Best practices for analyzing imputed genotypes from low-pass sequencing in dogs. Mamm Genome. 2022;33:213–29. CAS PubMed Google Scholar Srikanth K, von Pfeil DJF, Stanley BJ, Griffitts C, Huson HJ. Genome wide association study with imputed whole genome sequence data identifies a 431 kb...
41 To ensure that effect-size changes could not be attributed to reduced sample size alone, we first recomputed covariate-adjusted associations in the genomically confirmed European ancestry subsample (n = 4591). We then tested whether any significant estimates (P < .05 for any contrast...
Hudson RR, Kreitman M, Aguade M: A test of neutral molecular evolution based on nucleotide data. Genetics. 1987, 116: 153-159. PubMed Central CAS Google Scholar Wang RL, Hey J: The speciation history of Drosophila pseudoobscura and close relatives: inferences from DNA sequence variation at...
DNA motif recognition analysis of genome-wide significant SNPs We used the function “variation-scan” of the online tool RSAT (http://rsat.sb-roscoff.fr/index.php, accessed on 01/15/2020) (Nguyen et al. 2018) to predict the binding effect of all the significant SNPs in the 3p21.31 lo...
(ii) triple-negative breast cancer diagnosed at or before age 60; (iii) two or more primary breast cancers in the same person; (iv) ovarian, Fallopian tube, or primary peritoneal cancer; (v) Ashkenazi Jewish ancestry and breast or pancreatic cancer at any age; or (vi) male breast ...
Specifically, the exclusion of samples and SNPs with call rates o95%, non-European (CEU) ancestry, relatedness (duplicates or related within or between each case– control series) and sex discrepancy. Furthermore, there was no evidence of systematic inflation of the test statistic in any study...
(26.7%) had best matches to bilaterian sequences and were subsequently removed (Additional file1). Following the removal of these putative contaminants, preliminary phylogenetic analyses showed that the myxozoan sequences procured by the Agalma pipeline still retained many contaminants, as these species...
Bread wheat (Triticum aestivum) is an important crop and serves as a significant source of protein and calories for humans, worldwide. Nevertheless, its la
Best practices and joint calling of the HumanExome BeadChip: the CHARGE Consortium. PLoS ONE 2013; 8: e68095. Further replication in different populations is thus required. In conclusion, the results of our study using SNP-set analyses of both dichotomous and quantitative phenotypes and subsequent...
The best known example of interaction of germline and somatic mutation is the 'two-hit' model for carcinogenesis in retinoblastoma (Knudson, 1971). Under this model, the first-hit could be either a germline susceptibility variant or a somatic mutation in an important cancer predisposition gene. ...