Cis-Phased Block

The Cis-Phased Block is a set of Alleles that are found in-cis: occurring on the same physical molecule. The CisPhasedBlock structure is useful for representing genetic Haplotypes, which are commonly described with respect to locations on a gene, a set of nearby genes, or other physically proximal genetic markers that tend to be transmitted together. Unlike haplotypes, the CisPhasedBlock is not also used to convey information about genetic ancestry.

New in v2

In VRS v1, a class with the same computational use as the CisPhasedBlock was defined and named the Haplotype class. This term is not used to describe this concept in v2, as the use of the Haplotype name created confusion in the community, due to the additional semantics of the term around genetic linkage and ancestry. In practice, implementations transitioning from v1 to v2 should find the CisPhasedBlock able to accommodate the same information content from v1 Haplotypes.

Definition and Information Model

Note

This data class is at a trial use maturity level and may change in future releases. Maturity levels are described in the GKS Maturity Model.

Computational Definition

An ordered set of co-occurring variants on the same molecule.

GA4GH Digest

Prefix	Inherent
CPB	[‘members’, ‘type’]

Information Model

Some CisPhasedBlock attributes are inherited from Variation.

Field	Flags	Type	Limits	Description
id		string	0..1	The ‘logical’ identifier of the Entity in the system of record, e.g. a UUID. This ‘id’ is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
name		string	0..1	A primary name for the entity.
description		string	0..1	A free-text description of the Entity.
aliases	⋮	string	0..m	Alternative name(s) for the Entity.
extensions	⋮	Extension	0..m	A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
digest		string	0..1	A sha512t24u digest created using the VRS Computed Identifier algorithm.
expressions	⋮	Expression	0..m
type		string	1..1	MUST be “CisPhasedBlock”
members	⋮	Allele | iriReference	2..m	A list of Alleles that are found in-cis on a shared molecule.
sequenceReference		Sequence Reference	0..1	An optional Sequence Reference on which all of the in-cis Alleles are found. When defined, this may be used to implicitly define the sequenceReference attribute for each of the CisPhasedBlock member Alleles.

Example

{
   "id": "ga4gh:CPB.YAWwnFF0e-T7fnuT4wRzZW4Lzg7jc-zQ",
   "type": "CisPhasedBlock",
   "members": [
      {
         "location": {
            "start": 601,
            "end": 602,
            "type": "SequenceLocation"
         },
         "state": {
            "sequence": "C",
            "type": "LiteralSequenceExpression"
         },
         "type": "Allele"
      },
      {
         "location": {
            "start": 701,
            "end": 702,
            "type": "SequenceLocation"
         },
         "state": {
            "sequence": "C",
            "type": "LiteralSequenceExpression"
         },
         "type": "Allele"
      }
   ],
   "sequenceReference": {
      "type": "SequenceReference",
      "refgetAccession": "SQ.S_KjnFVz-FE7M0W6yoaUDgYxLPc1jyWU",
      "residueAlphabet": "na",
      "id": "NC_000001.10"
   }
}