Diminishing Return for Increased Mappability with Longer Sequencing Reads: Implications of the k-mer Distributions in the Human Genome

The amount of non-unique sequence (non-singletons) in a genome directly affects the difficulty of read alignment to a reference assembly for high throughput-sequencing data. Although a greater length increases the chance for reads being uniquely mapped to the reference genome, a quantitative analysis of the influence of read lengths on mappability has been lacking. To address this question, we evaluate the k-mer distribution of the human reference genome. The k-mer frequency is determined for k ranging from 20 to 1000 basepairs. We use the proportion of non-singleton k-mers to evaluate the mappability of reads for a corresponding read length. We observe that the proportion of non-singletons decreases slowly with increasing k, and can be fitted by piecewise power-law functions with different exponents at different k ranges. A faster decay at smaller values for k indicates more limited gains for read lengths > 200 basepairs. The frequency distributions of k-mers exhibit long tails in a power-law-like trend, and rank frequency plots exhibit a concave Zipf's curve. The location of the most frequent 1000-mers comprises 172 kilobase-ranged regions, including four large stretches on chromosomes 1 and X, containing genes with biomedical implications. Even the read length 1000 would be insufficient to reliably sequence these specific regions.Comment: 5 figure

Accelerated matrix-vector multiplications for matrices involving genotype covariates with applications in genomic prediction

In the last decade, a number of methods have been suggested to deal with large amounts of genetic data in genomic predictions. Yet, steadily growing population sizes and the suboptimal use of computational resources are pushing the practical application of these approaches to their limits. As an extension to the C/CUDA library miraculix, we have developed tailored solutions for the computation of genotype matrix multiplications which is a critical bottleneck in the empirical evaluation of many statistical models. We demonstrate the benefits of our solutions at the example of single-step models which make repeated use of this kind of multiplication. Targeting modern Nvidia® GPUs as well as a broad range of CPU architectures, our implementation significantly reduces the time required for the estimation of breeding values in large population sizes. miraculix is released under the Apache 2.0 license and is freely available at https://github.com/alexfreudenberg/miraculix

A Simple Method for Analyzing Exome Sequencing Data Shows Distinct Levels of Nonsynonymous Variation for Human Immune and Nervous System Genes

To measure the strength of natural selection that acts upon single nucleotide variants (SNVs) in a set of human genes, we calculate the ratio between nonsynonymous SNVs (nsSNVs) per nonsynonymous site and synonymous SNVs (sSNVs) per synonymous site. We transform this ratio with a respective factor f that corrects for the bias of synonymous sites towards transitions in the genetic code and different mutation rates for transitions and transversions. This method approximates the relative density of nsSNVs (rdnsv) in comparison with the neutral expectation as inferred from the density of sSNVs. Using SNVs from a diploid genome and 200 exomes, we apply our method to immune system genes (ISGs), nervous system genes (NSGs), randomly sampled genes (RSGs), and gene ontology annotated genes. The estimate of rdnsv in an individual exome is around 20% for NSGs and 30–40% for ISGs and RSGs. This smaller rdnsv of NSGs indicates overall stronger purifying selection. To quantify the relative shift of nsSNVs towards rare variants, we next fit a linear regression model to the estimates of rdnsv over different SNV allele frequency bins. The obtained regression models show a negative slope for NSGs, ISGs and RSGs, supporting an influence of purifying selection on the frequency spectrum of segregating nsSNVs. The y-intercept of the model predicts rdnsv for an allele frequency close to 0. This parameter can be interpreted as the proportion of nonsynonymous sites where mutations are tolerated to segregate with an allele frequency notably greater than 0 in the population, given the performed normalization of the observed nsSNV to sSNV ratio. A smaller y-intercept is displayed by NSGs, indicating more nonsynonymous sites under strong negative selection. This predicts more monogenically inherited or de-novo mutation diseases that affect the nervous system

