ok

nanopore.typ → TAGC_CT_2024.typ

@@ -63,6 +63,7 @@
     )
   ],
 )
+
 #simple_dia(
   [👨‍⚕️ Model --- T-ALL ],
   [
@@ -147,7 +148,7 @@
           [
             #set align(center + horizon)
             #v(10pt)
-            Cases *refractory* to chemotherapy as well as *relapses* (UKALL12: adults at 5
+            *Refractory* cases to standard chemotherapy as well as *relapses* (UKALL12: adults at 5
             years 42%) have a poor prognosis.
             #v(10pt)
           ],
@@ -180,8 +181,7 @@
           [
             #set align(center + horizon)
             #v(10pt)
-            We also believe that the tumor phenotype results from modifications in the
-            genotype.
+            The tumor phenotype emerges from alterations in their genotype.
 
             #sym.arrow.r.stroked A better description of the genotype will lead to a better
             understanding of oncogenic mechanisms and to the discovery of more *effective
@@ -203,7 +203,9 @@
       auto,
       auto,
       [
-        *Somatic intergenic alterations are responsible for the deregulation of
+        #set align(center + horizon)
+
+        *Somatic intergenic alterations are responsible of the deregulation of
     oncogenes.*
         #image("./Images/bradner_cis_small.png")
       ],
@@ -220,8 +222,8 @@
       auto,
       auto,
       [
-        - Our laboratory has shown that an insertion upstream of _TAL1_ leads to the
-          formation of a *neo-enhancer* and thus the overexpression of _TAL1_.
+        - Our laboratory has shown that a somatic insertion upstream of _TAL1_ leads to the
+          formation of a *neo-enhancer* and thus leads to the overexpression of _TAL1_.
         #set align(center)
         #image("./Images/tal_ins.png", height: 66%)
       ],
@@ -240,17 +242,25 @@
       auto,
       auto,
       [
-        - Implement a method for sequencing the *whole tumoral genome*.
-        - Detect structural variations (SV) and SNV with good sensitivity/specificity.
-        - Describe a set of somatic intergenic alterations likely responsible for the
-          deregulation of known oncogenes.
-        - Identify similar alterations deregulating genes not known to be oncogenes.
-      ],
+        - *Implement* a method for sequencing the *whole tumoral genome*.
+        #uncover(
+          (2, 3, 4, 5),
+          [- *Detect* structural variations (SV) and SNV with good sensitivity/specificity.],
+        )
+        #uncover(
+          (3, 4, 5),
+          [- *Describe* a set of somatic intergenic alterations likely responsible for the deregulation of known oncogenes.],
+        )
+        #uncover(
+          (4, 5),
+          [- *Discover* similar alterations deregulating genes not known to be oncogenes.
+          ],
+        )],
       [],
     )
 
     #uncover(
-      2,
+      5,
       [
         #double_boxes(
           auto,
@@ -258,7 +268,7 @@
           [
             #set align(center)
             *#sym.arrow.r.stroked* Implementation of the *Oxford Nanopore sequencing
-        method*.
+        method* and integrate multi-omics data.
           ],
           [],
         )
@@ -386,8 +396,8 @@
       [
         1. *Base calling* and *Alignement* on hs1 (T2T).
 
-        Latest version of Dorado 0.6.0 with latest AI model of 5mC 5hmC modified
-        basecalling (v4.3).
+        Latest version of Dorado 0.8.1 with latest AI model of 5mC 5hmC modified
+        basecalling (v5.0).
 
