SNP Genotyping Research Articles

Two genetic variants in the HIBCH and FTCDNL1 genes are associated with susceptibility to developmental dysplasia of the hips among the Han Chinese population of Southwest China

BackgroundDevelopmental dysplasia of the hip (DDH) is a common cause of childhood disability, and the incidence of DDH shows significant familial aggregation. As the genetic factors of DDH remain unknown, the correlation between five candidate single nucleotide polymorphisms (SNPs) and DDH was evaluated in the Han Chinese population of Southwest China.MethodsA case‒control association study was conducted in 276 patients with DDH and 318 healthy controls. SNP genotyping in the case and control groups was performed by SNPshot and multiple PCR. SNPs were genotyped in the case and control groups by multiplex PCR. The relationship between DDH and candidate SNPs was evaluated using the χ2 test.ResultsThe genotype distributions of rs291412 in HIBCH and rs769956 in FTCDNL1 were different between the case and control groups (P < 0.05). After genetic model analysis, logistic regression analysis revealed that the C allele of rs291412 had a protective effect on DDH (OR = 0.605, P = 0.010) and that the G allele of rs769956 was a risk factor (OR = 2.939, P = 0.010).s.ConclusionThese SNPs could be associated with susceptibility to DDH but larger population-based studies should confirm the current results.

Genotypic and phenotypic characterisation of three local chicken ecotypes of Ghana based on principal component analysis and body measurements.

This study aimed to characterise three Ghanaian local chicken ecotypes, namely, Interior Savannah, Forest, and Coastal Savannah, based on morphological data and single nucleotide polymorphism (SNP) genotypes. Morphological data including body weight, shank length, body girth, back length, thigh length, beak length, comb length, and wattle length were collected from 250 local chickens. DNA isolated from blood of 1,440 local chickens was used for SNP genotyping with the Affymetrix chicken 600k SNP chip. Principal component analysis showed that Forest and Coastal Savannah birds were closely related. Generally, all three ecotypes exhibited high genetic diversity, especially birds from the Interior Savannah zone. Morphological characterisation showed that ecotype (p = 0.016) and sex (p = 0.000) had significant effects on body weight. Birds of the Interior Savannah ecotype were the heaviest (p = 0.004), with mean weights of 1.23 kg for females and 1.40 kg for males. Sex also had a strong significant effect on most of the morphological measurements, but the sex * ecotype interaction effect was not significant. Very few of the feather phenotypes previously reported to be associated with heat resistance-frizzle (2%) and naked neck (1.6%)-were found in the studied populations. It is concluded that the three local ecotypes are genetically diverse but with similar morphological features and the information provided would be useful for future selection decisions.

Comprehensive breast cancer risk analysis with whole exome sequencing and the prevalence of BRCA1 and ABCG2 mutations and oncogenic HPV.

Breast cancer is the most prevalent cancer and also the leading cause of cancer death in women worldwide. A comprehensive understanding of breast cancer risk factors and their incidences is useful information for breast cancer prevention and control planning. The present study aimed to provide information on single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) in breast cancer, the allele frequency of two SNPs in breast cancer-related genes BRCA1 DNA repair associated (BRCA1; rs799917) and ATP binding cassette subfamily G member 2 (ABCG2; rs2231142), and the prevalence of human papillomavirus (HPV) infections in a normal population living in Phayao Province, Northern Thailand. One breast cancer and 10 healthy samples were investigated by whole exome sequencing (WES) and compared for genetic variation. The WES data contained SNPs in genes previously implicated in breast cancer and provided data on CNVs. The allele frequencies for SNPs rs799917 and rs2231142 were also examined. The SNP genotype frequencies were 35.88% CC, 46.54% CT, and 17.58% TT for rs799917 and 33.20% CC, 46.88% CA, and 19.92% AA for rs2231142. A total of 825 human whole blood samples were examined for HPV infection by PCR, and the pooled DNA was tested for HPV infection using metagenomic sequencing. No HPV infections were detected among all 825 samples or the pooled blood samples. The incidence of breast cancer among the tested samples was estimated based on acceptable breast cancer risk factors and demographic data and was 1.47%. The present study provided data on SNPs and CNVs in breast cancer-related genes. The associations between SNPs rs2231142 and rs799917 and breast cancer should be further investigated in a case-control study since heterozygous and homozygous variants are more common. Based on the detection of HPV infection in the blood samples, HPV may not be associated with breast cancer, at least in the Northern Thai population.

