Genome-wide Single Nucleotide Polymorphism Research Articles

What makes a giant fruit? Assembling a genomic toolkit underlying various fruit traits of the mammoth group of Cucurbita maxima.

Since their introduction in Europe, pumpkins (Cucurbita maxima Duch.) have rapidly dispersed throughout the world. This is mainly because of their wide genetic diversity and Plasticity to thrive in a wide range of geographical regions across the world, their high nutritional value and suitability to integrate with local cuisines, and their long shelf life. Competition for growing the showy type or mammoth-sized pumpkins that produce the largest fruit of the entire plant kingdom has drawn attention. In this study, we used genome-wide single nucleotide polymorphisms to resolve admixture among different pumpkin groups. Also, to resolve population differentiation, genome-wide divergence and evolutionary forces underlying the evolution of mammoth-sized pumpkin. The admixture analysis indicates that the mammoth group (also called Display or Giant) evolved from the hubbard group with genome-wide introgressions from the buttercup group. We archived a set of private alleles underlying fruit development in mammoth group, and resolved haplotype level divergence involved in the evolutionary mechanisms. Our genome-wide association study identified three major allelic effects underlying various fruit-size genes in this study. For fruit weight, a missense variant in the homeobox-leucine zipper protein ATHB-20-like (S04_18528409) was significantly associated (false discovery rate = 0.000004) with fruit weight, while high allelic effect was consistent across the 3 years of the study. A cofactor (S08_217549) on chromosome 8 is strongly associated with fruit length, having superior allelic effect across the 3 years of this study. A missense variant (S10_4639871) on translocation protein SEC62 is a cofactor for fruit diameter. Several known molecular mechanisms are likely controlling giant fruit size, including endoreduplication, hormonal regulation, CLV-WUS signaling pathway, MADS-box family, and ubiquitin-proteasome pathway. This study provides a general framework for the evolutionary relationship among horticulture groups of C. maxima and elucidates the origins of rare variants contributing to the giant pumpkin fruit size.

Genetic diversity and population structure of locally adapted Brazilian horse breeds assessed using genome-wide single nucleotide polymorphisms

Animals first introduced in Brazil with the discovery were submitted to various selective pressures over five centuries, developing adaptive traits specific to the hostile environments found in the country. A high quantity of genotypic information can be generated quickly and with high repeatability and reliability using genome-wide Single Nucleotide Polymorphism (SNP) panels. Blood samples from 285 horses belonging to eight Brazilian breeds (Baixadeiro, Lavradeiro, Marajoara, Puruca, Campeiro, Crioulo, Mangalarga Marchador and Pantaneiro) and two commercial breeds sampled in Brazil (Arabian and English Thoroughbred) were genotyped focusing on elucidating the genetic structure and composition within and among Brazilian horse breeds and some of their possible founders. Data from the GGP Equine BeadChip (GeneSeek® Genomic Profiler™ Equine, 65.157 SNPs) was used to assess basic diversity parameters, genetic distance (pairwise FST and Nei), Principal Component Analysis (PCA), Analysis of Molecular Variance (AMOVA) and population structure (ADMIXTURE). Results showed that Crioulo (few animals), Pantaneiro, Mangalarga Marchador, and Campeiro breeds possess distinct genetic bases from the others and each other. The Lavradeiro, Baixadeiro, Puruca, and Marajoara breeds have a shared genetic basis, hindering their differentiation. The results also reflected a geographic division of the Brazilian equine breeds, with those originally from the North and Northeast regions (Lavradeiro, Marajora, Puruca and Baixadeiro) grouped. On the other hand, animals from the South and Southeast regions (Crioulo, Campeiro and Mangalarga Marchador) were genetically closer although distinguished. The Pantaneiro breed originating from Pantanal Matogrossense in the Midwest region of Brazil, separated from all the others. Overall, high values of genetic variability and low values of FIS were observed for the Brazilian naturalized breeds. Both Arabian and English Thoroughbred sampled in Brazil presented a similar genetic variability to the Brazilian breeds but were genetically differentiated. This study aims to understand better the genetic variability and relation among Brazilian naturalized horse breeds and their possible origins. This information helps establish and maintain conservation nuclei and programs for each horse breed. Results found here can be used as a base for backup decisions regarding management to optimize conservation programs and other support sampling strategies for the National Animal Germplasm Program.

An Extremes of Phenotype Approach Confirms Significant Genetic Heterogeneity in Patients with Ulcerative Colitis.