Key Role of Splenic Myeloid DCs in the IFN-αβ Response to Adenoviruses In Vivo

The early systemic production of interferon (IFN)-αβ is an essential component of the antiviral host defense mechanisms, but is also thought to contribute to the toxic side effects accompanying gene therapy with adenoviral vectors. Here we investigated the IFN-αβ response to human adenoviruses (Ads) in mice. By comparing the responses of normal, myeloid (m)DC- and plasmacytoid (p)DC-depleted mice and by measuring IFN-αβ mRNA expression in different organs and cells types, we show that in vivo, Ads elicit strong and rapid IFN-αβ production, almost exclusively in splenic mDCs. Using knockout mice, various strains of Ads (wild type, mutant and UV-inactivated) and MAP kinase inhibitors, we demonstrate that the Ad-induced IFN-αβ response does not require Toll-like receptors (TLR), known cytosolic sensors of RNA (RIG-I/MDA-5) and DNA (DAI) recognition and interferon regulatory factor (IRF)-3, but is dependent on viral endosomal escape, signaling via the MAP kinase SAPK/JNK and IRF-7. Furthermore, we show that Ads induce IFN-αβ and IL-6 in vivo by distinct pathways and confirm that IFN-αβ positively regulates the IL-6 response. Finally, by measuring TNF-α responses to LPS in Ad-infected wild type and IFN-αβR−/− mice, we show that IFN-αβ is the key mediator of Ad-induced hypersensitivity to LPS. These findings indicate that, like endosomal TLR signaling in pDCs, TLR-independent virus recognition in splenic mDCs can also produce a robust early IFN-αβ response, which is responsible for the bulk of IFN-αβ production induced by adenovirus in vivo. The signaling requirements are different from known TLR-dependent or cytosolic IFN-αβ induction mechanisms and suggest a novel cytosolic viral induction pathway. The hypersensitivity to components of the microbial flora and invading pathogens may in part explain the toxic side effects of adenoviral gene therapy and contribute to the pathogenesis of adenoviral disease

Transancestral mapping of the MHC region in systemic lupus erythematosus identifies new independent and interacting loci at MSH5, HLA-DPB1 and HLA-G

OBJECTIVES: Systemic lupus erythematosus (SLE) is a chronic multisystem genetically complex autoimmune disease characterised by the production of autoantibodies to nuclear and cellular antigens, tissue inflammation and organ damage. Genome-wide association studies have shown that variants within the major histocompatibility complex (MHC) region on chromosome 6 confer the greatest genetic risk for SLE in European and Chinese populations. However, the causal variants remain elusive due to tight linkage disequilibrium across disease-associated MHC haplotypes, the highly polymorphic nature of many MHC genes and the heterogeneity of the SLE phenotype. METHODS: A high-density case-control single nucleotide polymorphism (SNP) study of the MHC region was undertaken in SLE cohorts of Spanish and Filipino ancestry using a custom Illumina chip in order to fine-map association signals in these haplotypically diverse populations. In addition, comparative analyses were performed between these two datasets and a northern European UK SLE cohort. A total of 1433 cases and 1458 matched controls were examined. RESULTS: Using this transancestral SNP mapping approach, novel independent loci were identified within the MHC region in UK, Spanish and Filipino patients with SLE with some evidence of interaction. These loci include HLA-DPB1, HLA-G and MSH5 which are independent of each other and HLA-DRB1 alleles. Furthermore, the established SLE-associated HLA-DRB1*15 signal was refined to an interval encompassing HLA-DRB1 and HLA-DQA1. Increased frequencies of MHC region risk alleles and haplotypes were found in the Filipino population compared with Europeans, suggesting that the greater disease burden in non-European SLE may be due in part to this phenomenon. CONCLUSION: These data highlight the usefulness of mapping disease susceptibility loci using a transancestral approach, particularly in a region as complex as the MHC, and offer a springboard for further fine-mapping, resequencing and transcriptomic analysis

