Merge pull request #4418 from broadinstitute/sex-aneuploidy

Sex aneuploidy

matchmaker/models.py

@@ -8,7 +8,10 @@
 
 class MatchmakerSubmission(ModelWithGUID):
 
-    SEX_LOOKUP = {Individual.SEX_MALE: 'MALE', Individual.SEX_FEMALE: 'FEMALE'}
+    SEX_LOOKUP = {
+        **{sex: 'MALE' for sex in Individual.MALE_SEXES},
+        **{sex: 'FEMALE' for sex in Individual.FEMALE_SEXES},
+    }
 
     individual = models.OneToOneField(Individual, on_delete=models.PROTECT)
 

seqr/fixtures/1kg_project.json

@@ -444,7 +444,7 @@
         "individual_id": "NA19675_1",
         "mother_id": 3,
         "father_id": 2,
-        "sex": "M",
+        "sex": "XXY",
         "affected": "A",
         "display_name": "",
         "notes": "",
@@ -536,7 +536,7 @@
         "individual_id": "HG00731",
         "mother_id": 6,
         "father_id": 5,
-        "sex": "F",
+        "sex": "X0",
         "affected": "A",
         "proband_relationship": "S",
         "display_name": "HG00731_a",

seqr/migrations/0076_alter_individual_sex.py

@@ -0,0 +1,18 @@
+# Generated by Django 4.2.13 on 2024-10-10 20:51
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('seqr', '0075_alter_individual_primary_biosample'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='individual',
+            name='sex',
+            field=models.CharField(choices=[('M', 'Male'), ('F', 'Female'), ('U', 'Unknown'), ('XXY', 'XXY'), ('XYY', 'XYY'), ('XXX', 'XXX'), ('X0', 'X0')], default='U', max_length=3),
+        ),
+    ]

seqr/models.py

@@ -447,10 +447,16 @@ class Individual(ModelWithGUID):
     SEX_MALE = 'M'
     SEX_FEMALE = 'F'
     SEX_UNKNOWN = 'U'
+    FEMALE_ANEUPLOIDIES = ['XXX', 'X0']
+    MALE_ANEUPLOIDIES = ['XXY', 'XYY']
+    FEMALE_SEXES = [SEX_FEMALE] + FEMALE_ANEUPLOIDIES
+    MALE_SEXES = [SEX_MALE] + MALE_ANEUPLOIDIES
     SEX_CHOICES = (
         (SEX_MALE, 'Male'),
         ('F', 'Female'),
         ('U', 'Unknown'),
+        *[(sex, sex) for sex in MALE_ANEUPLOIDIES],
+        *[(sex, sex) for sex in FEMALE_ANEUPLOIDIES],
     )
 
     AFFECTED_STATUS_AFFECTED = 'A'
@@ -603,7 +609,7 @@ class Individual(ModelWithGUID):
     mother = models.ForeignKey('seqr.Individual', null=True, blank=True, on_delete=models.SET_NULL, related_name='maternal_children')
     father = models.ForeignKey('seqr.Individual', null=True, blank=True, on_delete=models.SET_NULL, related_name='paternal_children')
 
-    sex = models.CharField(max_length=1, choices=SEX_CHOICES, default='U')
+    sex = models.CharField(max_length=3, choices=SEX_CHOICES, default='U')
     affected = models.CharField(max_length=1, choices=AFFECTED_STATUS_CHOICES, default=AFFECTED_STATUS_UNKNOWN)
 
     # TODO once sample and individual ids are fully decoupled no reason to maintain this field

seqr/utils/search/hail_search_utils.py

@@ -141,7 +141,7 @@ def _get_sample_data(samples, inheritance_filter=None, inheritance_mode=None, **
         affected=F('individual__affected'),
     )
     if inheritance_mode == X_LINKED_RECESSIVE:
-        sample_values['is_male'] = Case(When(individual__sex=Individual.SEX_MALE, then=True), default=False)
+        sample_values['is_male'] = Case(When(individual__sex__in=Individual.MALE_SEXES, then=True), default=False)
     sample_data = samples.order_by('guid').values('individual__individual_id', 'dataset_type', 'sample_type', **sample_values)
 
     custom_affected = (inheritance_filter or {}).pop('affected', None)

