Moment estimators of relatedness from low-depth whole-genome sequencing data.

BACKGROUND: Estimating relatedness is an important step for many genetic study designs. A variety of methods for estimating coefficients of pairwise relatedness from genotype data have been proposed. Both the kinship coefficient [Formula: see text] and the fraternity coefficient [Formula: see text] for all pairs of individuals are of interest. However, when dealing with low-depth sequencing or imputation data, individual level genotypes cannot be confidently called. To ignore such uncertainty is known to result in biased estimates. Accordingly, methods have recently been developed to estimate kinship from uncertain genotypes. RESULTS: We present new method-of-moment estimators of both the coefficients [Formula: see text] and [Formula: see text] calculated directly from genotype likelihoods. We have simulated low-depth genetic data for a sample of individuals with extensive relatedness by using the complex pedigree of the known genetic isolates of Cilento in South Italy. Through this simulation, we explore the behaviour of our estimators, demonstrate their properties, and show advantages over alternative methods. A demonstration of our method is given for a sample of 150 French individuals with down-sampled sequencing data. CONCLUSIONS: We find that our method can provide accurate relatedness estimates whilst holding advantages over existing methods in terms of robustness, independence from external software, and required computation time. The method presented in this paper is referred to as LowKi (Low-depth Kinship) and has been made available in an R package ( https://github.com/genostats/LowKi ).

The Time Knowledge Questionnaire for children.

Based on a definition of time knowledge as the correct representation and use of the various time units, a validated questionnaire, the Time Knowledge Questionnaire (TKQ) has been developed with norms for typically developing children aged 6-11 years. The TKQ is a relatively short (10-45 min) and innovative tool, comprising 25 questions broken down into 7 categories. The TKQ has good internal consistency. A total score and two summary scores are provided, assessing conventional time and estimative time respectively. A clinical application of the tool was shown to be of interest for children with disorders or disabilities.

HLA-DRB1*15 allele influences the later course of relapsing remitting multiple sclerosis.

Most of the published works so far have aimed at finding genes associated with multiple sclerosis (MS) susceptibility. Very few studies have attempted to correlate disease features with DNA variants. In a well-characterized sample (651 patients) representative of multiple sclerosis natural history, we engaged a comprehensive study of the role of human leukocyte antigen (HLA) in the course of the disease. We investigated the role of HLA-DRB1*15 allele in samples stratified according to severity evaluated by the Multiple Sclerosis Severity Score (MSSS), time to reach EDSS 6.0 and disease type. We found that HLA-DRB1*15 genotype does not influence MS severity even among patients presenting with a given type of the disease. However, we show for the first time that HLA-DRB1*15 allele modulates the course of MS for relapsing-remitting (RR) onset patients likely by precipitating the secondary progressive (SP) phase.