brazilian population. A detailed list of alleles from the registry, presented at a two-field resolution and supplemented with grouped ARD levels, including three- or four-field resolution when available, serves as an essential reference for HLA typing frequencies specific to the Brazilian population.

MLNe: Simulating and Estimating Effective Size and Migration Rate from Temporal Changes in Allele Frequencies

In studies of molecular ecology, conservation biology and evolutionary biology, the current or recent effective size (Ne) of a population is frequently estimated from the marker genotype data of two or more temporally spaced samples of individuals taken from the population. Despite the developments of numerous Bayesian, likelihood and moment estimators, only a couple of them can use both temporally and spatially spaced samples of individuals to estimate jointly the effective size (Ne) of and the migration rate (m) into a population. In this note I describe new implementations of these joint estimators of Ne and m in software MLNe which runs on multiple platforms (Windows, Mac, Linux) with or without a graphical user interface (GUI), has an integrated simulation module to simulate genotype data for investigating the impacts of various factors (such as sample size and sampling interval) on estimation precision and accuracy, exploits both Message Passing Interface (MPI) and openMP for parallel computations using multiple cores and nodes to speed up analysis. The program does not require data pre-processing and accepts multiple formats of a file of original genotype data and a file of parameters as input. The GUI facilitates data and parameter inputs and produces publication-quality output graphs, while the non-GUI version of software is convenient for batch analysis of multiple datasets as in simulations. MLNe will help advance the analysis of temporal genetic marker data for estimating Ne of and m between populations, which are important parameters that will help biologists for the conservation management of natural and managed populations. MLNe can be downloaded free from the website http://www.zsl.org/science/research/software/.