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index.html

@@ -17,7 +17,7 @@
         <div class="logo-badge">
           <div class="pulse-dot"></div>
           <span class="logo-title">MVA SYNDROME</span>
-          <span class="logo-sub">5D GENOMIC STUDIO</span>
+          <span class="logo-sub">MULTI-DIMENSIONAL GENOMIC STUDIO</span>
         </div>
         <div class="patient-badge">
           <span class="patient-label">PROBAND:</span>
@@ -67,6 +67,12 @@
       <button class="nav-tab" data-tab="tab-syndromic-diff">
         <span class="tab-icon">🩺</span> Phenotype Differential Matrix
       </button>
+      <button class="nav-tab" data-tab="tab-acmg-matrix">
+        <span class="tab-icon">🧪</span> ACMG Variant Classification
+      </button>
+      <button class="nav-tab" data-tab="tab-therapeutic-targets">
+        <span class="tab-icon">💊</span> Precision Oncology Targets
+      </button>
       <button class="nav-tab" data-tab="tab-mosaic-strat">
         <span class="tab-icon">⚡</span> Mosaic Allelic Stratification
       </button>
@@ -80,7 +86,7 @@
         <span class="tab-icon">🔬</span> Mosaicism & VAF Spectrum
       </button>
       <button class="nav-tab" data-tab="tab-wgs">
-        <span class="tab-icon">📊</span> WGS Sequencing & Flowcells
+        <span class="tab-icon">📊</span> 4-Lane Sequencing QC Audit
       </button>
       <button class="nav-tab" data-tab="tab-pathway">
         <span class="tab-icon">⚙️</span> Mitotic Checkpoint Pathway
@@ -246,129 +252,7 @@
       </div>
     </section>
 
-    <!-- Tab 3: Mosaicism & VAF Spectrum -->
-    <section id="tab-mosaic" class="tab-content">
-      <div class="mosaic-grid">
-        <div class="card">
-          <div class="card-header">
-            <h3>🔬 Variant Allele Frequency (VAF) Spectrum & Mosaicism Analysis</h3>
-            <span class="badge-cyan">Somatic vs Germline Resolution</span>
-          </div>
-          <div class="card-body">
-            <p class="section-desc">
-              In Mosaic Variegated Aneuploidy, post-zygotic somatic mutations and mitotic nondisjunction events exhibit non-Mendelian allele frequencies. Variants with <strong>VAF between 5% and 38% (0.05 – 0.38)</strong> represent high-confidence mosaic somatic candidates.
-            </p>
-
-            <div class="vaf-distribution-chart">
-              <div class="vaf-bracket bracket-mosaic">
-                <div class="bracket-header">
-                  <span>MOSAIC SOMATIC SPECTRUM</span>
-                  <strong>5% – 38% VAF</strong>
-                </div>
-                <div class="bracket-body" id="mosaicListSummary">
-                  <!-- JS generated -->
-                </div>
-              </div>
-
-              <div class="vaf-bracket bracket-het">
-                <div class="bracket-header">
-                  <span>GERMLINE HETEROZYGOUS</span>
-                  <strong>40% – 60% VAF</strong>
-                </div>
-                <div class="bracket-body" id="hetListSummary">
-                  <!-- JS generated -->
-                </div>
-              </div>
-
-              <div class="vaf-bracket bracket-hom">
-                <div class="bracket-header">
-                  <span>GERMLINE HOMOZYGOUS</span>
-                  <strong>85% – 100% VAF</strong>
-                </div>
-                <div class="bracket-body" id="homListSummary">
-                  <!-- JS generated -->
-                </div>
-              </div>
-            </div>
-          </div>
-        </div>
-
-        <div class="card">
-          <div class="card-header">
-            <h3>⭐ Top Mosaic Somatic Candidate Loci</h3>
-            <span class="badge-gold">Prioritized SAC & Centrosome Mutants</span>
-          </div>
-          <div class="card-body">
-            <div id="topMosaicTable" class="top-mosaic-container">
-              <!-- Rendered via JS -->
-            </div>
-          </div>
-        </div>
-      </div>
-    </section>
-
-    <!-- Tab 4: WGS Sequencing & Flowcells -->
-    <section id="tab-wgs" class="tab-content">
-      <div class="wgs-grid">
-        <div class="card">
-          <div class="card-header">
-            <h3>📊 Illumina NovaSeq 6000 Flowcell Metrics</h3>
-            <span class="badge-cyan">Flowcell ID: HGWCNDSX7</span>
-          </div>
-          <div class="card-body">
-            <div class="stats-overview-row">
-              <div class="overview-box">
-                <span class="box-label">Total Sequencing Data</span>
-                <span class="box-val font-cyan">78.86 GB</span>
-              </div>
-              <div class="overview-box">
-                <span class="box-label">Total Paired Reads</span>
-                <span class="box-val">805.8 Million</span>
-              </div>
-              <div class="overview-box">
-                <span class="box-label">Mean Genome Coverage</span>
-                <span class="box-val font-green">36.2×</span>
-              </div>
-              <div class="overview-box">
-                <span class="box-label">Bases ≥ Q30</span>
-                <span class="box-val font-gold">93.45%</span>
-              </div>
-              <div class="overview-box">
-                <span class="box-label">Mean Insert Size</span>
-                <span class="box-val">380 bp</span>
-              </div>
-              <div class="overview-box">
-                <span class="box-label">Duplication Rate</span>
-                <span class="box-val">8.4%</span>
-              </div>
-            </div>
-
-            <h4 class="subhead">Lane-by-Lane Sequencing Breakdown (4 Flowcell Lanes)</h4>
-            <div class="lanes-table-wrapper">
-              <table class="lane-table">
-                <thead>
-                  <tr>
-                    <th>Lane</th>
-                    <th>Read 1 (R1) FASTQ</th>
-                    <th>R1 Size</th>
-                    <th>Read 2 (R2) FASTQ</th>
-                    <th>R2 Size</th>
-                    <th>Total Reads</th>
-                    <th>Q30 %</th>
-                    <th>Est. Coverage</th>
-                  </tr>
-                </thead>
-                <tbody id="laneTableBody">
-                  <!-- Rendered via JS -->
-                </tbody>
-              </table>
-            </div>
-          </div>
-        </div>
-      </div>
-    </section>
-
-    <!-- Tab 6: Candidate Gene Burden & ACMG Matrix -->
+    <!-- Tab 3: Candidate Gene Burden & ACMG Matrix -->
     <section id="tab-gene-burden" class="tab-content">
       <div class="infotable-card">
         <div class="infotable-header">
@@ -404,7 +288,7 @@
       </div>
     </section>
 
