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feat: integrate ClinGen, sHet, rCNV gene information (#1119)
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@holtgrewe
holtgrewe authored Aug 29, 2023
1 parent 0111247 commit 1fbaf40
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Showing 3 changed files with 332 additions and 21 deletions.
154 changes: 145 additions & 9 deletions svs/vueapp/src/components/SvDetails/Genes.vue
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Original file line number Diff line number Diff line change
Expand Up @@ -45,12 +45,12 @@ const headers: Header[] = [
},
{
text: 'OMIM',
value: 'dbnsfp.mim_disease.length',
value: 'omim',
sortable: true,
},
{
text: 'Orphanet',
value: 'dbnsfp.orphanet_disorder.length',
value: 'orpha',
sortable: true,
},
{
Expand All @@ -70,6 +70,34 @@ const headers: Header[] = [
width: 50,
value: 'dbnsfp.haploinsufficiency',
},
{
text: 'sHet',
width: 100,
value: 'shet.s_het',
sortable: true,
},
{
text: 'pHaplo',
width: 100,
value: 'rcnv.p_haplo',
sortable: true,
},
{
text: 'pTriplo',
width: 100,
value: 'rcnv.p_triplo',
sortable: true,
},
{
text: 'CG haploin.',
width: 100,
value: 'clingen.haplo_summary',
},
{
text: 'CG triploin.',
width: 100,
value: 'clingen.triplo_summary',
},
]
/** The SV details store. */
Expand Down Expand Up @@ -136,7 +164,54 @@ const geneInfoBadge = (geneInfo: any): string | null => {
/** Compute list of gene infos to protect against empty `props.genesInfos`. */
const items: ComputedRef<GeneInfo[]> = computed(() => {
if (props.genesInfos) {
return props.genesInfos
const genesInfos = JSON.parse(JSON.stringify(props.genesInfos))
for (const geneInfo of genesInfos) {
if (geneInfo.clingen) {
const haploLabels = new Map<number, string>()
const triploLabels = new Map<number, string>()
for (const diseaseRecord of geneInfo.clingen.disease_records) {
if (diseaseRecord.dosage_haploinsufficiency_assertion?.length) {
const val = parseInt(
diseaseRecord.dosage_haploinsufficiency_assertion.split(' ')[0],
)
haploLabels.set(
val,
diseaseRecord.dosage_haploinsufficiency_assertion,
)
}
if (diseaseRecord.dosage_triplosensitivity_assertion?.length) {
const val = parseInt(
diseaseRecord.dosage_triplosensitivity_assertion.split(' ')[0],
)
triploLabels.set(
val,
diseaseRecord.dosage_triplosensitivity_assertion,
)
}
}
if (haploLabels.size) {
geneInfo.clingen.haplo_summary = Math.max(...haploLabels.keys())
geneInfo.clingen.haplo_label = haploLabels.get(
geneInfo.clingen.haplo_summary,
)
} else {
geneInfo.clingen.haplo_summary = null
geneInfo.clingen.haplo_label = null
}
if (triploLabels.size) {
geneInfo.clingen.triplo_summary = Math.max(...triploLabels.keys())
geneInfo.clingen.triplo_label = triploLabels.get(
geneInfo.clingen.triplo_summary,
)
} else {
geneInfo.clingen.triplo_summary = null
geneInfo.clingen.triplo_label = null
}
}
}
return genesInfos
} else {
return []
}
Expand Down Expand Up @@ -181,16 +256,38 @@ const onRowClicked = (item: ClickRowArgument) => {
</span>
</template>

<template #item-dbnsfp.mim_disease.length="geneInfo">
<template v-if="geneInfo.dbnsfp?.mim_disease.length">
{{ geneInfo.dbnsfp?.mim_disease.join(' // ') }}
<template #item-omim="{ omim }">
<template v-if="omim?.omim_diseases?.length">
<template v-for="(disease, idx) in omim?.omim_diseases">
<template v-if="idx > 0">, </template>
<a
:href="`https://www.omim.org/entry/${disease.omim_id.replace(
'OMIM:',
'',
)}`"
target="_blank"
>
{{ disease.label }}
</a>
</template>
</template>
<template v-else> &mdash; </template>
</template>

<template #item-dbnsfp.orphanet_disorder.length="geneInfo">
<template v-if="geneInfo.dbnsfp?.orphanet_disorder.length">
{{ geneInfo.dbnsfp?.orphanet_disorder.join(' // ') }}
<template #item-orpha="{ orpha }">
<template v-if="orpha?.orpha_diseases?.length">
<template v-for="(disease, idx) in orpha?.orpha_diseases">
<template v-if="idx > 0">, </template>
<a
:href="`https://www.orpha.net/consor/cgi-bin/OC_Exp.php?Expert=${disease.orpha_id.replace(
'ORPHA:',
'',
)}`"
target="_blank"
>
{{ disease.label }}
</a>
</template>
</template>
<template v-else> &mdash; </template>
</template>
Expand All @@ -217,6 +314,45 @@ const onRowClicked = (item: ClickRowArgument) => {
</template>
<template v-else> &mdash; </template>
</template>

<template #item-shet.s_het="{ shet }">
<template v-if="shet?.s_het">
<span v-html="roundIt(shet.s_het, 3)" />
</template>
<template v-else> &mdash; </template>
</template>

<template #item-rcnv.p_haplo="{ rcnv }">
<template v-if="rcnv?.p_haplo">
<span v-html="roundIt(rcnv.p_haplo, 3)" />
</template>
<template v-else> &mdash; </template>
</template>

<template #item-rcnv.p_triplo="{ rcnv }">
<template v-if="rcnv?.p_triplo">
<span v-html="roundIt(rcnv.p_triplo, 3)" />
</template>
<template v-else> &mdash; </template>
</template>

<template #item-clingen.haplo_summary="{ clingen }">
<template v-if="clingen?.haplo_summary">
<abbr :title="clingen.haplo_label">{{
clingen.haplo_summary
}}</abbr>
</template>
<template v-else> &mdash; </template>
</template>

<template #item-clingen.triplo_summary="{ clingen }">
<template v-if="clingen?.triplo_summary">
<abbr :title="clingen.triplo_label">{{
clingen.triplo_summary
}}</abbr>
</template>
<template v-else> &mdash; </template>
</template>
</EasyDataTable>
</div>

Expand Down
2 changes: 2 additions & 0 deletions varfish/vueapp/components.d.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -113,6 +113,8 @@ declare module 'vue' {
IMdiSquareEditOutline: typeof import('~icons/mdi/square-edit-outline')['default']
IMdiStar: typeof import('~icons/mdi/star')['default']
IMdiStarOutline: typeof import('~icons/mdi/star-outline')['default']
IMdiTableColumnWidth: typeof import('~icons/mdi/table-column-width')['default']
IMdiTableMergeCells: typeof import('~icons/mdi/table-merge-cells')['default']
IMdiToggleSwitchOutline: typeof import('~icons/mdi/toggle-switch-outline')['default']
IMdiTools: typeof import('~icons/mdi/tools')['default']
IMdiUndoVariant: typeof import('~icons/mdi/undo-variant')['default']
Expand Down
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