Glossary

The Accelerating Medicines Partnership (AMP) is a public-private partnership between the National Institutes of Health (NIH), the U.S. Food and Drug Administration (FDA), multiple biopharmaceutical and life science companies and non-profit organizations to transform the current model for developing new diagnostics and treatments by jointly identifying and validating promising biological targets for therapeutics. See NIH AMP homepage.

The AMP PD Access and Compliance Team (ACT) monitors public activities on the AMP PD Knowledge Platform through periodic audits to assess compliance with the AMP PD governance policies. Email the AMP PD ACT: ACT@amp-pd.org.

All AMP PD clinical data includes a baseline visit, which is defined as the participant’s first clinical evaluation as part of the cohort.*  All visit months are calculated relative to the participant's baseline visit (e.g., “Month 12” indicates data obtained 1 year after the baseline visit).   Other clinical data, such as diagnosis date, medication start date, etc. are calculated in months, relative to the baseline visit date, in order to allow researchers to establish a timeline for disease progression and treatment milestones.

For studies in which post-mortem samples were collected, such as the Postmortem Sequencing Data cohort, the date of death is used as a substitute for the baseline visit.  When premortem clinical data are available for a participant in a postmortem study, visit dates will be negative, indicating the number of months prior to death the event occurred.

*BioFIND participants had an initial screening visit, followed by a more comprehensive evaluation and biospecimen collection visit 2 weeks later.  Most BioFIND clinical and biospecimen data is therefore recorded as “Month 0.5”

Binary Alignment Map (BAM) is the comprehensive raw data of genome sequencing. BAM files consist of the lossless, compressed binary representation of the Sequence Alignment Map.

BioFIND is a collaboration between MJFF and the National Institute of Neurological Disorders and Stroke (NINDS). BioFIND is one of the core AMP PD cohorts and study data contributors. See BioFIND. 

Brigham and Women's Hospital (BWH), an affiliate of Harvard Medical School, is recognized internationally for its excellence and innovation in patient care, biomedical research, and education and training programs for physicians, scientists and health care professionals.

The AMP PD Clinical Data Harmonization (CDH) working group is tasked with coordinating the harmonization and intake of clinical data from multiple existing cohorts into the AMP PD knowledge portal. The subgroup includes representation from experts on all but one of the main AMP PD cohorts as well as from industry and NIH.

The Clinical Data Interchange Standards Consortium (CDISC) develops data standards by analyzing and transforming incompatible formats, inconsistent methodologies, and diverse perspectives into a powerful framework for generating clinical research data that is as accessible and reusable.

The Common Workflow Language (CWL) is an open standard for describing analysis workflows and tools in a way that makes them portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments.

CRAM is a compressed columnar file format for storing biological sequences aligned to a reference sequence.

The Data Management Resource (DMR) is part of the Parkinson's Disease Biomarkers Program (PDBP). The DMR enables web-based data entry for clinical studies supporting PD biomarker development, as well as broad data sharing (imaging, clinical, genetic, and biospecimen analysis) across the entire PD research community. See DMR.

The AMP PD governing policy that defines how users to should interact with the AMP PD system and data. Users of the system are required to sign and adhere to the DUA. See DUA.

The AMP PD Data Use Policies (DUP) working group is responsible for establishing AMP PD policies and recommending procedures for dealing with policy enforcement and changes.

Deep Brain Stimulation (DBS) is a surgical treatment for Parkinson's which delivers electrical pulses to brain cells to decrease symptoms.

The eRA Commons is an online interface where signing officials, principal investigators, trainees and post-docs at institutions/organizations can access and share administrative information relating to research grants. 
 

FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. Both the sequence letter and quality score are each encoded with a single ASCII character for brevity.

In the context used on this site federation is used when describing the inter-operation of two distinct, formally disconnected, independently governed platforms (occasionally geographically separated) computing clouds that may have different internal structures.

The Food and Drug Administration (FDA) is a federal government partner affiliated with AMP PD. See FDA.

The Foundation for the National Institutes of Health (FNIH) procures funding and manages alliances with public and private institutions in support of the mission of the National Institutes of Health (NIH), the premier medical research agency. FNIH is a non-profit AMP PD partner. See FNIH.