seqr/views/apis/anvil_workspace_api_tests.py

@@ -730,7 +730,7 @@ def _assert_valid_operation(self, project, test_add_data=True):
                 ['R0001_1kg', 'F000001_1', '1', 'NA19675_1', 'NA19678', '', 'F'],
                 ['R0001_1kg', 'F000001_1', '1', 'NA19678', '', '', 'M'],
                 ['R0001_1kg', 'F000001_1', '1', 'NA19679', '', '', 'F'],
-                ['R0001_1kg', 'F000002_2', '2', 'HG00731', 'HG00732', 'HG00733', 'F'],
+                ['R0001_1kg', 'F000002_2', '2', 'HG00731', 'HG00732', 'HG00733', 'X0'],
                 ['R0001_1kg', 'F000002_2', '2', 'HG00732', '', '', 'M'],
                 ['R0001_1kg', 'F000002_2', '2', 'HG00733', '', '', 'F'],
                 ['R0001_1kg', 'F000003_3', '3', 'NA20870', '', '', 'M'],

seqr/views/apis/data_manager_api_tests.py

@@ -390,10 +390,10 @@
 
 PEDIGREE_HEADER = ['Project_GUID', 'Family_GUID', 'Family_ID', 'Individual_ID', 'Paternal_ID', 'Maternal_ID', 'Sex']
 EXPECTED_PEDIGREE_ROWS = [
-    ['R0001_1kg', 'F000001_1', '1', 'NA19675_1', 'NA19678', 'NA19679', 'M'],
+    ['R0001_1kg', 'F000001_1', '1', 'NA19675_1', 'NA19678', 'NA19679', 'XXY'],
     ['R0001_1kg', 'F000001_1', '1', 'NA19678', '', '', 'M'],
     ['R0001_1kg', 'F000001_1', '1', 'NA19679', '', '', 'F'],
-    ['R0001_1kg', 'F000002_2', '2', 'HG00731', 'HG00732', 'HG00733', 'F'],
+    ['R0001_1kg', 'F000002_2', '2', 'HG00731', 'HG00732', 'HG00733', 'X0'],
 ]
 
 PROJECT_OPTION = {

seqr/views/apis/individual_api.py

@@ -29,12 +29,6 @@
 from seqr.views.utils.individual_utils import delete_individuals, add_or_update_individuals_and_families
 from seqr.views.utils.variant_utils import bulk_create_tagged_variants
 
-_SEX_TO_EXPORTED_VALUE = dict(Individual.SEX_LOOKUP)
-_SEX_TO_EXPORTED_VALUE['U'] = ''
-
-__AFFECTED_TO_EXPORTED_VALUE = dict(Individual.AFFECTED_STATUS_LOOKUP)
-__AFFECTED_TO_EXPORTED_VALUE['U'] = ''
-
 
 @login_and_policies_required
 def update_individual_handler(request, individual_guid):

seqr/views/apis/individual_api_tests.py

@@ -453,7 +453,8 @@ def test_individuals_table_handler_errors(self):
 
         rows += [
             '"1"	"NA19675_1"	"NA19675_1"	"F"	"Father"',
-            '"2"	"NA19675_2"	"NA19675_1"	"M"	""',
+            '"2"	"NA19675_2"	"NA19675_1"	"XXX"	"Nephew"',
+            '"2"	"NA19677"	"NA19675_2"	"M"	""',
         ]
         response = self.client.post(individuals_url, {
             'f': SimpleUploadedFile('test.tsv', '\n'.join(rows).encode('utf-8'))})
@@ -463,8 +464,10 @@ def test_individuals_table_handler_errors(self):
                 'Invalid proband relationship "Father" for NA19675_1 with given gender Female',
                 'NA19675_1 is recorded as their own father',
                 'NA19675_1 is recorded as Female sex and also as the father of NA19675_1',
+                'Invalid proband relationship "Nephew" for NA19675_2 with given gender XXX',
                 'NA19675_1 is recorded as Female sex and also as the father of NA19675_2',
                 'NA19675_1 is recorded as the father of NA19675_2 but they have different family ids: 1 and 2',
+                'NA19675_2 is recorded as XXX sex and also as the father of NA19677',
                 'NA19675_1 is included as 2 separate records, but must be unique within the project',
             ],
             'warnings': [missing_entry_warning],
@@ -477,7 +480,7 @@ def test_individuals_table_handler(self):
 
