Add v3 SV dataset

browser/help/topics/structural-variants/sv-effect-overview.md

@@ -3,7 +3,7 @@ id: sv-effect-overview
 title: 'Genic consequences of structural variants'
 ---
 
-We annotated each SV for multiple potential genic effects using an approach described in [the gnomAD SV paper](https://broad.io/gnomad_sv).  In brief, this approach considers SV size, class, position, and overlap with exons from canonical transcripts of [GENCODE v19](https://www.gencodegenes.org/human/release_19.html) protein-coding genes.
+We annotated each SV for multiple potential genic effects using an approach described in [the gnomAD SV paper](https://broad.io/gnomad_sv). In brief, this approach considers SV size, class, position, and overlap with exons from canonical transcripts of [GENCODE v19](https://www.gencodegenes.org/human/release_19.html) protein-coding genes.
 
 ### Representation in the gnomAD Browser
 
@@ -13,16 +13,20 @@ The functional consequence per SV was determined in the order below:
 
 ### Main functional consequences
 
-  1. ![](https://placehold.it/15/D43925/000000?text=+) **Predicted loss-of-function (pLoF)**: SV is predicted to delete the gene or truncate the gene product.
-  2. ![](https://placehold.it/15/7459B2/000000?text=+) **Intragenic exonic duplication (IED)**: SV is predicted to result in duplicated exons within the gene, without extending beyond the boundaries of the open reading frame.
-  3. ![](https://placehold.it/15/2376B2/000000?text=+) **Copy gain (CG)**: SV is predicted to result in an entire additional intact copy of the gene.
+1. ![](https://placehold.it/15/D43925/000000?text=+) **Predicted loss-of-function (pLoF)**: SV is predicted to delete the gene or truncate the gene product.
+2. ![](https://placehold.it/15/7459B2/000000?text=+) **Intragenic exonic duplication (IED)**: SV is predicted to result in duplicated exons within the gene, without extending beyond the boundaries of the open reading frame. (New in gnomAD v4)
+3. **Partial exon duplication (PED)**: SV is predicted to duplicate part of one or more exons without resulting in a whole-gene copy gain. (New in gnomAD v4)
+4. ![](https://placehold.it/15/2376B2/000000?text=+) **Copy gain (CG)**: SV is predicted to result in an entire additional intact copy of the gene.
 
 ### Other consequences
 
-  4. **MCNV overlap**: MCNV overlaps one or more protein-coding exons; exact consequence depends on the number of copies and their orientation.
-  5. **Partial duplication**: SV is predicted to partially duplicate the gene while leaving the original copy of the gene intact.
-  6. **UTR**: SV does not directly disrupt coding sequence, but overlaps one of the gene's untranslated regions (UTRs).
-  7. **Promoter**: SV does not directly disrupt coding sequence or promoter, but is within 2kb of the gene's transcription start site.
-  8. **Inversion span**: gene is entirely spanned by an inversion SV without being directly disrupted.
-  9. **Intronic**: SV does not directly disrupt coding sequence, but is wholly contained within an intron.
-  10. **Intergenic**: SV does not meet any of the above categories.
+4. **Transcription start site duplication**: SV is predicted to result in a duplication of a transcription start site but not result in any other, more severe consequences. (New in gnomAD v4).
+5. **MCNV overlap**: MCNV overlaps one or more protein-coding exons; exact consequence depends on the number of copies and their orientation.
+
+6. **Partial duplication**: SV is predicted to partially duplicate the gene while leaving the original copy of the gene intact.
+7. **Exonic breakend**: breakend localizes to exonic locus, but consequence is unclear as SV is incompletely resolved. (New in gnomAD v4).
+8. **UTR**: SV does not directly disrupt coding sequence, but overlaps one of the gene's untranslated regions (UTRs).
+9. **Promoter**: SV does not directly disrupt coding sequence or promoter, but is within 2kb of the gene's transcription start site.
+10. **Inversion span**: gene is entirely spanned by an inversion SV without being directly disrupted.
+11. **Intronic**: SV does not directly disrupt coding sequence, but is wholly contained within an intron.
+12. **Intergenic**: SV does not meet any of the above categories.