The Genome Analysis Toolkit (GATK) is developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping.

The Global Parkinson’s Genetics Program (GP2), supported by the Aligning Science Across Parkinson’s (ASAP) initiative, is an international collaborative effort aimed at making transformational progress in Parkinson’s disease (PD) genetics. 

The Global Unique Identifier (GUID) is a Global Unique Identifier for each study participant that allows researchers to aggregate and share a participant’s data without exposing personally identifiable information (PII). The GUID is made up of random alpha-numeric characters and is not generated from PII/PHI.

Good clinical practice (GCP) is an international quality standard for conducting clinical trials. The principles of GCP help assure the safety, integrity, and quality of clinical trials by addressing elements related to the design, conduct, and reporting of clinical trials.

The Harvard Biomarkers Study (HBS) is one of the core AMP PD cohorts and study data contributors. See HBS.

The Health Insurance Portability and Accountability Act of 1996 (HIPAA) is a set of regulations protecting the privacy and security of certain health information.

The Hoehn and Yahr scale is a commonly used system for describing how the symptoms of Parkinson's disease progress.

Adult cells that have been genetically reprogrammed to an embryonic stem cell–like state by being forced to express genes and factors important for maintaining the defining properties of embryonic stem cells.

Institutional review boards (IRBs) or research ethics committees provide a core protection for human research participants through advance and periodic independent review of the ethical acceptability of proposals for human research.

International LBD Genomics Consortium (iLBDGC) study overview: Genome Sequencing in Lewy Body Dementia and Neurologically Healthy Controls: A Resource for the Research Community. These data were generated by the International LBD Genomics Consortium (iLBDGC), under the co-directorship by Dr. Bryan J. Traynor and Dr. Sonja W. Scholz from the Intramural Research Program of the U.S. National Institutes of Health. For a complete list of contributors, please see attached document.

The LBD cohort was collected by the International Lewy Body Dementia Genomics Consortium (iLBDGC) for the purpose of understanding the genetic architecture of Lewy Body Dementia (LBD).  The cohort includes 4623 subjects with the diagnosis of LBD (69% pathologically confirmed) and normal controls recruited from 44 European and North American sites.  See LBD.

The LRRK2 Cohort Consortium (LCC) was created to assemble and study groups of people with and without Parkinson’s disease who carry mutations in the LRRK2 gene. It comprises three closed studies that followed standardized data acquisition protocols: the LRRK2 Cross-sectional Study, LRRK2 Longitudinal Study and the 23andMe Blood Collection Study. See LCC.

Machine learning (ML) is a method of data analysis that automates analytical model building. It is based on the idea that systems can learn from data and make decisions with minimal human intervention.

The Movement Disorder Society – Unified Parkinson’s Disease Rating Scale (MDS-UPDRS) is a tool to assess Parkinson's disease. The goal of the UPDRS was to provide a comprehensive, practical, and easy to administer scale that can be used across all patients regardless of severity, medication treatment, or age

The Michael J. Fox Foundation (MJFF) is a non-profit AMP PD partner and parent organization for the BioFIND and PPMI cohorts. See MJFF.

The Montreal Cognitive Assessment (MoCA) assessment is a rapid screening instrument for mild cognitive dysfunction. It assesses different cognitive domains: attention and concentration, executive functions, memory, language, visuoconstructional skills, conceptual thinking, calculations, and orientation. 

The National Institute of Health (NIH) is a federal government partner affiliated with AMP PD. See NIH.

The National Institutes of Neurological Disorders and Stroke (NINDS) is an NIH Institute that seeks fundamental knowledge about the brain and nervous system and to use that knowledge to reduce the burden of neurological disease. NINDS is a federal government partner affiliated with AMP PD. See NINDS.

Parkinson's disease is a chronic, degenerative neurological disorder. 

The National Institute of Neurological Disorders and Stroke (NINDS) Parkinson's Disease Biomarkers Program (PDBP) was developed to accelerate the discovery of promising new diagnostic and progression biomarkers for Parkinson's Disease. PDBP is made up of researchers, patients, family members, and healthcare professionals who are dedicated to accelerating the pace of biomarkers research and is one of the core AMP PD cohorts and study data contributors. See PDBP. 

