{% extends "layout_bs4.html" %} {% from "cases/collapsible_actionbar.html" import action_bar, research_modal, rerun_modal %} {% from "utils.html" import comments_panel, activity_panel, pedigree_panel %} {% from "cases/utils.html" import causatives_list, suspects_list, remove_form, matching_causatives %} {% from "cases/individuals_table.html" import cancer_individuals_table, individuals_table %} {% from "cases/phenotype.html" import cohort_panel, diagnosis_phenotypes, diagnosis_genes, phenotype_groups_panel, phenotype_terms_panel, phenotypes_panel %} {% from "cases/gene_panel.html" import genepanels_table, hpo_genelist_panel %} {% from "cases/case_ideograms.html" import case_ideograms %} {% block title %} {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} {% endblock %} {% block css %} {{ super() }} {% endblock %} {% block top_nav %} {{ super() }} {% endblock %} {% block content_main %}
{{ action_bar(institute, case, collaborators) }} {{ case_page() }}
{% endblock %} {% macro case_page() %}

Case: {{case.display_name}}

status: {{case.status}}

{{ variants_buttons() }}
{% if other_causatives|length > 1%}
{{ matching_causatives(other_causatives, institute, case) }}
{% endif %}
{{ causatives_list(causatives, partial_causatives, institute, case) }}
{{ suspects_list(suspects, institute, case, manual_rank_options, cancer_tier_options) }}
{% if case.track == 'cancer' %}
{{ cancer_individuals_table(case, institute, tissue_types) }}
{% else %}
{{ individuals_table(case, institute, tissue_types) }}
{% endif %}
{% if case.madeline_info and case.individuals|length > 1 %} {{ pedigree_panel(case) }} {% else %}

No pedigree picture available.

{% endif %}
{{ synopsis_panel() }} {{ comments_panel(institute, case, current_user, comments) }}
 Diagnoses
{{ diagnosis_phenotypes(case, institute, omim_terms) }}
{{ diagnosis_genes(case, institute, omim_terms) }}
{{ cohort_panel(case, institute, cohort_tags) }}
{{ phenotype_groups_panel(case, institute, hpo_groups) }}
{{ phenotype_terms_panel(case, institute) }}
{{ phenotypes_panel(case, institute, config) }}
{{ genepanels_table(case, institute) }}
{{ hpo_genelist_panel(case, institute, config) }}
{% if case.clinvar_variants %}
{{ clinvar_panel() }}
{% endif %} {% if 'mme_submitter' in current_user.roles %}
{{ matchmaker_panel() }}
{% endif %}
{{activity_panel(events)}}
{{ modal_synopsis() }} {{ rerun_modal(institute, case) }} {{ research_modal(institute, case) }}
{% endmacro %} {% macro variants_buttons() %}
{% if case.vcf_files.vcf_snv %} Clinical SNV and INDELs {% endif %} {% if case.vcf_files.vcf_sv %} Clinical structural variants {% endif %} {% if case.vcf_files.vcf_str %} Clinical STR variants {% endif %} {% if case.smn_tsv %} SMN CN {% endif %} {% if case.vcf_files.vcf_cancer %} Clinical SNV and INDELs {% endif %} {% if case.vcf_files.vcf_cancer_sv %} Clinical structural variants {% endif %}
{% if case.is_research%}
{% if case.track=="cancer" %} Research SNV and INDELs Research structural variants {% else %} Research SNV and INDELs Research structural variants {% endif %}
{% endif %} {% endmacro %} {% macro synopsis_panel() %}
Synopsis
{{ case.synopsis|markdown if case.synopsis else 'Nothing written yet...' }}
{% endmacro %} {% macro roh_panel() %} {% if case.chromograph_prefixes %}
Ideogram, UPD, ROH

{% endif %} {% endmacro %} {% macro modal_synopsis() %}
{% endmacro %} {% macro clinvar_panel() %}
Variants in Clinvar submissions
{% endmacro %} {% macro matchmaker_panel() %}
Matching patients
{% if case.mme_submission %}

This case is in MatchMaker!

Matches
Modify submission

{% else %}

This case is not yet in MatchMaker! Submission form

{% endif %}
  • Include patient gender
  • Include HPO terms
  • Include OMIM diagnoses
  • Share variants
  • Gene names only

{% if case.mme_submission %} {{ modal_mme_delete() }} {% endif %}
{% endmacro %} {% macro modal_mme_delete() %}
{% endmacro %} {% macro remove_form(url, hidden_input=None, button_name=None, button_value=None) %}
{% if hidden_input %} {% endif %}
{% endmacro %} {% block scripts %} {{ super() }} {% if case.chromograph_prefixes %} {{ case_ideograms(institute, case) }} {% endif %} {% endblock %}