         #set align(center + horizon)
         #grid(
@@ -466,13 +476,14 @@
       auto,
       [
         3. Annotations
-        - VEP for variant consequence prediction (ensembl v110.1)
-        - Cosmic (latest)
+        - VEP for variant consequence prediction (ensembl v112)
+        - Cosmic DB (latest)
+        - dbSNP
         - NCBI genomic regions (latest)
       ],
       [],
     )
-    #image("./Images/vep_consequences.svg", height: 65%)
+    #image("./Images/vep_consequences.svg", height: 60%)
   ],
 )
 
@@ -519,10 +530,10 @@
       auto,
       [
         Implementation of _de novo assemblage_ for LRS: \
-        Inspired by *SV-finder* (local de novo assemblage)
+        Inspired by *SV-finder* (local de novo assembly)
         - *Scan* alignements and select locally misaligned reads (outliers detection).
         - *Assemble* them together (wtdbg2 v2.5 and spades v4.0).
-        - *Describe* the consensus sequence (Blast, minimap2).
+        - *Describe* the resulting consensus sequence (Blast, minimap2).
       ],
       [],
     )
@@ -569,33 +580,39 @@
       80%,
       [
         #set align(center + horizon)
-        After the interpretation of the results and the redaction of a conclusion.
+        After the manual interpretation of the results and the redaction of a conclusion.
       ],
       [],
     )
 
-    #double_boxes(
-      auto,
-      80%,
-      [
-        #set align(left)
-        The system generates a detailed PDF report that seamlessly integrates:
+    #uncover(
+      (2, 3),
+      double_boxes(
+        auto,
+        80%,
+        [
+          #set align(left)
+          The system generates a detailed PDF report that seamlessly integrates:
 
-        + Detailed quality metrics (with graphics generation)
-        + Interpreted genetic mutations (Pathogenic, ...)
-        + Analytical conclusions
-      ],
-      [],
+          + Detailed quality metrics (with graphics generation)
+          + Interpreted genetic mutations (Pathogenic, ...)
+          + Analytical conclusions
+        ],
+        [],
+      ),
     )
 
-    #double_boxes(
-      auto,
-      25%,
-      align(
-        center,
-        link("http://localhost/data/longreads_basic_pipe/CHAMPION/diag/report/CHAMPION_report.pdf")[Example...],
+    #uncover(
+      3,
+      double_boxes(
+        auto,
+        25%,
+        align(
+          center,
+          link("http://localhost/data/longreads_basic_pipe/CHAMPION/diag/report/CHAMPION_report.pdf")[Example...],
+        ),
+        [],
       ),
-      [],
     )
   ],
 )
@@ -612,9 +629,9 @@
       [
         Initially, to investigate our hypothesis, we decided to sequence T-ALLs
         harboring deregulation of the expression of known frequent oncogenes in T-ALL:
-        - * _TAL1_ *,
-        - * _HOXA9_ * and
-        - * _TLX1_* deregulated without genetic explanation.
+        - *_TAL1_* (cis-deregulated),
+        - *_HOXA9_* (RT-MLPA neg),
+        - * _TLX1_* deregulated without genetic explanation (FISH neg and NGS panel neg).
       ],
       [],
     )
@@ -957,7 +974,13 @@
   [🧬 Interesting results: TAL1],
   align(
     center + horizon,
-    double_boxes(auto, 60%, align(center)[show CAMA MYB insertion on line…], []),
+    double_boxes(
+      auto,
+      60%,
+      align(center)[🌐 show CAMA MYB insertion on line…],
+
+      [],
+    ),
   ),
 )
 
@@ -977,18 +1000,24 @@
               #v(12pt)
 
               - Surexpression of TLX1.
-              - Inv10
-              - Modification of 3' UTR.
+              #uncover((2, 3), [- Inv10 ])
+              #uncover(3, [- Modification of 3' UTR.])
             ],
             [],
           )
-          #double_boxes(auto, auto, image("./Images/utr_tlx1.png"), [])
+          #uncover(
+            3,
+            double_boxes(auto, auto, image("./Images/utr_tlx1.png"), []),
+          )
         ],
-        double_boxes(
-          auto,
-          auto,
-          image("./Images/LEV_inv10_tlx1.png", height: 75%),
-          [],
+        uncover(
+          (2, 3),
+          double_boxes(
+            auto,
+            auto,
+            image("./Images/LEV_inv10_tlx1.png", height: 75%),
+            [],
+          ),
         ),
       ),
     )