scout-browser 4.99.0__py3-none-any.whl → 4.100.1__py3-none-any.whl

scout/server/blueprints/alignviewers/templates/alignviewers/igv_viewer.html

@@ -132,6 +132,16 @@
                         sourceType: 'file'
                       },
                       {% endfor %}
+                      {% for maftrack in minor_allele_frequency_wigs %}
+                      {
+                        type: "wig",
+                        format: 'bw',
+                        name: '{{ maftrack.name }}',
+                        url: '{{ url_for("alignviewers.remote_static", file=maftrack.url) }}',
+                        color: "rgb(60, 60, 140)",
+                        sourceType: 'file'
+                      },
+                      {% endfor %}
                       {% for ptrack in paraphase_alignments %}
                       {
                         type: "alignment",

scout/server/blueprints/cases/controllers.py

@@ -40,7 +40,12 @@ from scout.constants.variant_tags import (
     MANUAL_RANK_OPTIONS,
 )
 from scout.export.variant import export_mt_variants
-from scout.parse.matchmaker import genomic_features, hpo_terms, omim_terms, parse_matches
+from scout.parse.matchmaker import (
+    genomic_features,
+    hpo_terms,
+    omim_terms,
+    parse_matches,
+)
 from scout.server.blueprints.variant.controllers import variant as variant_decorator
 from scout.server.blueprints.variants.controllers import get_manual_assessments
 from scout.server.extensions import (
@@ -61,6 +66,7 @@ from scout.server.utils import (
     case_has_mt_alignments,
     case_has_mtdna_report,
     case_has_rna_tracks,
+    get_case_mito_chromosome,
     institute_and_case,
 )
 from scout.utils.acmg import get_acmg_temperature
@@ -788,11 +794,11 @@ def mt_excel_files(store, case_obj, temp_excel_dir):
 
     # Check if coverage and MT copy number stats are available via chanjo2 or chanjo
     if case_obj.get("chanjo2_coverage"):
-        coverage_stats: Dict[str, dict] = chanjo2.mt_coverage_stats(individuals=samples)
+        coverage_stats: Dict[str, dict] = chanjo2.mt_coverage_stats(case_obj=case_obj)
     elif case_obj.get("chanjo_coverage"):
         coverage_stats: Dict[str, dict] = chanjo_report.mt_coverage_stats(individuals=samples)
 
-    query = {"chrom": "MT"}
+    query = {"chrom": get_case_mito_chromosome(case_obj)}
     mt_variants = list(
         store.variants(case_id=case_obj["_id"], query=query, nr_of_variants=-1, sort_key="position")
     )