Local versus regional patterns in zoospore dispersal of the kelp Eisenia bicyclis (Laminariales, Phaeophyceae)

SummaryIt is generally accepted that kelp populations have a metapopulation structure. Most zoospores settle near to their parent individual, and infrequent but long‐distance dispersal of zoospores contributes to gene flow between local populations. Population genetic analysis of single nucleotide polymorphism genotyping by MIG‐seq (i.e. multiplexed inter‐simple sequence repeats genotyping by sequencing) was performed on the dominant kelp, Eisenia bicyclis, in two areas: Kitsunezaki (a sheltered area) and Shimoda (an exposed site). Regional scale analysis of genetic structure was conducted at six sites in Kitsunezaki and three sites in Shimoda. When viewed on a regional scale based on the inbreeding coefficient within the local population, the inbreeding ratio was higher in Shimoda than in Kitsunezaki, probably as a result of the limited vertical zonal distribution in the exposed environment. Vertically wide distribution in the sheltered environment apparently enabled frequent crossing among individuals in Kitsunezaki. By contrast, when viewed on a local scale based on the pairwise kinship coefficient (FST) between populations, gene flow among local populations in Shimoda occurred over a wide area, but was limited in Kitsunezaki. In Shimoda, genetic exchange between local populations, even if inbreeding is locally active, is likely to support metapopulation maintenance and rapid recovery of local populations. In Kitsunezaki, however, genetic exchange among local populations is limited within few 100 m, and the metapopulation structure will decline in the long term because of inbreeding depression. Local dispersal distance of zoospores was investigated based on parent–offspring analysis in the Kitsunezaki population, which revealed that zoospores mainly settled within 5 m of their parent. However, some zoospores traveled over 27 m within the 4 × 30 m study area. The present study shows the importance of examination at different spatial scales when investigating zoospore dispersal of laminarialean kelps.

Assessment of DNA quality for whole genome library preparation

In recent years, more sophisticated DNA technologies for genotyping have enabled considerable progress in various fields such as clinical genetics, archaeogenetics and forensic genetics. DNA samples previously rejected as too challenging to analyze due to low amounts of degraded DNA can now provide useful information. To increase the chances of success with the new methodologies, it is crucial to know the fragment size of the template DNA molecules, and whether the DNA in a sample is mostly single or double stranded. With this knowledge, an appropriate library preparation method can be chosen, and the DNA shearing parameters of the protocol can be adjusted to the DNA fragment size in the sample. In this study, we first developed and evaluated a user-friendly fluorometry-based protocol for estimation of DNA strandedness. We also evaluated different capillary electrophoresis methods for estimation of DNA fragmentation levels. Next, we applied the developed methodologies to a broad variety of DNA samples processed with different DNA extraction protocols. Our findings show that both the applied DNA extraction method and the sample type affect the DNA strandedness and fragmentation. The established protocols and the gained knowledge will be applicable for future sequencing-based high-density SNP genotyping in various fields.

Gene‒Environment Interaction Between CAST Gene and Eye-Rubbing in the Chinese Keratoconus Cohort Study: A Case-Only Study.