Ulcerative colitis [UC] is a major form of inflammatory bowel disease globally. Phenotypic heterogeneity is defined by several variables including age of onset and disease extent. The genetics of disease severity remains poorly understood. To further investigate this, we performed a genome wide association [GWA] study using an extremes of phenotype strategy. We conducted GWA analyses in 311 patients with medically refractory UC [MRUC], 287 with non-medically refractory UC [non-MRUC] and 583 controls. Odds ratios [ORs] were calculated for known risk variants comparing MRUC and non-MRUC, and controls. MRUC-control analysis had the greatest yield of genome-wide significant single nucleotide polymorphisms [SNPs] [2018], including lead SNP = rs111838972 [OR = 1.82, p = 6.28 × 10-9] near MMEL1 and a locus in the human leukocyte antigen [HLA] region [lead SNP = rs144717024, OR = 12.23, p = 1.7 × 10-19]. ORs for the lead SNPs were significantly higher in MRUC compared to non-MRUC [p < 9.0 × 10-6]. No SNPs reached significance in the non-MRUC-control analysis (top SNP, rs7680780 [OR 2.70, p = 5.56 × 10-8). We replicate findings for rs4151651 in the Complement Factor B [CFB] gene and demonstrate significant changes in CFB gene expression in active UC. Detailed HLA analyses support the strong associations with MHC II genes, particularly HLA-DQA1, HLA-DQB1 and HLA-DRB1 in MRUC. Our MRUC subgroup replicates multiple known UC risk variants in contrast to non-MRUC and demonstrates significant differences in effect sizes compared to those published. Non-MRUC cases demonstrate lower ORs similar to those published. Additional risk and prognostic loci may be identified by targeted recruitment of individuals with severe disease.

Genetic diversity, population structure, linkage disequilibrium and GWAS for resistance to WSSV in Pacific white shrimp (Litopenaeus vannamei) using a 50K SNP chip

The objectives of this research were to assess the genetic diversity, population structure, linkage disequilibrium and perform a genome-wide association study (GWAS) to search for single nucleotide polymorphisms (SNPs) that associate with the resistance of Pacific white shrimp (Litopenaeus vannamei) to White Spot Syndrome Virus (WSSV). The line here analyzed was formerly founded with animals originated from different origins (Ecuador, Panama, and United States of America), with a history of resistance to WSSV and they have undergone a selection process, currently reaching up to F6 generation. In a controlled challenge to WSSV, this line showed a binary survival (39.0% ± 1.1%) and time to death (109.7 ± 0.9 h post-infection) (n = 1944). The population was genotyped using a commercially available 50 K SNP chip and ∼32 K SNPs remained after quality control of genotypes. Population structure, extent and decay of linkage disequilibrium (LD), and genetic variability in the population were evaluated. The principal component analysis (PCA) did not show apparent genetic stratification in the population. The LD decay estimated, revealed a rapid decrease in r2 as the physical distance between markers increased. The most significant decrease was observed in the first 30Kb of distance, suggesting the need to use a higher density of informative markers to meet the requirement of a genome-wide association study in L. vannamei. The observed and expected heterozygosities were both = 0.38, which indicates that the population presents acceptable genetic variability for WSSV resistance. Two SNPs were significantly associated to WSSV resistance at a genome-wide level, which in turn together explained 0.17% of the genetic variance for the trait. One identified SNP surpassing the genome-wide significance threshold (chromosome 1 at 51207389 bp) is located near potential candidate genes, such as Arylsulfatase B-like (ARSB), and D-beta-hydroxybutyrate dehydrogenase mitochondrial-like (βhyD); which was linked to the humoral immune response to WSSV, in addition to the Putative mediator of RNA polymerase II transcription subunit 26 (PMed26); which are associated with the hepatopancreas immune response against infection of WSSV and acute hepatopancreatic necrosis disease (AHPND). Our results indicate a polygenic architecture for WSSV resistance in L. vannamei, suggesting that incorporating genome-wide SNP information, through genomic selection, might be the most appropriate approach to accelerate the genetic progress for this trait.

