SIMULATING PEDIGREES ASCERTAINED ON THE BASIS OF OBSERVED IBD SHARING.

In large genotyping datasets, individuals often have thousands of distant cousins with whom they share detectable segments of DNA identically by descent (IBD). The ability to simulate these distant relationships is important for developing and testing methods, carrying out power analyses, and performing population genetic analyses. Because distant relatives are unlikely to share detectable IBD segments by chance, many simulation replicates are needed to sample IBD between any given pair of distant relatives.

CORRECTING MODEL MISSPECIFICATION IN RELATIONSHIP ESTIMATES.

The datasets of large genotyping biobanks and direct-to-consumer genetic testing companies contain many related individuals. Until now, it has been widely accepted that the most distant relationships that can be detected are around fifteen degrees (approximately 8 cousins) and that practical relationship estimates have a ceiling around ten degrees (approximately 5 cousins). However, we show that these assumptions are incorrect and that they are due to a misapplication of relationship estimators.

Reconstructing parent genomes using siblings and other relatives.

Reconstructing the DNA of ancestors from their descendants has the potential to empower phenotypic analyses (including association and genetic nurture studies), improve pedigree reconstruction, and shed light on the ancestral population and phenotypes of ancestors. We developed HAPI-RECAP, a method that reconstructs the DNA of parents from full siblings and their relatives. This tool leverages HAPI2's output, a new phasing approach that applies to siblings (and optionally one or both parents) and reliably infers parent haplotypes but does not link the ungenotyped parents' DNA across chromosomes or between segments flanking ambiguities.

The genetic legacy of African Americans from Catoctin Furnace.

Few African Americans have been able to trace family lineages back to ancestors who died before the 1870 United States Census, the first in which all Black people were listed by name. We analyzed 27 individuals from Maryland's Catoctin Furnace African American Cemetery (1774-1850), identifying 41,799 genetic relatives among consenting research participants in 23andMe, Inc.'s genetic database.

A prospective multicenter study to evaluate the impact of cryotherapy on dysphagia and quality of life in patients with inoperable esophageal cancer.

Background: Dysphagia palliation in inoperable esophageal cancer continues to be a challenge. Self-expandable metal stents have been the mainstay of endoscopic palliation but have a significant risk of adverse events (AEs). Liquid nitrogen spray cryotherapy is an established modality that can be used with systemic therapy.

30 years of [C]methyl triflate.

Some scientific discoveries are well known only to a core group of researchers working on technical subjects. Nevertheless, they open new research directions, allow existing knowledge to be viewed in entirely new and useful ways, or provide a way to make something that was hard or impossible to make before. Carbon-11 methyl triflate ([C]MeOTf) is one such advance, facilitating the synthesis of many carbon-11 radio tracers and broadening the range of applications of carbon-11 radiochemistry.

Impact of implant-based breast reconstruction on bra fit.

Comfortable and well-fitting bras are necessary for good quality of life but hard to find for women who undergo reconstruction after breast cancer treatment. This study aimed to provide data to inform bra designs for breast cancer survivors. We measured anatomical distances used in bra design on 3D clinical photographs of patients who underwent unilateral and bilateral implant-based reconstruction to quantify changes after reconstruction relative to the measured values before the person underwent surgery.

Microplastics and Their Impact on Reproduction-Can we Learn From the Model?

Biologically active environmental pollutants have significant impact on ecosystems, wildlife, and human health. Microplastic (MP) and nanoplastic (NP) particles are pollutants that are present in the terrestrial and aquatic ecosystems at virtually every level of the food chain. Moreover, recently, airborne microplastic particles have been shown to reach and potentially damage respiratory systems.

Bonsai: An efficient method for inferring large human pedigrees from genotype data.

Pedigree inference from genotype data is a challenging problem, particularly when pedigrees are sparsely sampled and individuals may be distantly related to their closest genotyped relatives. We present a method that infers small pedigrees of close relatives and then assembles them into larger pedigrees. To assemble large pedigrees, we introduce several formulas and tools including a likelihood for the degree separating two small pedigrees, a generalization of the fast DRUID point estimate of the degree separating two pedigrees, a method for detecting individuals who share background identity-by-descent (IBD) that does not reflect recent common ancestry, and a method for identifying the ancestral branches through which distant relatives are connected.

Nonsteroidal sulfamate derivatives as new therapeutic approaches for Neurofibromatosis 2 (NF2).

Background: Neurofibromatosis 1 and 2, although involving two different tumour suppressor genes (neurofibromin and merlin, respectively), are both cancer predisposition syndromes that disproportionately affect cells of neural crest origin. New therapeutic approaches for both NF1 and NF2 are badly needed. In promising previous work we demonstrated that two non-steroidal analogues of 2-methoxy-oestradiol (2ME2), STX3451(2-(3-bromo-4,5-dimethoxybenzyl)-7-methoxy-6-sulfamoyloxy-1,2,3,4-tetrahydroisoquinoline), and STX2895 (7-Ethyl-6-sulfamoyloxy-2-(3,4,5-trimethoxybenzyl)-1,2,3,4-tetrahydroisoquinoline) reduced tumour cell growth and induced apoptosis in malignant and benign human Neurofibromatosis 1 (NF1) tumour cells.

