False positives in a Genome-Wide Association Study (GWAS) can be effectively controlled by fixed effect and random Mixed Linear Model (MLM) that incorporates population structure kinship among individuals to adjust association tests on markers; however, the adjustment also compromises true positives. The modified MLM method, Multiple Loci (MLMM), multiple markers simultaneously as covariates stepwise partially remove confounding between testing kinship. To completely eliminate confounding,...

Big datasets, accumulated from biomedical and agronomic studies, provide the potential to identify genes that control complex human diseases agriculturally important traits through genome-wide association studies (GWAS). However, big datasets also lead extreme computational challenges, especially when sophisticated statistical models are employed simultaneously reduce false positives negatives. The newly developed fixed random model circulating probability unification (FarmCPU) method uses a...

Preharvest sprouting (PHS), the germination of grain on mother plant under cool and wet conditions, is a recurring problem for wheat farmers worldwide. α-amylase enzyme produced during PHS degrades starch resulting in baked good with poor end-use quality. The Hagberg-Perten Falling Number (FN) test used to measure this industry, determines how much farmer's discounted damage. tolerance associated higher dormancy. Thus, breeding programs use germination-based assays such as spike-wetting...

Soft white wheat is used in domestic and foreign markets for various end products requiring specific quality profiles. Phenotyping end-use traits can be costly, time-consuming destructive nature, so it advantageous to use molecular markers select experimental lines with superior traits. An association mapping panel of 469 soft winter cultivars advanced generation breeding was developed from regional programs the U.S. Pacific Northwest. This genotyped on a wheat-specific 90 K iSelect single...

Histone methylation plays crucial roles in the development, gene regulation, and maintenance of stem cell pluripotency mammals. Recent work shows that histone is associated with aging, yet underlying mechanism remains unclear. In this work, we identified a class putative 3 lysine 9 mono/dimethyltransferase genes (met-2, set-6, set-19, set-20, set-21, set-32, set-33), mutations which induce synergistic lifespan extension long-lived DAF-2 (insulin growth factor 1 [IGF-1] receptor) mutant...

We report a repertoire of diverse aneuploids harbored by newly synthesized segmental allotetraploid rice population with fully sequenced sub-genomes and demonstrate their retention features phenotypic consequences. Aneuploidy, defined as unequal numbers different chromosomes, is large-effect genetic variant may produce cellular organismal phenotypes. Polyploids are more permissive to chromosomal content imbalance than diploid haploid counterparts, therefore, enable in-depth investigation the...

Calling tandem repeat (TR) variants from DNA sequences is of both theoretical and practical significance. Some bioinformatics tools have been developed for detecting or genotyping TRs. However, little study has done to TR alleles long-read sequencing data, the accuracy next-generation data still needs be improved. Herein, a novel algorithm described retrieve regions sequence alignment, software program TRcaller integrated into web portal call short- sequences, whole genome targeted generated...

Temperature greatly affects numerous biological processes in all organisms. How multicellular organisms respond to and are impacted by hypothermic stress remains elusive. Here, we found that cold-warm stimuli induced depletion of the RNA exosome complex nucleoli but enriched it nucleoplasm. To further understand function mechanism stimuli, conducted forward genetic screening identified ZTF-7, which is required for from upon transient exposure C . elegans ZTF-7 a putative ortholog human...

Hip dysplasia (HD), elbow (ED), and rupture of the cranial (anterior) cruciate ligament (RCCL) are most common complex orthopedic traits dogs all result in debilitating osteoarthritis. We reanalyzed previously reported data: Norberg angle (a quantitative measure HD) 921 dogs, ED 113 cases 633 controls, RCCL 271 399 controls their genotypes at ~185,000 single nucleotide polymorphisms. A novel fixed random model with a circulating probability unification (FarmCPU) function, marker-based...

Big data, accumulated from biomedical and agronomic studies, provides the potential to identify genes controlling complex human diseases agriculturally important traits through genome-wide association studies (GWAS). However, big data also leads extreme computational challenges, especially when sophisticated statistical models are employed simultaneously reduce false positives negatives. The newly developed Fixed random model Circulating Probability Unification (FarmCPU) method uses a bin...

Wheat (Triticumaestivum L.) is a major cereal crop grown across wide range of environments, but its productivity around the world challenged by various biotic and abiotic factors. landraces from are source unexploited genetic diversity that can be essential for modern wheat-breeding programs in search resistance to stresses like freezing tolerance. This study 553 winter wheat based on single-nucleotide polymorphisms (SNPs) revealed separate clusters related latitude origin. Linkage block...