         data = 'Family ID	Individual ID	Previous Individual ID	Paternal ID	Maternal ID	Sex	Affected Status	Notes	familyNotes\n\
 "1"	" NA19675_1 "	""	"NA19678 "	"NA19679"	"Female"	"Affected"	"A affected individual, test1-zsf"	""\n\
-"1"	"NA19678"	""	""	""	"Male"	"Unaffected"	"a individual note"	""\n\
+"1"	"NA19678"	""	""	""	"XXY"	"Unaffected"	"a individual note"	""\n\
 "4"	"NA20872_update"	"NA20872"	""	""	"Male"	"Affected"	""	""\n\
 "21"	" HG00735"	""	""	""	"Female"	"Unaffected"	""	"a new family""'
 
@@ -525,6 +528,7 @@ def test_individuals_table_handler(self):
         self.assertEqual(response_json['individualsByGuid']['I000001_na19675']['sex'], 'F')
         self.assertEqual(
             response_json['individualsByGuid']['I000001_na19675']['notes'], 'A affected individual, test1-zsf')
+        self.assertEqual(response_json['individualsByGuid']['I000002_na19678']['sex'], 'XXY')
         self.assertEqual(response_json['individualsByGuid'][new_indiv_guid]['individualId'], 'HG00735')
         self.assertEqual(response_json['individualsByGuid'][new_indiv_guid]['sex'], 'F')
         self.assertEqual(response_json['individualsByGuid']['I000008_na20872']['individualId'], 'NA20872_update')
@@ -899,7 +903,7 @@ def _is_expected_individuals_metadata_upload(self, response, expected_families=F
             response_json['individualsByGuid']['I000001_na19675']['absentFeatures'],
             [{'id': 'HP:0012469', 'category': 'HP:0025031', 'label': 'Infantile spasms'}]
         )
-        self.assertEqual(response_json['individualsByGuid']['I000001_na19675']['sex'], 'M')
+        self.assertEqual(response_json['individualsByGuid']['I000001_na19675']['sex'], 'XXY')
         self.assertEqual(response_json['individualsByGuid']['I000001_na19675']['birthYear'], 2000)
         self.assertTrue(response_json['individualsByGuid']['I000001_na19675']['affectedRelatives'])
         self.assertEqual(response_json['individualsByGuid']['I000001_na19675']['onsetAge'], 'J')

seqr/views/apis/report_api_tests.py

@@ -526,11 +526,11 @@
         'missing_variant_case',
     ], [
         'Broad_NA19675_1', 'Broad_1kg project nme with unide', 'BROAD', 'HMB', 'Yes', 'IKBKAP|CCDC102B|CMA - normal',
-        '34415322', 'Broad_1', 'Broad_NA19678', 'Broad_NA19679', '', 'Self', '', 'Male', '',
+        '34415322', 'Broad_1', 'Broad_NA19678', 'Broad_NA19679', '', 'Self', '', 'Male', 'XXY',
         'Middle Eastern or North African', '', '', '21', 'Affected', 'myopathy', '18', 'Unsolved', 'No',
     ], [
         'Broad_HG00731', 'Broad_1kg project nme with unide', 'BROAD', 'HMB', '', '', '', 'Broad_2', 'Broad_HG00732',
-        'Broad_HG00733', '', 'Self', '', 'Female', '', '', 'Hispanic or Latino', 'Other', '', 'Affected',
+        'Broad_HG00733', '', 'Self', '', 'Female', 'X0', '', 'Hispanic or Latino', 'Other', '', 'Affected',
         'microcephaly; seizures', '', 'Unsolved', 'No',
     ], [
         'Broad_HG00732', 'Broad_1kg project nme with unide', 'BROAD', 'HMB', '', '', '', 'Broad_2', '0', '0', '',
@@ -875,14 +875,14 @@ def _test_gregor_export(self, url, mock_subprocess, mock_temp_dir, mock_open, mo
             [c for c in PARTICIPANT_TABLE[0] if c not in {'pmid_id', 'ancestry_detail', 'age_at_last_observation', 'missing_variant_case'}],
             [
             'Broad_NA19675_1', 'Broad_1kg project nme with unide', 'BROAD', 'HMB', 'Yes', 'IKBKAP|CCDC102B|CMA - normal',
-            'Broad_1', 'Broad_NA19678', 'Broad_NA19679', '', 'Self', '', 'Male', '', 'Middle Eastern or North African',
+            'Broad_1', 'Broad_NA19678', 'Broad_NA19679', '', 'Self', '', 'Male', 'XXY', 'Middle Eastern or North African',
             '', 'Affected', 'myopathy', '18', 'Unsolved',
         ], [
             'Broad_NA19678', 'Broad_1kg project nme with unide', 'BROAD', 'HMB', '', '', 'Broad_1', '0', '0', '', '',
             '', 'Male', '', '', '', 'Unaffected', 'myopathy', '', 'Unaffected',
         ], [
             'Broad_HG00731', 'Broad_1kg project nme with unide', 'BROAD', 'HMB', '', '', 'Broad_2', 'Broad_HG00732',
-            'Broad_HG00733', '', 'Self', '', 'Female', '', '', 'Hispanic or Latino', 'Affected',
+            'Broad_HG00733', '', 'Self', '', 'Female', 'X0', '', 'Hispanic or Latino', 'Affected',
             'microcephaly; seizures', '', 'Unsolved',
         ]], additional_calls=10)
         self._assert_expected_file(read_file, [READ_TABLE_HEADER, [

