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| # Genetic Descriptor | ||
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| Support for genetic descriptors was developed as a [BIDS Extension Proposal](https://github.com/bids-standard/bids-specification/blob/master/src/06-extensions.md#bids-extension-proposals). | ||
| The extension was primarily developped by Cyril Pernet and Clara Moreau with contributions from Tom Nichols and Jessica Turner. | ||
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| The goal of the genetic descriptor is to link imaging and genetic data. | ||
| This is necessary as genetic data are typically stored in dedicated repositories, separately from the imaging data. | ||
| The descriptor provides basics information about: | ||
| - where to find genetic information associated with the imaging data | ||
| - what type of genetic information is available | ||
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| ## dataset_description.json | ||
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| In order to link a genetic database entry, the key `Genetics` MUST be present and | ||
| the value is an object with the following fields: | ||
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| | Field name | Definition | | ||
| |----------------------|--------------------------------------------------------------------------------| | ||
| | Genetics.Dataset | REQUIRED. URI where data can be retrieved. | | ||
| | Genetics.Database | OPTIONAL. URI of database where the dataset is hosted. | | ||
| | Genetics.Descriptors | OPTIONAL. List of relevant descriptors (*e.g.*, journal articles) for dataset. | | ||
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| `dataset_description.json` example: | ||
| ```JSON | ||
| { | ||
| "Name": "Human Connectom Project", | ||
| "BIDSVersion": "1.2.0", | ||
| "License": "CC0", | ||
| "Authors": ["1st author", "2nd author"], | ||
| "Funding": "list your funding sources", | ||
| "Genetics": { | ||
| "Dataset": "dataset", | ||
| "Database": "database", | ||
| "Descriptors": "descriptors" | ||
| } | ||
| } | ||
| ``` | ||
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| ## Subject naming and Participants file | ||
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| If the same participants have different identifiers in the genetic and imaging datasets, | ||
| the column `GeneticID` SHOULD be added to the `participants.tsv` file to associate | ||
| the BIDS participant with a subject in the `Genetics.Dataset` referred to in the | ||
| `dataset_description.json` file. | ||
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| Information about the presence/absence of specific genetic markers MAY be duplicated | ||
| in the `participants.tsv` file by adding optional columns. | ||
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| `participants.tsv` example: | ||
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| ```Text | ||
| participant_id age sex group GeneticID IDH Mutation | ||
| sub-control01 34 M control 124587 yes | ||
| sub-control02 12 F control 548936 yes | ||
| sub-patient01 33 F patient 489634 no | ||
| ``` | ||
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| ## genetic_info.json | ||
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| This file is the descriptor of the genetic information available either in the participant tsv file and/or the genetic database described in the dataset_description.json. The `GeneticLevel` and `SampleOrigin` are the only two mandatory fields. | ||
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| | Field name | Definition | Values | | ||
| | :----------------- | :------------------------------------------------------------------------------- | :---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | ||
| | GeneticLevel | MANDATORY Describes the level of analysis | `Genetic`, `Genomic`, `Epigenomic`, `Transcriptomic`, `Metabolomic`, or `Proteomic` | | ||
| | AnalyticalApproach | OPTIONAL Methodology used to analyse the GeneticLevel | Value must be taken from [gapsolr](https://www.ncbi.nlm.nih.gov/projects/gapsolr/facets.html) under /Study/Molecular Data Type, for instance `SNP Genotypes (Array)` or `Methylation (CpG)` | | ||
| | SampleOrigin | MANDATORY Describes from which tissue the genetic information was extracted from | `blood`, `saliva`, `brain`, `csf`, `breast milk`, `bile`, `amniotic fluid`, `other biospecimen` | | ||
| | TissueOrigin | OPTIONAL Describes the type of tissue analyzed for SampleOrigin `brain` | `gray matter`, `white matter`, `csf`, `meninges`, `macrovascular` or `microvascular` | | ||
| | BrainLocation | OPTIONAL Refers to the location in space of the TissueOrigin | `MNI coordinate` or a `label` taken from the [Allen Brain Atlas](http://atlas.brain-map.org/atlas?atlas=265297125) possibly `layer` to refer to layer-specific gene expression, which can also tie up with laminar fMRI | | ||
| | CellType | OPTIONAL Describes the type of cell analyzed | Value should come from the [cell ontology](http://obofoundry.org/ontology/cl.html) | | ||
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| `genetic_info.json` example: | ||
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| ```JSON | ||
| { | ||
| "GeneticLevel": "Genetic", | ||
| "AnalyticalApproach": "SNP Genotypes", "SampleOrigin": "brain", | ||
| "TissueOrigin": "gray matter", | ||
| "CellType": "neuron", | ||
| "BrainLocation": "[-30 -15 10]" | ||
| } | ||
| ``` |