Genetic substructure of Guizhou Tai-Kadai-speaking people inferred from genome-wide single nucleotide polymorphisms data

The genome-wide characteristics and admixture history of the Tai-Kadai-speaking populations are essential for understanding the population genetic diversity in southern China. We genotyped about 700,000 single nucleotide polymorphisms (SNPs) of 239 individuals from six Tai-Kadai-speaking populations residing in the mountainous Guizhou Province of southwestern China. We merged the genome-wide data with available populations and ancients in East and Southeast Asia to infer Tai-Kadai-speaking populations’ admixture history and genetic structure. We observed a genetic substructure within the studied six populations in the PCA, ADMIXTURE, ChromoPainter, GLOBETROTTER, f-statistics, and qpWave analysis. The Dong, Zhuang, and Bouyei people had a strong genetic affinity with other Tai-Kadai-speaking and Austronesian groups in the surrounding area. However, Gelao showed an affinity to Sino-Tibetan groups, and Mulao people were genetically close to Hmong-Mien populations. qpAdm further illuminated that Gelao and Dong_Tongren composited more Han-related ancestry than Dong, Zhuang, Bouyei, and Mulao people. Meanwhile, we observed high frequencies of Y-chromosome haplogroup O in studied Tai-Kadai-speaking groups except for Gelao people with a high haplogroup N frequency. From the maternal side, haplogroup M7 was frequent in studied populations except for Tongren Dong, who had a high frequency of haplogroup B5. Our newly reported data are helpful for further exploring population dynamics in southern China.

Common genetic variants improve risk stratification after the atrial switch operation for transposition of the great arteries

BackgroundClinical factors are used to estimate late complication risk in adults after atrial switch operation (AtrSO) for transposition of the great arteries (TGA), but heterogeneity in clinical course remains. We studied whether common genetic variants are associated with outcome and add value to a clinical risk score in TGA-AtrSO patients. Methods and resultsThis multicenter study followed 133 TGA-AtrSO patients (aged 28 [IQR 24–35] years) for 13 (IQR 9–16) years and examined the association of genome-wide single-nucleotide polymorphisms (SNPs) with a composite endpoint of symptomatic ventricular arrhythmia, heart failure hospitalization, ventricular assist device implantation, heart transplantation, or mortality. Thirty-two patients (24%) reached the endpoint. The genome-wide association study yielded one genome-wide significant (p < 1 × 10−8) locus and 18 suggestive loci (p < 1 × 10−5). A genetic risk score constructed on the basis of independent SNPs with p < 1 × 10−5 was associated with outcome after correction for the clinical risk score (HR = 1.26/point increase [95%CI 1.17–1.35]). Risk stratification improved with a combined risk score (clinical score + genetic score) compared to the clinical score alone (p = 2 × 10−16, C-statistic 0.95 vs 0.85). In 51 patients with a clinical intermediate (5–20%) 5-year risk of events, the combined score reclassified 32 patients to low (<5%) and 5 to high (>20%) risk. Stratified by the combined score, observed 5-year event-free survival was 100%, 79% and 31% for low, intermediate, and high-risk patients, respectively. ConclusionsCommon genetic variants may explain some variation in the clinical course in TGA-AtrSO and improve risk stratification over clinical factors alone, especially in patients at intermediate clinical risk. These findings support the hypothesis that including genetic variants in risk assessment may be beneficial.

G × EBLUP: A novel method for exploring genotype by environment interactions and genomic prediction.

Genotype by environment (G × E) interaction is fundamental in the biology of complex traits and diseases. However, most of the existing methods for genomic prediction tend to ignore G × E interaction (GEI). In this study, we proposed the genomic prediction method G × EBLUP by considering GEI. Meanwhile, G × EBLUP can also detect the genome-wide single nucleotide polymorphisms (SNPs) subject to GEI. Using comprehensive simulations and analysis of real data from pigs and maize, we showed that G × EBLUP achieved higher efficiency in mapping GEI SNPs and higher prediction accuracy than the existing methods, and its superiority was more obvious when the GEI variance was large. For pig and maize real data, compared with GBLUP, G × EBLUP showed improvement by 3% in the prediction accuracy for backfat thickness, while our findings indicated that the trait of days to 100 kg of pig was not affected by GEI and G × EBLUP did not improve the accuracy of genomic prediction for the trait. A significant advantage was observed for G × EBLUP in maize; the prediction accuracy was improved by ∼5.0 and 7.7% for grain weight and water content, respectively. Furthermore, G × EBLUP was not influenced by the number of environment levels. It could determine a favourable environment using SNP Bayes factors for each environment, implying that it is a robust and useful method for market-specific animal and plant breeding. We proposed G × EBLUP, a novel method for the estimation of genomic breeding value by considering GEI. This method identified the genome-wide SNPs that were susceptible to GEI and yielded higher genomic prediction accuracies and lower mean squared error compared with the GBLUP method.

Genomic analysis of a reef-building coral, Acropora digitifera, reveals complex population structure and a migration network in the Nansei Islands, Japan.