Keratoconus (KC), characterized by progressive corneal protrusion and thinning, is a complex disease influenced by the combination of genetic and environmental factors. The purpose of this study was to explore potential gene‒environment interaction between the calpastatin (CAST) gene and eye-rubbing in KC. A case-only study including 930 patients (676 patients with eye-rubbing and 254 patients without eye-rubbing) from the Chinese Keratoconus (CKC) cohort study was performed in the present study. Genotyping of single nucleotide polymorphism (SNP) was conducted using the Illumina Infinium Human Asian Screening Array (ASA) Beadchip. The gene‒environment interactions between CAST gene and eye-rubbing were analyzed using PLINK version 1.90. The interactions between CAST genotypes and eye-rubbing were analyzed by logistic regression models. The SNP-SNP-environment interactions were analyzed using generalized multifactor dimensionality reduction (GMDR). Three SNPs in CAST gene, namely, rs26515, rs27991, and rs9314177, reached the significance threshold for interactions (defined as P < 2.272 × 10-3). Notably, the minor alleles of these three SNPs exhibited negative interactions with eye-rubbing in KC. The results of logistic regression models revealed that the minor allele homozygotes and heterozygotes of rs26515, rs27991, and rs9314177 also exhibited negative interactions with eye-rubbing. Furthermore, GMDR analysis revealed the significant SNP-SNP-environment interactions among rs26515, rs27991, rs9314177, and eye-rubbing in KC. This study identified rs26515, rs27991, and rs9314177 in CAST gene existed gene-environment interactions with eye-rubbing in KC, which is highly important for understanding the underlying biological mechanisms of KC and guiding precision prevention and proper management.

Genotyping SNPs and Indels: A method to improve the scope and sensitivity of High-Resolution melt (HRM) analysis based applications

High-resolution melt (HRM) analysis is a closed-tube technique for detecting single nucleotide polymorphisms (SNPs). However, it has limited use in high-resolution melting devices, even those with high thermal accuracy (HTA). In addition to the cost of switching to these specialized devices, the presence of nearest neighbour neutral changes (class III, IV SNPs and small indels) made HRM-based assays a challenging task due to reduced sensitivity. This study aimed to design a common modified competitive amplification of differently melting amplicons (CADMA)-based assay to address these challenges by generating allele-specific qPCR products that are detectable on most qPCR platforms.For this study, SNPs were selected from all four classes of SNPs (class I: C/T or G/A mutation; class II: C/A or G/T mutation; class III: G/C mutation; class IV: A/T mutation). A single base pair and 19 bp indels were also chosen to simulate how CADMA primers could be designed for indels of varying lengths. The melting temperatures (Tm) were determined using IDT oligoAnalyzer. qPCR and melt data acquisition were performed on the CFX96 qPCR platform, and the melt curve data were analyzed using Precision Melt software (Bio-Rad, USA). The clusters for different genotypes were successfully identified with the aid of the control samples, and Tm predictions were carried out using the uMelt batch and Tm online tools for comparison.Using HRM-qPCR assays based on the modified CADMA method, genotyping of various SNPs was successfully carried out. For some SNPs, similarly shaped melt curves were observed for homozygotes and heterozygotes, making shape-based genotype prediction difficult. The Tm values calculated via the Blake and Delcourts (1998) method were the closest to the experimental Tm values after adjusting for the salt concentration.Since HRM assays usually depend on the ΔTm caused by mutations, they are prone to a high error rate due to nearest neighbour neutral changes. The technique developed in this study significantly reduces the failure rates in HRM-based genotyping and could be applied to any SNP or indel in any platform. It is crucial to have a deep understanding of the melt instrument, its accuracy and the nature of the target (SNP class or indel length and GC content of the flanking region). Furthermore, the availability of controls is essential for a high success rate.

Optimizing Strategy for Whole-Genome Genotype Imputation in Scallops

Advancements in sequencing technologies have facilitated low-coverage whole-genome sequencing (lcWGS) for detecting millions of single nucleotide polymorphisms (SNPs) in large populations at low cost. The effectiveness of this approach relies on genotype imputation following lcWGS. While several imputation methods have been applied in human and other terrestrial animals, their performance in aquaculture organisms, particularly mollusks, remains unassessed. Mollusks contribute 70% of mariculture production in China and are characterized by high genetic polymorphism. In this study, we aimed to optimize reference panel construction and evaluate imputation strategies for SNP detection in two scallops, Chlamys farreri and Patinopecten yessoensis, both important bivalve species. High-coverage whole-genome sequencing (hcWGS) data were used to construct haplotype reference panels, and three imputation methods were applied: Beagle5.4, GLIMPSE2, and QUILT. QUILT outperformed other methods, achieving imputation quality scores (IQS) exceeding 0.930 in C. farreri and 0.946 in P. yessoensis, and yielded the highest number of imputed loci in both species. Furthermore, panel construction was optimized by adjusting for genotype quality (GQ) and minor allele frequency (MAF); we determined that a GQ threshold > 20 and an MAF threshold > 0.01 were optimal. We observed that imputation quality improved with increased sequencing depth, plateauing at 0.5×, and varied with sample size depending on the imputation method. A negative correlation was observed between imputation quality and the ratio of non-synonymous to synonymous substitution rates (Ka/Ks) across chromosomal segments, highlighting the influence of selection pressure on imputation efficacy. Collectively, our findings provide an optimized framework for SNP genotyping using lcWGS in scallops, with implications for aquaculture breeding and genetic research.

