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Metadata Annotation Guidelines

Metadata Annotation Guidelines#

Purpose of this Document#

This document describes the RECOMMENDED ways to provide metadata annotation for various experimental setups.

Clarification of Terms#

  • The key words “MUST”, “MUST NOT”, “REQUIRED”, “SHOULD”, “SHOULD NOT”, “RECOMMENDED”, “MAY”, and “OPTIONAL” in this document are to be interpreted as described in [RFC2119].

Individual fields#

library_generation_method#

The library_generation_method describes how the nucleic acid annotated in template_class that encodes the V(D)J-rearrangement it reverse-transcribed, amplified and/or otherwise prepared for further processing. Typically this procedure will precede further NGS platform- specific steps, however these procedures MAY be combined. The field uses a controlled vocabulary, the individual values are described below:

template_class

library_generation_method

Methodology

DNA

PCR

Conventional PCR on genomic DNA of a vertebrate host (requires: synthetic == false )

Conventional PCR on DNA of a synthetic library (requires: synthetic == true )

RNA

RT(RHP)+PCR

RT-PCR using random hexamer primers

RT(oligo-dT)+PCR

RT-PCR using oligo-dT primers

RT(oligo-dT)+TS+PCR

5’-RACE PCR (i.e. RT is followed by a template switch (TS) step) using oligo-dT primers

RT(oligo-dT)+TS(UMI)+PCR

5’-RACE PCR using oligo-dT primers and template switch primers containing unique molecular identifiers (UMI), i.e., the 5’ end is UMI-coded

RT(specific)+PCR

RT-PCR using transcript-specific primers

RT(specific)+TS+PCR

5’-RACE PCR using transcript- specific primers

RT(specific)+TS(UMI)+PCR

5’-RACE PCR using transcript- specific primers and template switch primers containing UMIs

RT(specific+UMI)+PCR

RT-PCR using transcript-specific primers containing UMIs (i.e., the 3’ end is UMI-coded)

RT(specific+UMI)+TS+PCR

5’-RACE PCR using transcript- specific primers containing UMIs (i.e., the 3’ end is UMI-coded)

RT(specific)+TS

RT-based generation of dsDNA without subsequent PCR. This is used by RNA-seq kits.

any

other

Any methodology not covered above

*_pcr_primer_target_location#

The fields forward_pcr_primer_target_location and reverse_pcr_primer_target_location describe the location of the innermost primer used for a given locus. This information is critical to determine which positions of a sequence reflect a biological process and which are an artifact of the experiment.

The terms “proximal” and “distal” in the field description refer to the start of the respective V or C gene. Using human TRAC and a hypothetical primer as an example:

1   5    10   15   20   25   30   35   40   45   50   55  60   position (+1 = start of exon 1)
|...|....|....|....|....|....|....|....|....|....|....|....|
                   TGCCGTGTACCAGCTGAGAG                        TRAC primer (reverse complement)
ATATCCAGAACCCTGACCCTGCCGTGTACCAGCTGAGAGACTCTAAATCCAGTGACAAGT   Chr. 14:22,547,506-22,547,565 (GRCh38)
                  ^^                  ^
                [a][b]               [c]                       markers

In this case:

  • +19 (marker [a]) is the most distal untemplated nucleotide

  • +20 (marker [b]) is the most proximal templated nucleotide

  • +39 (marker [c]) is the most distal templated nucleotide

cell_subset#

The cell_subset field is ontology-controlled, i.e., if present, it MUST refer to a Cell Ontology (CL) term via its id field. The field SHOULD NOT be used for values other than lymphocyte (CL:0000542) and its descendents. The reasoning behind this is that rearrangements of IG and TR loci are typically confined to this population, so that other nodes, do not provide further information. In addition, the field SHOULD only be used if the subset has been purified to a level that is comparable to flow cytometric cell sorting.

  • In general, the provided annotation MUST NOT contradict the experimentally determined phenotype. E.g., if the experiment shows that the population is CD27+ a term that is explicitly defined in CL as CD27- MUST NOT be used.

  • However, this does not mean that all markers listed in the description of an ontology term need to be confirmed, as long as the existing information is considered sufficient for classification and not contradictory (see above).

