LSDB - Controlled vocabulary terms

Note: This is a working document. Final information will be collected into the VarioML wiki pages.

Misc

Evidence codes

• GO Evidence codes
• dbSNP validation codes for variants
• Evidence code ontology

Mutation events

•  Types of mutation events and their discreet affects on RNA and polypeptide

Inheritance pattern (of phenotype, note: look also inheritance ontology. http://www.human-phenotype-ontology.org/index.php/hpo_docu.html)

• 'familial'
• 'familial, consanguineous parents'
• 'familial, autosomal dominant'
• 'familial, autosomal recessive'
• 'familial, X-linked'
• 'sporadic'
• 'sporadic, consanguineous parents'
• 'sporadic, consanguineous parents (1st degree)'
• 'sporadic, consanguineous parents (2nd degree)'
• 'sporadic, consanguineous parents (3rd degree)'
• 'sporadic, non-consanguineous parents'
• 'sporadic, consanguinity parents?'
• 'sporadic? (parents not tested)'

Genetic source

• 'de novo'
• 'de novo, maternal chromosome'
• 'de novo, paternal chromosome'
• 'de novo, from either parent'
• 'inherited'
• 'inherited, maternal chromosome'
• 'inherited, paternal chromosome'
• 'inherited, from either parent
• somatic

Variant

Consequence

See for example sequence ontology: List of variant effect terms

From DMuDB:

Complex frameshift: Frameshift involving insertions and deletions

Exon deletion: Deletion encompassing a whole exon or exons, frameshift status unknown

Exon duplication: Duplication of one of more exons, frameshift status unknown

Frameshift: Deletion or insertion causing reading frame shift

In-frame deletion: Deletion of a whole codon or codons.  Can include deletion of one or 
more exons

In-frame duplication: A duplication that does not change the reading frame.  Can include 
one or more exons

In-frame insertion: An insertion of a whole codon or codons.  Can include one or more 
exons

Intronic variant: A variant in an intron which has not been shown to affect splicing

Missense: Substitution resulting in a change to a different amino acid

Nonsense: Substitution resulting in a change to a stop codon

Out of frame deletion: Deletion of part of a codon or number of codons resulting in a 
frameshift.  Can include one or more exons

Out of frame duplication: A duplication that changes the reading frame.  Can include one or more 
exons

Out of frame insertion: An insertion of part of a codon or number of codons resulting in a 
frameshift.  Can include one or more exons

Silent: A nucleotide change that does not change the amino acid

Splice site variant: A mutation that affects splicing

Number of independent observations of a DNA variant (Frequency in XML)

Example values from the Data sharing between LSDBs paper

found once (should it be "found at least once" ?. Same with other terms)

2–10 times 

11–99 times

over 100 times

Origin (note this field will be replaced by genetic source and inheritance pattern . JM DEC 2010)

Source LOVD

in vitro (cloned)
familial
familial, consanguineous parents
familial, autosomal dominant
familial, autosomal recessive
familial, X-linked
sporadic
sporadic, consanguineous parents
sporadic, consanguineous parents (1st degree)
sporadic, consanguineous parents (2nd degree)
sporadic, consanguineous parents (3rd degree)
sporadic, non-consanguineous parents
sporadic, consanguinity parents?
sporadic? (parents not tested)
uniparental disomy
de novo
de novo, somatic mosaicism
de novo, germline mosaicism
de novo, germline and somatic mosaicism
de novo, in patient
de novo, in patient (maternal allele)
de novo, in patient (paternal allele)
de novo, in mother
de novo, in mother (grandmaternal allele)
de novo, in mother (grandpaternal allele)
de novo, in father
de novo, in father (grandmaternal allele)
de novo, in father (grandpaternal allele)
uniparental disomy, maternal allele
uniparental disomy, paternal allele

Tissue distribution (Note. This will be normalized with other fields JM May 2011)

• constitutional
• mosaci
• mosaic in germline

Parental origin

Source LOVD

Parent #1
Parent #2 
Paternal (inferred)
Paternal (confirmed)
Maternal (inferred)
Maternal (confirmed)
de novo
de novo, on paternal allele 
de novo, maternal allele

Pathogenicity

See the paper From LOVD:

No known pathogenicity

Probably no pathogenicity

Unknown
Probably pathogenic
Pathogenic

From DMuDB:

Non-Pathogenic

Probably Not Pathogenic

Not Known
Probably Pathogenic
Pathogenic
Unclassified

From CMGS/VKGL paper as by Alamut:

Class 1 – Certainly not pathogenic
Class 2 – Unlikely to be pathogenic but cannot be formally proven
Class 3 – Likely to be pathogenic but cannot be formally proven
Class 4 - Certainly pathogenic

Class 5 - Unknown (not in spec)

Other comments:

Not Known implies that a submitter has given no data on pathogenicity. Unclassified implies that the submitter has specifically indicated that they are unable to classify the pathogenicity of the variant.

Patient

Gender

Source iso5218 (codes 0,1,2,9)

not known 

male

female

not applicable

Geographical region

• Country (iso-3166 codes)
• dbSNP population classes
• See also geonames datatabase / web servcies

Ethnicity

• Continetal population groups from MeSH

Detection Technique

From DMuDB:

ARMS
CF20: CF Common Mutation Test
CF29: Analysis of 29 mutations using the Elucigene CF29 kit
CSCE: Conformation sensitive capillary electrophoresis
DGGE: Denaturing gradient gel electrophoresis
dHPLC: Denaturing high performance liquid chromatography
Heteroduplex analysis
Loss of heterozygosity analysis
Meta-PCR
MLPA: Multiplex ligation-dependent probe amplification
MS-PCR: Mutagenically separated PCR
Multiplex PCR
Not Known: The information has not been recorded or provided
Not Specified: Test information cannot be determined
PCR-PAGE
PTT: Protein Trucation Test
RNA: RNA work performed
Sequencing
SNPlex: The SNPlex™ Genotyping System from ABI
SSCP
SSCP/Heteroduplex