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updated CNV term mapping table #147

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updated CNV term mapping table #147

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updated CNV term mapping table
mbaudis Jul 13, 2024
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Merge branch 'main' into website-docs
costero-e Jul 16, 2024
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33 changes: 17 additions & 16 deletions docs/variant-queries.md
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Expand Up @@ -374,18 +374,19 @@ values to underlying genomic variations had not been precisely defined.

This table is maintained in parallel with the [hCNV community documentation](https://cnvar.org/resources/CNV-annotation-standards/#cnv-term-use-comparison-in-computational-fileschema-formats).

| [EFO](https://www.ebi.ac.uk/efo/EFO_0030063) | Beacon | [VCF](https://samtools.github.io/hts-specs/) | SO | GA4GH [VRS](https://vrs.ga4gh.org/en/latest/terms_and_model.html#relativecopynumber) &rArr;<br/>[VRS proposal](https://github.com/ga4gh/vrs/issues/404)[^1] | Notes |
| [EFO](http://www.ebi.ac.uk/efo/EFO_0030063) | Beacon | [VCF](https://samtools.github.io/hts-specs/) | SO | GA4GH [VRS](https://vrs.ga4gh.org/en/latest/terms_and_model.html#copynumberchange)[^1] | Notes |
| ------------------------------------------- | ------------------------------------------------------------------------------ | -------------------------------------------- | -------- | ------------------------------------------------------------------------------------------------------------------------------------------------- | ----- |
| <nobr>[`EFO:0030070`](https://www.ebi.ac.uk/efo/EFO_0030070)</nobr> copy number gain | `DUP`[^2] or<br/><nobr>[`EFO:0030070`](https://www.ebi.ac.uk/efo/EFO_0030070)</nobr> | `DUP`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001742`](https://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain | [`low-level gain`](https://vrs.ga4gh.org/en/latest/terms_and_model.html#relativecopynumber) (implicit) &rArr; [`EFO:0030070`](https://www.ebi.ac.uk/efo/EFO_0030070) copy&nbsp;number&nbsp;gain | a sequence alteration whereby the copy number of a given genomic region is greater than the reference sequence |
| [`EFO:0030071`](https://www.ebi.ac.uk/efo/EFO_0030071) low-level copy number gain| `DUP`[^2] or<br/><nobr>[`EFO:0030071`](https://www.ebi.ac.uk/efo/EFO_0030071)</nobr> | `DUP`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001742`](https://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain | [`low-level gain`](https://vrs.ga4gh.org/en/latest/terms_and_model.html#relativecopynumber) &rArr; [`EFO:0030071`](https://www.ebi.ac.uk/efo/EFO_0030071) low-level copy number gain | |
| [`EFO:0030072`](https://www.ebi.ac.uk/efo/EFO_0030072) high-level copy number gain | `DUP`[^2] or<br/><nobr>[`EFO:0030072`](https://www.ebi.ac.uk/efo/EFO_0030072)</nobr> | `DUP`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001742`](https://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain | [`high-level gain`](https://vrs.ga4gh.org/en/latest/terms_and_model.html#relativecopynumber) &rArr; [`EFO:0030072`](https://www.ebi.ac.uk/efo/EFO_0030072) high-level copy number gain | commonly but not consistently used for >=5 copies on a bi-allelic genome region |
| [`EFO:0030073`](https://www.ebi.ac.uk/efo/EFO_0030073) focal genome amplification | `DUP`[^2] or<br/><nobr>[`EFO:0030073`](https://www.ebi.ac.uk/efo/EFO_0030073)</nobr> | `DUP`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001742`](https://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain | [`high-level gain`](https://vrs.ga4gh.org/en/latest/terms_and_model.html#relativecopynumber) &rArr; [`EFO:0030073`](https://www.ebi.ac.uk/efo/EFO_0030073) focal genome amplification | commonly but not consistently used for >=5 copies on a bi-allelic genome region, of limited size (operationally max. 1-5Mb) |
| [`EFO:0030067`](https://www.ebi.ac.uk/efo/EFO_0030067) copy number loss | `DEL`[^2] or<br/><nobr>[`EFO:0030067`](https://www.ebi.ac.uk/efo/EFO_0030067)</nobr> | `DEL`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001743`](https://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | [`partial loss`](https://vrs.ga4gh.org/en/latest/terms_and_model.html#relativecopynumber) (implicit) &rArr; [`EFO:0030067`](https://www.ebi.ac.uk/efo/EFO_0030067) copy number loss | a sequence alteration whereby the copy number of a given genomic region is smaller than the reference sequence |
| [`EFO:0030068`](https://www.ebi.ac.uk/efo/EFO_0030068) low-level copy number loss | `DEL`[^2] or<br/><nobr>[`EFO:0030068`](https://www.ebi.ac.uk/efo/EFO_0030068)</nobr> | `DEL`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001743`](https://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | [`partial loss`](https://vrs.ga4gh.org/en/latest/terms_and_model.html#relativecopynumber) &rArr; [`EFO:0030068`](https://www.ebi.ac.uk/efo/EFO_0030068) low-level copy number loss | |
| [`EFO:0020073`](https://www.ebi.ac.uk/efo/EFO_0020073) high-level copy number loss | `DEL`[^2] or<br/><nobr>[`EFO:0020073`](https://github.com/EBISPOT/efo/issues/1941)</nobr> | `DEL`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001743`](https://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | [`partial loss`](https://vrs.ga4gh.org/en/latest/terms_and_model.html#relativecopynumber) &rArr; [`EFO:0020073`](https://github.com/EBISPOT/efo/issues/1941) high-level copy number loss | a loss of several copies; also used in cases where a complete genomic deletion cannot be asserted |
| [`EFO:0030069`](https://www.ebi.ac.uk/efo/EFO_0030069) complete genomic deletion | `DEL`[^2] or<br/><nobr>[`EFO:0030069`](https://www.ebi.ac.uk/efo/EFO_0030069)</nobr> | `DEL`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001743`](https://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | [`complete loss`](https://vrs.ga4gh.org/en/latest/terms_and_model.html#relativecopynumber) &rArr; [`EFO:0030069`](https://www.ebi.ac.uk/efo/EFO_0030069) complete genomic deletion | complete genomic deletion (e.g. homozygous deletion on a bi-allelic genome region) |

