Haplotypes versus genotypes on pedigrees

Abstract. Genome sequencing will soon produce haplotype data for individuals. For pedigrees of related individuals, sequencing appears to be an attractive alternative to genotyping. However, methods for pedigree analysis with haplotype data have not yet been developed, and the computational complexity of such problems has been an open question. Furthermore, it is not clear in which scenarios haplotype data would provide better estimates than genotype data for quantities such as recombination rates. To answer these questions, a reduction is given from genotype problem instances to haplotype problem instances, and it is shown that solving the haplotype problem yields the solution to the genotype problem, up to constant factors or coefficients. The pedigree analysis problems we will consider are the likelihood, maximum probability haplotype, and minimum recombination haplotype problems. Two algorithms are introduced: an exponential-time hidden Markov model (HMM) for haplotype data where some individuals are untyped, and a linear-time algorithm for pedigrees having haplotype data for all individuals. Recombination estimates from the general haplotype HMM algorithm are compared to recombination estimates produced by a genotype HMM. Having haplotype data on all individuals produces better estimates. However, having several untyped individuals can drastically reduce the utility of haplotype data. Pedigree analysis, both linkage and association studies, has a long history of important contributions to genetics, including disease-gene finding and some of the first genetic maps for humans. Recent contributions include fine-scale recombination maps in humans [4], regions linked to Schizophrenia that might be missed by genome-wide association studies [11], and insights into the relationship between cystic fibrosis and fertility [13]. Algorithms for pedigree problems are of great interest to the computer science community, in part because of connections to machine learning algorithms, optimization methods, and combinatorics [7, 16

The Near-Earth Object Surveyor Mission

The Near-Earth Object (NEO) Surveyor mission is a NASA observatory designed to discover and characterize near-Earth asteroids and comets. The mission's primary objective is to find the majority of objects large enough to cause severe regional impact damage ($>$140 m in effective spherical diameter) within its five-year baseline survey. Operating at the Sun-Earth L1 Lagrange point, the mission will survey to within 45 degrees of the Sun in an effort to find the objects in the most Earth-like orbits. The survey cadence is optimized to provide observational arcs long enough to reliably distinguish near-Earth objects from more distant small bodies that cannot pose an impact hazard. Over the course of its survey, NEO Surveyor will discover $\sim$200,000 - 300,000 new NEOs down to sizes as small as $\sim$10 m and thousands of comets, significantly improving our understanding of the probability of an Earth impact over the next century.Comment: accepted to PS

The Brief Aggression Questionnaire : structure, validity, reliability, and generalizability

In contexts that increasingly demand brief self-report measures (e.g., experience sampling, longitudinal and field studies), researchers seek succinct surveys that maintain reliability and validity. One such measure is the 12-item Brief Aggression Questionnaire (BAQ; Webster et al., 2014), which uses 4 3-item subscales: Physical Aggression, Verbal Aggression, Anger, and Hostility. Although prior work suggests the BAQ's scores are reliable and valid, we addressed some lingering concerns. Across 3 studies (N = 1,279), we found that the BAQ had a 4-factor structure, possessed long-term test–retest reliability across 12 weeks, predicted differences in behavioral aggression over time in a laboratory experiment, generalized to a diverse nonstudent sample, and showed convergent validity with a displaced aggression measure. In addition, the BAQ's 3-item Anger subscale showed convergent validity with a trait anger measure. We discuss the BAQ's potential reliability, validity, limitations, and uses as an efficient measure of aggressive traits