Abstract
The Ensembl software resources are a stable infrastructure to store, access and manipulate genome assemblies and their functional annotations. The Ensembl ‘Core’ database and Application ...Programming Interface (API) was our first major piece of software infrastructure and remains at the centre of all of our genome resources. Since its initial design more than fifteen years ago, the number of publicly available genomic, transcriptomic and proteomic datasets has grown enormously, accelerated by continuous advances in DNA-sequencing technology. Initially intended to provide annotation for the reference human genome, we have extended our framework to support the genomes of all species as well as richer assembly models. Cross-referenced links to other informatics resources facilitate searching our database with a variety of popular identifiers such as UniProt and RefSeq. Our comprehensive and robust framework storing a large diversity of genome annotations in one location serves as a platform for other groups to generate and maintain their own tailored annotation. We welcome reuse and contributions: our databases and APIs are publicly available, all of our source code is released with a permissive Apache v2.0 licence at http://github.com/Ensembl and we have an active developer mailing list (http://www.ensembl.org/info/about/contact/index.html).
Database URL: http://www.ensembl.org
An overview of Ensembl Birney, Ewan; Andrews, T Daniel; Bevan, Paul ...
Genome research,
05/2004, Letnik:
14, Številka:
5
Journal Article
Recenzirano
Odprti dostop
Ensembl (http://www.ensembl.org/) is a bioinformatics project to organize biological information around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of ...individual genomes, and of the synteny and orthology relationships between them. It is also a framework for integration of any biological data that can be mapped onto features derived from the genomic sequence. Ensembl is available as an interactive Web site, a set of flat files, and as a complete, portable open source software system for handling genomes. All data are provided without restriction, and code is freely available. Ensembl's aims are to continue to "widen" this biological integration to include other model organisms relevant to understanding human biology as they become available; to "deepen" this integration to provide an ever more seamless linkage between equivalent components in different species; and to provide further classification of functional elements in the genome that have been previously elusive.
To measure in vitro fertilization (IVF) outcomes following 24-chromosome single‒nucleotide-polymorphism (SNP)–based preimplantation genetic testing for aneuploidy (PGT-A) and euploid embryo transfer.
...Retrospective.
Fertility clinics and laboratory.
Women 20–46 years of age undergoing IVF treatment.
Twenty-four-chromosome SNP-based PGT-A of day 5/6 embryo biopsies.
Maternal age–stratified implantation, clinical pregnancy, and live birth rates per embryo transfer; miscarriage rates; and number of embryo transfers per patient needed to achieve a live birth.
An implantation rate of 69.9%, clinical pregnancy rate per transfer of 70.6%, and live birth rate per transfer of 64.5% were observed in 1,621 nondonor frozen cycles with the use of SNP-based PGT-A. In addition, SNP-based PGT-A outcomes, when measured per cycle with transfer, remained relatively constant across all maternal ages; when measured per cycle initiated, they decreased as maternal age increased. Miscarriage rates were ∼5% in women ≤40 years old. No statistically significant differences in pregnancy outcomes were found for single-embryo transfers (SET) versus double-embryo transfers with SNP-based PGT-A. On average, 1.38 embryo transfers per patient were needed to achieve a live birth in nondonor cycles.
Our findings that SNP-based PGT-A can mitigate the negative effects of maternal age on IVF outcomes in cycles with transfer, and that pregnancy outcomes from SET cycles are not significantly different from those of double-embryo transfer cycles, support the use of SET when transfers are combined with SNP-based PGT-A.
Resultados de embarazos de más de 1800 ciclos de fecundación in vitro mediante polimorfismosde nucleótido único en 24 cromosomas basado en el diagnóstico genético preimplantacional para aneuploidías
Medir los resultados de fecundación in vitro (FIV) con el uso de polimorfismos de nucleótido único en 24 cromosomas (SNP) basado en el estudio genético preimplantacional para aneuploidías (PGT-A) y transferencia de embriones euploides.
