v3 Portal Data Dictionary

Study

Field	Field Description	Permitted Values	Value Description
Study Code	Unique identifier for each Study	ABC-DS	Alzheimer's Biomarker Consortium - Down Syndrome
		BRI-DSR	Benaroya Research Institute Down Syndrome Registry
		DS360-CHD	INCLUDE: (Sherman) Genomic Analysis of Congenital Heart Defects and Acute Lymphoblastic Leukemia in Children with Down Syndrome
		DS-COG-ALL	INCLUDE: (Lupo) Genomic Analysis of Congenital Heart Defects and Acute Lymphoblastic Leukemia in Children with Down Syndrome
		DS-NEXUS	Nexus
		DS-PCGC	INCLUDE: (PCGC) Genomic Analysis of Congenital Heart Defects and Acute Lymphoblastic Leukemia in Children with Down Syndrome
		DS-Sleep	Dimensional, Sleep, and Genomic Analyses of Down Syndrome to Elucidate Phenotypic Variability
		DSC	DS-Connect-The Down Syndrome Registry
		HTP	Crnic Institute Human Trisome Project
		X01-deSmith	The epidemiology of transient leukemia in newborns with Down syndrome
		X01-Hakonarson	Genetic Underpinnings of the Multifactorial Phenotype of Trisomy 21 Patients Unveiled by Multi-Omics Approaches
Study Name	Full name of Study
Program	Funding source for Study	INCLUDE	NIH INCLUDE (INvestigation of Co-occurring conditions across the Lifespan to Understand Down syndromE) Project
		KF	Gabriella Miller Kids First Pediatric Research Program
dbGaP	dbGaP accession code

Participant

Field	Field Description	Permitted Values	Value Description	Study-Specific Notes
Participant ID	Unique Global identifier for Participant, assigned by INCLUDE DCC. Clicking on the ID brings up a detailed page of information about the Participant
External Participant ID	Unique identifier for Participant, assigned by data contributor. This column may not be shown by default but can be accessed using the "settings" gear in the upper right
Sex	Sex of Participant	Male
		Female
		Other
		Unknown
Race	Race of Participant	American Indian or Alaska Native
		Asian		For X01-deSmith, this includes participants whose race was listed as "East Asian (Chinese)", "East Asian (Japanese)", or "South Asian"
		Black or African American
		Native Hawaiian or Other Pacific Islander
		White		For X01-deSmith, this includes participants whose race was listed as "Arabic"
		More than one race
		Other		For X01-deSmith, this includes participants whose race was listed as "Latino" (these participants will also have Ethnicity = Latino)
		Asked but Unknown
Ethnicity	Ethnicity of Participant	Hispanic or Latino		For X01-deSmith, this includes participants whose race was listed as "Latino" (these participants will also have Race = Other)
		Not Hispanic or Latino
		Asked but Unknown
Family Unit	Structure of family members participating in the study, relative to Proband	Proband-only	Proband only, no family members participating in study
		Duo	Proband + one parent
		Trio	Proband + two parents
		Trio+	Proband + two parents + other relatives
		Other	Other family structure, e.g. Proband + sibling, or twin Probands
		Control-only	Unrelated control, no family members with Down syndrome
Family ID	[download only] Unique identifer for family to which Participant belongs		NA if study did not include any family members
Father ID	[download only] Participant ID for Participant's father		NA if Participant is not the Proband
Mother ID	[download only] Participant ID for Participant's mother		NA if Participant is not the Proband
Family Member Relationship	[download only] Relationship of Participant to Proband	Proband	The first affected family member to join the study (some families may have two Probands, usually siblings)
		Father
		Mother
		Sibling
		Other relative
		Unrelated control
DS Status	Down syndrome status of Participant	T21	Trisomy 21
		D21	Disomy 21 (euploid)
Vital Status	[download only] Whether Participant is alive or dead	Alive
		Dead
		Unknown or not available
Age at the Last Vital Status (Days)	[download only] Age in days when participant's vital status was last recorded
Condition (Source Text)	[download only] Co-occurring Condition (phenotype or diagnosis), as described by data contributor. The Down Syndrome Genetic Diagnosis is also provided in this field.			Measures for ABC-DS participants are available by request from ABC-DS. For additional info and request form, visit https://www.nia.nih.gov/research/abc-ds#data
Age At Phenotype Assignment/Age at Diagnosis (Days)	[download only] Age in days at which Condition or Measure was observed, recorded, or diagnosed
Interpretation	[download only] Whether Condition was observed or not	Observed	Condition was observed or reported
		Not Observed	Participant was specifically examined or medical record queried for condition and found to be negative
Diagnosis (MONDO)	Mondo Disease Ontology term
Biospecimens	Number of biospecimens associated with this participant
Files	Number of data files associated with this participant