browser/src/ConstraintTable/__snapshots__/ConstraintTable.spec.tsx.snap

@@ -6510,6 +6510,42 @@ exports[`ConstraintTable with "gnomad_sv_r2_1_non_neuro" dataset selected with a
 </p>
 `;
 
+exports[`ConstraintTable with "gnomad_sv_r4" dataset selected and gene with available constraint has no unexpected changes 1`] = `
+<p>
+  Constraint not yet available for gnomAD v3.
+</p>
+`;
+
+exports[`ConstraintTable with "gnomad_sv_r4" dataset selected and transcript with available constraint has no unexpected changes 1`] = `
+<p>
+  Constraint not yet available for gnomAD v3.
+</p>
+`;
+
+exports[`ConstraintTable with "gnomad_sv_r4" dataset selected with a minimal gene has no unexpected changes 1`] = `
+<p>
+  Constraint not yet available for gnomAD v3.
+</p>
+`;
+
+exports[`ConstraintTable with "gnomad_sv_r4" dataset selected with a minimal transcript has no unexpected changes 1`] = `
+<p>
+  Constraint not yet available for gnomAD v3.
+</p>
+`;
+
+exports[`ConstraintTable with "gnomad_sv_r4" dataset selected with a mitochondrial gene has no unexpected changes 1`] = `
+<p>
+  Constraint not yet available for gnomAD v3.
+</p>
+`;
+
+exports[`ConstraintTable with "gnomad_sv_r4" dataset selected with a mitochondrial transcript has no unexpected changes 1`] = `
+<p>
+  Constraint not yet available for gnomAD v3.
+</p>
+`;
+
 exports[`ConstraintTable with exac dataset and gene with available constraints has no unexpected changes 1`] = `
 [
   <table

browser/src/DatasetSelector.spec.tsx

@@ -15,4 +15,24 @@ forAllDatasets('DataSelector with "%s" dataset selected', (datasetId) => {
     )
     expect(tree).toMatchSnapshot()
   })
+
+  test('has no unexpected changes when showing all possible datasets', () => {
+    const tree = renderer.create(
+      withDummyRouter(
+        <DatasetSelector
+          selectedDataset={datasetId}
+          datasetOptions={{
+            includeShortVariants: true,
+            includeStructuralVariants: true,
+            includeExac: true,
+            includeGnomad2: true,
+            includeGnomad2Subsets: true,
+            includeGnomad3: true,
+            includeGnomad3Subsets: true,
+          }}
+        />
+      )
+    )
+    expect(tree).toMatchSnapshot()
+  })
 })

browser/src/DatasetSelector.tsx

@@ -14,6 +14,8 @@ import {
   hasShortVariants,
   hasStructuralVariants,
   referenceGenome,
+  shortVariantDatasetId,
+  structuralVariantDatasetId,
 } from '@gnomad/dataset-metadata/metadata'
 
 const NavigationMenuWrapper = styled.ul`
@@ -124,7 +126,6 @@ const SubNavigationLink = styled.a`
   }
 `.withComponent(Link)
 
-
 const ItemDescription = styled.div`
   margin-top: 0.125em;
   margin-left: 5px;
@@ -148,13 +149,13 @@ type ChildDataset = {
 }
 
 type Props = {
-  items: ({
+  items: {
     id: string
     isActive?: boolean
     label: string
     url: string | any
     children: ChildDataset[]
-  })[]
+  }[]
 }
 