-    <!-- Tab 7: Phenotype Differential Matrix -->
+    <!-- Tab 4: Phenotype Differential Matrix -->
     <section id="tab-syndromic-diff" class="tab-content">
       <div class="infotable-card">
         <div class="infotable-header">
@@ -436,7 +320,76 @@
       </div>
     </section>
 
-    <!-- Tab 8: Mosaic Allelic Stratification -->
+    <!-- Tab 5: ACMG Variant Classification Table -->
+    <section id="tab-acmg-matrix" class="tab-content">
+      <div class="infotable-card">
+        <div class="infotable-header">
+          <div class="infotable-title-box">
+            <h3>🧪 ACMG / AMP Diagnostic Variant Pathogenicity Classification Table</h3>
+            <p class="infotable-desc">Formal ACMG/AMP clinical evidence tiering of prioritized candidate mutations across Spindle Assembly Checkpoint and sarcoma driver loci.</p>
+          </div>
+          <div class="table-search-box">
+            <input type="text" id="searchAcmgMatrix" placeholder="Filter by gene or classification..." class="search-input">
+          </div>
+        </div>
+        <div class="table-scroll-lg">
+          <table class="infotable">
+            <thead>
+              <tr>
+                <th>Gene</th>
+                <th>HGVSc / Protein Change</th>
+                <th>Genomic Coordinate (GRCh38)</th>
+                <th>Ref → Alt</th>
+                <th>Variant Type</th>
+                <th>VAF</th>
+                <th>ACMG Evidence Criteria</th>
+                <th>gnomAD v4.1 AF</th>
+                <th>REVEL / CADD</th>
+                <th>Final ACMG Tier</th>
+              </tr>
+            </thead>
+            <tbody id="acmgMatrixTableBody">
+              <!-- Rendered via JS -->
+            </tbody>
+          </table>
+        </div>
+      </div>
+    </section>
+
+    <!-- Tab 6: Precision Oncology Targets -->
+    <section id="tab-therapeutic-targets" class="tab-content">
+      <div class="infotable-card">
+        <div class="infotable-header">
+          <div class="infotable-title-box">
+            <h3>💊 Precision Oncology & Therapeutic Target Matrix</h3>
+            <p class="infotable-desc">Targeted therapies, synthetic lethality vulnerabilities, and investigational small molecules exploiting chromosomal instability (CIN) and mitotic spindle defects.</p>
+          </div>
+          <div class="table-search-box">
+            <input type="text" id="searchTherapeuticTargets" placeholder="Filter by drug, target, or mechanism..." class="search-input">
+          </div>
+        </div>
+        <div class="table-scroll-lg">
+          <table class="infotable">
+            <thead>
+              <tr>
+                <th>Drug / Small Molecule</th>
+                <th>Target Gene</th>
+                <th>Pharmacological Class</th>
+                <th>Mechanism of Action</th>
+                <th>Synergy with MVA Phenotype</th>
+                <th>Clinical Trial Status</th>
+                <th>Evidence Tier</th>
+              </tr>
+            </thead>
+            <tbody id="therapeuticTargetsTableBody">
+              <!-- Rendered via JS -->
+            </tbody>
+          </table>
+        </div>
+      </div>
+    </section>
+
+    <!-- Tab 7: Mosaic Allelic Stratification -->
     <section id="tab-mosaic-strat" class="tab-content">
       <div class="infotable-card">
         <div class="infotable-header">
@@ -466,7 +419,7 @@
       </div>
     </section>
 
