160 lines
No EOL
6.3 KiB
HTML
160 lines
No EOL
6.3 KiB
HTML
<!DOCTYPE HTML>
|
|
<html>
|
|
<head>
|
|
<title>Variation</title>
|
|
<script type="text/javascript" src="/core/jquery/jquery-3.6.0.min.js">
|
|
</script>
|
|
<script type="text/javascript">
|
|
jQuery.getScript("/core/alerts/alerts.js", function () { galert(['pre']) });
|
|
</script>
|
|
</head>
|
|
<body>
|
|
<h3>Variation</h3><pre>Defined in file <a href="variation.asn.html">variation.asn</a>
|
|
C++ class: <a href="../doxyhtml/classCVariation.html">CVariation</a>
|
|
|
|
|
|
Variation ::= 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 <a href="Dbtag.html">Dbtag</a> OPTIONAL,
|
|
parent-id <a href="Dbtag.html">Dbtag</a> OPTIONAL,
|
|
sample-id SET OF <a href="Object-id.html">Object-id</a> OPTIONAL,
|
|
other-ids SET OF <a href="Dbtag.html">Dbtag</a> 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,
|
|
|
|
-- where this beast is seen
|
|
-- note that this is a set of locations, and there are no restrictions to
|
|
-- the contents to this set.
|
|
placements SEQUENCE OF <a href="VariantPlacement.html">VariantPlacement</a> OPTIONAL,
|
|
|
|
-- phenotype
|
|
phenotype SET OF <a href="Phenotype.html">Phenotype</a> OPTIONAL,
|
|
|
|
-- sequencing / acuisition method
|
|
method <a href="VariationMethod.html">VariationMethod</a> 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 <a href="Variation-inst.html">Variation-inst</a>, all at the same location, would
|
|
-- describe individual alleles.
|
|
|
|
-- population data
|
|
population-data SET OF <a href="Population-data.html">Population-data</a> OPTIONAL,
|
|
|
|
-- variant properties bit fields
|
|
variant-prop <a href="VariantProperties.html">VariantProperties</a> OPTIONAL,
|
|
|
|
-- publication support; same type as in seq-feat
|
|
pub <a href="Pub-set.html">Pub-set</a> OPTIONAL,
|
|
|
|
-- References to external
|
|
clinical-test <a href="Dbtag.html">Dbtag</a> OPTIONAL,
|
|
|
|
data CHOICE {
|
|
unknown NULL,
|
|
note VisibleString, --free-form
|
|
uniparental-disomy NULL,
|
|
|
|
-- actual sequence-edit at feat.location
|
|
instance <a href="Variation-inst.html">Variation-inst</a>,
|
|
|
|
-- 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
|
|
chimeric (10), -- e.g. c.[1C>T//2G>T]
|
|
other (255)
|
|
},
|
|
variations SET OF <a href="Variation.html">Variation</a>,
|
|
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,
|
|
|
|
seq <a href="Bioseq.html">Bioseq</a> -- Sequnece as it exists post-alteration
|
|
},
|
|
|
|
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 <a href="Variation.html">Variation</a>,
|
|
|
|
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,
|
|
|
|
-- Frameshift-related info. Applies only to protein-level variations.
|
|
-- see http://www.hgvs.org/mutnomen/recs-prot.html
|
|
frameshift SEQUENCE {
|
|
phase INTEGER OPTIONAL,
|
|
x-length INTEGER OPTIONAL
|
|
} OPTIONAL,
|
|
|
|
-- Additional undescribed extensions
|
|
ext SET OF <a href="User-object.html">User-object</a> OPTIONAL,
|
|
|
|
somatic-origin SET OF SEQUENCE {
|
|
-- description of the somatic origin itself
|
|
source <a href="SubSource.html">SubSource</a> OPTIONAL,
|
|
-- condition related to this origin's type
|
|
condition SEQUENCE {
|
|
description VisibleString OPTIONAL,
|
|
-- reference to BioTerm / other descriptive database
|
|
object-id SET OF <a href="Dbtag.html">Dbtag</a> OPTIONAL
|
|
} OPTIONAL
|
|
} OPTIONAL,
|
|
|
|
exceptions SET OF <a href="VariationException.html">VariationException</a> OPTIONAL,
|
|
|
|
so-terms SET OF INTEGER OPTIONAL
|
|
}</pre>
|
|
</body>
|
|
</html> |