A method for low-coverage single-gamete sequence analysis demonstrates adherence to Mendel’s first law across a large sample of human sperm

Recently published single-cell sequencing data from individual human sperm (n=41,189; 969–3377 cells from each of 25 donors) offer an opportunity to investigate questions of inheritance with improved statistical power, but require new methods tailored to these extremely low-coverage data (∼0.01× per cell). To this end, we developed a method, named rhapsodi, that leverages sparse gamete genotype data to phase the diploid genomes of the donor individuals, impute missing gamete genotypes, and discover meiotic recombination breakpoints, benchmarking its performance across a wide range of study designs. We then applied rhapsodi to the sperm sequencing data to investigate adherence to Mendel’s Law of Segregation, which states that the offspring of a diploid, heterozygous parent will inherit either allele with equal probability. While the vast majority of loci adhere to this rule, research in model and non-model organisms has uncovered numerous exceptions whereby ‘selfish’ alleles are disproportionately transmitted to the next generation. Evidence of such ‘transmission distortion’ (TD) in humans remains equivocal in part because scans of human pedigrees have been under-powered to detect small effects. After applying rhapsodi to the sperm data and scanning for evidence of TD, our results exhibited close concordance with binomial expectations under balanced transmission. Together, our work demonstrates that rhapsodi can facilitate novel uses of inferred genotype data and meiotic recombination events, while offering a powerful quantitative framework for testing for TD in other cohorts and study systems

Synthesis, thiol-yne "click" photopolymerization, and physical properties of networks derived from novel multifunctional alkynes

Multifunctional alkynes (2, 3, or 4 ynes per monomer) were prepared utilizing the nucleophile-catalyzed thio-Michael addition reaction from commercially available multifunctional thiols (2, 3, or 4 thiols) and propargyl acrylate. Real-time FTIR (RTIR) and NMR spectroscopies indicate that the conjugate addition under these conditions proceeds to high conversions within seconds using the nucleophilic catalyst dimethylphenylphosphine, in the absence of solvent, at ambient temperature, and with no side products. A family of polymer networks was prepared by the photoinitiated thiol-yne reaction employing a 2:1 ratio of thiol to alkyne, which resulted in uniformly cross-linked materials of systematically increasing cross-link density. Photopolymerization kinetic profiles indicate that the thiol-yne reaction proceeded rapidly to high conversion with conversions decreasing with increasing functionality of the thiol and/or alkyne groups. Differential scanning calorimetry (DSC) and dynamic mechanical thermal analysis (DMTA) results clearly indicate that the glass transition temperature increases as the overall cross-link density increases (from -10 to 42 °C by DMTA). An increase in the rubbery modulus (from 6 to 23 MPa at 70 °C) results as the functionality increases, with a concomitant decrease in the molecular weight between cross-links. © 2010 American Chemical Society