Imputation of single nucleotide polymorphism genotypes in ungenotyped sport horses from the genotypes of their progeny

Many sport horse studbooks worldwide use microsatellite markers for parentage verification. However, many have expressed a desire to introduce genomic selection using genome-wide dense single nucleotide polymorphism (SNP) genotypes to complement their current breeding programmes. Hence, it does not make sense to genotype the same animal for both microsatellite markers and SNP markers. Transitioning to SNP-based parentage verification is an obvious solution but one barrier to this transition is the lack of SNP data on parents from which to verify parentage against. Therefore, the objective of this study was to assess the ability to impute the SNP genotype of a stallion from the genotypes of its progeny, with or without the consideration of the genotype of the progeny’s dam. Genotype information from 55 935 SNPs was available on 13 327 horses. A total of 98 stallions had genotype data on 10 progeny and the genotypes of these stallions were used as a test population. Genome-wide genotype imputation was undertaken by combining a family- and population-based imputation approach. Several different scenarios were assessed to quantify the ability to accurately impute the genotype of a stallion based on genotype data of incrementally more half-sibling progeny. Using genomic information from four progeny the average genotype concordance of the imputed sire genotype compared to the actual sire’s genotype was 0.932. The average genotype concordance rate increased to 0.960 when the genotypes of 10 progeny were included in the imputation process. The inclusion of the genotypes of the dams of the progeny improved the concordance rate from 0.932 to 0.977 when based on the genotype of just four progeny and their dams and from 0.960 to 0.996 when based on the genotype of 10 progeny and their dams. These results suggest it is possible to impute the genotype of a non-genotyped horse from the genotypes of its progeny and that the inclusion of the genotypes of the dams of the progeny improves this imputation accuracy further.

Multi-polygenic score prediction of mathematics, reading, and language abilities independent of general cognitive ability.

Specific cognitive abilities (SCA) correlate genetically about 0.50, which underpins general cognitive ability (g), but it also means that there is considerable genetic specificity. If g is not controlled, then genomic prediction of specific cognitive abilities is not truly specific because they are all perfused with g. Here, we investigated the heritability of mathematics, reading, and language ability independent of g (SCA.g) using twins and DNA, and the extent to which multiple genome-wide polygenic scores (multi-PGS) can jointly predict these SCA.g as compared to SCA uncorrected for g. We created SCA and SCA.g composites from a battery of 14 cognitive tests administered at age 12 to 5,000 twin pairs in the Twins Early Development Study (TEDS). Univariate twin analyses yielded an average heritability estimate of 40% for SCA.g, compared to 53% for uncorrected SCA. Using genome-wide SNP genotypes, average SNP-based heritabilities were 26% for SCA.g and 35% for SCA. We then created multi-PGS from at least 50 PGS to predict each SCA and SCA.g using elastic net penalised regression models. Multi-PGS predicted 4.4% of the variance of SCA.g on average, compared to 11.1% for SCA uncorrected for g. The twin, SNP and PGS heritability estimates for SCA.g provide further evidence that the heritabilities of SCA are not merely a reflection of g. Although the relative reduction in heritability from SCA to SCA.g was greater for PGS heritability than for twin or SNP heritability, this decrease is likely due to the paucity of PGS for SCA. We hope that these results encourage researchers to conduct genome-wide association studies of SCA, and especially SCA.g, that can be used to predict PGS profiles of SCA strengths and weaknesses independent of g.

