ABSTRACT
GWAS summary statistics are fundamental for a variety of research applications yet no common storage format has been widely adopted. Existing tabular formats ambiguously or incompletely store information about genetic variants and associations, lack essential metadata and are typically not indexed yielding poor query performance and increasing the possibility of errors in data interpretation and post-GWAS analyses. To address these issues, we adapted the variant call format to store GWAS summary statistics (GWAS-VCF) and developed open-source tools to use this format in downstream analyses. We provide open access to over 10,000 complete GWAS summary datasets converted to this format ( https://gwas.mrcieu.ac.uk ).
Subject(s)
Databases, Genetic , Genome-Wide Association Study/methods , Genomics , Humans , SoftwareABSTRACT
The mycalesine butterfly Bicyclus anynana, the "Squinting bush brown," is a model organism in the study of lepidopteran ecology, development, and evolution. Here, we present a draft genome sequence for B. anynana to serve as a genomics resource for current and future studies of this important model species. Seven libraries with insert sizes ranging from 350 bp to 20 kb were constructed using DNA from an inbred female and sequenced using both Illumina and PacBio technology; 128 Gb of raw Illumina data was filtered to 124 Gb and assembled to a final size of 475 Mb (â¼×260 assembly coverage). Contigs were scaffolded using mate-pair, transcriptome, and PacBio data into 10 800 sequences with an N50 of 638 kb (longest scaffold 5 Mb). The genome is comprised of 26% repetitive elements and encodes a total of 22 642 predicted protein-coding genes. Recovery of a BUSCO set of core metazoan genes was almost complete (98%). Overall, these metrics compare well with other recently published lepidopteran genomes. We report a high-quality draft genome sequence for Bicyclus anynana. The genome assembly and annotated gene models are available at LepBase (http://ensembl.lepbase.org/index.html).
Subject(s)
Butterflies/genetics , Genome, Insect , Animals , Molecular Sequence Annotation , Whole Genome SequencingABSTRACT
Basal-like breast cancer (BLBC) is a heterogeneous disease with poor prognosis; however, its cellular origins and aetiology are poorly understood. In this study, we show that inhibitor of differentiation 4 (ID4) is a key regulator of mammary stem cell self-renewal and marks a subset of BLBC with a putative mammary basal cell of origin. Using an ID4GFP knock-in reporter mouse and single-cell transcriptomics, we show that ID4 marks a stem cell-enriched subset of the mammary basal cell population. ID4 maintains the mammary stem cell pool by suppressing key factors required for luminal differentiation. Furthermore, ID4 is specifically expressed by a subset of human BLBC that possess a very poor prognosis and a transcriptional signature similar to a mammary stem cell. These studies identify ID4 as a mammary stem cell regulator, deconvolute the heterogeneity of BLBC and link a subset of mammary stem cells to the aetiology of BLBC.
Subject(s)
Breast Neoplasms/genetics , Inhibitor of Differentiation Proteins/genetics , Mammary Glands, Animal/cytology , RNA, Messenger/metabolism , Stem Cells/metabolism , Animals , Breast Neoplasms/metabolism , Cell Line, Tumor , Female , Gene Knock-In Techniques , Humans , Inhibitor of Differentiation Proteins/metabolism , Mammary Glands, Animal/metabolism , Mice , Neoplasm Transplantation , Phenotype , Real-Time Polymerase Chain ReactionABSTRACT
SUMMARY: High-quality draft genomes are now easy to generate, as sequencing and assembly costs have dropped dramatically. However, building a user-friendly searchable Web site and database for a newly annotated genome is not straightforward. Here we present Badger, a lightweight and easy-to-install genome exploration environment designed for next generation non-model organism genomes. AVAILABILITY: Badger is released under the GPL and is available at http://badger.bio.ed.ac.uk/. We show two working examples: (i) a test dataset included with the source code, and (ii) a collection of four filarial nematode genomes. CONTACT: mark.blaxter@ed.ac.uk.
Subject(s)
Genomics/methods , Software , Genes , Genome , InternetABSTRACT
We used authentication tests developed for ancient DNA to evaluate claims by Asara et al. (Reports, 13 April 2007, p. 280) of collagen peptide sequences recovered from mastodon and Tyrannosaurus rex fossils. Although the mastodon samples pass these tests, absence of amino acid composition data, lack of evidence for peptide deamidation, and association of alpha1(I) collagen sequences with amphibians rather than birds suggest that T. rex does not.
Subject(s)
Bone and Bones/chemistry , Collagen/chemistry , Dinosaurs , Elephants , Fossils , Amino Acid Sequence , Animals , Mass Spectrometry , PhylogenyABSTRACT
A molecular survey technique was used to investigate the diversity of terrestrial tardigrades from three sites within Scotland. Ribosomal small subunit sequence was used to classify specimens into molecular operational taxonomic units (MOTU). Most MOTU were identified to the generic level using digital voucher photography. Thirty-two MOTU were defined, a surprising abundance given that the documented British fauna is 68 species. Some tardigrade MOTU were shared between the two rural collection sites, but no MOTU were found in both urban and rural sites, which conflicts with models of ubiquity of meiofaunal taxa. The patterns of relatedness of MOTU were particularly intriguing, with some forming clades with low levels of divergence, suggestive of taxon flocks. Some morphological taxa contained well-separated MOTU, perhaps indicating the existence of cryptic taxa. DNA sequence-based MOTU proved to be a revealing method for meiofaunal diversity studies.