 type State = any
@@ -394,27 +395,29 @@ class NavigationMenu extends Component<Props, State> {
                     ).map((childReferenceGenome) => (
                       <li key={childReferenceGenome}>
                         <GroupedNav>{childReferenceGenome}</GroupedNav>
-                          {item.children
-                            .filter((childItem) => childItem.childReferenceGenome === childReferenceGenome)
-                            .map((childItem) => (
-                              <li key={childItem.id}>
-                                <SubNavigationLink
-                                  data-item={childItem.id}
-                                  to={childItem.url}
-                                  onBlur={this.onBlur}
-                                  onClick={() => {
-                                    this.setState({ expandedItem: null })
-                                    this.focusItem(item.id)
-                                  }}
-                                  onKeyDown={this.onKeyDownSubMenuItem}
-                                >
-                                  {childItem.label}
-                                  {childItem.description && (
-                                    <ItemDescription>{childItem.description}</ItemDescription>
-                                  )}
-                                </SubNavigationLink>
-                              </li>
-                            ))}
+                        {item.children
+                          .filter(
+                            (childItem) => childItem.childReferenceGenome === childReferenceGenome
+                          )
+                          .map((childItem) => (
+                            <li key={childItem.id}>
+                              <SubNavigationLink
+                                data-item={childItem.id}
+                                to={childItem.url}
+                                onBlur={this.onBlur}
+                                onClick={() => {
+                                  this.setState({ expandedItem: null })
+                                  this.focusItem(item.id)
+                                }}
+                                onKeyDown={this.onKeyDownSubMenuItem}
+                              >
+                                {childItem.label}
+                                {childItem.description && (
+                                  <ItemDescription>{childItem.description}</ItemDescription>
+                                )}
+                              </SubNavigationLink>
+                            </li>
+                          ))}
                       </li>
                     ))}
                   </SubNavigationMenu>
@@ -444,10 +447,8 @@ const DatasetSelector = withRouter(({ datasetOptions, history, selectedDataset }
     search: queryString.stringify({ dataset: datasetId }),
   })
 
-  const defaultTopLevelShortVariantDataset = includeGnomad2 ? 'gnomad_r2_1' : 'gnomad_r3'
-  const topLevelShortVariantDataset = hasShortVariants(selectedDataset)
-    ? selectedDataset
-    : defaultTopLevelShortVariantDataset
+  const topLevelShortVariantDataset = shortVariantDatasetId(selectedDataset)
+  const topLevelStructuralVariantDataset = structuralVariantDatasetId(selectedDataset)
 
   let datasets: any = []
 
@@ -580,10 +581,6 @@ const DatasetSelector = withRouter(({ datasetOptions, history, selectedDataset }
   }
 
   if (includeStructuralVariants) {
-    const topLevelStructuralVariantDataset = hasStructuralVariants(selectedDataset)
-      ? selectedDataset
-      : 'gnomad_sv_r2_1'
-
     datasets.push(
       {
         id: 'current_sv_dataset',
@@ -596,6 +593,13 @@ const DatasetSelector = withRouter(({ datasetOptions, history, selectedDataset }
         isActive: hasStructuralVariants(selectedDataset),
         label: 'More datasets',
         children: [
+          {
+            id: 'gnomad_sv_r4',
+            label: labelForDataset('gnomad_sv_r4'),
+            url: datasetLink('gnomad_sv_r4'),
+            description: `${sampleCounts.gnomad_sv_r4.total.toLocaleString()} samples`,
+            childReferenceGenome: referenceGenome('gnomad_sv_r4'),
+          },
           {
             id: 'gnomad_sv_r2_1',
             label: labelForDataset('gnomad_sv_r2_1'),

browser/src/GenePage/StructuralVariantsInGene.tsx

@@ -4,6 +4,7 @@ import { referenceGenome } from '@gnomad/dataset-metadata/metadata'
 import Query from '../Query'
 import { filterStructuralVariantsInZoomRegion } from '../RegionViewer/filterVariantsInZoomRegion'
 import StructuralVariants from '../StructuralVariantList/StructuralVariants'
+import { StructuralVariant } from '../StructuralVariantPage/StructuralVariantPage'
 
 type OwnProps = {
   datasetId: string
@@ -61,15 +62,20 @@ const StructuralVariantsInGene = ({ datasetId, gene, zoomRegion, ...rest }: Prop
       success={(data: any) => data.gene && data.gene.structural_variants}
     >
       {({ data }: any) => {
+        const structural_variants = filterStructuralVariantsInZoomRegion(
+          data.gene.structural_variants,
+          zoomRegion
+        ).map((variant: StructuralVariant) => ({
+          ...variant,
+          variant_id: variant.variant_id.toUpperCase(),
+        }))
+
         return (
           <StructuralVariants
             {...rest}
             context={gene}
             exportFileName={`gnomad_structural_variants_${gene.gene_id}`}
-            variants={filterStructuralVariantsInZoomRegion(
-              data.gene.structural_variants,
-              zoomRegion
-            )}
+            variants={structural_variants}
           />
         )
       }}