Interleukin-7 Risk Allele, Lymphocyte Counts, and Autoantibodies for Prediction of Risk of Immune-Related Adverse Events in Patients Receiving Atezolizumab plus Bevacizumab Therapy for Unresectable Hepatocellular Carcinoma.

Atezolizumab plus bevacizumab (AB) therapy was the effective immune checkpoint inhibitor (ICI) for unresectable hepatocellular carcinoma (u-HCC). However, immune-related adverse events (irAEs) are common in patients receiving ICI therapies. Our research aimed to explore the risk factors for irAE development, with attention to interleukin-7 (IL-7) risk alleles, lymphocyte counts, and autoantibodies. Seventy-six patients receiving AB therapy for u-HCC were recruited. Single nucleotide polymorphism genotyping was done for the analysis of rs16906115 polymorphism near IL-7-expressing genes using 20 μL of stored buffy coat at baseline. The association between IL-7 risk alleles, lymphocyte counts, autoantibodies, and irAE development was investigated. irAEs were found in 14 (18%) patients. The incidence of irAEs did not differ significantly between the groups showing IL-7 AG/AA and the GG group (p = 0.72). The incidence in the group with a lymphocyte count of 1,130/µL or more at baseline was higher than in that with a value below 1,130/µL (p = 0.0093). The group showing IL-7 AG/AA or lymphocyte count &gt;1,130/μL had a higher irAE prevalence rate than the others (p = 0.019). IL-7 AG/AA or lymphocyte count &gt;1,130/μL and positivity for autoantibodies at baseline were the prognostic factors for irAE development. irAE incidence could be stratified using a combination of IL-7 AG/AA or lymphocyte counts ≥1,130/µL and positive autoantibodies (p = 0.016). Patients with IL-7 risk alleles, high lymphocyte counts, and autoantibodies at baseline may require careful monitoring for irAE development.

Insight into adiponectin gene impact on coronary artery disease from a polymorphism case-control study in Iraqi individuals

BackgroundCoronary artery disease (CAD) is a group of diseases caused by plaque formation in the wall of arteries supplying blood to the heart. Adiponectin (ADIPOQ) is an adipocytokine that controls carbohydrate and lipid metabolism, has anti-diabetic properties, and correlates well with cardio-metabolic risk. ADIPOQ gene polymorphism is reported to be associated with CAD in numerous populations. ObjectiveTo explore the impact of adiponectin gene polymorphism, rs2241766 T > G, rs1501299 G > T, rs17300539 G > A, rs266729 G > A, and rs822395 A > C SNPs, on the CAD in the Iraqi population. MethodsA case-control study of 317 healthy individuals and 302 CAD patients was conducted. Standard protocols for measuring serum lipid profile levels were followed. ADIPOQ and insulin levels were estimated using the ELISA method. Genotyping of ADIPOQ gene was carried out using the RFLP technique. ResultsGenotype assessment of rs2241766, rs1501299, rs266729, and rs17300539 SNPs under several inheritance models pointed out significant (P = 0.012–10−4) elevations of the variant alleles in CAD patients in comparison to the control group. The haplotype analysis of the five analyzed SNPs exhibited five disease-susceptible haplotypes; they were GTCGA (OR: 7.6, 95 % CI: 2.55–21.76), TGCAA (P = 0.013), TGGGA (P = 0.046), TGGAA (P = 0.017), and GGGGA (P = 0.032). The linkage disequilibrium (LD) analysis of the five SNPs in the control versus the patient groups revealed significant LD. The variant genotype of the rs2241766 SNP was found to significantly increase the atherogenic lipids and HOMA values and decrease the ADIPOQ and high-density cholesterol (HDL-c) levels. Those of the rs1501299, rs17300539, and rs266729 SNPs were indicated to increase the metabolic parameter values except ADIPOQ and HDL-c magnitudes, which are reduced in the variant carriers. ConclusionThe rs2241766, rs1501299, rs266729, and rs17300539 SNPs of the ADIPOQ gene are risk factors for CAD in Iraqi individuals. Both single nucleotide and haplotype analyses suggested the implication of the ADIPOQ gene in the pathogenesis of the disease. This implication has occurred through lowering ADIPOQ levels and increasing atherogenic lipids.

