| ARCHETYPE ID | openEHR-EHR-CLUSTER.genetic_variant.v0 |
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| Concept | Genetic variant |
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| Description | Result of a genetic test for a single variant. |
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| Use | This archetype is meant to be used in the "Test result" SLOT of the Laboratory test result observation archetype. |
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| Purpose | Used to report observations and annotations related to a single mutation found in the genome through a sequencing test. |
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| References | Description of sequence variants follows the recommentations of HGVS nomenclature v19.01 url:http://varnomen.hgvs.org/
H.L. Rehm, S.J. Bale, P. Bayrak-Toydemir, J.S. Berg, K.K. Brown, J.L. Deignan, M.J. Friez, B.H. Funke, M.R. Hegde, E. Lyon, ACMG clinical laboratory standards for next-generation sequencing, Genet. Med. 15 (2013) 733–747. doi:10.1038/gim.2013.92.
S. Richards, N. Aziz, S. Bale, D. Bick, S. Das, J. Gastier-Foster, W.W. Grody, M. Hegde, E. Lyon, E. Spector, K. Voelkerding, H.L. Rehm, Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology, Genet. Med. 17 (2015) 405–423. doi:10.1038/gim.2015.30. |
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| Copyright | © openEHR Foundation |
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| Authors | Author name: Cecilia Mascia
Organisation: CRS4, Italy
Email: cecilia.mascia@crs4.it
Date originally authored: 2019-01-15
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| Other Details Language | Author name: Cecilia Mascia
Organisation: CRS4, Italy
Email: cecilia.mascia@crs4.it
Date originally authored: 2019-01-15
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| Other Details (Language Independent) | - Licence: This work is licensed under the Creative Commons Attribution-ShareAlike 4.0 License. To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/4.0/.
- Custodian Organisation: Ocean Informatics
- References: Description of sequence variants follows the recommentations of HGVS nomenclature v19.01 url:http://varnomen.hgvs.org/
H.L. Rehm, S.J. Bale, P. Bayrak-Toydemir, J.S. Berg, K.K. Brown, J.L. Deignan, M.J. Friez, B.H. Funke, M.R. Hegde, E. Lyon, ACMG clinical laboratory standards for next-generation sequencing, Genet. Med. 15 (2013) 733–747. doi:10.1038/gim.2013.92.
S. Richards, N. Aziz, S. Bale, D. Bick, S. Das, J. Gastier-Foster, W.W. Grody, M. Hegde, E. Lyon, E. Spector, K. Voelkerding, H.L. Rehm, Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology, Genet. Med. 17 (2015) 405–423. doi:10.1038/gim.2015.30.
- Original Namespace: com.oceaninformatics
- Custodian Namespace: com.oceaninformatics
- Original Publisher: Ocean Informatics
- MD5-CAM-1.0.1: 9B5FB614F18F5C55BD29D222CC5A68B7
- Build Uid: e592c58c-a0d4-4f41-82dd-a02224e0cb38
- Revision: 0.0.1-alpha
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| Keywords | variation, VCF, variant, genetic, genomic, variant calling, sequence, mutation |
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| Lifecycle | in_development |
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| UID | a57f6859-fdfb-4ff0-b9f1-5e5bbc955a82 |
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| Language used | en |
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| Citeable Identifier | 1013.1.2342 |
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| Revision Number | 0.0.1-alpha |
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| items | |
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| Tissue specimen identifier | Tissue specimen identifier: Identifier for the specimen used for the genetic test. |
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| Bioinformatic analysis workflow | Bioinformatic analysis workflow: Structured details about the bioinformatic analysis workflow or a link to a protocol.
Include:
openEHR-EHR-CLUSTER.knowledge_base.v0 or
openEHR-EHR-CLUSTER.device.v1 |
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| Reference Genome | Reference Genome: Structured details about the specific version of the human sequence assembly used for annotation.
For example, "GCF_000001405.38"
Source name: NCBI
Accession number: GCF_000001405
Version number: GCF_000001405.38
URL: https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.38/
Include:
openEHR-EHR-CLUSTER.reference_sequence.v0 and specialisations |
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| Variant identifier | Variant identifier: A reference to a specific variation recorded into a biological variation database. |
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| Source name | Source name: The name of the public data source that gives the variant identification. |
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| Identification | Identification: The ID of a variation record. |
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| Version | Version: The version of the record. |
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| URL | URL: A reference to a specific variation recorded into a biological variation database. |
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| Variant | Variant: Structured description of the genetic variant.