Y chromosome Short Tandem Repeat (STR) haplotypes have been used in assisting forensic investigations primarily for identification and male lineage determination. The current SWGDAM interpretation guidelines Y-STR typing provide helpful guidance on those purposes but do not address the issue of kinship analysis with haplotypes. Because high mutation rate Y-STRs, there are complex missing person cases which inconsistent between true paternal relatives will arise two or more references same...

Abstract Accurate estimation of grain yield potential in soybean [ Glycine max (L.) Merr.] progeny rows (PRs) by measuring itself is challenging due to the small number seeds available. To obtain more precise estimates and control nongenetic sources variability, breeders United States use secondary traits, visual selection (VIS), adjustments for field spatial variation, pedigree (PED) information, unmanned aerial systems–based plant phenotypes; however, there are limited comparisons among...

e22093 Background: The epithermal growth factor receptor(EGFR) signaling pathways has been implicated in self-renewal of breast cancer stem cells. It proved that the EGFR tyrosine kinase inhibitor-gefitinib significantly decreased mammosphere- forming efficiency(MFE) ductal carcinoma situ (DCIS) derived We investigated response cells cell line MCF-7 to MAbs C225(cetuximab). Methods: Cells were used for nonadherent (i.e.,mammosphere) culture and divided into four groups according different...

Motivation: Genotyping error can impact downstream single nucleotide polymorphism (SNP)-based analyses. Simulating various modes and levels of help investigators better understand potential biases caused by miscalled genotypes. Methods: We have developed validated vcferr, a tool to probabilistically simulate genotyping missingness in variant call format (VCF) files. demonstrate how vcferr could be used address research question introducing varying different type into sample simulated...

Canine hip dysplasia (CHD) and rupture of the cranial cruciate ligament (RCCL) are two complex inherited orthopedic traits dogs. These may occur concurrently in same dog. Genomic prediction these diseases would benefit veterinary medicine, dog’s owner, dog breeders because their high prevalence, both result painful debilitating osteoarthritis affected joints. In this study, 842 unique dogs from 6 breeds with stifle phenotypes were genotyped on a customized Illumina density 183 k single...

Background: Single nucleotide polymorphism (SNP)-based kinship analysis is now a cornerstone of modern forensic genomics. Imputation can be used to augment genome-wide SNP data from low-coverage whole-genome sequencing (LCWGS). The impact imputation after LCWGS on genotyping error and its subsequent are unknown. Methods: We assessed the LCWGS+imputation using 1 × unidentified human remains paired with direct reference samples. characterized before implementing postimputation filters quality...

e13542 Objective: To explore the different effects of epirubicin on MCF-7 mammosphere cells and monolayer cells. Methods: were cultured in suspension to generate primary mammospheres. The inhibitory by measured MTT assay. change CD44 + CD24 - expression cell cycle distribution under condition was analyzed flow cytometry. Results: inhibition lower than that when induced same concentration (>100 ng/ml),(P<0.01). significantly higher 400 ng/μl for 72 h, (22.8% ± 4.8% Vs 3.3%...

Abstract Calling tandem repeat (TR) variants from DNA sequences is of both theoretical and practical significance. A large number software tools have been developed for detecting TRs. However, little study has done to detect TR alleles long-read sequences, the effectiveness whole genome sequence (WGS) data still needs be improved. Herein, a novel algorithm described retrieve regions alignment, program, TRcaller, call short- targeted generated multiple sequencing platforms. The results showed...

Estimating the relationships between individuals is one of fundamental challenges in many fields. In particular, relationship.ip estimation could provide valuable information for missing persons cases. The recently developed investigative genetic genealogy approach uses high-density single nucleotide polymorphisms (SNPs) to determine close and more distant relationships, which hundreds thousands tens millions SNPs are generated either by microarray genotyping or whole-genome sequencing....

Abstract Motivation Genotyping error can impact downstream SNP-based analyses. Simulating various modes and levels of help investigators better understand potential biases caused by miscalled genotypes. Results We have developed validated vcferr , a tool to probabilistically simulate genotyping missigness in VCF files. demonstrate how could be used address research question introducing varying different type into sample simulated pedigree, assessed kinship analysis degrades as function kind...

Abstract Background The increasing size of genotype data has led to the loading VCF files becoming a computational bottleneck in various analyses, including imputation and genome-wide association studies (GWAS). To address this issue, we developed software library, FM3VCF (fast M3VCF), that utilizes multiple CPU threads accelerate process. Findings can convert into exclusive format MINIMAC4[1], M3VCF[1], efficiently read parse from files. In comparison m3vcftools[1], is approximately 20...