Publications by authors named "Glenn Proctor"

14 Publications

  • Page 1 of 1

Pregnancy outcomes from more than 1,800 in vitro fertilization cycles with the use of 24-chromosome single-nucleotide polymorphism-based preimplantation genetic testing for aneuploidy.

Fertil Steril 2018 07 13;110(1):113-121. Epub 2018 Jun 13.

Natera, San Carlos, California. Electronic address:

Objective: 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.

Design: Retrospective.

Setting: Fertility clinics and laboratory.

Patient(s): Women 20-46 years of age undergoing IVF treatment.

Intervention(s): Twenty-four-chromosome SNP-based PGT-A of day 5/6 embryo biopsies.

Main Outcome Measure(s): 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.

Result(s): 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.

Conclusion(s): 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.
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http://dx.doi.org/10.1016/j.fertnstert.2018.03.026DOI Listing
July 2018

Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation.

Database (Oxford) 2017 01;2017(1)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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.
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http://dx.doi.org/10.1093/database/bax020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5467575PMC
January 2017

Ensembl 2012.

Nucleic Acids Res 2012 Jan 15;40(Database issue):D84-90. Epub 2011 Nov 15.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK.

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.
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http://dx.doi.org/10.1093/nar/gkr991DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245178PMC
January 2012

Ensembl BioMarts: a hub for data retrieval across taxonomic space.

Database (Oxford) 2011 23;2011:bar030. Epub 2011 Jul 23.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

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/.
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http://dx.doi.org/10.1093/database/bar030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3170168PMC
November 2011

Ensembl 2011.

Nucleic Acids Res 2011 Jan 2;39(Database issue):D800-6. Epub 2010 Nov 2.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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.
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http://dx.doi.org/10.1093/nar/gkq1064DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013672PMC
January 2011

Consistent annotation of gene expression arrays.

BMC Genomics 2010 May 11;11:294. Epub 2010 May 11.

European Bioinformatics Institute EMBL, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Background: 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.

Results: 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.

Conclusions: Consistent, accurate and updated gene expression array annotations remain critical for biological research. Our annotations facilitate accurate biological interpretation of gene expression profiles.
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http://dx.doi.org/10.1186/1471-2164-11-294DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2894801PMC
May 2010

Locus Reference Genomic sequences: an improved basis for describing human DNA variants.

Genome Med 2010 Apr 15;2(4):24. Epub 2010 Apr 15.

Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK.

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.
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http://dx.doi.org/10.1186/gm145DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2873802PMC
April 2010

Ensembl's 10th year.

Nucleic Acids Res 2010 Jan 11;38(Database issue):D557-62. Epub 2009 Nov 11.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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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http://dx.doi.org/10.1093/nar/gkp972DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808936PMC
January 2010

Solutions for data integration in functional genomics: a critical assessment and case study.

Brief Bioinform 2008 Nov;9(6):532-44

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

The torrent of data emerging from the application of new technologies to functional genomics and systems biology can no longer be contained within the traditional modes of data sharing and publication with the consequence that data is being deposited in, distributed across and disseminated through an increasing number of databases. The resulting fragmentation poses serious problems for the model organism community which increasingly rely on data mining and computational approaches that require gathering of data from a range of sources. In the light of these problems, the European Commission has funded a coordination action, CASIMIR (coordination and sustainability of international mouse informatics resources), with a remit to assess the technical and social aspects of database interoperability that currently prevent the full realization of the potential of data integration in mouse functional genomics. In this article, we assess the current problems with interoperability, with particular reference to mouse functional genomics, and critically review the technologies that can be deployed to overcome them. We describe a typical use-case where an investigator wishes to gather data on variation, genomic context and metabolic pathway involvement for genes discovered in a genome-wide screen. We go on to develop an automated approach involving an in silico experimental workflow tool, Taverna, using web services, BioMart and MOLGENIS technologies for data retrieval. Finally, we focus on the current impediments to adopting such an approach in a wider context, and strategies to overcome them.
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http://dx.doi.org/10.1093/bib/bbn040DOI Listing
November 2008

Mouse Phenotype Database Integration Consortium: integration [corrected] of mouse phenome data resources.

Mamm Genome 2007 Mar 10;18(3):157-63. Epub 2007 Apr 10.