scout/server/blueprints/cases/templates/cases/case_report.html

@@ -63,7 +63,7 @@
 </nav>
 
 <div id="container" class="container">
-  <h4>Scout case analysis report</h4> - created on:&nbsp;<strong>{{report_created_at}}</strong> using <strong>Scout v.{{current_scout_version}}</strong><br><br>
+  <h4>Scout case analysis report</h4> - created on:&nbsp;<strong>{{report_created_at}}</strong> using <strong>Scout v{{current_scout_version}}</strong> for genome build <strong>{{case.genome_build }}</strong>.<br><br>
    {{ phenotype_panel() }}
    {{ gene_panels_panel()}}
    {{ causatives_panel()}}
@@ -104,7 +104,7 @@
                 <td>Case created: <strong>{{case.created_at.strftime('%Y-%m-%d')}}</strong></td>
 	              <td>Last updated: <strong>{{case.updated_at.strftime('%Y-%m-%d') if case.updated_at else "n.a." }}</strong></td>
                 {% if case.scout_load_version %}
-                  <td> Loaded with <strong>Scout v.{{case.scout_load_version}}</strong></td>
+                  <td> Loaded with <strong>Scout v{{case.scout_load_version}}</strong></td>
                 {% endif %}
 	            </tr>
 	          </table>
@@ -383,7 +383,7 @@
     {% set duplicated_variants = [] %}
     {% if variants.classified_detailed %}
       {% for variant in variants.classified_detailed|sort(attribute='variant_rank') %}
-        {% if variant['_id'] not in printed_vars %}
+        {% if variant['_id'] not in printed_vars and variant not in variants.dismissed_detailed %}
           {% do printed_vars.append(variant['_id']) %}
           {{ variant_content(variant, loop.index) }}
           <br>
@@ -395,7 +395,7 @@
       No ACMG-classified variants available for this case
     {% endif %}
     {% if variants.classified_detailed and duplicated_variants|length == variants.classified_detailed|length %}
-      All ACMG-classified variants are already described in the previous views
+      All ACMG-classified variants are already described in the other panels
     {% endif %}
   </div>
 </div>
@@ -410,7 +410,7 @@
     {% set duplicated_variants = [] %}
     {% if variants.ccv_classified_detailed %}
       {% for variant in variants.ccv_classified_detailed|sort(attribute='variant_rank') %}
-        {% if variant['_id'] not in printed_vars %}
+        {% if variant['_id'] not in printed_vars and variant not in variants.dismissed_detailed %}
           {% do printed_vars.append(variant['_id']) %}
           {{ variant_content(variant, loop.index) }}
           <br>
@@ -422,7 +422,7 @@
       No ClinGen-CGC-VICC-classified variants available for this case
     {% endif %}
     {% if variants.ccv_classified_detailed and duplicated_variants|length == variants.ccv_classified_detailed|length %}
-      All ClinGen-CGC-VICC-classified variants are already described in the previous views
+      All ClinGen-CGC-VICC-classified variants are already described in the other panels
     {% endif %}
   </div>
 </div>
@@ -437,7 +437,7 @@
     {% set duplicated_variants = [] %}
     {% if variants.tagged_detailed %}
       {% for variant in variants.tagged_detailed|sort(attribute='variant_rank') %}
-        {% if variant['_id'] not in printed_vars %}
+        {% if variant['_id'] not in printed_vars and variant not in variants.dismissed_detailed %}
           {% do printed_vars.append(variant['_id']) %}
           {{ variant_content(variant, loop.index) }}
           <br>
@@ -461,7 +461,7 @@
       No tagged variants for this case
     {% endif %}
     {% if (variants.tagged_detailed or variants.tier_detailed) and duplicated_variants|length == (variants.tagged_detailed|length+variants.tier_detailed|length) %}
-      All tagged variants are already described in the previous views
+      All tagged variants are already described in the other panels
     {% endif %}
   </div>
 </div>
@@ -500,7 +500,7 @@
     {% set duplicated_variants = [] %}
     {% if variants.commented_detailed %}
       {% for variant in variants.commented_detailed|sort(attribute='variant_rank') %}
-        {% if variant['_id'] not in printed_vars %}
+        {% if variant['_id'] not in printed_vars and variant not in variants.dismissed_detailed %}
           {% do printed_vars.append(variant['_id']) %}
           {% if variant.category == 'snv' %}
             {{ sn_variant_content(variant, loop.index) }}
@@ -520,7 +520,7 @@
       No commented variants for this case
     {% endif %}
     {% if variants.commented_detailed and duplicated_variants|length == variants.commented_detailed|length %}
-      All commented variants are already described in the previous views
+      All commented variants are already described in the other panels
     {% endif %}
   </div>
 </div>
@@ -845,7 +845,8 @@
                 <th class="w-5"></th>
                 <th class="w-25"><strong>Variant</strong></th>
                 <th class="w-5"><strong>Category</strong></th>
-  	            <th class="w-25"><strong>Genes</strong></th>
+  	            <th class="w-20"><strong>Genes</strong></th>
+                <th class="w-5"><strong>Classification</strong></th>
                 <th class="w-45"><strong>Dismissed description</strong></th>
             </tr>
           </thead>
@@ -867,7 +868,14 @@
               <td style="width:15%;"
                 {{ dismissed_gene_list(variant) }}
               </td>
-
+              <td>
+                {% if variant.acmg_classification %}
+                  <span class="badge rounded-pill bg-{{variant.acmg_classification['color'] if variant.acmg_classification['color'] else 'secondary'}}" title="{{variant.acmg_classification['code']}}">{{variant.acmg_classification['short'] }}</span>
+                {% endif %}
+                {% if variant.ccv_classification %}
+                  <span class="badge rounded-pill bg-{{variant.ccv_classification['color'] if variant.ccv_classification['color'] else 'secondary'}}" title="{{variant.ccv_classification['code']}}">{{variant.ccv_classification['short'] }}</span>
+                {% endif %}
+              </td>
               <td rowspan="2">
                 <ul>
                   {% for reason in variant.dismiss_variant if not reason == "Select a tag"  %}
@@ -1531,7 +1539,11 @@
   <td>
     {% if variant.acmg_classification %}
       <span class="badge rounded-pill bg-{{variant.acmg_classification['color'] if variant.acmg_classification['color'] else 'secondary'}}" title="{{variant.acmg_classification['code']}}">{{variant.acmg_classification['short'] }}</span>
-    {% elif variant.manual_rank %}
+    {% endif %}
+    {% if variant.ccv_classification%}
+      <span class="badge rounded-pill bg-{{variant.ccv_classification['color'] if variant.ccv_classification['color'] else 'secondary'}}" title="{{variant.ccv_classification['code']}}">{{variant.ccv_classification['short'] }}</span>
+    {% endif%}
+    {% if variant.manual_rank %}
       <span class="badge rounded-pill bg-secondary" title="Manual rank">{{ manual_rank_options[variant.manual_rank]['label'] }}</span>
     {% else %}
       -