  • In case the experimentally isolated cells to not match any “leaf” term, e.g., due to the isolation of multiple populations that contradict the definitions, the general advice is to move up the CL hierarchy to the most distal term that is no-contradictory. In this case, cell_phenotype should be used to define the markers that were used experimentally.

  • Note that ontology-controlled fields allow exactly one term. Therefore, mixtures of defined cell populations either need to be demultiplexed, or – if this is not possible – use the last (i.e,, most distal) common term of all cell populations involved. Again, cell_phenotype can be used to provide the markers used in the experiment.

Specific Use Cases and Experimental Setups#

Peripheral Blood Mononuclear Cells (PBMCs)#

PBMCs are frequently used starting material for AIRR-seq studies in humans and are prepared by a density-gradient centrifugation using Ficoll. As they constitute a mixture of myeloid and lymphoid cells, the following points should be taken into consideration when annotating experiments using PBMCs:

  • The cell_population and cell_phenotype fields should be NULL as PBMCs are neither sufficiently pure nor do they exclusively contain cells of the lymphocytic lineage (see cell_subset).

  • Note that while Cell Ontology does provide a term peripheral blood mononuclear cell (CL:2000001), this is a sister node of lymphocyte (CL:0000542) and therefore outside of the current specification.

  • The typical annotation for PBMC is therefore as follows:

    sample_type:"peripheral venous puncture"
tissue:
   label:"venous blood"
   id:"UBERON:0013756"
tissue_processing"Ficoll gradient"
cell_subset:NULL
cell_phenotype:NULL

Synthetic libraries#

In synthetic libraries (e.g., phage or yeast display), particles present genetically engineered constructs (e.g., scFv fusion receptors) on their surface. As this deviates substantially from other workflows, the following annotation SHOULD/MUST be used:

  • In general, Subject should be interpreted as the initial library that undergoes a mutation/selection procedure.

  • synthetic: MUST be set to true

  • species: It is assumed that every synthetic library is derived from V and J genes that exist in some vertebrate species. This field SHOULD encode that species. Importantly, it MUST NOT encode the phage vector, the bacterial host or a comparable biological component of the library system that constitutes the presenting particle.

  • sample_type: SHOULD be NULL.

  • single_cell: Only true if individual particles are isolated and sequenced. Note that colonies or plaques, even if containing genetically identical particles, per se do not match this definition and therefore MUST be annotated as false.

  • cell_storage: SHOULD be used for non-cellular particles analogously.

  • physical_linkage: For scFv constructs the hetero_prelinkeded term MUST be used. VHH (i.e., camelid) libraries SHOULD annotate none as there is only a single rearrangement envolved.

10X Chromium#

The current 10X V(D)J Kits (07/2020, Rev. G) perform a fully nested PCR, in which only the reverse primers (i.e., complementary to the constant region) are Ig/TCR specific, while the forward primers anneal to the sequence of the template switch primer. For the purpose of annotation, this is considered a gene-specific amplification, therefore such experiments SHOULD be annotated as follows:

  • single_cell: MUST be true

  • library_generation_method: SHOULD be RT(specific)+TS(UMI)+PCR

  • pcr_target MAY contain multiple entries, one for each locus that is potentially amplified. Within each entry (i.e., each PCRTarget object) the following annotations SHOULD be provided:

    • pcr_target_locus: The locus described by this object, using the controlled vocabulary defined in the AIRR schema. Note that each object can only describe one locus, multiple loci require multiple PCRTarget objects.

    • forward_pcr_primer_target_location: NULL (as it cannot be reliably determined.

    • reverse_pcr_primer_target_location: Locus and position according to the respective set of reverse primers.

Geolocation information#

For questions regarding population genetics, the information about the membership of a given individual in a (potentially) distinct population group is of high interest. However, no reasonably complete ontology exists for the concept of “ethnicity”, which in addition is limited to humans (not to mention the challenge of assigning consistent values to this property). Therefore, the AIRR Schema uses annotation of the location of birth of an individual and the location where a given sample was taken as imperfect but at least operationalizable substitute.

The respective properties Subject.``location_birth`` and Sample.``collection_location`` are ontology controlled and expect values that are geographic locations. The provided value SHOULD allow to resolve at least the country-level information of the annotated location. Higher granularity SHOULD only be provided, if this does not exposed the data subject to the risk of being re-identified via based on or assisted by this information.

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