Understanding the structure and connectivity of coral populations is fundamental for developing marine conservation policies, especially in patchy environments such as archipelagos. The Nansei Islands, extending more than 1000 km in southwestern Japan, are characterized by high levels of biodiversity and endemism, supported by coral reefs, which make this region ideal for assessing genetic attributes of coral populations. In this study, we conducted population genomic analyses based on genome-wide, single-nucleotide polymorphisms (SNPs) of Acropora digitifera, a common species in the Nansei Islands. By merging newly obtained genome resequencing data with previously published data, we identified more than 4 million genome-wide SNPs in 303 colonies collected at 22 locations, with sequencing coverage ranging from 3.91× to 27.41×. While population structure analyses revealed genetic similarities between the southernmost and northernmost locations, separated by >1000 km, several subpopulations in intermediate locations suggested limited genetic admixture, indicating conflicting migration tendencies in the Nansei Islands. Although migration networks revealed a general tendency of northward migration along the Kuroshio Current, a substantial amount of southward migration was also detected, indicating important contributions of minor ocean currents to coral larval dispersal. Moreover, heterogeneity in the transition of effective population sizes among locations suggests different histories for individual subpopulations. The unexpected complexity of both past and present population dynamics in the Nansei Islands implies that heterogeneity of ocean currents and local environments, past and present, have influenced the population structure of this species, and similar unexpected population complexities may be expected for other marine species with similar reproductive modes.

The genetic mechanisms underlying the convergent evolution of pollination syndromes in the Neotropical radiation of Costus L.

Selection together with variation in floral traits can act to mold floral form, often driven by a plant’s predominant or most effective pollinators. To investigate the evolution of traits associated with pollination, we developed a phylogenetic framework for evaluating tempo and mode of pollination shifts across the genus Costus L., known for its evolutionary toggle between traits related to bee and bird pollination. Using a target enrichment approach, we obtained 957 loci for 171 accessions to expand the phylogenetic sampling of Neotropical Costus. In addition, we performed whole genome resequencing for a subset of 20 closely related species with contrasting pollination syndromes. For each of these 20 genomes, a high-quality assembled transcriptome was used as reference for consensus calling of candidate loci hypothesized to be associated with pollination-related traits of interest. To test for the role these candidate genes may play in evolutionary shifts in pollinators, signatures of selection were estimated as dN/dS across the identified candidate loci. We obtained a well-resolved phylogeny for Neotropical Costus despite conflict among gene trees that provide evidence of incomplete lineage sorting and/or reticulation. The overall topology and the network of genome-wide single nucleotide polymorphisms (SNPs) indicate that multiple shifts in pollination strategy have occurred across Costus, while also suggesting the presence of previously undetected signatures of hybridization between distantly related taxa. Traits related to pollination syndromes are strongly correlated and have been gained and lost in concert several times throughout the evolution of the genus. The presence of bract appendages is correlated with two traits associated with defenses against herbivory. Although labellum shape is strongly correlated with overall pollination syndrome, we found no significant impact of labellum shape on diversification rates. Evidence suggests an interplay of pollination success with other selective pressures shaping the evolution of the Costus inflorescence. Although most of the loci used for phylogenetic inference appear to be under purifying selection, many candidate genes associated with functional traits show evidence of being under positive selection. Together these results indicate an interplay of phylogenetic history with adaptive evolution leading to the diversification of pollination-associated traits in Neotropical Costus.

Effect of schizophrenia risk gene polymorphisms on cognitive and neural plasticity

A recent Chinese genome-wide association study found evidence for 58 out of the 128 schizophrenia-associated variants previously discovered in Western samples by the Schizophrenia Working Group of the Psychiatric Genomics Consortium (PGC). However, the functional impact of these trans-ancestry genome-wide single-nucleotide polymorphisms (SNPs) is not clear. In the current study, we examined the roles of trans-ancestry SNPs in cognitive and neural plasticity. We first performed a behavioral study of 547 healthy volunteers, who received month-long working memory training, and working memory capability assessment both before and after the training. A separate sample of 101 subjects received the same training and received fMRI scans during a working memory task, both before and after the training. The behavioral study found a significant association between the polygenic risk score (PRS) and behavioral plasticity, with higher schizophrenia risk scores being linked to less plasticity. At the SNP level, rs36068923 showed a significant signal, with the risk allele being associated with less plasticity. The fMRI study further found that the PRS and rs36068923 polymorphism were associated with training-induced changes in striatal activation, with higher PRS and the risk allele of rs36068923 being linked to less brain plasticity. In sum, this study found that a high genetic risk for schizophrenia was associated with less plasticity at both behavioral and neural levels. These results provide new insights into the neural and cognitive mechanisms linking genes to schizophrenia.