-    <!-- Tab 9: Mitotic Machinery & Interactome Functional Table -->
+    <!-- Tab 8: Mitotic Machinery & Interactome Functional Table -->
     <section id="tab-mitotic-machinery" class="tab-content">
       <div class="infotable-card">
         <div class="infotable-header">
@@ -499,7 +452,7 @@
       </div>
     </section>
 
-    <!-- Tab 10: 24-Chromosome Karyotype & Instability Matrix -->
+    <!-- Tab 9: 24-Chromosome Karyotype & Instability Matrix -->
     <section id="tab-karyotype-matrix" class="tab-content">
       <div class="infotable-card">
         <div class="infotable-header">
@@ -534,6 +487,147 @@
       </div>
     </section>
 
+    <!-- Tab 10: Mosaicism Spectrum -->
+    <section id="tab-mosaic" class="tab-content">
+      <div class="mosaic-grid">
+        <div class="card">
+          <div class="card-header">
+            <h3>🔬 Variant Allele Frequency (VAF) Spectrum & Mosaicism Analysis</h3>
+            <span class="badge-cyan">Somatic vs Germline Resolution</span>
+          </div>
+          <div class="card-body">
+            <p class="section-desc">
+              In Mosaic Variegated Aneuploidy, post-zygotic somatic mutations and mitotic nondisjunction events exhibit non-Mendelian allele frequencies. Variants with <strong>VAF between 5% and 38% (0.05 – 0.38)</strong> represent high-confidence mosaic somatic candidates.
+            </p>
+
+            <div class="vaf-distribution-chart">
+              <div class="vaf-bracket bracket-mosaic">
+                <div class="bracket-header">
+                  <span>MOSAIC SOMATIC SPECTRUM</span>
+                  <strong>5% – 38% VAF</strong>
+                </div>
+                <div class="bracket-body" id="mosaicListSummary">
+                  <!-- JS generated -->
+                </div>
+              </div>
+
+              <div class="vaf-bracket bracket-het">
+                <div class="bracket-header">
+                  <span>GERMLINE HETEROZYGOUS</span>
+                  <strong>40% – 60% VAF</strong>
+                </div>
+                <div class="bracket-body" id="hetListSummary">
+                  <!-- JS generated -->
+                </div>
+              </div>
+
+              <div class="vaf-bracket bracket-hom">
+                <div class="bracket-header">
+                  <span>GERMLINE HOMOZYGOUS</span>
+                  <strong>85% – 100% VAF</strong>
+                </div>
+                <div class="bracket-body" id="homListSummary">
+                  <!-- JS generated -->
+                </div>
+              </div>
+            </div>
+          </div>
+        </div>
+
+        <div class="card">
+          <div class="card-header">
+            <h3>⭐ Top Mosaic Somatic Candidate Loci</h3>
+            <span class="badge-gold">Prioritized SAC & Centrosome Mutants</span>
+          </div>
+          <div class="card-body">
+            <div id="topMosaicTable" class="top-mosaic-container">
+              <!-- Rendered via JS -->
+            </div>
+          </div>
+        </div>
+      </div>
+    </section>
+
+    <!-- Tab 11: 4-Lane Sequencing QC Audit -->
+    <section id="tab-wgs" class="tab-content">
+      <div class="wgs-grid">
+        <div class="card">
+          <div class="card-header">
+            <h3>📊 Illumina NovaSeq 6000 Flowcell Quality Audit (4 Lanes)</h3>
+            <span class="badge-cyan">Flowcell ID: HGWCNDSX7</span>
+          </div>
+          <div class="card-body">
+            <div class="stats-overview-row">
+              <div class="overview-box">
+                <span class="box-label">Total Sequencing Data</span>
+                <span class="box-val font-cyan">78.86 GB</span>
+              </div>
+              <div class="overview-box">
+                <span class="box-label">Total Paired Reads</span>
+                <span class="box-val">805.8 Million</span>
+              </div>
+              <div class="overview-box">
+                <span class="box-label">Mean Genome Coverage</span>
+                <span class="box-val font-green">36.2×</span>
+              </div>
+              <div class="overview-box">
+                <span class="box-label">Bases ≥ Q30</span>
+                <span class="box-val font-gold">93.45%</span>
+              </div>
+              <div class="overview-box">
