Variation-ref
Defined in file seqfeat.asn
C++ class: CVariation_ref
Variation-ref ::= SEQUENCE {
-- ids (i.e., SNP rsid / ssid, dbVar nsv/nssv)
-- expected values include 'dbSNP|rs12334', 'dbSNP|ss12345', 'dbVar|nsv1'
--
-- we relate three kinds of IDs here:
-- - our current object's id
-- - the id of this object's parent, if it exists
-- - the sample ID that this item originates from
id Dbtag OPTIONAL,
parent-id Dbtag OPTIONAL,
sample-id Object-id OPTIONAL,
other-ids SET OF Dbtag OPTIONAL,
-- names and synonyms
-- some variants have well-known canonical names and possible accepted
-- synonyms
name VisibleString OPTIONAL,
synonyms SET OF VisibleString OPTIONAL,
-- tag for comment and descriptions
description VisibleString OPTIONAL,
-- phenotype
phenotype SET OF Phenotype OPTIONAL,
-- sequencing / acuisition method
method SET OF INTEGER {
unknown (0),
bac-acgh (1),
computational (2),
curated (3),
digital-array (4),
expression-array (5),
fish (6),
flanking-sequence (7),
maph (8),
mcd-analysis (9),
mlpa (10),
oea-assembly (11),
oligo-acgh (12),
paired-end (13),
pcr (14),
qpcr (15),
read-depth (16),
roma (17),
rt-pcr (18),
sage (19),
sequence-alignment (20),
sequencing (21),
snp-array (22),
snp-genoytyping (23),
southern (24),
western (25),
optical-mapping (26),
other (255)
} OPTIONAL,
-- Note about SNP representation and pretinent fields: allele-frequency,
-- population, quality-codes:
-- The case of multiple alleles for a SNP would be described by
-- parent-feature of type Variation-set.diff-alleles, where the child
-- features of type Variation-inst, all at the same location, would
-- describe individual alleles.
-- population data
-- DEPRECATED - do not use
population-data SET OF Population-data OPTIONAL,
-- variant properties bit fields
variant-prop VariantProperties OPTIONAL,
-- has this variant been validated?
-- DEPRECATED: new field = VariantProperties.other-validation
validated BOOLEAN OPTIONAL,
-- link-outs to GeneTests database
-- DEPRECATED - do not use
clinical-test SET OF Dbtag OPTIONAL,
-- origin of this allele, if known
-- note that these are powers-of-two, and represent bits; thus, we can
-- represent more than one state simultaneously through a bitwise OR
-- DEPRECATED: new field = VariantProperties.allele-origin
allele-origin INTEGER {
unknown (0),
germline (1),
somatic (2),
inherited (4),
paternal (8),
maternal (16),
de-novo (32),
biparental (64),
uniparental (128),
not-tested (256),
tested-inconclusive (512),
-- stopper - 2^31
other (1073741824)
} OPTIONAL,
-- observed allele state, if known
-- DEPRECATED: new field = VariantProperties.allele-state
allele-state INTEGER {
unknown (0),
homozygous (1),
heterozygous (2),
hemizygous (3),
nullizygous (4),
other (255)
} OPTIONAL,
-- NOTE:
-- 'allele-frequency' here refers to the minor allele frequency of the
-- default population
-- DEPRECATED: new field = VariantProperties.allele-frequency
allele-frequency REAL OPTIONAL,
-- is this variant the ancestral allele?
-- DEPRECATED: new field = VariantProperties.is-ancestral-allele
is-ancestral-allele BOOLEAN OPTIONAL,
-- publication support.
-- Note: made this pub instead of pub-equiv, since
-- Pub can be pub-equiv and pub-equiv is a set of pubs, but it looks like
-- Pub is more often used as top-level container
-- DEPRECATED - do not use; use Seq-feat.dbxref instead
pub Pub OPTIONAL,
data CHOICE {
unknown NULL,
note VisibleString, --free-form
uniparental-disomy NULL,
-- actual sequence-edit at feat.location
instance Variation-inst,
-- Set of related Variations.
-- Location of the set equals to the union of member locations
set SEQUENCE {
type INTEGER {
unknown (0),
compound (1), -- complex change at the same location on the
-- same molecule
products (2), -- different products arising from the same
-- variation in a precursor, e.g. r.[13g>a,
-- 13_88del]
haplotype (3), -- changes on the same allele, e.g
-- r.[13g>a;15u>c]
genotype (4), -- changes on different alleles in the same
-- genotype, e.g. g.[476C>T]+[476C>T]
mosaic (5), -- different genotypes in the same individual
individual (6), -- same organism; allele relationship unknown,
-- e.g. g.[476C>T(+)183G>C]
population (7), -- population
alleles (8), -- set represents a set of observed alleles
package (9), -- set represents a package of observations at
-- a given location, generally containing
-- asserted + reference
other (255)
},
variations SET OF Variation-ref,
name VisibleString OPTIONAL
},
-- variant is a complex and undescribed change at the location
-- This type of variant is known to occur in dbVar submissions
complex NULL
},
consequence SET OF CHOICE {
unknown NULL,
splicing NULL, --some effect on splicing
note VisibleString, --freeform
-- Describe resulting variation in the product, e.g. missense,
-- nonsense, silent, neutral, etc in a protein, that arises from
-- THIS variation.
variation Variation-ref,
-- see http://www.hgvs.org/mutnomen/recs-prot.html
frameshift SEQUENCE {
phase INTEGER OPTIONAL,
x-length INTEGER OPTIONAL
},
loss-of-heterozygosity SEQUENCE {
-- In germline comparison, it will be reference genome assembly
-- (default) or reference/normal population. In somatic mutation,
-- it will be a name of the normal tissue.
reference VisibleString OPTIONAL,
-- Name of the testing subject type or the testing tissue.
test VisibleString OPTIONAL
}
} OPTIONAL,
-- Observed location, if different from the parent set or feature.location.
-- DEPRECATED - do not use
location Seq-loc OPTIONAL,
-- reference other locs, e.g. mapped source
-- DEPRECATED - do not use
ext-locs SET OF Ext-loc OPTIONAL,
-- DEPRECATED - do not use; use Seq-feat.exts instead
ext User-object OPTIONAL,
somatic-origin SET OF SEQUENCE {
-- description of the somatic origin itself
source SubSource OPTIONAL,
-- condition related to this origin's type
condition SEQUENCE {
description VisibleString OPTIONAL,
-- reference to BioTerm / other descriptive database
object-id SET OF Dbtag OPTIONAL
} OPTIONAL
} OPTIONAL
}