Retrospectivo.
Clínicas y Laboratorios de Fertilidad.
Mujeres de 20 a 46 años de edad sometidas a tratamientos de FIV.
Polimorfismo de nucleótido único de 24 cromosomas basado en el estudio genético preimplantacional para aneuploidías de biopsias de embriones de día 5/6.
Implantación estratificada por edad materna, embarazo clínico y tasa de recién nacido vivo por embrión transferido; tasas de pérdida/aborto y número de transferencias embrionarias por paciente necesarias para lograr un recién nacido vivo.
Se observó una tasa de implantación de 69,9%, una tasa de embarazo clínico por transferencia de 70,6% y una tasa de recién nacido vivo por transferencia de 64,5% en 1621 ciclos congelados de pacientes no donantes con el uso del SNP PGT-A. Además al medir los resultados de SNP PGT-A en ciclos donde hubo transferencias, estos se mantuvieron relativamente constantes a través de todas las edades maternas; al momento de medir los resultados por ciclo iniciado, estos disminuyeron a la vez que la edad materna aumentaba. La tasa de pérdida/aborto fue de aproximadamente 5% en mujeres ≤ 40 años de edad. No se hallaron diferencias estadísticamente significativas en los embarazos donde hubo transferencia de un solo embrión (SET) versus aquellos con transferencias de dos embriones y el uso de SNP PGT-A. Un promedio de 1,38 transferencias embrionarias por paciente fueron necesarias para lograr un recién nacido vivo en ciclos de no donantes.
Nuestros hallazgos muestran que el uso de SNP PGT-A puede mitigar los efectos negativos de la edad materna en los resultados de FIV en los ciclos donde hubo transferencias; y que los resultados de embarazo con ciclos de SET no son significativamente diferentes a aquellos ciclos en los que hubo transferencias de dos embriones, lo que apoya el uso de SET cuando las transferencias embrionarias son combinadas con el uso de SNP PGT-A.
Gene expression arrays are valuable and widely used tools for biomedical research. Today's commercial arrays attempt to measure the expression level of all of the genes in the genome. Effectively ...translating the results from the microarray into a biological interpretation requires an accurate mapping between the probesets on the array and the genes that they are targeting. Although major array manufacturers provide annotations of their gene expression arrays, the methods used by various manufacturers are different and the annotations are difficult to keep up to date in the rapidly changing world of biological sequence databases.
We have created a consistent microarray annotation protocol applicable to all of the major array manufacturers. We constantly keep our annotations updated with the latest Ensembl Gene predictions, and thus cross-referenced with a large number of external biomedical sequence database identifiers. We show that these annotations are accurate and address in detail reasons for the minority of probesets that cannot be annotated. Annotations are publicly accessible through the Ensembl Genome Browser and programmatically through the Ensembl Application Programming Interface. They are also seamlessly integrated into the BioMart data-mining tool and the biomaRt package of BioConductor.
Consistent, accurate and updated gene expression array annotations remain critical for biological research. Our annotations facilitate accurate biological interpretation of gene expression profiles.
A decision tree model was created to investigate pregnancy rates, as well as cost factors associated with rigid vs. flexible catheters. Although the flexible catheter costs more than the rigid ...catheter, it is associated with a higher pregnancy rate, which decreases costs of IUI treatment because fewer cycles are needed.
For a number of years the BioMart data warehousing system has proven to be a valuable resource for scientists seeking a fast and versatile means of accessing the growing volume of genomic data ...provided by the Ensembl project. The launch of the Ensembl Genomes project in 2009 complemented the Ensembl project by utilizing the same visualization, interactive and programming tools to provide users with a means for accessing genome data from a further five domains: protists, bacteria, metazoa, plants and fungi. The Ensembl and Ensembl Genomes BioMarts provide a point of access to the high-quality gene annotation, variation data, functional and regulatory annotation and evolutionary relationships from genomes spanning the taxonomic space. This article aims to give a comprehensive overview of the Ensembl and Ensembl Genomes BioMarts as well as some useful examples and a description of current data content and future objectives. Database URLs: http://www.ensembl.org/biomart/martview/; http://metazoa.ensembl.org/biomart/martview/; http://plants.ensembl.org/biomart/martview/; http://protists.ensembl.org/biomart/martview/; http://fungi.ensembl.org/biomart/martview/; http://bacteria.ensembl.org/biomart/martview/.