FecalSeq enrichment with RAD Sequencing from non-invasive environmental samples holds promise for genetic monitoring of an imperiled lagomorph

Despite advances in genomic sequencing and bioinformatics, conservation genomics is still often hindered by a reliance on non-invasive samples. The presence of exogenous DNA and the low quantity and poor quality of DNA in non-invasive samples have been a roadblock to sequencing, thereby limiting the potential for genomic monitoring of endangered species. Recent molecular advances, such as host DNA enrichment, hold promise for facilitating sequencing from non-invasive samples. We used the FecalSeq method to enrich DNA extracted from wild-collected fecal pellets of the imperiled New England cottontail and identified SNPs from 3RAD Sequencing. We obtained SNPs from rabbit pellets, including pellets that were collected in poor environmental conditions and samples that performed poorly with microsatellites. Measures of sequencing success improved with greater amounts of starting DNA and 32% of samples generated SNP genotypes that passed quality control filtering. Genotyping error rates were high, however, and the approach was unable to consistently distinguish unique individuals or matching genotypes, while it was suitable for recovering the expected population structure. Pairing FecalSeq enrichment with RADseq is a promising low-cost method for monitoring wild populations using non-invasive samples in an environmental context, but it may be better suited for informing conservation through population genomics.

An enzyme-free fluorescence sensing platform based on multiplex toehold-mediated strand displacement for point-of-care testing of single nucleotide polymorphisms

Single nucleotide polymorphisms (SNPs) are biomarkers for the prediction and diagnosis of biomedical diseases, as well as important reference markers for intelligent design and breeding of animals and plants. Therefore, the development of high-sensitivity, practicability, and convenient SNPs sensing strategies and detection platforms is of great significance. In this study, we pioneered an ultra-sensitive universal sensing strategy for single base mutation detection and an enzyme-free FRET fluorescence sensing point-of-care testing (POCT) platform for SNP detection. Based on the thermodynamically regulated strand replacement mechanism, the system rationally introduced extra base mismatches and combined multiple toehold-mediated strand displacement (TMSD) reactions to achieve enzyme-free recognition of the single base mutation and double amplification of the detection signal. Finally, the biological signal of the mutant target (MT) was recognized, amplified, and transduced into a fluorescence resonance energy transfer (FRET) signal between Cy3 and Cy5 for output. Overall, the proposed biosensing strategy demonstrated high sensitivity for MT, with a detection limit as low as 0.37 fM, and could achieve detection of targets with mutant abundances as low as 0.1 %. Moreover, a portable detection system was assembled in conjunction with this sensing strategy to form a POCT platform for SNP genotyping. This POCT platform was validated to accurately identify SNPs from human cancer cells and soybean leaf genome extracts. In summary, this study will provide new insights into the design of enzyme-free biosensors for SNP detection, and will provide important technical support tools for the prevention and diagnosis of major diseases, animal and plant breeding, etc.

Development and validation of a 40 K liquid SNP array for the mud crab (Scylla paramamosain)