Evaluating the suitability of close-kin mark-recapture as a demographic modelling tool for a critically endangered elasmobranch population.

Estimating the demographic parameters of contemporary populations is essential to the success of elasmobranch conservation programmes, and to understanding their recent evolutionary history. For benthic elasmobranchs such as skates, traditional fisheries-independent approaches are often unsuitable as the data may be subject to various sources of bias, whilst low recapture rates can render mark-recapture programmes ineffectual. Close-kin mark-recapture (CKMR), a novel demographic modelling approach based on the genetic identification of close relatives within a sample, represents a promising alternative approach as it does not require physical recaptures. We evaluated the suitability of CKMR as a demographic modelling tool for the critically endangered blue skate (Dipturus batis) in the Celtic Sea using samples collected during fisheries-dependent trammel-net surveys that ran from 2011 to 2017. We identified three full-sibling and 16 half-sibling pairs among 662 skates, which were genotyped across 6291 genome-wide single nucleotide polymorphisms, 15 of which were cross-cohort half-sibling pairs that were included in a CKMR model. Despite limitations owing to a lack of validated life-history trait parameters for the species, we produced the first estimates of adult breeding abundance, population growth rate, and annual adult survival rate for D.batis in the Celtic Sea. The results were compared to estimates of genetic diversity, effective population size (N e ), and to catch per unit effort estimates from the trammel-net survey. Although each method was characterized by wide uncertainty bounds, together they suggested a stable population size across the time-series. Recommendations for the implementation of CKMR as a conservation tool for data-limited elasmobranchs are discussed. In addition, the spatio-temporal distribution of the 19 sibling pairs revealed a pattern of site fidelity in D.batis, and supported field observations suggesting an area of critical habitat that could qualify for protection might occur near the Isles of Scilly.

QTL associated with Gummy Stem Blight (GSB) resistance in watermelon

BackgroundGummy stem blight (GSB), caused by Didymella bryoniae (syn. Stagonosporopsis cucurbitacearum), produces devastating symptoms on whole plants of watermelon (Citrullus lanatus) and other cucurbits, significantly reducing yield and quality. Identification of genetic determinants and sources of resistance to this devastating GSB disease in watermelon is essential for developing resistant varieties.ResultsIn this study, we aimed at identifying quantitative trait loci (QTLs) linked to GSB resistance in melon. We identified the genome-wide single nucleotide polymorphisms (SNPs) by genotyping by sequencing (GBS) of an F2 population developed from C. lanatus lines, ‘PI 279461’ (resistant) ✕ ‘PI 223764’ (susceptible). Inheritance analysis indicated that resistance to GSB is a multi-genic trait in this population. Three QTLs namely, ClGSB1.1, ClGSB10.1, and ClGSB11.1 associated with GSB resistance, explaining approximately 10% of the phenotypic variation, were identified. Among these, the QTL ClGSB1.1 on chromosome 1 is identified as a major QTL harboring five candidate genes associated with GSB resistance including two RLKs (ClC01G014900 and ClC01G015010), two WRKY transcription factors (ClC01G014910 and ClC01G014990), and one AvrRpt-cleavage domain protein (ClC01G015130).ConclusionTwo high resolution melting (HRM) markers, WmGSB1.1–2 and WmGSB1.1–7 having a high positive correlation with the phenotypic variations, were developed. Five potential candidate genes were predicted to be associated with GSB resistance. These findings will help breeders to develop watermelon cultivars resistant to GSB.

Lung‐ and liver‐dominant phenotypes of Korean eight constitution medicine have different profiles of genotype associated with each organ function

Eight Constitution Medicine (ECM), a ramification of traditional Korean medicine, has categorized people into eight constitutions. The main criteria of classification are inherited differences or predominance in the functions of organs, such as the liver or lung, diagnosed through ECM‐specific pulse patterns. This study investigated the association between single nucleotide polymorphism (SNP) genotypes and ECM phenotypes and explored candidate genetic makeups responsible for each constitution using a genome‐wide association study (GWAS). Sixty‐three healthy volunteers, who were either categorized as the Hepatonia (HEP, n = 32) or Pulmotonia (PUL, n = 31) constitution, were enrolled. HEP and PUL are two contrasting ECM types representing the dominant liver and lung phenotypes, respectively. SNPs were analyzed from the oral mucosa DNA using a commercially available microarray chip that can identify 820,000 SNPs. We conducted GWAS using logistic regression analysis and additive mode genotypes and constructed phylogenetic trees using the SNPhylo program with 8 SNPs specific for the liver phenotype and 15 SNPs for the lung phenotype. Although genome‐wide significant SNPs were not found, the phylogenetic tree showed a clear difference between the two constitutions. This is the first observation suggesting genetic involvement in the ECM and can be extended to all ECM constitutions.