Include:
openEHR-EHR-CLUSTER.repeated_sequence_variant.v0 or
openEHR-EHR-CLUSTER.inversion_variant.v0 or
openEHR-EHR-CLUSTER.substitution_variant.v0 or
openEHR-EHR-CLUSTER.indel_variant.v0 or
openEHR-EHR-CLUSTER.duplication_variant.v0 or
openEHR-EHR-CLUSTER.deletion_variant.v0 or
openEHR-EHR-CLUSTER.conversion_variant.v0 or
openEHR-EHR-CLUSTER.insertion_variant.v0 or
openEHR-EHR-CLUSTER.copy_number_variant.v0 or
openEHR-EHR-CLUSTER.translocation_variant.v0 |
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| Transcript | Transcript: Structured details about the transcript which is potentially affected by the variant. |
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| Transcript reference sequence | Transcript reference sequence: Structured details about the transcribed reference sequence.
Example:
Source name: NCBI
Accession number: NM_015557
Version number: NM_015557.2
URL: https://www.ncbi.nlm.nih.gov/nuccore/304361774
Include:
openEHR-EHR-CLUSTER.reference_sequence.v0 and specialisations |
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| DNARegionName | DNARegionName: A human readable name for the region of interest. Typically Exon #, Intron # or other. |
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| DNA change | DNA change: Description of the variation at the DNA-level following the HGVS nomenclature.
For example: "c.5249C>T"
NC_000023.10:g.33038255C>A |
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| Amino Acid Change | Amino Acid Change: Description of the variation at the protein-level following the HGVS nomenclature.
For example "p.T1750M" |
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| Amino Acid Change Type | Amino Acid Change Type: Codified type for associated Amino Acid Marker.
Choice of:
 Coded Text
- at0085::Wild Type [Wild Type.]
[LOINC(2.65)::LA9658-1] - at0086::Deletion [A deletion in the amino acid sequence.]
[LOINC(2.65)::LA6692-3] - at0087::Duplication [A duplication in the amino acid sequence.]
[LOINC(2.65)::LA6686-5] - at0088::Frameshift [A frameshift in the amino acid sequence.]
[LOINC(2.65)::LA6694-9] - at0089::Initiating Methionine [Initiating Methionine.]
[LOINC(2.65)::LA6695-6] - at0090::Insertion [A insertion in the amino acid sequence.]
[LOINC(2.65)::LA6687-3] - at0091::Insertion and Deletion [An insertion/deletion in the amino acid sequence.]
[LOINC(2.65)::LA9659-9] - at0092::Missense [Missense.]
[LOINC(2.65)::LA6698-0] - at0093::Nonsense [Nonsense.]
[LOINC(2.65)::LA6699-8] - at0094::Silent [Silent.]
[LOINC(2.65)::LA6700-4] - at0095::Stop Codon Mutation [Stop Codon Mutation.]
[LOINC(2.65)::LA6701-2]
 Text
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| Predicted impact | Predicted impact: Estimate of the effects that each variant may have on the transcript.
Calculation is based on a precise data source and only done by software. |
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| Predicted impact analysis | Predicted impact analysis: Structured details about the tool used to calculate the predicted impact.
For example "CADD", "SIFT", etc.
Include:
openEHR-EHR-CLUSTER.knowledge_base.v0 or
openEHR-EHR-CLUSTER.device.v1 |
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| Score | Score: The calculated value.
Property: Qualified real
Units: (UCUM: 1) |
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| Qualitative prediction | Qualitative prediction: Human readable version of the predicted impact. |
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| Reported impact | Reported impact: Intepretation of the Mutation linked to a specific paper (e.g. activation, deactivating, dysfunction…). |
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| Source | Source: A reference to the specific research paper.
Include:
openEHR-EHR-CLUSTER.citation.v1 and specialisations |
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| Impact | Impact: Interpretative data about the specific variant. |
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| Gene | Gene: Structured details about the gene harboring the variant. |
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| Gene symbol | Gene symbol: The official gene symbol approved by the HGNC, which is a short abbreviated form of the gene name.
For example "CHD5". |
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| Full name | Full name: The full gene name approved by the HGNC that convey the character or function of the gene.
For example "Chromodomain helicase DNA binding protein 5". |
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| Copy number overlap | Copy number overlap: The fraction of gene region covered by copy number. |
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| Part of fusion | Part of fusion: States if the Gene is part of a Fusion Gene and if it is the first or second part of the Fusion Gene.
- at0096::First [First part of a Fusion Gene.]
- at0097::Second [Second part of a Fusion Gene.]
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| ACMG classification | ACMG classification: Single DNA marker or individual allele interpretation in the context of the assessed genetic disease according to the ACMG recommendations.
- at0071::Pathogenic [Pathogenic variant.]
[LOINC(2.65)::LA6668-3] - at0072::Likely pathogenic [Likely pathogenic variant.]
[LOINC(2.65)::LA26332-9] - at0073::Uncertain significance [Variant of uncertain significance.]
[LOINC(2.65)::LA26333-7] - at0074::Likely benign [Likely benign variant.]
[LOINC(2.65)::LA26334-5] - at0075::Benign [Benign variant.]
