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gene_known_for_phenotype from tags #3982

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Mar 20, 2024
Merged

gene_known_for_phenotype from tags #3982

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eb3a67b
use tags to determine gene_known_for_phenotype
hanars Mar 19, 2024
c8c8b4d
update tests
hanars Mar 19, 2024
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1 change: 0 additions & 1 deletion seqr/views/apis/report_api.py
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Original file line number Diff line number Diff line change
Expand Up @@ -893,7 +893,6 @@ def _add_row(row, family_id, row_type):
individual_data_types={i.individual_id: i.data_types for i in individuals},
add_row=_add_row,
variant_json_fields=['clinvar', 'variantId'],
saved_variant_annotations={'tags': ArrayAgg('varianttag__variant_tag_type__name', distinct=True)},
mme_values={'variant_ids': ArrayAgg('matchmakersubmissiongenes__saved_variant__saved_variant_json__variantId')},
include_metadata=True,
include_mondo=True,
Expand Down
12 changes: 6 additions & 6 deletions seqr/views/apis/report_api_tests.py
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Expand Up @@ -616,7 +616,7 @@ def test_anvil_export(self, mock_google_authenticated, mock_zip):
'1_248367227_HG00731', 'HG00731', 'HG00731', 'RP11', 'Known', 'paternal',
'Homozygous', 'GRCh37', '1', '248367227', 'TC', 'T', '-', '-', '-', '-', '-', '-', '-'], discovery_file)
self.assertIn([
'21_3343353_NA19675_1', 'NA19675_1', 'NA19675', 'RP11', 'Known', 'de novo',
'21_3343353_NA19675_1', 'NA19675_1', 'NA19675', 'RP11', 'Candidate', 'de novo',
'Heterozygous', 'GRCh37', '21', '3343353', 'GAGA', 'G', 'c.375_377delTCT', 'p.Leu126del', 'ENST00000258436',
'-', '-', '-', '-'], discovery_file)
self.assertIn([
Expand Down Expand Up @@ -993,7 +993,7 @@ def _assert_expected_gregor_files(self, mock_open, has_second_project=False):
])
self.assertIn([
'Broad_NA19675_1_21_3343353', 'Broad_NA19675_1', '', 'SNV/INDEL', 'GRCh37', '21', '3343353', 'GAGA', 'G', '',
'RP11', 'ENST00000258436', 'c.375_377delTCT', 'p.Leu126del', 'Heterozygous', '', 'de novo', '', '', 'Known',
'RP11', 'ENST00000258436', 'c.375_377delTCT', 'p.Leu126del', 'Heterozygous', '', 'de novo', '', '', 'Candidate',
'Myasthenic syndrome, congenital, 8, with pre- and postsynaptic defects', 'OMIM:615120', 'Autosomal recessive|X-linked',
'Full', '', '', 'SR-ES', '',
], genetic_findings_file)
Expand All @@ -1006,12 +1006,12 @@ def _assert_expected_gregor_files(self, mock_open, has_second_project=False):
self.assertIn([
'Broad_NA20889_1_248367227', 'Broad_NA20889', '', 'SNV/INDEL', 'GRCh37', '1', '248367227', 'TC', 'T',
'', 'OR4G11P', 'ENST00000505820', 'c.3955G>A', 'c.1586-17C>G', 'Heterozygous', '', 'unknown',
'Broad_NA20889_1_249045487', '', 'Known', 'IRIDA syndrome', 'MONDO:0008788', 'Autosomal dominant',
'Broad_NA20889_1_249045487', '', 'Candidate', 'IRIDA syndrome', 'MONDO:0008788', 'Autosomal dominant',
'Full', '', '', 'SR-ES', '',
], genetic_findings_file)
self.assertIn([
'Broad_NA20889_1_249045487', 'Broad_NA20889', '', 'SNV/INDEL', 'GRCh37', '1', '249045487', 'A', 'G', '',
'OR4G11P', '', '', '', 'Heterozygous', '', 'unknown', 'Broad_NA20889_1_248367227', '', 'Known',
'OR4G11P', '', '', '', 'Heterozygous', '', 'unknown', 'Broad_NA20889_1_248367227', '', 'Candidate',
'IRIDA syndrome', 'MONDO:0008788', 'Autosomal dominant', 'Full', '', '', 'SR-ES', '',
], genetic_findings_file)