The Parkinson's Progression Markers Initiative is a longitudinal study of a cohort of individuals with early stage Parkinson's disease, towards the goal of validation of biomarkers. PPMI is funded by the Michael J. Fox Foundation (MJFF). PPMI is one of the core AMP PD cohorts and study data contributors. See PPMI. 

Principal component analysis (PCA) is a statistical procedure that can be used for exploratory data analysis. PCA uses linear combinations of the original data (e.g. gene expression values) to define a new set of unrelated variables (principal components).

Principal Investigators (PIs) lead and conduct biomedical or behavioral research programs supported by medical research organizations.

The AMP PD Publication Coordination Team (PCT) works directly with researchers interested in submitting a manuscript(s) on behalf of AMP PD to validate author list submission and compliance with the AMP PD publication policy. The AMP PD PCT consists of 1 NIH representative, 1 representative from each of the cohort studies and 1 non-NIH partner representative. See PCT. 

The RNA integrity number (RIN) is an algorithm for assigning integrity values to RNA measurements.

Safety, Tolerability and Efficacy Assessment of Dynacirc CR in Parkinson Disease (STEADY-PD3) was conducted as a randomized Phase 3, 2-arm, double-blind, parallel group trial with subjects randomized to Isradipine immediate release 5 mg or matching placebo twice daily for 36 months. The primary efficacy measure was the change in the total UPDRS score in the active treatment arm versus placebo between the baseline and 36 months. If patients needed to start symptomatic therapy, they continued on their randomized treatment assignment in conjunction with the symptomatic therapyand primary outcome was assessed in the medications ON state. The primary analysis was based on the intent-to-treat principle and included all subjects who had 36 month data. The study had 95 % retention rate. 

The study was negative for the primary outcome, showing no difference in PD symptoms over the 3 years of the study between the active and placebo arms. See STEADY-PD3.

Salmon is a tool for fast transcript quantification from RNA-seq data. See Salmon.

Single nucleotide polymorphisms, frequently called SNPs (pronounced “snips”), are the most common type of genetic variation among people. Each SNP represents a difference in a single DNA building block, called a nucleotide.

The Spliced Transcripts Alignment to a Reference (STAR) software package performs mapping of large sets of high-throughput sequencing reads to a reference genome for RNA-seq data analysis. See STAR.

Study of Urate Elevation in Parkinson's Disease, Phase 3 (SURE-PD3) was a randomized, double-blind, placebo-controlled trial of urate-elevating inosine treatment to slow clinical decline in early PD. The primary aim of this study was to determine whether oral inosine dosed to moderately elevate serum urate (from ≤5.7 mg/dL to 7.1-8.0 mg/dL) over 2 years slows clinical decline in early PD, assessed as change in the primary outcome variable of the Movement Disorders Society-Unified Parkinson’s Disease Rating Scale (MDS-UPDRS). Secondary aims include assessing long-term safety and effects on a) the development of disability warranting dopaminergic medication, b) short-term changes in parkinsonian symptoms, c) changes in functional disability and quality of life, d) non-motor measures of cognition, mood and autonomic function, and e) loss of striatal dopamine transporter signal.

The Trans-Omics for Precision Medicine (TOPMed) program, sponsored by NIH, is part of a broader Precision Medicine Initiative, which aims to provide disease treatments tailored to an individual’s unique genes and environment. TOPMed contributes to this Initiative through the integration of whole-genome sequencing (WGS) and other omics (e.g., metabolic profiles, protein and RNA expression patterns) data with molecular, behavioral, imaging, environmental, and clinical data.

Transcripts Per Million (TPM) is a normalization method for RNA-seq that directly measures the relative abundance of transcripts.

Variant Call Format (VCF) is a common file format developed by the genomics scientific community. It contains information about variants found at specific positions in a reference genome.

VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.

Whole Genome Sequencing (WGS) is the process of determining the complete DNA sequence of an organism's genome at a single time. 

Workflow Description Language (WDL) is meant to be a human readable and writable way to express tasks and workflows.