GA4GH Connect - April 2024

Initial work on the VRS 2.0 draft specification, including:

• Application of maturity model to VRS data classes
• SV support: Adjacency model
• Class refactor: Haplotype / CisPhasedBlock
• GA4GH Digest key support
• Reference Length Expression encoding

1.3.0 Release: Genotype, Copy Changes, and Composed SEs

Release summary

The v1.3.0 release of VRS includes two new systemic variation concepts:

1. the Genotype model for representing all variants present at a given genomic locus
2. the CopyNumberChange model for representing copy number changes from a regional base ploidy

It also includes support for composed sequence expressions, for expressing sequences composed of multiple underlying expressions.

Additional minor changes include cleanup of the allele normalization guidance, haplotype member minimum, and updates to the processing tools (i.e. gks.metaschema) used to build and represent the schema artifacts. This has also enabled explicity class inheritance and explicit declaration of array ordinality for processing computed digests.

What's Changed

• remove ComposedSequenceExpression from 1.2, belongs in 1.3+ by @ahwagner in #380
• relative copy number by @ahwagner in #382
• Update validation models for Copy Number variation by @korikuzma in #383
• Fix Allele state type priority by @jsstevenson in #384
• 386: revise base64url description by @ahwagner in #387
• explain ref agree normalization rules by @reece in #381
• Add default value for types + update readme for using smoketests by @korikuzma in #390
• C & P error fix in CytobandInterval by @mbaudis in #392
• fix: get smoketests to pass by @korikuzma in #402
• VRS Hackathon Genotype draft by @ahwagner in #394
• Update validation models by @korikuzma in #407
• fix: models.yaml to take ordered property in account by @korikuzma in #409
• Add tests to check schema validation in models.yaml (#406) by @korikuzma in #412
• Add tests for ComposedSequenceExpression (#408) by @korikuzma in #413
• 1.2: Add default value for type in schemas, update smoketests readme by @korikuzma in #391
• Issue 404 by @ahwagner in #416
• relative_copy_class -> copy_assessment in CopyNumberChange example by @mbaudis in #419
• v1.3 release candidate by @ahwagner in #418

New Contributors

• @jsstevenson made their first contribution in #384
• @mbaudis made their first contribution in #392

Full Changelog: 1.2.1...1.3.0

Definition reconciliation and metaschema

This patch version release shores up inconsistencies in the JSON Schema and definitions, and adds a single source-of-truth document from which the JSON Schema and .rst documentation is derived.

New variation Types, SequenceExpressions, CopyNumber

Deprecations

• SimpleInterval and SequenceState are deprecated. They will be removed in VRS 2.0.

Major Changes

• New classification of variation types.

  • Molecular Variation refers to variation within or of a contiguous molecular
  • Systemic Variation refers to variation in the context of a system, such as a genome, sample, or homologous chromosomes
  • Utility Variation classes provide useful representations for certain technical operations

• New SequenceExpressions subclasses replace SequenceState. Subtypes are:

  • DerivedSequenceExpression, which representations sequence notionally derived from a SequenceLocation
  • RepeatedSequenceExpression, which represents contiguous repeats of a sequence
  • LiteralSequenceExpression, which wraps a Sequence and provides data structure parity with other SequenceExpressions

• CopyNumber, a form of SystemicVariation, represents the copies of a molecule within a genome, and can be used to express concepts such as amplification and copy loss.

• Gene enables reference to an external definition of a gene, particularly for useas a subject of copy number expressions.

• DefiniteRange and IndefiniteRange represent bounded and half-bounded ranges respectively. A new Number type wraps integers so that some attributes may assume values of any of these three types.

For more changes, see the release notes

1.1.2

This patch version makes the following corrections and clarifications:

• Adds the intended ChromosomeLocation prefix to the Computed Identifiers table.
• Revises the Cytoband information model to align with ISCN conventions.
• Updates the Cytoband regex to match the specified model.

1.1 Release: Haplotypes, VariationSets, ChromosomeLocations

See release notes, which has links to more information.

New classes

• ChromosomeLocation: A region of a chromosomed specified by species and name using cytogenetic naming conventions
• CytobandInterval: A contiguous region specified by chromosomal bands features.
• Haplotype: A set of zero or more Alleles.
• VariationSet: A set of Variation objects.

Other data model changes

• Interval was renamed to SequenceInterval. Interval was an internal class that was never instantiated, so this change should not be visable to users.

Documentation changes

• Added Relationship of VRS to existing standards to describe how VRS relates to other standards.
• Updated Normalization to clarify handling of reference alleles and generalize terminology to apply to all VRS objects.
• Updated current and future schema diagrams.
• Included a discussion of the Release Cycle.

1.0 GA4GH Approved

The approved Variation Representation specification of the Global Alliance for Genomics and Health.

1.0 Release Candidate 2

Second release candidate for the Variation Representation specification of the Global Alliance for Genomics and Health.

1.0 Release Candidate 1

First release candidate for the Variation Representation specification of the Global Alliance for Genomics and Health.