##### Last updated 2023-03-22 by @mbaudis (EFO:0020073)
| <nobr>[`EFO:0030070`](http://www.ebi.ac.uk/efo/EFO_0030070)</nobr> copy number gain | `DUP`[^2] or<br/><nobr>[`EFO:0030070`](http://www.ebi.ac.uk/efo/EFO_0030070)</nobr> | `DUP`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001742`](http://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain | <nobr>[`EFO:0030070`](http://www.ebi.ac.uk/efo/EFO_0030070) gain | a sequence alteration whereby the copy number of a given genomic region is greater than the reference sequence |
| [`EFO:0030071`](http://www.ebi.ac.uk/efo/EFO_0030071) low-level copy number gain| `DUP`[^2] or<br/><nobr>[`EFO:0030071`](http://www.ebi.ac.uk/efo/EFO_0030071)</nobr> | `DUP`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001742`](http://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain | <nobr>[`EFO:0030071`](http://www.ebi.ac.uk/efo/EFO_0030071)</nobr> low-level gain | |
| [`EFO:0030072`](http://www.ebi.ac.uk/efo/EFO_0030072) high-level copy number gain | `DUP`[^2] or<br/><nobr>[`EFO:0030072`](http://www.ebi.ac.uk/efo/EFO_0030072)</nobr> | `DUP`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001742`](http://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain | <nobr>[`EFO:0030072`](http://www.ebi.ac.uk/efo/EFO_0030072)</nobr> high-level gain | commonly but not consistently used for >=5 copies on a bi-allelic genome region |
| [`EFO:0030073`](http://www.ebi.ac.uk/efo/EFO_0030073) focal genome amplification | `DUP`[^2] or<br/><nobr>[`EFO:0030073`](http://www.ebi.ac.uk/efo/EFO_0030073)</nobr> | `DUP`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001742`](http://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain | <nobr>[`EFO:0030072`](http://www.ebi.ac.uk/efo/EFO_0030072)</nobr> high-level gain[^4] | commonly but not consistently used for >=5 copies on a bi-allelic genome region, of limited size (operationally max. 1-5Mb) |
| [`EFO:0030067`](http://www.ebi.ac.uk/efo/EFO_0030067) copy number loss | `DEL`[^2] or<br/><nobr>[`EFO:0030067`](http://www.ebi.ac.uk/efo/EFO_0030067)</nobr> | `DEL`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001743`](http://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | <nobr>[`EFO:0030067`](http://www.ebi.ac.uk/efo/EFO_0030067)</nobr> loss | a sequence alteration whereby the copy number of a given genomic region is smaller than the reference sequence |
| [`EFO:0030068`](http://www.ebi.ac.uk/efo/EFO_0030068) low-level copy number loss | `DEL`[^2] or<br/><nobr>[`EFO:0030068`](http://www.ebi.ac.uk/efo/EFO_0030068)</nobr> | `DEL`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001743`](http://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | <nobr>[`EFO:0030068`](http://www.ebi.ac.uk/efo/EFO_0030068)</nobr> low-level loss | |
| [`EFO:0020073`](http://www.ebi.ac.uk/efo/EFO_0020073) high-level copy number loss | `DEL`[^2] or<br/><nobr>[`EFO:0020073`](https://github.com/EBISPOT/efo/issues/1941)</nobr> | `DEL`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001743`](http://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | <nobr>[`EFO:0020073`](https://github.com/EBISPOT/efo/issues/1941)</nobr> high-level loss | a loss of several copies; also used in cases where a complete genomic deletion cannot be asserted |
| [`EFO:0030069`](http://www.ebi.ac.uk/efo/EFO_0030069) complete genomic deletion | `DEL`[^2] or<br/><nobr>[`EFO:0030069`](http://www.ebi.ac.uk/efo/EFO_0030069)</nobr> | `DEL`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001743`](http://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | <nobr>[`EFO:0030069`](http://www.ebi.ac.uk/efo/EFO_0030069)</nobr> complete genomic loss | complete genomic deletion (e.g. homozygous deletion on a bi-allelic genome region) |