Expand Down Expand Up @@ -1225,7 +1225,7 @@ def test_variant_metadata(self):
'family_history': 'Yes',
'gene': 'OR4G11P',
'gene_id': 'ENSG00000240361',
'gene_known_for_phenotype': 'Known',
'gene_known_for_phenotype': 'Candidate',
'genetic_findings_id': 'NA20889_1_248367227',
'hgvsc': 'c.3955G>A',
'hgvsp': 'c.1586-17C>G',
Expand Down Expand Up @@ -1253,7 +1253,7 @@ def test_variant_metadata(self):
'family_history': 'Yes',
'gene': None,
'gene_id': None,
'gene_known_for_phenotype': 'Known',
'gene_known_for_phenotype': 'Candidate',
'genetic_findings_id': 'NA20889_1_249045487',
'participant_id': 'NA20889',
'pos': 249045487,
Expand Down
7 changes: 5 additions & 2 deletions seqr/views/apis/summary_data_api_tests.py
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Original file line number Diff line number Diff line change
Expand Up @@ -37,8 +37,8 @@
"num_saved_variants": 2,
"solve_status": "Unsolved",
"sample_id": "NA20889",
"gene_known_for_phenotype-1": "Known",
"gene_known_for_phenotype-2": "Known",
"gene_known_for_phenotype-1": "Candidate",
"gene_known_for_phenotype-2": "Candidate",
"variant_inheritance-1": "unknown",
"variant_inheritance-2": "unknown",
'genetic_findings_id-1': 'NA20889_1_248367227',
Expand Down Expand Up @@ -105,6 +105,8 @@
'allele_balance_or_heteroplasmy_percentage-2': None,
'notes-1': None,
'notes-2': None,
'tags-1': ['Tier 1 - Novel gene and phenotype'],
'tags-2': ['Tier 1 - Novel gene and phenotype'],
}
EXPECTED_SAMPLE_METADATA_ROW = {
"dbgap_submission": "No",
Expand Down Expand Up @@ -147,6 +149,7 @@
'alt-1': 'T',
'chrom-1': '1',
'gene_known_for_phenotype-1': 'Candidate',
'tags-1': ['Tier 1 - Novel gene and phenotype'],
'pos-1': 248367227,
'end-1': None,
'ref-1': 'TC',
Expand Down
17 changes: 5 additions & 12 deletions seqr/views/utils/anvil_metadata_utils.py
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Expand Up @@ -126,7 +126,7 @@ def parse_anvil_metadata(
variant_json_fields: Iterable[str] = None, post_process_variant: Callable[[dict, list[dict]], dict] = None,
include_no_individual_families: bool = False, omit_airtable: bool = False, include_metadata: bool = False,
include_discovery_sample_id: bool = False, include_mondo: bool = False, include_parent_mnvs: bool = False,
proband_only_variants: bool = False, saved_variant_annotations: dict = None):
proband_only_variants: bool = False):

individual_samples = individual_samples or (_get_loaded_before_date_project_individual_samples(projects, max_loaded_date) \
if max_loaded_date else _get_all_project_individual_samples(projects))
Expand All @@ -147,7 +147,6 @@ def parse_anvil_metadata(

saved_variants_by_family = _get_parsed_saved_discovery_variants_by_family(
list(family_data_by_id.keys()), variant_filter=variant_filter, variant_json_fields=variant_json_fields,
saved_variant_annotations=saved_variant_annotations,
)

condition_map = _get_condition_map(family_data_by_id.values())
Expand Down Expand Up @@ -285,21 +284,14 @@ def _post_process_variant_metadata(v, gene_variants, include_parent_mnvs=False):


def _get_parsed_saved_discovery_variants_by_family(
families: Iterable[Family], variant_filter: dict, variant_json_fields: list[str], saved_variant_annotations: dict,
families: Iterable[Family], variant_filter: dict, variant_json_fields: list[str],
):
tag_types = VariantTagType.objects.filter(project__isnull=True, category=DISCOVERY_CATEGORY)

annotations = {
'gene_known_for_phenotype': Case(When(
Q(family__post_discovery_omim_numbers__len=0, family__mondo_id__isnull=True),
then=Value('Candidate')), default=Value('Known')
),
**(saved_variant_annotations or {}),
}
project_saved_variants = SavedVariant.objects.filter(
varianttag__variant_tag_type__in=tag_types, family__id__in=families,
**(variant_filter or {}),
).order_by('created_date').distinct().annotate(**annotations)
).order_by('created_date').distinct().annotate(tags=ArrayAgg('varianttag__variant_tag_type__name', distinct=True))

variants = []
gene_ids = set()
Expand All @@ -321,8 +313,9 @@ def _get_parsed_saved_discovery_variants_by_family(
'hgvsc': (main_transcript.get('hgvsc') or '').split(':')[-1],
'hgvsp': (main_transcript.get('hgvsp') or '').split(':')[-1],
'seqr_chosen_consequence': main_transcript.get('majorConsequence'),
'gene_known_for_phenotype': 'Known' if 'Known gene for phenotype' in variant.tags else 'Candidate',
**{k: variant_json.get(k) for k in ['genotypes', 'svType', 'svName', 'end'] + (variant_json_fields or [])},
**{k: getattr(variant, k) for k in ['family_id', 'ref', 'alt', *annotations.keys()]},
**{k: getattr(variant, k) for k in ['family_id', 'ref', 'alt', 'tags']},
})

genes_by_id = get_genes(gene_ids)
Expand Down
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