Genomic selection (GS) and genome-wide association studies (GWAS) have been widely implemented to accelerate the genetic improvement of important economic traits. Developing an efficient and reliable high-throughput genotyping tool is the premise and basis of implementing GS and GWAS on the mud crab (Scylla paramamosain). In this study, leveraging the whole-genome resequencing data of 146 mud crabs from the southeast coast of China, a total of 16,714,943 high-quality SNPs were discovered. Based on polymorphic information content and evenly distribution on 49 chromosomes, a total of 40,352 SNPs was selected to develop a 40 K liquid SNP array (named “Xiexin No. 1”) using the genotyping by target sequencing (GBTS) technology. The genotyping performance test showed that this SNP array had a high site polymorphism (over 92.70%) and individual calling rate (97.02%). Furthermore, the mean of SNP concordance, genotype concordance, non-reference sensitivity, and non-reference discrepancy between “Xiexin No. 1” SNP array and resequencing were identified to be 0.986, 0.954, 0.942, and 0.097, respectively. Using this SNP array data, the genomic heritabilities were evaluated as 0.887 ± 0.065, 0.643 ± 0.108, 0.599 ± 0.111, and 0.624 ± 0.111 for body weight (BW), carapace length (CL), carapace length (CW), and body height (BH) in a cultured population (233 crabs). Furthermore, five significant SNPs associated with growth traits were identified by GWAS. After annotation, one candidate gene (XP_027221997.1) associated with BW and one candidate gene (XP_027210446.1) associated with CW and BH were identified. Most importantly, the prediction accuracy of GBLUP for BW, BH, CL, and CW were 0.535 ± 0.064, 0.544 ± 0.101, 0.574 ± 0.087, and 0.585 ± 0.083, with the unbiasedness values of 0.988 ± 0.22, 1.015 ± 0.274, 1.011 ± 0.196 and 1.037 ± 0.235. In conclusion, the “Xiexin No. 1” SNP array provides an efficient and reliable platform for high-quality genotyping, which would greatly promote the genetic studies and thus accelerate the genetic improvement of mud crabs.

Generation of genome-wide SNP markers from minimally invasive sampling in endangered animals and applications in species ecology and conservation.

High-density genotyping methods have revolutionized the field of population and conservation genetics in the past decade. To exploit the technological and analytical advances in the field, access to high-quality genetic material is a key component. However, access to such samples in endangered and rare animals is often challenging or even impossible. Here, we used a minimally invasive sampling method (MIS) in the endangered cave salamander Proteus anguinus, the olm, to generate thousands of genetic markers using ddRADseq for population and conservation genomic analyses. Using tail clips and MIS skin swabs taken from the same individual, we investigated genotyping data properties of the two different sampling types. We found that sufficient DNA can be extracted from swab samples to generate up to 200,000 polymorphic SNPs in divergent Proteus lineages. Swab and tissue samples were highly reproducible exhibiting low SNP genotyping error rates. We found that SNPs were most frequently (~50%) located within genic regions, while the rest mapped to mostly flanking regions of repetitive DNA. The vast majority of DNA recovered from swabbing was host DNA. However, a fraction of DNA recovered from swabs contained additional ecological information on the species, including eDNA from the surrounding environment and bacterial skin fauna. Most exogenous DNA recovered from swabs were bacteria (~80%), followed by vertebrates (~20%). Our results demonstrate that MIS can be used to (i) generate tens of thousands of ddRADseq markers for conservation and population genomic analyses and (ii) inform on the species health status and ecology from exogenous DNA.

Recipient IL-17A polymorphism rs2275913 is associated with acute graft-versus-host disease after single-unit cord blood transplantation

BackgroundInterleukin-17 (IL-17) is elevated in human inflammatory and autoimmune diseases. The polymorphism in the promoter region of the IL-17 A gene is associated with susceptibility to several inflammatory diseases, including acute graft-versus-host disease (GVHD) following allogeneic hematopoietic cell transplantation from adult donors. However, the impacts of IL-17 A polymorphism on cord blood transplantation (CBT) outcomes remain unclear. ObjectiveThe objective of this study was to assess the impact of IL-17 A polymorphism rs2275913 on GVHD, survival, relapse, non-relapse mortality (NRM), and hematopoietic recovery after CBT. Study DesignWe conducted a retrospective analysis of data from adult patients who underwent single-unit CBT at our institution from January 2005 to March 2023 for whose recipient or donor DNA samples were available. IL-17 A genotyping was performed using real-time polymerase chain reaction with the TaqMan® SNP genotyping assay for rs2275913. ResultsA total of 158 recipients and 136 donors were evaluated in this study. Multivariate analysis showed that rs2275913 GA or AA recipients were associated with increased risk of grades II to IV acute GVHD compared to GG recipients (hazard ratio [HR], 1.46; 95% confidence interval [CI], 1.00–2.13; P = 0.047). Serum IL-17 A levels at eight weeks were significantly higher in rs2275913 GA or AA recipients compared to GG. The rs2275913 polymorphism did not affect survival, relapse, NRM, or hematopoietic recovery after single-unit CBT. ConclusionOur data showed recipient IL-17 A polymorphism rs2275913 was associated with the risk of grade II to IV acute GVHD in adults undergoing single-unit CBT. However, the rs2275913 polymorphism in recipients and donors did not affect survival or relapse. Thus, the polymorphism of IL-17 A rs2275913 in recipients might predict the risk of acute GVHD after single-unit CBT.