Functionalized tetrapodal diazatriptycenes for electrostatic dipole engineering in n-type organic thin film transistors

V.R., F.S.B., S.H., M.M., M.-M.B., S.H., J.F., W.K., W.J., A.K., A.P., U.H.F.B., and K.M. acknowledge the German Federal Ministry of Education and Research (BMBF) for financial support within the INTERPHASE project (nos. 13N13656, 13N13657, 13N13658, 13N13659). V.R. thanks the German Research Foundation for financial support within the SFB1249 project and the Heidelberg Graduate School of Fundamental research.The authors also appreciate financial support by the German Research Foundation (grant ZH 63/39-1) and by the DAAD-ACEH Scholarship of Excellence (A.A.).A diazatriptycene‐based tetrapodal scaffold with thiol anchors enforces a nearly upright orientation of functional groups, introduced to its quinoxaline subunit, with respect to the substrate upon formation of self‐assembled monolayers (SAMs). Substitution with electron‐withdrawing fluorine and cyano as well as electron‐rich dimethylamino substituents allows tuning of the molecular dipole and, consequently, of the work function of gold over a range of 1.0 eV (from 3.9 to 4.9 eV). The properties of the SAMs are comprehensively investigated by infrared reflection absorption spectroscopy, near edge X‐ray absorption fine structure spectroscopy, and X‐ray photoelectron spectroscopy. As prototypical examples for the high potential of the presented SAMs in devices, organic thin‐film transistors are fabricated.Publisher PDFPeer reviewe

Interplay of structural dynamics and electronic effects in an engineered assembly of pentacene in a metal–organic framework

Charge carrier mobility is an important figure of merit to evaluate organic semiconductor (OSC) materials. In aggregated OSCs, this quantity is determined by inter-chromophoric electronic and vibrational coupling. These key parameters sensitively depend on structural properties, including the density of defects. We have employed a new type of crystalline assembly strategy to engineer the arrangement of the OSC pentacene in a structure not realized as crystals to date. Our approach is based on metal–organic frameworks (MOFs), in which suitably substituted pentacenes act as ditopic linkers and assemble into highly ordered π-stacks with long-range order. Layer-by-layer fabrication of the MOF yields arrays of electronically coupled pentacene chains, running parallel to the substrate surface. Detailed photophysical studies reveal strong, anisotropic inter-pentacene electronic coupling, leading to efficient charge delocalization. Despite a high degree of structural order and pronounced dispersion of the 1D-bands for the static arrangement, our experimental results demonstrate hopping-like charge transport with an activation energy of 64 meV dominating the band transport over a wide range of temperatures. A thorough combined quantum mechanical and molecular dynamics investigation identifies frustrated localized rotations of the pentacene cores as the reason for the breakdown of band transport and paves the way for a crystal engineering strategy of molecular OSCs that independently varies the arrangement of the molecular cores and their vibrational degrees of freedom

Singlet exciton fission in a modified acene with improved stability and high photoluminescence yield

Abstract: We report a fully efficient singlet exciton fission material with high ambient chemical stability. 10,21-Bis(triisopropylsilylethynyl)tetrabenzo[a,c,l,n]pentacene (TTBP) combines an acene core with triphenylene wings that protect the formal pentacene from chemical degradation. The electronic energy levels position singlet exciton fission to be endothermic, similar to tetracene despite the triphenylenes. TTBP exhibits rapid early time singlet fission with quantitative yield of triplet pairs within 100 ps followed by thermally activated separation to free triplet excitons over 65 ns. TTBP exhibits high photoluminescence quantum efficiency, close to 100% when dilute and 20% for solid films, arising from triplet-triplet annihilation. In using such a system for exciton multiplication in a solar cell, maximum thermodynamic performance requires radiative decay of the triplet population, observed here as emission from the singlet formed by recombination of triplet pairs. Combining chemical stabilisation with efficient endothermic fission provides a promising avenue towards singlet fission materials for use in photovoltaics