Biospecimen

Field	Field Description	Permitted Values	Value Description	Study-Specific Notes
Collection ID	Identifier for the eldest sample in a lineage of processed, pooled, or aliquoted samples - typically the material actually collected from the participant. This may be the same as Parent Sample ID or Sample ID (if no processing was performed). Clicking on the Collection ID shows all samples derived from that collection.
Collection Sample Type	Type of biological material comprising the collected sample	E.g. Whole blood, Not reported, Saliva, Derived cell line
Sample ID	Unique identifier for sample, assigned by INCLUDE DCC. A sample is a unique biological material; two samples with two different IDs are biologically distinct, but may come from the same Parent Sample and Collection.
External Sample ID	Unique identifier for sample, assigned by data contributor.
Sample Type	Type of biological material comprising the sample	E.g. Plasma, White blood cells, Red blood cells, DNA, RNA, Peripheral blood mononuclear cells, CD4+ Tconv cells, NK cells, Monocytes, CD8+ T cells, B cells, Granulocytes, Treg cells
Parent Sample ID	Identifier for the direct parent from which Sample was derived, processed, pooled, etc. (if applicable)
Parent Sample Type	Type of biological material comprising the parent sample	E.g. Not Reported, Peripheral Whole Blood, Derived Cell Line, Saliva, Whole blood, WBCs
Age At Biospecimen Collection	Age in years and days of participant at time of sample collection
Sample Availability	Whether Sample is potentially available for sharing through the Virtual Biorepository	Available	Sample is potentially available to be requested through the Virtual Biorepository (see VBR contact info in Study page)	Biospecimens for ABC-DS participants may be available by request from ABC-DS. For additional info and request form, visit https://www.nia.nih.gov/research/abc-ds#data
		Unavailable	Sample either was available through Virtual Biorepository but has been used up, or is part of a study that is not participating in the VBR
Container ID	Identifier for specific container/aliquot of sample, if applicable. Distinct aliquots of a sample will have the same Sample ID but different Container IDs.
Volume	Amount of sample in container
Volume Unit	Unit of sample volume
Laboratory Procedure	Procedure by which Sample was derived from Parent Sample	E.g. Centrifugation, RBC lysis, Lyse/fix buffer, FACS, PAXgene DNA, PAXgene RNA, Qiagen Allprep, Ficoll
Biospecimen Storage	Method by which Sample is stored	E.g. Minus 80 degrees Celsius, Liquid nitrogen storage
Files	Number of data files associated with this biospecimen

Data File

Field	Field Description	Permitted Values	Value Description	Study-Specific Notes
File Authorization	Whether user is authorized to access this file	Locked icon	Unauthorized
		Unlocked icon	Authorized
Data Access	Type of access control for data file	C	Controlled
		R	Registered
File Name	Name of data file, assigned by data contributor
File ID	Unique identifier for data file, assigned by INCLUDE DCC. Clicking on the ID brings up a detailed page of information about the File
Data Category	General category of data in file	e.g. Genomics, Proteomics, Metabolomics, Transcriptomics
Data Type	Specific type of data contained in file	E.g. Preprocessed metabolite relative abundance, Absolute protein concentration, Aligned reads, Simple nucleotide variations, GVCF, Gene expression quantifications, Raw gene fusions, Annotated gene fusions, Somatic copy number variations, Somatic structural variations
Experimental Strategy	Experimental method used to obtain data in file	e.g. Whole genome sequencing, RNAseq, Multiplex immunoassay, LCMS metabolomics
Access URL	Storage location for this file	DRS URI or other repository URL		Data Files for ABC-DS participants are available by request from ABC-DS. For additional info and request form, visit https://www.nia.nih.gov/research/abc-ds#data
File Format	Format of data file	E.g. tsv, cram, gvcf, vcf, maf, txt, pdf, html, png
File Size	Size (and unit) of file. Size in file export is given in bytes.
Participants	Number of participants associated with this file
Biospecimens	Number of biospecimens associated with this file