{% extends "layout_bs4.html" %} {% from "cases/collapsible_actionbar.html" import action_bar, research_modal, rerun_modal %} {% from "utils.html" import comments_panel, activity_panel %} {% from "cases/utils.html" import individuals_table %} {% from "cases/case_ideograms.html" import case_ideograms %} {% from "variants/utils.html" import tier_cell %} {% 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() }}
{{ candidates_list() }}
{{ related_causatives_list() }}
{% if case.track == 'cancer' %}
{{ cancer_individuals_table() }}
{% else %}
{{ individuals_table(case, institute, tissue_types) }}
{% endif %}
{{ roh_panel() }}
{% if case.madeline_info and case.individuals|length > 1 %} {{ pedigree_panel() }} {% else %}

No pedigree picture available.

{% endif %}
{{ synopsis_panel() }} {{ comments_panel(institute, case, current_user, comments) }}
{{ cohort_panel() }}
{{ diagnosis_panel() }}
{{ phenotype_groups_panel() }}
{{ phenotypes_panel() }}
{{ genepanels_table() }}
{{ hpo_genelist_panel() }}
{% 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.vcf_files.vcf_cancer %} Clinical SNV and INDELs {% endif %} {% if case.vcf_files.vcf_cancer_sv %} Clinical structural variants {% endif %}
{% if case.is_research %}
Research SNV and INDELs Research structural variants
{% endif %} {% endmacro %} {% macro related_causatives_list() %}
Matching causatives from other cases
{% endmacro %} {% macro cancer_individuals_table() %}
Individuals
{% for ind in case.individuals %} {% endfor %}
Sample Tumor Type Phenotype Sequencing TMB MSI Tumor Purity Tissue
{{ ind.display_name }} {{ ind.tumor_type or 'Unknown'}} {{ ind.phenotype_human }} {{ ind.analysis_type|upper }} {{ ind.tmb or 'N/A' }} {{ ind.msi or 'N/A' }} {{ ind.tumor_purity or 'N/A' }} {{ ind.tissue_type or 'unknown' }}
{% endmacro %} {% macro pedigree_panel() %}
Pedigree
{{ case.madeline_info|safe }}
{% 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 candidates_list() %}
Causative variants
Pinned variants
{% endmacro %} {% macro diagnosis_panel() %}
Diagnosis phenotypes
{{ diagnosis_form('phenotype') }}
Diagnosis genes
{{ diagnosis_form('gene') }}
{% endmacro %} {% macro diagnosis_form(type) %}
{% endmacro %} {% macro cohort_panel() %}
Cohort tag
{% 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 phenotype_groups_panel() %}
Phenotype groups
{% set url = 'http://hpo.jax.org/app/browse/term/HP:0000018' %}
Phenotype terms (HPO web)
{% endmacro %} {% macro hpo_group_item(hpo_term) %}
  • {{ hpo_term.feature }} {{ hpo_term.phenotype_id }}
    {{ remove_form(url_for('cases.phenotypes', institute_id=institute._id, case_name=case.display_name, phenotype_id=hpo_term.phenotype_id, is_group='yes')) }}
  • {% endmacro %} {% macro phenotypes_panel() %}
    Added phenotypes
    {% if config.PHENOMIZER_USERNAME %}
    {% endif %}
    Add gene to the dynamic panel
    {% endmacro %} {% macro hpo_item(hpo_term) %}
  • {{ hpo_term.feature }} {{ hpo_term.phenotype_id }}
  • {% endmacro %} {% macro remove_form(url, hidden_input=None, button_name=None, button_value=None) %}
    {% if hidden_input %} {% endif %}
    {% endmacro %} {% macro hpo_genelist_panel() %}
    HPO gene panel ({{ case.dynamic_gene_list|length }} genes) {%- if case.dynamic_panel_phenotypes %}, {{ case.dynamic_panel_phenotypes|length }} phenotypes {% endif %}) {% if config.SQLALCHEMY_DATABASE_URI and case.dynamic_gene_list|length > 0 %} Coverage
    {% endif %}
    {% if case.dynamic_gene_list %} {% endif %}
    {% endmacro %} {% macro genepanels_table() %}
    Gene panels
    {% for panel in case.panels %} {% else %} {% endfor %}
    Panel Version Genes
    {{ panel.display_name|truncate(30, True) }} {% if panel.is_default %} Default {% endif %} {{ panel.version }} ({{ panel.updated_at.date() }}) {{ panel.nr_genes }}
    No panels linked to case
    {% endmacro %} {% block scripts %} {{ super() }} {% if case.chromograph_prefixes %} {{ case_ideograms(institute, case) }} {% endif %} {% endblock %}