Copy Number Variation Analysis Facilitates Identification of Genetic Causation in Patients with Congenital Anomalies of the Kidney and Urinary Tract

BackgroundCongenital anomalies of the kidneys and urinary tract (CAKUT) are the most common cause of chronic kidney disease among children and adults younger than 30 yr. In our previous study, whole-exome sequencing (WES) identified a known monogenic cause of isolated or syndromic CAKUT in 13% of families with CAKUT. However, WES has limitations and detection of copy number variations (CNV) is technically challenging, and CNVs causative of CAKUT have previously been detected in up to 16% of cases. ObjectiveTo detect CNVs causing CAKUT in this WES cohort and increase the diagnostic yield. Design, setting, and participantsWe performed a genome-wide single nucleotide polymorphism (SNP)-based CNV analysis on the same CAKUT cohort for whom WES was previously conducted. Outcome measurements and statistical analysisWe evaluated and classified the CNVs using previously published predefined criteria. Results and limitationsIn a cohort of 170 CAKUT families, we detected a pathogenic CNV known to cause CAKUT in nine families (5.29%, 9/170). There were no competing variants on genome-wide CNV analysis or WES analysis. In addition, we identified novel likely pathogenic CNVs that may cause a CAKUT phenotype in three of the 170 families (1.76%). ConclusionsCNV analysis in this cohort of 170 CAKUT families previously examined via WES increased the rate of diagnosis of genetic causes of CAKUT from 13% on WES to 18% on WES + CNV analysis combined. We also identified three candidate loci that may potentially cause CAKUT. Patient summaryWe conducted a genetics study on families with congenital anomalies of the kidney and urinary tract (CAKUT). We identified gene mutations that can explain CAKUT symptoms in 5.29% of the families, which increased the percentage of genetic causes of CAKUT to 18% from a previous study, so roughly one in five of our patients with CAKUT had a genetic cause. These analyses can help patients with CAKUT and their families in identifying a possible genetic cause.

925P Analytical performance of a next-generation sequencing (NGS) assay kit for assessing homologous recombination deficiency (HRD) from solid tumor samples

HRD status is predictive of response to PARP inhibitors (PARPi) in ovarian cancer. Developing reliable methods to assess HRD status is important to enable genomic profiling of tumor types with PARPi indications. Here we describe the analytical performance of the TruSight™ Oncology 500 HRD (TSO 500 HRD) research assay, an in-development NGS kit for assessing HRD using DNA from solid tumor samples. The TSO 500 HRD assay was developed by adding an HRD probe pool targeting genome-wide single nucleotide polymorphisms (SNPs) to the TruSight Oncology 500 (TSO 500) assay to enable Genomic Instability Score (GIS) assessment. For each sample, the DNA library was split into two hybridization reactions, one with TSO 500 probes and the other with HRD probes. Both libraries were pooled for sequencing with 8 samples per NextSeq™ 550 run. The GIS algorithm was licensed from Myriad, re-implemented as part of the DRAGEN Bio-IT software suite and integrated into the TSO 500 analysis workflow. Forty nanograms of DNA extracted from formalin-fixed, paraffin-embedded (FFPE) samples was used as assay input. Samples were also tested with a reference assay as the orthogonal test. Testing of serial dilutions of 8 ovarian cancer samples showed the limit of detection for small variant calling in BRCA1/2 genes is at 5-10% variant allele frequency (VAF), for large rearrangement variant calling in BRCA1/2 genes is at 30-50% VAF, and for GIS is at 30%-40% tumor content. The false positive rate for GIS status and BRCA variants is 0%. Testing of ovarian cancer samples and control samples with multiple operators, reagent lots, and library preparation start days showed >95% concordance in BRCA variant calling and GIS status. The GIS scores were highly concordant with the reference method assay (R = 0.98). The results were robust on both NextSeq 550 and NovaSeq™ 6000 with SP flowcells. The TSO 500 HRD assay demonstrated high analytical sensitivity and specificity in detecting BRCA variants and GIS status for HRD status assessment in ovarian cancer samples. TSO 500 HRD enables high resolution comprehensive genomic profiling alongside HRD assessment to maximize biomarker detection from limited amount of sample.