Ensembl 2012 Flicek, Paul; Amode, M. Ridwan; Barrell, Daniel ...
Nucleic acids research,
01/2012, Letnik:
40, Številka:
D1
Journal Article
Recenzirano
Odprti dostop
The Ensembl project (http://www.ensembl.org) provides genome resources for chordate genomes with a particular focus on human genome data as well as data for key model organisms such as mouse, rat and ...zebrafish. Five additional species were added in the last year including gibbon (Nomascus leucogenys) and Tasmanian devil (Sarcophilus harrisii) bringing the total number of supported species to 61 as of Ensembl release 64 (September 2011). Of these, 55 species appear on the main Ensembl website and six species are provided on the Ensembl preview site (Pre!Ensembl; http://pre.ensembl.org) with preliminary support. The past year has also seen improvements across the project.
The Ensembl project (http://www.ensembl.org) seeks to enable genomic science by providing high quality, integrated annotation on chordate and selected eukaryotic genomes within a consistent and ...accessible infrastructure. All supported species include comprehensive, evidence-based gene annotations and a selected set of genomes includes additional data focused on variation, comparative, evolutionary, functional and regulatory annotation. The most advanced resources are provided for key species including human, mouse, rat and zebrafish reflecting the popularity and importance of these species in biomedical research. As of Ensembl release 59 (August 2010), 56 species are supported of which 5 have been added in the past year. Since our previous report, we have substantially improved the presentation and integration of both data of disease relevance and the regulatory state of different cell types.
As our knowledge of the complexity of gene architecture grows, and we increase our understanding of the subtleties of gene expression, the process of accurately describing disease-causing gene ...variants has become increasingly problematic. In part, this is due to current reference DNA sequence formats that do not fully meet present needs. Here we present the Locus Reference Genomic (LRG) sequence format, which has been designed for the specific purpose of gene variant reporting. The format builds on the successful National Center for Biotechnology Information (NCBI) RefSeqGene project and provides a single-file record containing a uniquely stable reference DNA sequence along with all relevant transcript and protein sequences essential to the description of gene variants. In principle, LRGs can be created for any organism, not just human. In addition, we recognize the need to respect legacy numbering systems for exons and amino acids and the LRG format takes account of these. We hope that widespread adoption of LRGs - which will be created and maintained by the NCBI and the European Bioinformatics Institute (EBI) - along with consistent use of the Human Genome Variation Society (HGVS)-approved variant nomenclature will reduce errors in the reporting of variants in the literature and improve communication about variants affecting human health. Further information can be found on the LRG web site: http://www.lrg-sequence.org.
Ensembl (http://www.ensembl.org) integrates genomic information for a comprehensive set of chordate genomes with a particular focus on resources for human, mouse, rat, zebrafish and other high-value ...sequenced genomes. We provide complete gene annotations for all supported species in addition to specific resources that target genome variation, function and evolution. Ensembl data is accessible in a variety of formats including via our genome browser, API and BioMart. This year marks the tenth anniversary of Ensembl and in that time the project has grown with advances in genome technology. As of release 56 (September 2009), Ensembl supports 51 species including marmoset, pig, zebra finch, lizard, gorilla and wallaby, which were added in the past year. Major additions and improvements to Ensembl since our previous report include the incorporation of the human GRCh37 assembly, enhanced visualisation and data-mining options for the Ensembl regulatory features and continued development of our software infrastructure.
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