scout/server/blueprints/cases/templates/cases/chanjo2_form.html

@@ -1,6 +1,6 @@
 {% macro chanjo2_report_form(institute_obj, case_obj, panel_name, report_type, hgnc_ids, link_text, link_class = "link-primary") %}
 
-  {% set form_name = "chanjo2_"+panel_name+"_"+report_type %}
+  {% set form_name = "chanjo2_" ~ panel_name ~ "_" ~ report_type %}
   {% set form_action = config.CHANJO2_URL+"/"+report_type %}
   {% set build = "GRCh38" if "38" in case_obj.get("genome_build", "37") else "GRCh37" %}
   {% set default_level = institute_obj.coverage_cutoff %}

scout/server/blueprints/cases/templates/cases/collapsible_actionbar.html

@@ -196,7 +196,7 @@
   <div href="#" class="bg-dark list-group-item text-white" data-bs-toggle="tooltip" title="Scout version used for loading the case" data-bs-placement="right">
     <div class="d-flex w-100 justify-content-start align-items-center">
       <span class="fa fa-gear fa-fw me-3"></span>
-      <span class="menu-collapsed">v.{{ case.scout_load_version }}</span>
+      <span class="menu-collapsed">v{{ case.scout_load_version }}</span>
     </div>
   </div>
 {% endif %}

scout/server/blueprints/cases/templates/cases/gene_panel.html

@@ -18,7 +18,7 @@
           {% for panel in case.panels %}
             <tr {% if panel.is_default %} class="bg-info" {% endif %}>
               <td>
-                <a {% if panel.is_default %} class="text-white" {% endif %} href="{{ url_for('panels.panel', panel_id=panel.panel_id, case_id=case._id, institute_id=institute._id) }}">
+                <a {% if panel.is_default %} class="text-white" {% endif %} href="{{ url_for('panels.panel', panel_id=panel.panel_id, case_id=case._id, institute_id=institute._id) }}" target="_blank" rel="noopener">
                   {{ panel.display_name|truncate(30, True) }}
                 </a>
                 {% if panel.removed %}