##### Last updated 2023-07-13 to align with 2023-03-22 hCNV documentation (VRS 1.3 adjustment) by @mbaudis
##### updated 2023-03-20 by @mbaudis (VRS proposal)

## Query Parameter Change Log
Expand Down Expand Up @@ -417,17 +418,17 @@ recommended for query forms
and `alternateBases`


[^1]: The VRS annotations refer to the status at v1.2 (2022). The GA4GH VRS team
is currently (Spring 2023) preparing an updated specification which will introduce
the new class `CopyNumberChange` ([discussion...](https://github.com/ga4gh/vrs/issues/404#issuecomment-1472599849)) with the use of the EFO terms (including a new term
for `high level deletion (EFO:0020073)` in the April 2023 EFO release).
[^1]: The VRS annotations refer to the status from v1.3 (2022) when
the new class `CopyNumberChange` ([discussion...](https://github.com/ga4gh/vrs/issues/404#issuecomment-1472599849))
with the use of the EFO terms.
[^2]: While the use of VCF derived (`DUP`, `DEL`) values had been introduced with
beacon v1, usage of these terms has always been a _recommendation_ rather than an integral part
of the API. We now encourage the support of more specific terms (particularly EFO)
by Beacon developers. As example, the Progentix Beacon API [uses EFO terms](https://progenetix.org/search/) but
by Beacon developers. As example, the Progentix Beacon API [uses EFO terms](http://progenetix.org/search/) but
provides an internal term expansion for legacy `DUP`, `DEL` support.
[^3]: VCFv4.4 introduces an `SVCLAIM` field to disambiguate between _in situ_ events (such as
tandem duplications; known _adjacency_/ _break junction_: `SVCLAIM=J`) and events where e.g. only the
change in _abundance_ / _read depth_ (`SVCLAIM=D`) has been determined. Both **J** and **D** flags can be combined.
[^4]: VRS did not adopt the "amplification" term due to possible inconsistencies


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