+                <span class="box-label">Mean Insert Size</span>
+                <span class="box-val">380 bp</span>
+              </div>
+              <div class="overview-box">
+                <span class="box-label">Duplication Rate</span>
+                <span class="box-val">8.4%</span>
+              </div>
+            </div>
+
+            <h4 class="subhead">Comprehensive Lane-by-Lane Telemetry Audit</h4>
+            <div class="lanes-table-wrapper">
+              <table class="lane-table">
+                <thead>
+                  <tr>
+                    <th>Lane ID</th>
+                    <th>Read Pairs FASTQ Files</th>
+                    <th>Total Size</th>
+                    <th>Paired Reads</th>
+                    <th>Q30 %</th>
+                    <th>GC %</th>
+                    <th>Est. Coverage</th>
+                    <th>Dup Rate</th>
+                    <th>Mapping Rate</th>
+                    <th>Flowcell Status</th>
+                  </tr>
+                </thead>
+                <tbody id="flowcellQcTableBody">
+                  <!-- Rendered via JS -->
+                </tbody>
+              </table>
+            </div>
+          </div>
+        </div>
+      </div>
+    </section>
+
+    <!-- Tab 12: Mitotic Checkpoint Pathway Network -->
+    <section id="tab-pathway" class="tab-content">
+      <div class="pathway-grid">
+        <div class="card">
+          <div class="card-header">
+            <h3>⚙️ Spindle Assembly Checkpoint (SAC) & Centrosomal Protein Network</h3>
+            <span class="badge-rare">Mitotic Machinery</span>
+          </div>
+          <div class="card-body">
+            <div class="pathway-diagram" id="pathwayComplexes">
+              <!-- Rendered via JS -->
+            </div>
+          </div>
+        </div>
+      </div>
+    </section>
+
     <!-- Variant Detail Modal -->
     <div id="modalVariant" class="modal-overlay hidden">
       <div class="modal-card">
@@ -551,7 +645,7 @@
     <div id="modalHelp" class="modal-overlay hidden">
       <div class="modal-card">
         <div class="modal-header">
-          <h2>⌨ 5D Studio Keyboard Shortcuts</h2>
+          <h2>⌨ Studio Keyboard Shortcuts</h2>
           <button id="btnCloseHelpModal" class="modal-close">✕</button>
         </div>
         <div class="modal-body">
@@ -560,12 +654,14 @@
             <div class="shortcut-item"><kbd>2</kbd><span>Chromosome & Variant Navigator (5.01M WGS)</span></div>
             <div class="shortcut-item"><kbd>3</kbd><span>Candidate Gene Burden & ACMG Matrix</span></div>
             <div class="shortcut-item"><kbd>4</kbd><span>Phenotype Differential Matrix</span></div>
-            <div class="shortcut-item"><kbd>5</kbd><span>Mosaic Allelic Stratification Table</span></div>
-            <div class="shortcut-item"><kbd>6</kbd><span>Mitotic Machinery Interactome</span></div>
-            <div class="shortcut-item"><kbd>7</kbd><span>24-Chromosome Karyotype Matrix</span></div>
-            <div class="shortcut-item"><kbd>8</kbd><span>Mosaicism & VAF Spectrum</span></div>
-            <div class="shortcut-item"><kbd>9</kbd><span>WGS Sequencing & Flowcells</span></div>
-            <div class="shortcut-item"><kbd>0</kbd><span>Mitotic Checkpoint Pathway Network</span></div>
+            <div class="shortcut-item"><kbd>5</kbd><span>ACMG Diagnostic Variant Classification</span></div>
+            <div class="shortcut-item"><kbd>6</kbd><span>Precision Oncology Targets</span></div>
+            <div class="shortcut-item"><kbd>7</kbd><span>Mosaic Allelic Stratification Table</span></div>
+            <div class="shortcut-item"><kbd>8</kbd><span>Mitotic Machinery Interactome</span></div>
+            <div class="shortcut-item"><kbd>9</kbd><span>24-Chromosome Karyotype Matrix</span></div>
+            <div class="shortcut-item"><kbd>0</kbd><span>Mosaicism & VAF Spectrum</span></div>
+            <div class="shortcut-item"><kbd>Q</kbd><span>4-Lane Sequencing QC Audit</span></div>
+            <div class="shortcut-item"><kbd>W</kbd><span>Mitotic Checkpoint Pathway Network</span></div>
             <div class="shortcut-item"><kbd>/</kbd><span>Focus Variant Search bar</span></div>
             <div class="shortcut-item"><kbd>Esc</kbd><span>Close modals</span></div>
           </div>