scout/server/blueprints/cases/templates/cases/utils.html

@@ -313,6 +313,22 @@
 
       {{ display_genes|join(", ") }}
 
+    {% elif variant.category == "outlier" %}
+      {{ variant.sub_category|upper }} - {% if variant.genes %}
+        {% for gene in variant.genes %}
+           {% if gene.hgnc_symbol %}
+             {{ gene.hgnc_symbol }}
+           {% else %}
+             {{gene.hgnc_id}}
+           {% endif %}
+        {% endfor %} - {%  if variant.sub_category == "splicing" %}
+          {{ variant.delta_psi }}Δψ  {{ variant.potential_impact }} - fs {{ variant.causes_frameshift }}
+        {% else %}
+          {{ variant.l2fc }}{% if variant.l2fc > 0 %}&uarr;{% elif variant.l2fc < 0 %}&darr;{% endif %}
+        {% endif %}
+      {% else %}
+        {{ variant.gene_name_orig }}
+      {% endif %}
     {% else %} <!-- structural variants -->
       {{ variant.sub_category|upper }}({{ variant.chromosome }}{{ variant.cytoband_start }}-{{ variant.end_chrom }}{{ variant.cytoband_end }})
     {% endif %}
@@ -335,6 +351,9 @@
                    case_name=case.display_name,
                    variant_id=variant._id) }}' target='_blank'>
     {% endif %}
+  {% elif variant.category == "outlier" %}
+    <a href='{{ url_for('omics_variants.outliers',
+       institute_id=variant.institute, case_name=case.display_name) }}' target='_blank'>
   {% else %} <!-- structural variants -->
     <a href='{{ url_for('variant.sv_variant',
                               institute_id=variant.institute,

scout/server/blueprints/clinvar/controllers.py

@@ -619,8 +619,12 @@ def remove_item_from_submission(submission: str, object_type: str, subm_variant_
     if object_type == "variant_data":
         variant_id: str = subm_variant_id.split("_")[-1]
         variant_obj: dict = store.variant(document_id=variant_id)
+        if not variant_obj:
+            return
+        case_obj = store.case(case_id=variant_obj["case_id"])
+        if not case_obj:
+            return
         institute_obj: dict = store.institute(institute_id=variant_obj["institute"])
-        case_obj: dict = store.case(case_id=variant_obj["case_id"])
         user_obj: dict = store.user(user_id=current_user._id)
         for category in ["case", "variant"]:
             store.create_event(

