Mutation discovery in mice by whole exome sequencing

We report the development and optimization of reagents for in-solution, hybridization-based capture of the mouse exome. By validating this approach in a multiple inbred strains and in novel mutant strains, we show that whole exome sequencing is a robust approach for discovery of putative mutations, irrespective of strain background. We found strong candidate mutations for the majority of mutant exomes sequenced, including new models of orofacial clefting, urogenital dysmorphology, kyphosis and autoimmune hepatitis

Mining a Cathepsin Inhibitor Library for New Antiparasitic Drug Leads

The targeting of parasite cysteine proteases with small molecules is emerging as a possible approach to treat tropical parasitic diseases such as sleeping sickness, Chagas' disease, and malaria. The homology of parasite cysteine proteases to the human cathepsins suggests that inhibitors originally developed for the latter may be a source of promising lead compounds for the former. We describe here the screening of a unique ∼2,100-member cathepsin inhibitor library against five parasite cysteine proteases thought to be relevant in tropical parasitic diseases. Compounds active against parasite enzymes were subsequently screened against cultured Plasmodium falciparum, Trypanosoma brucei brucei and/or Trypanosoma cruzi parasites and evaluated for cytotoxicity to mammalian cells. The end products of this effort include the identification of sub-micromolar cell-active leads as well as the elucidation of structure-activity trends that can guide further optimization efforts

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

A draft assembly of the almond genome

Almond is one of the oldest cultivated nut crops with its origin in central and western Asia. The selection of the sweet type [i](Prunus dulcis[/i]) distinguishes the domesticated almond from its bitter wild relatives. It is economically important, especially in California with the highest worldwide production, followed by Australia and Spain. The almond belongs to the same subgenus as the peach, for which there already exists a reference genome. However, to fully understand the genetic underpinnings marking the key phenotypic differences between almond and peach, we have sequenced the genome of the ‘Texas’ almond, one of the traditional cultivars producing a sweet nut. Whole-genome shotgun sequencing of Illumina paired-end libraries gave an initial low-contiguity assembly of 512 Mbp, nearly double the estimated genome size. Counting of k-mers indicates a 275 Mbp genome with substantial heterozygosity as well as repetitive sequence. In order to tackle both problems, we constructed a fosmid library and sequenced 68 pools of ~500 clones per pool. We then assembled the pools, merged them and finished the assembly by scaffolding with paired end and mate pair libraries, which resulted in a 240 Mbp assembly with a scaffold N50 of 500 kbp, a contig N50 of 33.5 kbp and CEGMA completeness of 99%. Two thirds of the assembly was anchored to the peach-almond genetic map, and using re-sequencing data of peach-almond hybrids and their parents we inferred the two haplotypes of the sequenced almond tree. We performed additional validation of the assembly using Oxford Nanopore MinION sequencing

Selected anti-plasmodium lead compounds with associated enzyme and cell-based data.

<p>Selected anti-plasmodium lead compounds with associated enzyme and cell-based data.</p

Structural composition of the cathepsin inhibitor library.

<p>Illustrated are significantly represented chemotypes at three positions: warhead/P1, P2, and P3. Indicated in parentheses are the approximate number of library members possessing each substructural chemotype.</p

Anti-plasmodium lead compounds.

<p>Chemical structures of protease inhibitors discussed in the text. Associated enzyme inhibition and growth inhibition data is provided in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001023#pntd-0001023-t002" target="_blank">tables 2</a>–<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001023#pntd-0001023-t003" target="_blank"></a><a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001023#pntd-0001023-t004" target="_blank">4</a>.</p

Selected anti-trypanosomal lead compounds with associated enzyme and cell-based data.

<p>Selected anti-trypanosomal lead compounds with associated enzyme and cell-based data.</p

Growth inhibition of parasites.

<p>GI₅₀ (µM) data for selected library members against cultured <i>P. falciparum</i> (W2 strain), <i>T. brucei brucei</i>, or <i>T. cruzi</i> parasites. Data points above the dotted line had no measurable GI₅₀ (i.e., GI₅₀>25 µM). Data points are colored and shaped by chemotype as described in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001023#pntd-0001023-g002" target="_blank">Figure 2</a>. The relative area of data points reflects cytotoxicity to mammalian cell lines (larger squares demoting increasing % growth inhibition relative to a 100% inhibition control). Cytotoxicity evaluations were performed in Jurkat cells for the <i>T. brucei</i> and <i>P. falciparum</i> actives (at 10 µM test compound) and in BESM cells for the <i>T. cruzi</i> actives (at 20 test µM compound).</p