A microRNA-microRNA crosstalk network inferred from genome-wide single nucleotide polymorphism variants in natural populations of Arabidopsis thaliana.

To adapt to variable natural conditions, plants have evolved several strategies to respond to different environmental stresses. MicroRNA (miRNA)-mediated gene regulation is one of such strategies. Variants, e.g., single nucleotide polymorphisms (SNPs) within the mature miRNAs or their target sites may cause the alteration of regulatory networks and serious phenotype changes. In this study, we proposed a novel approach to construct a miRNA–miRNA crosstalk network in Arabidopsis thaliana based on the notion that two cooperative miRNAs toward common targets are under a strong pressure to be inherited together across ecotypes. By performing a genome-wide scan of the SNPs within the mature miRNAs and their target sites, we defined a “regulation fate profile” to describe a miRNA–target regulation being static (kept) or dynamic (gained or lost) across 1,135 ecotypes compared with the reference genome of Col-0. The cooperative miRNA pairs were identified by estimating the similarity of their regulation fate profiles toward the common targets. The reliability of the cooperative miRNA pairs was supported by solid expressional correlation, high PPImiRFS scores, and similar stress responses. Different combinations of static and dynamic miRNA–target regulations account for the cooperative miRNA pairs acting on various biological characteristics of miRNA conservation, expression, homology, and stress response. Interestingly, the targets that are co-regulated dynamically by both cooperative miRNAs are more likely to be responsive to stress. Hence, stress-related genes probably bear selective pressures in a certain group of ecotypes, in which miRNA regulations on the stress genes reprogram. Finally, three case studies showed that reprogramming miRNA–miRNA crosstalk toward the targets in specific ecotypes was associated with these ecotypes’ climatic variables and geographical locations. Our study highlights the potential of miRNA–miRNA crosstalk as a genetic basis underlying environmental adaptation in natural populations.

Genome–wide association study and genomic prediction of growth traits in bighead catfish (Clarias macrocephalus Günther, 1864)

Next-generation sequencing (NGS) enables cost-effective exploration of genome-wide single nucleotide polymorphisms (SNPs). This new technology has made enormous contributions in various fields including genetic improvement. This study was conducted to identify SNPs that associated with growth traits (body weight, standard length, and total length) of bighead catfish (Clarias macrocephalus Günther, 1864) using genome-wide association studies (GWAS), and to estimate genetic parameters of these growth traits using genomic best linear unbiased prediction (GBLUP). Individual DNA samples from 991 eight-month-old bighead catfish across 74 full-sibs and 31 half-sibs were collected and subjected to next-generation sequencing using the DArTSeq platform. In return, 9530 SNPs were obtained and used for analysis together with the recorded phenotypic data. The analysis was performed using weighted genomic best linear unbiased prediction (wGBLUP), facilitated by the BLUPF90 family of programs, and identified a set of 19 markers associated with all growth traits; the proportion of explained variance ranged from 1.02 to 6.59%. Four SNP sequences were annotated to Egl nine 2-like gene (egln2), zinc finger FYVE-type containing 21 gene (zfyve21), junctophilin 3a (jph3a), and a hypothetical protein. Furthermore, GBLUP was used to estimate GEBV and heritability of the growth traits. PBLUP was also performed using pedigrees obtained from SNP-based parentage information to estimate PEBV and heritability. The results revealed that GBLUP improved accuracy of EBV estimates over PBLUP. Heritability of growth traits estimated by GBLUP ranged between 0.29 ± 0.05 (for standard length) and 0.55 ± 0.06 (for body weight), with accuracy ranging from 0.672 to 0.724 and prediction bias close to one. When compared to GBLUP, heritability estimated by PBLUP was lower, and with lower accuracy, while bias was lower only for standard length. In conclusion, the growth-associated SNPs identified herein explained only a small portion of genetic variance, and thus using these SNPs for marker-assisted selection is not promising. Instead, genomic selection based on GEBV is a better approach, provided that genotyping cost can be optimized. The knowledge gained from this study is beneficial to genetic improvement of bighead catfish and other related species.