Understanding the functions encoded in the mouse genome will be central to an understanding of the genetic basis of human disease. To achieve this it will be essential to be able to characterize the phenotypic consequences of variation and alterations in individual genes. Data on the phenotypes of mouse strains are currently held in a number of different forms (detailed descriptions of mouse lines, first-line phenotyping data on novel mutations, data on the normal features of inbred lines) at many sites worldwide. For the most efficient use of these data sets, we have initiated a process to develop standards for the description of phenotypes (using ontologies) and file formats for the description of phenotyping protocols and phenotype data sets. This process is ongoing and needs to be supported by the wider mouse genetics and phenotyping communities to succeed. We invite interested parties to contact us as we develop this process further.
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http://dx.doi.org/10.1007/s00335-007-9004-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4230762PMC
March 2007

Flexible versus rigid intrauterine insemination catheters: a prospective, randomized, controlled study.

Fertil Steril 2005 May;83(5):1544-6

Division of Reproductive Endocrinology and Infertility, Center for Women's Medicine, Greenville Hospital System, Greenville, South Carolina 29605, USA.

Objective: To prospectively compare pregnancy rates for couples undergoing IUI by a single healthcare provider with random assignment to either rigid (Tomcat; Kendall Sovereign, Mansfield, MA) or flexible (Soft Pass; Cook, Spencer, IN) catheters.

Design: Randomized, controlled study.

Setting: Tertiary care infertility practice.

Patient(s): One hundred infertile women enrolled from a single infertility practice who met the inclusion and exclusion criteria for IUI were enrolled. Of the 100 patients, 95 underwent ovarian stimulation before IUI: 35 with clomiphene citrate alone, 60 with clomiphene citrate combined with a single dose of gonadotropins.

Intervention(s): Timed IUI was performed with either rigid (Tomcat) or flexible (Cook) insemination catheters.

Main Outcome Measure(s): Pregnancy rate per cycle.

Result(s): No differences were noted between groups for the following: age, length of infertility, day-3 FSH level, number of prior IUI cycles, total motile sperm count, days of abstinence, infertility diagnoses, insemination ratings, and stimulation protocols. No difference in pregnancy rates was observed between rigid and flexible catheter groups.

Conclusion(s): There is no statistically significant difference between flexible and rigid catheters for IUI.
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http://dx.doi.org/10.1016/j.fertnstert.2004.11.069DOI Listing
May 2005

Does seasonality alter intrauterine insemination outcomes: a 5-year study.

J Assist Reprod Genet 2004 Jul;21(7):263-70

Department of Obstetrics and Gynecology, Greenville Hospital System, Greenville, South Carolina, USA.

Purpose: To determine if seasonal changes alter pregnancy rate in intrauterine insemination (IUI) patients.

Methods: One-thousand and eighty semen analyses prepared for IUI were evaluated in this retrospective cohort study of 496 patients.

Results: Volume, pH, sperm concentration, and pregnancy rates were not altered by season. However, the percent motility, the total motile spermatozoa in the ejaculate, the straight-line velocity (VSL) of spermatozoa, as well as the morphology of sperm were altered by season. In a subset of these patients that were defined as normal, only the VSL and the morphology of the spermatozoa were altered by seasonal changes.

Conclusions: Seasonality alters sperm motility parameters as well as morphology, but these changes are not significant enough to alter pregnancy rates.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3455185PMC
http://dx.doi.org/10.1023/b:jarg.0000042012.12958.9eDOI Listing
July 2004

The Ensembl core software libraries.

Genome Res 2004 May;14(5):929-33

EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK.

Systems for managing genomic data must store a vast quantity of information. Ensembl stores these data in several MySQL databases. The core software libraries provide a practical and effective means for programmers to access these data. By encapsulating the underlying database structure, the libraries present end users with a simple, abstract interface to a complex data model. Programs that use the libraries rather than SQL to access the data are unaffected by most schema changes. The architecture of the core software libraries, the schema, and the factors influencing their design are described. All code and data are freely available.
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http://dx.doi.org/10.1101/gr.1857204DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC479122PMC
May 2004

An overview of Ensembl.

Genome Res 2004 May 12;14(5):925-8. Epub 2004 Apr 12.

EMBL European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

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.
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http://dx.doi.org/10.1101/gr.1860604DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC479121PMC
May 2004
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