seqr/views/apis/summary_data_api_tests.py

@@ -73,6 +73,7 @@
     'seqr_chosen_consequence-1': 'intron_variant',
     "ancestry": "Ashkenazi Jewish",
     "sex": "Female",
+    'sex_detail': None,
     "chrom-1": "1",
     "alt-1": "T",
     "gene_of_interest-1": "OR4G11P",
@@ -154,6 +155,7 @@
     'pmid_id': None,
     'proband_relationship': 'Self',
     'sex': 'Female',
+    'sex_detail': None,
     'solve_status': 'Unsolved',
     'alt-1': 'T',
     'chrom-1': '1',

seqr/views/apis/variant_search_api_tests.py

@@ -836,7 +836,7 @@ def test_variant_lookup(self, mock_variant_lookup):
                     'vlmContactEmail': 'test@broadinstitute.org,vlm@broadinstitute.org',
                 },
                 'I2_F0_1-10439-AC-A': {
-                    'affected': 'A', 'familyGuid': 'F0_1-10439-AC-A', 'individualGuid': 'I2_F0_1-10439-AC-A', 'sex': 'F',
+                    'affected': 'A', 'familyGuid': 'F0_1-10439-AC-A', 'individualGuid': 'I2_F0_1-10439-AC-A', 'sex': 'X0',
                     'features': [{'category': 'HP:0000707', 'label': '1 terms'}, {'category': 'HP:0001626', 'label': '1 terms'}],
                     'vlmContactEmail': 'test@broadinstitute.org,vlm@broadinstitute.org',
                 },

seqr/views/utils/anvil_metadata_utils.py

@@ -293,7 +293,7 @@ def _get_genotype_zygosity(genotype, individual=None, variant=None):
     num_alt = genotype.get('numAlt')
     cn = genotype.get('cn')
     if num_alt == 2 or cn == 0 or (cn != None and cn > 3):
-        return HEMI if (variant or {}).get('chrom') == 'X' and individual.sex == Individual.SEX_MALE else HOM_ALT
+        return HEMI if (variant or {}).get('chrom') == 'X' and individual.sex in Individual.MALE_SEXES else HOM_ALT
     if num_alt == 1 or cn == 1 or cn == 3:
         return HET
     return None
@@ -420,9 +420,18 @@ def _get_transcript_field(field, config, transcript):
 def _get_subject_row(individual, has_dbgap_submission, airtable_metadata, individual_ids_map, get_additional_individual_fields, format_id):
     paternal_ids = individual_ids_map.get(individual.father_id, ('', ''))
     maternal_ids = individual_ids_map.get(individual.mother_id, ('', ''))
+    sex = individual.sex
+    sex_detail = None
+    if sex in Individual.MALE_ANEUPLOIDIES:
+        sex_detail = sex
+        sex = Individual.SEX_MALE
+    elif sex in Individual.FEMALE_ANEUPLOIDIES:
+        sex_detail = sex
+        sex = Individual.SEX_FEMALE
     subject_row = {
         'participant_id': format_id(individual.individual_id),
-        'sex': Individual.SEX_LOOKUP[individual.sex],
+        'sex': Individual.SEX_LOOKUP[sex],
+        'sex_detail': sex_detail,
         'reported_race': ANCESTRY_MAP.get(individual.population, ''),
         'ancestry_detail': ANCESTRY_DETAIL_MAP.get(individual.population, ''),
         'reported_ethnicity': ETHNICITY_MAP.get(individual.population, ''),

seqr/views/utils/individual_utils.py

@@ -13,13 +13,6 @@
 from seqr.views.utils.pedigree_info_utils import JsonConstants
 