On the joint distribution of tree height and tree length under the coalescent.

Many statistics that examine genetic variation depend on the underlying shapes of genealogical trees. Under the coalescent model, we investigate the joint distribution of two quantities that describe genealogical tree shape: tree height and tree length. We derive a recursive formula for their exact joint distribution under a demographic model of a constant-sized population.

Loci associated with skin pigmentation identified in African populations.

Despite the wide range of skin pigmentation in humans, little is known about its genetic basis in global populations. Examining ethnically diverse African genomes, we identify variants in or near , , , , , and that are significantly associated with skin pigmentation. Genetic evidence indicates that the light pigmentation variant at was introduced into East Africa by gene flow from non-Africans.

Parallel Trajectories of Genetic and Linguistic Admixture in a Genetically Admixed Creole Population.

Joint analyses of genes and languages, both of which are transmitted in populations by descent with modification-genes vertically by Mendel's laws, language via combinations of vertical, oblique, and horizontal processes [1-4]-provide an informative approach for human evolutionary studies [5-10]. Although gene-language analyses have employed extensive data on individual genetic variation [11-23], their linguistic data have not considered corresponding long-recognized [24] variability in individual speech patterns, or idiolects. Genetically admixed populations that speak creole languages show high genetic and idiolectal variation-genetic variation owing to heterogeneity in ancestry within admixed groups [25, 26] and idiolectal variation owing to recent language formation from differentiated sources [27-31].

The Effects of Population Size Histories on Estimates of Selection Coefficients from Time-Series Genetic Data.

Many approaches have been developed for inferring selection coefficients from time series data while accounting for genetic drift. These approaches have been motivated by the intuition that properly accounting for the population size history can significantly improve estimates of selective strengths. However, the improvement in inference accuracy that can be attained by modeling drift has not been characterized.

Extraction, purification, methylation and GC-MS analysis of short-chain carboxylic acids for metabolic flux analysis.

Dynamic metabolic flux analysis requires efficient and effective methods for extraction, purification and analysis of a plethora of naturally-occurring compounds. One area of metabolism that would be highly informative to study using metabolic flux analysis is the tricarboxylic acid (TCA) cycle, which consists of short-chain carboxylic acids. Here, we describe a newly-developed method for extraction, purification, derivatization and analysis of short-chain carboxylic acids involved in the TCA cycle.

Social science as a tool in developing scientific thinking skills in underserved, low-achieving urban students.

Engagement in purposeful problem solving involving social science content was sufficient to develop a key set of inquiry skills in low-performing middle school students from an academically and economically disadvantaged urban public school population, with this skill transferring to a more traditional written scientific thinking assessment instrument 3weeks later. Students only observing their peers' activity or not participating at all failed to show these gains. Implications are addressed with regard to the mastery of scientific thinking skills among academically disadvantaged students.

SpectralTDF: transition densities of diffusion processes with time-varying selection parameters, mutation rates and effective population sizes.

Motivation: In the Wright-Fisher diffusion, the transition density function describes the time evolution of the population-wide frequency of an allele. This function has several practical applications in population genetics and computing it for biologically realistic scenarios with selection and demography is an important problem.

Results: We develop an efficient method for finding a spectral representation of the transition density function for a general model where the effective population size, selection coefficients and mutation parameters vary over time in a piecewise constant manner.

Theory and applications of a deterministic approximation to the coalescent model.

Under the coalescent model, the random number nt of lineages ancestral to a sample is nearly deterministic as a function of time when nt is moderate to large in value, and it is well approximated by its expectation E[nt]. In turn, this expectation is well approximated by simple deterministic functions that are easy to compute. Such deterministic functions have been applied to estimate allele age, effective population size, and genetic diversity, and they have been used to study properties of models of infectious disease dynamics.

Improvements to a class of distance matrix methods for inferring species trees from gene trees.

Among the methods currently available for inferring species trees from gene trees, the GLASS method of Mossel and Roch (2010), the Shallowest Divergence (SD) method of Maddison and Knowles (2006), the STEAC method of Liu et al. (2009), and a related method that we call Minimum Average Coalescence (MAC) are computationally efficient and provide branch length estimates. Further, GLASS and STEAC have been shown to be consistent estimators of tree topology under a multispecies coalescent model.

A coalescent model for genotype imputation.

The potential for imputed genotypes to enhance an analysis of genetic data depends largely on the accuracy of imputation, which in turn depends on properties of the reference panel of template haplotypes used to perform the imputation. To provide a basis for exploring how properties of the reference panel affect imputation accuracy theoretically rather than with computationally intensive imputation experiments, we introduce a coalescent model that considers imputation accuracy in terms of population-genetic parameters. Our model allows us to investigate sampling designs in the frequently occurring scenario in which imputation targets and templates are sampled from different populations.

iGLASS: an improvement to the GLASS method for estimating species trees from gene trees.

Several methods have been designed to infer species trees from gene trees while taking into account gene tree/species tree discordance. Although some of these methods provide consistent species tree topology estimates under a standard model, most either do not estimate branch lengths or are computationally slow. An exception, the GLASS method of Mossel and Roch, is consistent for the species tree topology, estimates branch lengths, and is computationally fast.