scout/server/blueprints/clinvar/templates/clinvar/clinvar_submissions.html

@@ -126,13 +126,19 @@
             </thead>
             <tbody>
               {% set var_key_name = {} %}
+
               {% for subm_variant in subm_obj.variant_data  %} <!-- loop over the submitted variants-->
+                {% set case_name = subm_obj.cases[subm_variant.case_id] %}
                 <tr>
                   <td>{{loop.index}}</td>
                     {% if subm_variant.category == 'sv' %}
                       {% do var_key_name.update( {subm_variant.local_id : '_'.join([subm_variant.var_type, subm_variant.chromosome, subm_variant.breakpoint1 or subm_variant.outer_start or ""]) }) %}
                       <td>
-                        <a href="{{ url_for('variant.sv_variant', institute_id=institute._id, case_name=subm_obj.cases[subm_variant.case_id], variant_id=subm_variant.local_id) }}" target="_blank" rel="noopener"><strong>{{var_key_name[subm_variant.local_id]|truncate(25,true,'..')}}</strong></a>
+                        {% if "N/A" not in case_name %}
+                          <a href="{{ url_for('variant.sv_variant', institute_id=institute._id, case_name=case_name, variant_id=subm_variant.local_id) }}" target="_blank" rel="noopener"><strong>{{var_key_name[subm_variant.local_id]|truncate(25,true,'..')}}</strong></a>
+                        {% else %}
+                          {{ var_key_name[subm_variant.local_id]|truncate(25,true,'..') }} (N/A)
+                        {% endif %}
                       </td>
                       <td><button id="{{subm_variant._id}}" type="button" class="btn btn-primary btn-xs var_btn"><span class="fa fa-search-plus" aria-hidden="true"></span></button></td>
                       <td><div class="badge bg-warning">SV</div></td>
@@ -143,21 +149,27 @@
                         {% do var_key_name.update({subm_variant.local_id : '_'.join([subm_variant.chromosome, subm_variant.start, subm_variant.ref[0:5], subm_variant.alt[0:5]]) }) %}
                       {% endif %}
                       <td>
-                        <a href="{{ url_for('variant.variant', institute_id=institute._id, case_name=subm_obj.cases[subm_variant.case_id], variant_id=subm_variant.local_id) }}" target="_blank" rel="noopener"><strong>{{var_key_name[subm_variant.local_id]|truncate(25,true,'..')}}</strong></a>
+                        {% if "N/A" not in case_name %}
+                          <a href="{{ url_for('variant.variant', institute_id=institute._id, case_name=case_name, variant_id=subm_variant.local_id) }}" target="_blank" rel="noopener"><strong>{{var_key_name[subm_variant.local_id]|truncate(25,true,'..')}}</strong></a>
+                        {% else %}
+                          {{ var_key_name[subm_variant.local_id]|truncate(25,true,'..') }} (N/A)
+                        {% endif %}
                       </td>
                       <td><button id="{{subm_variant._id}}" type="button" class="btn btn-primary btn-xs var_btn"><span class="fa fa-search-plus" aria-hidden="true"></span></button></td>
                       <td><div class="badge bg-success">SNV</div></td>
                     {% endif %}
                   </td>
-                  <td><a href="{{ url_for('cases.case', institute_id=institute._id, case_name=subm_obj.cases[subm_variant.case_id]) }}" target="_blank" rel="noopener">{{subm_obj.cases[subm_variant.case_id]}}</a></td>
+                  <td>{{ case_link(institute_id=institute._id, case_name=case_name) }}</td>
                   <td>{{subm_variant.ref_seq or '-'}}</td>
                   <td>{{subm_variant.gene_symbol or '-'}}</td>
                   <td>{{subm_variant.hgvs|truncate(100,true,'..') or '-'}}</td>
                   <td>{{subm_variant.clinsig}}</td>
                   <td>{{subm_variant.added_by or "N/A"}}</td>
-                  <form id="delete_variant_{{subm_variant._id}}" action="{{ url_for('clinvar.clinvar_delete_object', submission=subm_obj._id, object_type='variant_data') }}" method="POST">
-                    <td><button type="submit" name="delete_object" value="{{subm_variant._id}}" class="btn btn-danger btn-xs"><span class="fa fa-trash" aria-hidden="true"></span></button></td>
-                  </form>
+                  <td>
+                    <form id="delete_variant_{{subm_variant._id}}" action="{{ url_for('clinvar.clinvar_delete_object', submission=subm_obj._id, object_type='variant_data') }}" method="POST">
+                      <button type="submit" name="delete_object" value="{{subm_variant._id}}" class="btn btn-danger btn-xs"><span class="fa fa-trash" aria-hidden="true"></span></button>
+                    </form>
+                  </td>
                 </tr>
                 <tr>
                   <td colspan=11>
@@ -191,9 +203,9 @@
               <thead>
                 <tr>
                   <th></th>
-                  <th>Individual ID</th>
+                  <th>Individual</th>
                   <th></th>
-                  <th>Case ID</th>
+                  <th>Case</th>
                   <th>Variant</th>
                   <th>Allele origin</th>
                   <th></th>
@@ -209,12 +221,14 @@
                     </td>
                     </form>
                     <td><button id="{{case._id}}" type="button" class="btn btn-primary btn-xs cd_btn"><span class="fa fa-search-plus" aria-hidden="true"></span></button></td>
-                    <td><a href="{{ url_for('cases.case', institute_id=institute._id, case_name=subm_obj.cases[case.case_id]) }}" target="_blank" rel="noopener">{{subm_obj.cases[case.case_id]}}</a></td>
+                    <td>{{ case_link(institute_id=institute._id, case_name=subm_obj.cases[case.case_id]) }}</td>
                     <td>{{var_key_name[case.linking_id]|truncate(100,true,'..')}}</td>
                     <td>{{case.allele_origin}}</td>
-                    <form id="delete_casedata_{{case._id}}" action="{{ url_for('clinvar.clinvar_delete_object', submission=subm_obj._id, object_type='case_data') }}" method="POST">
-                      <td><button type="submit" name="delete_object" value="{{case._id}}" class="btn btn-danger btn-xs"><span class="fa fa-trash" aria-hidden="true"></span></button></td>
-                    </form>
+                    <td>
+                      <form id="delete_casedata_{{case._id}}" action="{{ url_for('clinvar.clinvar_delete_object', submission=subm_obj._id, object_type='case_data') }}" method="POST">
+                        <button type="submit" name="delete_object" value="{{case._id}}" class="btn btn-danger btn-xs"><span class="fa fa-trash" aria-hidden="true"></span></button>
+                      </form>
+                    </td>
                   </tr>
                   <tr>
                     <td colspan=8>
@@ -242,6 +256,14 @@
 </div>
 {% endmacro %}
 