[LOINC(2.65)::LA6675-8]
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| Fusion exon | Fusion exon: The number of the exon which is either the end or the beginning of the fusion. |
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| Best transcript candidate | Best transcript candidate: The ID of the transcript with the highest predicted impact. |
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| Conservation | Conservation: Structured details about the evolutionary conservation. |
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| Conservation score analysis | Conservation score analysis: Structured details about the tool used to calculate the conservation score.
For example "PhastCons7-way".
Include:
openEHR-EHR-CLUSTER.knowledge_base.v0 or
openEHR-EHR-CLUSTER.device.v1 |
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| Score | Score: The conservation score.
Property: Qualified real
Units: (UCUM: 1) |
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| Read depth | Read depth: Total number of reads mapped at this specific location. |
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| Allele depth | Allele depth: The number of reads that support the reported variant. |
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| Allele frequency | Allele frequency: The relative frequency of an allele at a particular locus, expressed as a number from 0 to 1.
Property: Qualified real
Units: 0.0..1.0 (UCUM: 1) |
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| Population allele frequency details | Population allele frequency details: The relative frequency of a particular allele in the population, expressed as a number from 0 to 1. |
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| Population allele frequency analysis | Population allele frequency analysis: Structured details about the database used to calculate the allele frequency.
Include:
openEHR-EHR-CLUSTER.knowledge_base.v0 or
openEHR-EHR-CLUSTER.device.v1 |
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| Population allele frequency | Population allele frequency: The population allele frequency.
Property: Qualified real
Units: 0.0..1.0 (UCUM: 1) |
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| VCF Quality Filter | VCF Quality Filter: Structured details about the quality filters that have been applied to the data.
This field is derived from the FILTER column of VCF.
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| Filter name | Filter name: Name of the quality filter.
For example "q10". |
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| Description | Description: Quality filter extended description.
For example "at this site the quality is below 10". |
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| Filter passed | Filter passed: Whether the variant passed the quality filter. |
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| Strand bias ratio | Strand bias ratio: The ratio of the strand bias.
Property: Qualified real
Units: (UCUM: 1) |
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| Strand bias p-value | Strand bias p-value: The Phred-scaled p-value of the strand bias.
Property: Qualified real
Units: (UCUM: 1) |
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| Genotype | Genotype: Genotype encoded as allele values separated by either of / or | (0 for the reference allele, 1 for the first alternate, etc.). |
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| Allelic State | Allelic State: The level of occurrence of a single DNA Marker within a set of chromosomes.
This is the human readable version of genotype, e.g.: Heterozygous, Homozygous.
Choice of:
- Coded Text
- at0076::Heteroplasmic [Heteroplasmic.]
[LOINC(2.65)::LA6703-8] - at0077::Homoplasmic [Homoplasmic.]
[LOINC(2.65)::LA6704-6] - at0078::Homozygous [Homozygous.]
[LOINC(2.65)::LA6705-3] - at0079::Heterozygous [Heterozygous.]
[LOINC(2.65)::LA6706-1] - at0080::Hemizygous [Hemizygous.]
[LOINC(2.65)::LA6707-9]
- Text
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| Genotype quality | Genotype quality: Conditional genotype quality, encoded as a phred quality. |
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| Genotype probability | Genotype probability: A comma separated list of the log10-scaled genotype likelihoods for all possible genotypes, given the reference and the alternate alleles. |
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| Genetic Variant Assessment | Genetic Variant Assessment: Assessment of the presence or absence of a specific DNA variants.
'No Call' is different from 'Absent', because 'No Call' did not result in the determination of the marker's presence or absence. This may be due to test failure or specimen specific context which renders the test ineffective.
- at0081::Present [The target variant is present.]
[LOINC(2.65)::LA9633-4] - at0082::Absent [The target variant is absent.]
[LOINC(2.65)::LA9634-2] - at0083::No call [No data are available to confirm the presence/absence of the variant.]
[LOINC(2.65)::LA18198-4] - at0084::Indeterminate [The result is indeterminate.]
[LOINC(2.65)::LA11884-6]
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| Extension | Extension: Additional details to be captured.
Include:
All not explicitly excluded archetypes |
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| Other contributors | Christina Jaeger-Schmidt, Heidelberg University Hospital, Germany
Florian Kaercher, Charité Berlin, Germany
Francesca Frexia, CRS4, Italy
Gianluigi Zanetti, CRS4, Italy
Heather Leslie, Atomica Informatics, Australia (openEHR Editor)
Gideon Giacomelli, Charité Berlin, Germany
Paolo Uva, CRS4, Italy
Silje Ljosland Bakke, Nasjonal IKT HF, Norway (openEHR Editor)
Simon Schumacher, HiGHmed, Germany |
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| Translators | German: Aurelie Tomczak, Institute of Pathology, University Hospital Heidelberg, au.tomczak@yahoo.com
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