Abbreviations and Glossary¶
| Abbreviation / Term | Description |
|---|---|
| 1000GENOMES_phase_3 | The 1000 Genomes Project ran between 2008 and 2015, creating the largest public catalogue of human variation and genotype data. As the project ended, the Data Coordination Centre at EMBL-EBI has received continued funding from the Wellcome Trust to maintain and expand the resource. |
| BAM | Binary Alignment Map of a participant’s genome. |
| CRAM | Compressed Reference-oriented Alignment Map file. A compressed efficient reference-based alternative to the BAM file. |
| Catalog (OpenCGA) | Catalog is been developed to provide authentication, ACLs and to keep track all of the files and sample annotation. |
| Cellbase | Annotation Database - https://github.com/opencb/cellbase |
| CIP | Clinical Interpretation Provider (CIP) is the software company which manages the CIP decision support system used by an NHS GMC user to interpret variants from a case. |
| CIP-API | Clinical Interpretation Provider Application Programming Interface (CIP-API) is the defined endpoint computer program that communicates between the CIP and the Genomics England bioinformatics pipeline using Genomics England data models. |
| CNV | Copy Number Variant |
| ESHG guidelines | The European Society of Human Genetics Guidelines |
| ESP_6500 | NHLBI GO Exome Sequencing Project (ESP) is to discover novel genes and mechanisms contributing to heart, lung and blood disorders by pioneering the application of next-generation sequencing of the protein coding regions of the human genome across diverse, richly-phenotyped populations and to share these datasets and findings with the scientific community to extend and enrich the diagnosis, management and treatment of heart, lung and blood disorders. |
| EuroGentest | EuroGentest is a project funded by the European Commission to harmonize the process of genetic testing, from sampling to counselling, across Europe. The ultimate goal is to ensure that all aspects of genetic testing are of high quality thereby providing accurate and reliable results for the benefit of the patients. |
| EVS | Exome Variant Server |
| ExAC | The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. |
| GeCIP | Genomics England Clinical Interpretation Partnership |
| GEL | Genomics England |
| GelPedigree | The Model of the pedigree is defined with the following parameters: 1. Model version number, 2. Family id which internally translates to a sample set, 3. Participants, members of a family with associated phenotypes as present in the record RD Participant, 4. Analysis Panels, in a family with associated phenotypes as present in the record Participants 5. Penetrance of a disease, in a family with associated phenotypes as present in the record Participants |
| NHS GLH | NHS Genomics Laboratory Hub |
| GnomAD | Genome Aggregation Database. This is a coalition of investigators seeking to aggregate and harmonize exome and genome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. |
| GONL | The Genome of the Netherlands is a consortium funded as part of the Netherlands Biobanking and Biomolecular Research Infrastructure. Samples where contributed by LifeLines, The Leiden Longevity Study, The Netherlands Twin Registry (NTR), The Rotterdam studies, and The Genetic Research in Isolated Populations program. |
| GRCh37 | The human genome assembly GRCh37 (also known as hg19) |
| GRCh38 | The human genome assembly GRCh38 |
| HPO | Human Phenotype Ontology |
| HPO terms | Human Phenotype Ontology terms |
| HTML | HyperText Markup Language – used to provide a human-readable presentation of key information from the JSON data export (a report). |
| Interpretation Browser | The Interpretation Browser is within the Genomics England Interpretation Portal enables the NHS GMC clinical scientists to review results of Genomics England Interpretation Services (e.g. Tiering and Exomiser) that have been applied to rare disease cases |
| Interpretation Portal | Webpage provided by Genomics England to host clinical reports and used to launch cases into a CIP, using the CIPAPI. |
| JSON | JavaScript Object Notation (JSON) is a lightweight data-interchange format used to encapsulate Genomics England’s interpreted genome and interpretation request through the CIP-API. |
| LabKey | Data Server hosting patient clinical and demographic information, excluding VCFs and BAMs. |
| LDAP | Lightweight Directory Access Protocol (LDAP) is a client/server protocol used to access and manage directory information. It reads and edits directories over IP networks and runs directly over TCP/IP using simple string formats for data transfer. |
| Main findings | Variants which have been found and potentially associated with the disease/disorder for which the patient has given consent for the genetic test. Referred to as ‘Primary Findings’ within Genomics England developed systems. |
| MDT | Multi-Disciplinary Team |
| OMIM | Online Mendelian Inheritance in Man |
| PanelApp | PanelApp (Open Source) was created to enable virtual gene panels to be viewed and commented on by experts |
| PID | Patient Identifiable Data |
| PMID | Unique identifier number used in PubMed. They are assigned to each article record when it enters the PubMed system, so an in-press publication will not have one unless it is issued as an electronic pre-pub |
| Primary findings | The variants that have been found and associated with the disease/disorder for which the patient has given consent for the genetic test. |
| SNV | Single Nucleotide Variant |
| STR | Short Tandem Repeat |
| SV | Structural variant |
| Tier | Flag used by Genomics England to signify variants of potential relevance to the patient’s condition - will be automatically categorised into Tiers to aid evaluation |
| UK10K_ALSPAC | The Avon Longitudinal Study of Parents and Children (ALSPAC) is a long-term health research project. More than 14,000 mothers enrolled during pregnancy in 1991 and 1992, and the health and development of their children has been followed in great detail ever since. The ALSPAC families have provided a vast amount of genetic and environmental information over the years. |
| UK10K_TWINSUK | The database used to study the genetic and environmental aetiology of age-related complex traits and diseases. It is one of the major departments of King's College London Division of Genetics and Molecular Medicine and is the most detailed clinical adult register in the world. |
| UPD | Uniparental Disomy |
| VCF | Variant Call Format |