 
-_SEX_TO_EXPORTED_VALUE = dict(Individual.SEX_LOOKUP)
-_SEX_TO_EXPORTED_VALUE['U'] = ''
-
-__AFFECTED_TO_EXPORTED_VALUE = dict(Individual.AFFECTED_STATUS_LOOKUP)
-__AFFECTED_TO_EXPORTED_VALUE['U'] = ''
-
-
 def _get_record_family_id(record):
     # family id will be in different places in the json depending on whether it comes from a flat uploaded file or from the nested individual object
     return record.get(JsonConstants.FAMILY_ID_COLUMN) or record.get('family', {})['familyId']

seqr/views/utils/pedigree_info_utils.py

@@ -134,7 +134,7 @@ def _parse_sex(sex):
         return 'F'
     elif sex == '0' or not sex or sex.lower() in {'unknown', 'prefer_not_answer'}:
         return 'U'
-    return None
+    return Individual.SEX_LOOKUP.get(sex)
 
 
 def _parse_affected(affected):
@@ -292,15 +292,15 @@ def validate_fam_file_records(project, records, fail_on_warnings=False, errors=N
         # check proband relationship has valid gender
         if r.get(JsonConstants.PROBAND_RELATIONSHIP) and r.get(JsonConstants.SEX_COLUMN):
             invalid_choices = {}
-            if r[JsonConstants.SEX_COLUMN] == Individual.SEX_MALE:
+            if r[JsonConstants.SEX_COLUMN] in Individual.MALE_SEXES:
                 invalid_choices = Individual.FEMALE_RELATIONSHIP_CHOICES
-            elif r[JsonConstants.SEX_COLUMN] == Individual.SEX_FEMALE:
+            elif r[JsonConstants.SEX_COLUMN] in Individual.FEMALE_SEXES:
                 invalid_choices = Individual.MALE_RELATIONSHIP_CHOICES
             if invalid_choices and r[JsonConstants.PROBAND_RELATIONSHIP] in invalid_choices:
                 message = 'Invalid proband relationship "{relationship}" for {individual_id} with given gender {sex}'.format(
                     relationship=Individual.RELATIONSHIP_LOOKUP[r[JsonConstants.PROBAND_RELATIONSHIP]],
                     individual_id=individual_id,
-                    sex=dict(Individual.SEX_CHOICES)[r[JsonConstants.SEX_COLUMN]]
+                    sex=Individual.SEX_LOOKUP[r[JsonConstants.SEX_COLUMN]]
                 )
                 if clear_invalid_values:
                     r[JsonConstants.PROBAND_RELATIONSHIP] = None
@@ -310,8 +310,8 @@ def validate_fam_file_records(project, records, fail_on_warnings=False, errors=N
 
         # check maternal and paternal ids for consistency
         for parent in [
-            ('father', JsonConstants.PATERNAL_ID_COLUMN, 'M'),
-            ('mother', JsonConstants.MATERNAL_ID_COLUMN, 'F')
+            ('father', JsonConstants.PATERNAL_ID_COLUMN, Individual.MALE_SEXES),
+            ('mother', JsonConstants.MATERNAL_ID_COLUMN, Individual.FEMALE_SEXES)
         ]:
             _validate_parent(r, *parent, individual_id, family_id, records_by_id, warnings, errors, clear_invalid_values)
 
@@ -345,7 +345,7 @@ def get_valid_hpo_terms(records, additional_feature_columns=None):
     return set(HumanPhenotypeOntology.objects.filter(hpo_id__in=all_hpo_terms).values_list('hpo_id', flat=True))
 