The association between endoplasmic reticulum aminopeptidase 2 gene single nucleotide polymorphisms and the risk of psoriasis and psoriatic arthritis in Egyptians.

Psoriasis (Ps) is a disorder attributed to the immune system that involves inflammation of the skin and joints. Psoriasis is a multifactorial disorder in which genetic factors represent about 70% of the disease risk. This study aims to establish the correlation between the ERAP2 gene's single nucleotide polymorphisms (SNPs) rs2910686 and rs2248374 with the susceptibility to Ps and/or psoriatic arthritis (PsA) among the Egyptian population. Genotyping of ERAP2 gene SNPs (rs2910686 and rs2248374) in 120 psoriatic patients with and without arthritis and 100 controls was done using real-time PCR. The genotype frequency and distribution of the ERAP2 SNP (rs2910686 and rs2248374) were in Hardy-Weinberg equilibrium (HWE). For rs2910686, the TC and CC genotypes and C allele frequency were significant risk factors for PsA compared to the controls (OR = 5.708, OR = 10.165, and OR = 4.282, respectively). They also were significant risk factors for Ps compared to the controls (OR = 5.165, OR = 5.040, and OR = 3.258, respectively). For rs2248374, the AG genotype significantly increased the risk of PsA (OR = 2.605) and Ps (OR = 3.768) compared to controls. The AG genotype was significantly related to the risk of Ps (OR = 3.369) G allele with PsA (OR = 1.608) and Ps (OR = 1.965) compared to controls. In Egyptian individuals, the ERAP2 gene polymorphisms (rs2248374 and rs2910686) may contribute genetically to the pathophysiology of psoriasis and PsA.

The heritability of fitness in a wild annual plant population with hierarchical size structure.

The relative magnitude of additive genetic vs. residual variation for fitness traits is important in models for predicting the rate of evolution and population persistence in response to changes in the environment. In many annual plants, lifetime reproductive fitness is correlated with end-of-season plant biomass, which can vary significantly from plant to plant in the same population. We measured end-of-season plant biomasses and obtained single nucleotide polymorphism (SNP) genotypes of plants in a dense, natural population of the annual plant species Impatiens capensis with hierarchical size structure. These data were used to estimate the amount of heritable variation for position in the size hierarchy and for plant biomass. Additive genetic variance for a position in the size hierarchy and plant biomass were both significantly different from zero. These results are discussed in relationship to the theory for the heritability of fitness in natural populations and ecological factors that potentially influence heritable variation for fitness in this species.

Genotypic variation in CYP2E1, GCKR, and PNPLA3 among nonalcoholic steatohepatitis patients of Turkish origin.

This study examines genetic variations in CYP2E1 (rs6413432, rs3813867), GCKR (rs780094, rs1260326), and PNPLA3 (rs738409) among Turkish patients to assess their influence on nonalcoholic steatohepatitis. Allele and genotype frequencies were compared between 245 NASH patients and 120 healthy controls using SNP genotyping via polymerase chain reaction-restriction fragment length polymorphism. Additionally, the deviation of the observed genotype frequencies from Hardy-Weinberg proportion was examined. No significant differences were found in the allelic and genotypic distributions of rs6413432, rs3813867, and rs780094 between NASH patients and healthy controls. However, significant disparities were noted for rs1260326 and rs738409. Gender and age-specific distributions showed no notable differences. The only observed deviation from Hardy-Weinberg proportion was in the genotype frequency of rs738409. Variants in GCKR (rs1260326) and PNPLA3 (rs738409) are significantly associated with increased NASH risk in the Turkish population, with the rs738409 variant potentially playing a more prominent role in NASH development.