+{% macro case_link(institute_id, case_name) %}
+{% if "N/A" in case_name %}
+  {{ case_name }}
+{% else %}
+  <a href="{{ url_for('cases.case', institute_id=institute_id, case_name=case_name) }}" target="_blank">{{case_name}}</a>
+{% endif %}
+{% endmacro %}
+
 {% macro action_modal(action_type, subm_id) %}
 <div class="modal fade" id="{{action_type}}Modal_{{subm_id}}" tabindex="-1">
   <div class="modal-dialog">

scout/server/blueprints/clinvar/templates/clinvar/multistep_add_variant.html

@@ -81,7 +81,7 @@
                   </div>
                   <div class="my-2 mx-lg-2" style="width:30%; display: inline">{{variant_data.var_form.assertion_method_cit_id(class="bg-white")}}</div>
                   </div>
-
+                <input type="button" name="previous" class="previous action-button-previous" value="Previous"/>
                 <input type="button" name="next" class="next action-button" value="Next"/>
               </fieldset>
               <fieldset data-step="3">

scout/server/blueprints/diagnoses/static/diagnoses.js

@@ -135,7 +135,14 @@ function initialiseTable(data) {
     $('#diagnoses_table').DataTable({
         data: data,
         paging: true,
-        dom: 'Brtip',
+        layout: {
+					topStart: 'buttons',
+					topEnd: {
+							search: {
+									placeholder: 'Filter further...'
+							}
+					}
+				},
         buttons: [
             {
                 extend: 'excelHtml5',

scout/server/blueprints/institutes/static/variants_list_scripts.js

@@ -1,7 +1,15 @@
 $(document).ready(function() {
   $('#variants_table').DataTable( {
       paging: false,
-      dom: 'Bfrtip',
+			searching: true,
+			layout: {
+				topStart: 'buttons',
+				topEnd: {
+            search: {
+                placeholder: 'Search'
+            }
+        }
+			},
       buttons: [
           'copyHtml5',
           'excelHtml5',