 
-def _validate_parent(row, parent_id_type, parent_id_field, expected_sex, individual_id, family_id, records_by_id, warnings, errors, clear_invalid_values):
+def _validate_parent(row, parent_id_type, parent_id_field, expected_sexes, individual_id, family_id, records_by_id, warnings, errors, clear_invalid_values):
     parent_id = row.get(parent_id_field)
     if not parent_id:
         return
@@ -367,8 +367,8 @@ def _validate_parent(row, parent_id_type, parent_id_field, expected_sex, individ
     # is father male and mother female?
     if JsonConstants.SEX_COLUMN in records_by_id[parent_id]:
         actual_sex = records_by_id[parent_id][JsonConstants.SEX_COLUMN]
-        if actual_sex != expected_sex:
-            actual_sex_label = dict(Individual.SEX_CHOICES)[actual_sex]
+        if actual_sex not in expected_sexes:
+            actual_sex_label = Individual.SEX_LOOKUP[actual_sex]
             errors.append(
                 "%(parent_id)s is recorded as %(actual_sex_label)s sex and also as the %(parent_id_type)s of %(individual_id)s" % locals())
 

ui/pages/Project/components/FamilyTable/IndividualRow.jsx

@@ -65,6 +65,15 @@ const IndividualContainer = styled.div`
 
 const PaddedRadioButtonGroup = styled(RadioButtonGroup)`
   padding: 10px;
+  
+  .button {
+    padding-left: 1em !important;
+    padding-right: 1em !important;
+    
+    &.labeled .label {
+      margin-left: 0px !important;
+    }
+  }
 `
 
 const POPULATION_MAP = {
@@ -414,6 +423,8 @@ const CASE_REVIEW_FIELDS = [
   ...INDIVIDUAL_FIELDS,
 ]
 
+const INDIVIDUAL_FIELD_CONFIG_SEX = INDIVIDUAL_FIELD_CONFIGS[INDIVIDUAL_FIELD_SEX]
+
 const NON_CASE_REVIEW_FIELDS = [
   {
     component: OptionFieldView,
@@ -430,6 +441,13 @@ const NON_CASE_REVIEW_FIELDS = [
       isVisible: caseReviewStatus === CASE_REVIEW_STATUS_MORE_INFO_NEEDED,
     }),
   },
+  {
+    field: INDIVIDUAL_FIELD_SEX,
+    fieldName: INDIVIDUAL_FIELD_CONFIG_SEX.label,
+    isEditable: false,
+    component: OptionFieldView,
+    tagOptions: INDIVIDUAL_FIELD_CONFIG_SEX.formFieldProps.options,
+  },
   ...[
     INDIVIDUAL_FIELD_ANALYTE_TYPE,
     INDIVIDUAL_FIELD_PRIMARY_BIOSAMPLE,

ui/pages/Project/selectors.js

@@ -12,6 +12,7 @@ import {
   INDIVIDUAL_HAS_DATA_FIELD,
   MME_TAG_NAME,
   TISSUE_DISPLAY,
+  SIMPLIFIED_SEX_LOOKUP,
 } from 'shared/utils/constants'
 import { toCamelcase, toSnakecase, snakecaseToTitlecase } from 'shared/utils/stringUtils'
 
@@ -639,8 +640,8 @@ export const getParentOptionsByIndividual = createSelector(
     ...individuals.reduce((indAcc, { individualGuid }) => ({
       ...indAcc,
       [individualGuid]: {
-        M: individuals.filter(i => i.sex === 'M' && i.individualGuid !== individualGuid).map(individualOption),
-        F: individuals.filter(i => i.sex === 'F' && i.individualGuid !== individualGuid).map(individualOption),
+        M: individuals.filter(i => SIMPLIFIED_SEX_LOOKUP[i.sex] === 'M' && i.individualGuid !== individualGuid).map(individualOption),
+        F: individuals.filter(i => SIMPLIFIED_SEX_LOOKUP[i.sex] === 'F' && i.individualGuid !== individualGuid).map(individualOption),
       },
     }), {}),
   }), {}),

ui/pages/SummaryData/components/IndividualMetadata.jsx

@@ -34,7 +34,7 @@ const CORE_COLUMNS = [
   { name: 'paternal_id', secondaryExportColumn: 'paternal_guid' },
   { name: 'maternal_id', secondaryExportColumn: 'maternal_guid' },
   { name: 'proband_relationship' },
-  { name: 'sex' },
+  { name: 'sex', format: ({ sex, sex_detail: sexDetail }) => (sexDetail ? `${sex} (${sexDetail})` : sex) },
   { name: 'ancestry' },
   { name: 'affected_status' },
   { name: 'hpo_present', style: { minWidth: '400px' } },