Associations of genetic liability for Alzheimer’s disease with cognition and eye movements in a large, population-based cohort study

To identify cognitive measures that may be particularly sensitive to early cognitive decline in preclinical Alzheimer’s disease (AD), we investigated the relation between genetic risk for AD and cognitive task performance in a large population-based cohort study. We measured performance on memory, processing speed, executive function, crystallized intelligence and eye movement tasks in 5182 participants of the Rhineland Study, aged 30 to 95 years. We quantified genetic risk for AD by creating three weighted polygenic risk scores (PRS) based on the genome-wide significant single-nucleotide polymorphisms coming from three different genetic association studies. We assessed the relation of AD PRS with cognitive performance using generalized linear models. Three PRS were associated with lower performance on the Corsi forward task, and two PRS were associated with a lower probability of correcting antisaccade errors, but none of these associations remained significant after correction for multiple testing. Associations between age and trail-making test A (TMT-A) performance were modified by AD genetic risk, with individuals at high genetic risk showing the strongest association. We conclude that no single measure of our cognitive test battery robustly captures genetic liability for AD as quantified by current PRS. However, Corsi forward performance and the probability of correcting antisaccade errors may represent promising candidates whose ability to capture genetic liability for AD should be investigated further. Additionally, our finding on TMT-A performance suggests that processing speed represents a sensitive marker of AD genetic risk in old age and supports the processing speed theory of age-related cognitive decline.

Genome-Wide Associative Study of Phenotypic Parameters of the 3D Body Model of Aberdeen Angus Cattle with Multiple Depth Cameras.

Simple SummaryThis article aims to develop a new approach to the lifetime evaluation of cattle by 3-D visualization of economic-biological and genetic features. The following indicators were selected as phenotypic features: chest width and chest girth retrieved by 3-D model and meat output on the bones. Correlation analysis showed a reliable positive relationship between chest width and meat output on the bones, which can potentially be used for lifetime evaluation of meat productivity of animals. Genome-wide associations analysis revealed the following potential loci of quantitative traits on cattle chromosomes for chest width, chest girth, and meat output on bones.In beef cattle breeding, genome-wide association studies (GWAS) using single nucleotide polymorphisms (SNPs) arrays can reveal many loci of various production traits, such as growth, productivity, and meat quality. With the development of genome sequencing technologies, new opportunities are opening up for more accurate identification of areas associated with these traits. This article aims to develop a novel approach to the lifetime evaluation of cattle by 3-D visualization of economic-biological and genetic features. The purpose of this study was to identify significant variants underlying differences in the qualitative characteristics of meat, using imputed data on the sequence of the entire genome. Samples of biomaterial of young Aberdeen-Angus breed cattle (n = 96) were the material for carrying out genome-wide SNP genotyping. Genotyping was performed using a high-density DNA chip Bovine GPU HD BeadChip (Illumina Inc., San Diego, CA, USA), containing ~150 thousand SNPs. The following indicators were selected as phenotypic features: chest width and chest girth retrieved by 3-D model and meat output on the bones. Correlation analysis showed a reliable positive relationship between chest width and meat output on the bones, which can potentially be used for lifetime evaluation of meat productivity of animals.

Prominence of NUDT15 genetic variation associated with 6-mercaptopurine tolerance in a genome-wide association study of Japanese children with acute lymphoblastic leukaemia.

Inherited genetic variation is associated with 6-mercaptopurine (6-MP) dose reduction and frequent toxicities induced by 6-MP. However, the tolerable dose for 6-MP is not fully predicted by the known variation in NUDT15 and TPMT among Asian children with acute lymphoblastic leukaemia (ALL). We performed a genome-wide association study (GWAS) related to 6-MP dose among Japanese children with ALL. This GWAS comprised 224 patients previously enrolled in Tokyo Children's Cancer Study Group clinical studies with replication attempted in 55 patients. Genome-wide single nucleotide polymorphism (SNP) genotypes were evaluated for association with average 6-MP dose during the initial 168 days of maintenance therapy. Possible associations were observed across five gene-coding regions, among which only variants at 13q14.2 were significant and replicated genome-wide (rs116855232, NUDT15, β=-10.99, p=3.7 × 10-13 ). Notable findings were observed for variants in AFF3 (rs75364948, p=2.05 × 10-6 ) and CHST11 (rs1148407, p=2.09 × 10-6 ), but were not replicated possibly due to small numbers. A previously reported candidate SNP in MTHFR was associated with higher average 6-MP dose (rs1801133, p=0.045), and FOLH1 (rs12574928) was associated in an evaluation of candidate regions (padjust =0.013). This study provides strong evidence that rs116855232 in NUDT15 is the genetic factor predominantly associated with 6-MP tolerable dose in children in Japan.