scout/server/blueprints/institutes/templates/overview/institute_sidebar.html

@@ -51,7 +51,15 @@
           </div>
       </a>
 
-    <!-- Variant filters -->
+     <!-- MME data menu item -->
+      <a href="{{ url_for('mme.mme_submissions', institute_id=institute._id) }}" class="bg-dark list-group-item list-group-item-action flex-column align-items-start">
+          <div class="d-flex w-100 justify-content-start align-items-center">
+              <span class="fas fa-people-arrows me-3"></span>
+              <span class="menu-collapsed">MME submissions</span>
+          </div>
+      </a>
+
+     <!-- Variant filters -->
       <a href="{{ url_for('overview.filters', institute_id=institute._id) }}" class="bg-dark list-group-item list-group-item-action flex-column align-items-start">
           <div class="d-flex w-100 justify-content-start align-items-center">
               <span class="fa fa-filter me-3"></span>

scout/server/blueprints/mme/__init__.py

@@ -0,0 +1 @@
+from .views import mme_bp

scout/server/blueprints/mme/controllers.py

@@ -0,0 +1,18 @@
+from typing import List
+
+from scout.server.extensions import store
+
+
+def institute_mme_cases(institute_id: str) -> List[dict]:
+    """Retrieves all cases for a given institute with an active MatchMaker Exchange submission."""
+    institute_mme_events = store.institute_events_by_verb(
+        category="case", institute_id=institute_id, verb="mme_add"
+    )
+    unique_case_ids = set([event["case"] for event in institute_mme_events])
+    mme_cases = []
+    for case_id in unique_case_ids:
+        case_obj = store.case(case_id=case_id)
+        if not case_obj or not case_obj.get("mme_submission"):
+            continue
+        mme_cases.append(case_obj)
+    return mme_cases

scout/server/blueprints/mme/templates/mme/mme_submissions.html

@@ -0,0 +1,153 @@
+{% extends "layout.html" %}
+{% from "overview/institute_sidebar.html" import institute_actionbar %}
+{% from "utils.html" import db_table_external_scripts, db_table_external_stylesheets %}
+
+{% block title %}
+{{ super() }} - Institutes
+{% endblock %}
+
+{% block css %}
+{{ super() }}
+ {{ db_table_external_stylesheets() }}
+{% endblock %}
+
+{% block top_nav %}
+  {{ super() }}
+  <li class="nav-item">
+    <a class="nav-link" href="{{ url_for('cases.index') }}">Institutes</a>
+  </li>
+  <li class="nav-item">
+    <a class="nav-link" href="{{ url_for('overview.cases', institute_id=institute._id) }}">{{ institute.display_name }}</a>
+  </li>
+  <li class="nav-item active d-flex align-items-center">
+    <span class="navbar-text">Cases in MatchMaker Exchange</span>
+  </li>
+{% endblock %}
+
+{% block content_main %}
+<div class="container-float">
+  <div class="row mt-3" id="body-row"> <!--sidebar and main container are on the same row-->
+    <div class="col">
+      {{ mme_submitted() }}
+    </div>
+  </div>
+</div>
+{% endblock %}
+
+{% macro mme_submitted() %}
+<table class="table table-bordered table-striped" id="mmeTable">
+  <thead>
+    <tr>
+      <th>Case Name</th>
+      <th>Synopsis</th>
+      <th>Status</th>
+      <th>Case Assignees</th>
+      <th>MME Submission Updated</th>
+      <th>MME Patient(s)</th>
+      <th>MME Phenotype Features</th>
+      <th>MME Genomic Features</th>
+    </tr>
+  </thead>
+  <tbody>
+    {% for case in mme_cases %}
+      <tr>
+        <td>
+          <a class="me-2" href="{{ url_for('cases.case', institute_id=case.owner, case_name=case.display_name) }}" target="_blank" rel="noopener">
+          {{ case.display_name }}
+          </a>
+        </td>
+        <td class="synopsis-cell" style="max-width: 300px;">
+          {% set collapse_id = 'collapse-' + case._id %}
+          {% set max_chars = 300 %}
+
+          {% if case.synopsis|length > max_chars %}
+            <div>
+              {{ case.synopsis[:max_chars] }}…
+            </div>
+
+            <a
+              class="btn btn-link p-0"
+              data-bs-toggle="collapse"
+              href="#{{ collapse_id }}"
+              role="button"
+              aria-expanded="false"
+              aria-controls="{{ collapse_id }}"
+            >More…</a>
+
+            <div class="collapse mt-1" id="{{ collapse_id }}">
+              <div class="card card-body p-2">
+                {{ case.synopsis }}
+              </div>
+            </div>
+          {% else %}
+            {{ case.synopsis }}
+          {% endif %}
+        </td>
+        <td>{{ case.status }}</td>
+        <td>
+          {% for assignee in case.assignees %}
+            <div>{{ assignee }}</div>
+          {% endfor %}
+        </td>
+        <td>
+          {{ case.mme_submission.updated_at.strftime('%Y-%m-%d %H:%M') }}
+        </td>
+        <td>
+          {% for patient in case.mme_submission.patients %}
+            <div>
+              <strong>{{ patient.label }}</strong> ({{ patient.sex }})<br>
+              <small>Contact: {{ patient.contact.name }} - <a href="{{ patient.contact.href }}">{{ patient.contact.href }}</a></small>
+            </div>
+          {% endfor %}
+        </td>
+        <td>
+          {% for disorder in case.mme_submission.disorders %}
+            <div>{{ disorder.label }} ({{ disorder.id }})</div>
+          {% endfor %}
+        </td>
+        <td>
+          {% for patient in case.mme_submission.patients %}
+            {% for gf in patient.genomicFeatures %}
+              <div>
+                <strong>{{ gf.gene.id }}</strong><br>
+                {% if gf.variant %}
+                  Chr{{ gf.variant.referenceName }}:
+                  {{ gf.variant.start|human_longint|safe }}-{{ gf.variant.end|human_longint|safe }}<br>
+                  {{ gf.variant.referenceBases }} → {{ gf.variant.alternateBases }}<br>
+                  Assembly: {{ gf.variant.assembly }}<br>
+                  Zygosity: {{ gf.zygosity }}
+                {% endif %}
+              </div>
+              <hr>
+            {% endfor %}
+          {% endfor %}
+        </td>
+      </tr>
+    {% endfor %}
+  </tbody>
+</table>
+{% endmacro %}
+
+
+{% block scripts %}
+  {{ super() }}
+    {{ db_table_external_scripts() }}
+  <script>
+    $(document).ready(function () {
+    $('#mmeTable').DataTable({
+      paging: true,
+      searching: true,
+      ordering: true,
+      responsive: true,
+      language: {
+        search: "Search all fields:",
+        lengthMenu: "Show _MENU_ entries",
+        info: "Showing _START_ to _END_ of _TOTAL_ cases",
+      },
+      columnDefs: [
+        { orderable: false, targets: [3, 5, 6, 7] }  // Disable sorting for multi-line complex columns
+      ]
+    });
+  });
+  </script>
+{% endblock %}

scout/server/blueprints/mme/views.py

@@ -0,0 +1,34 @@
+import logging
+
+from flask import (
+    Blueprint,
+    render_template,
+    url_for,
+)
+
+from scout.server.extensions import store
+from scout.server.utils import institute_and_case
+
+from . import controllers
+
+LOG = logging.getLogger(__name__)
+
+mme_bp = Blueprint(
+    "mme",
+    __name__,
+    template_folder="templates",
+    static_folder="static",
+    static_url_path="/mme/static",
+)
+
+
+@mme_bp.route("/<institute_id>/mme_submissions", methods=["GET"])
+def mme_submissions(institute_id: str):
+    """Retrieve all cases for an institute with associated a MME submission."""
+
+    institute_obj = institute_and_case(store, institute_id)
+    data = {
+        "institute": institute_obj,
+        "mme_cases": controllers.institute_mme_cases(institute_id=institute_id),
+    }
+    return render_template("mme/mme_submissions.html", **data)