presentation_241030_necker/nanopore_update_241030.typ

#import "@local/presentation_lib:0.1.0": *
#show: setup-emoji.with(font: noto)
#show: dia-theme.with("16-9")

#title_dia(
  [
    🧬 TAGC --- Implementation of whole genome longreads sequencing to decode somatic
    genotypes in T-ALL
  ],
  [
    Dr. Thomas Steimlé (MD)

    ---
    Thèse co-dirigée par Pr. Vahid Asnafi (PU-PH Necker) et Dr. Salvatore Spicuglia
    (DR1 Inserm)
  ],
)

#simple_dia(
  [
    ❓Main Hypothesis
  ],
  [
    #set align(center + horizon)
    #double_boxes(
      auto,
      auto,
      [
        #set align(center + horizon)
        #v(10pt)
        #set text(20pt)
        = Tumor proliferations harbor within their genome *intergenic somatic mutations* that disrupts the expression of oncogenes.
        #v(10pt)
      ],
      [],
    )
  ],
)

#simple_dia(
  [👨‍⚕️ Model --- T-ALL ],
  [
    #double_boxes(
      auto,
      auto,
      [
        #set align(center + horizon)
        #v(10pt)
        Acute lymphoblastic leukemia is a rare disease (#sym.tilde.eq 120/yr in Fr)
        resulting from a tumoral process driven by the clonal *proliferation of immature
        T lymphocytes*.
        #v(10pt)
      ],
      [],
    )
    #double_boxes(
      auto,
      auto,
      [
        #image("./Images/histo_ages.png")
      ],
      [Internal unpublished data],
    )
  ],
)

#simple_dia(
  [👨‍⚕️ Model --- T-ALL ],
  [
    #double_boxes(
      auto,
      auto,
      [
        #set align(center + horizon)
        #v(10pt)
        Acute lymphoblastic leukemia is a rare disease (#sym.tilde.eq 120/yr in Fr)
        resulting from a tumoral process driven by the clonal proliferation of *immature
        T lymphocytes*.
        #v(10pt)
      ],
      [],
    )
    #set align(horizon + center)
    #double_boxes(
      auto,
      auto,
      [
        #grid(
          columns: (50%, 50%),
          gutter: 5pt,
          [
            - Adults OS 3 years: 67% (GRAALL-2005)
          ],
          image("./Images/OS_graall.png", height: 67%),
        )
      ],
      [#set align(right)
        Trinquand A et al. J Clin Oncol. 2013;31(34):4333-4342],
    )
  ],
)

#simple_dia(
  [👨‍⚕️ Model --- T-ALL ],
  [
    #double_boxes(
      auto,
      auto,
      [
        #set align(center + horizon)
        #v(10pt)
        Acute lymphoblastic leukemia is a rare disease (#sym.tilde.eq 120/yr in Fr)
        resulting from a tumoral process driven by the clonal proliferation of *immature
        T lymphocytes*.
        #v(10pt)
      ],
      [],
    )
    #set align(horizon + center)
    #double_boxes(
      auto,
      auto,
      [
        #grid(
          columns: (50%, 50%),
          gutter: 5pt,
          [
            - Adults OS 3 years: 67% (GRAALL-2005)
            - Youths OS 5 years: 77% (FRALLE)
          ],
          align(center, image("./Images/os_KM_FRALLE2000.png", height: 67%)),
        )
      ],
      [Petit A et al. Blood. 2018;131(3):289-300.],
    )
  ],
)

#simple_dia(
  [👨‍⚕️ Model --- T-ALL ],
  [
    #uncover(
      (1, 2, 3),
      [
        #double_boxes(
          auto,
          auto,
          [
            #set align(center + horizon)
            #v(10pt)
            *Refractory* cases to standard chemotherapy as well as *relapses* (UKALL12: adults at 5
            years 42%) have a poor prognosis.
            #v(10pt)
          ],
          [],
        )
      ],
    )
    #uncover(
      (2, 3),
      [
        #double_boxes(
          auto,
          auto,
          [
            #set align(center + horizon)
            #v(10pt)
            *We need new treatments to address these cases !*
            #v(10pt)
          ],
          [],
        )
      ],
    )
    #uncover(
      3,
      [
        #double_boxes(
          auto,
          auto,
          [
            #set align(center + horizon)
            #v(10pt)
            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
            therapies tailored to specific alterations*.
            #v(10pt)
          ],
          [],
        )
      ],
    )
  ],
)

#simple_dia(
  [🦀 Intergenic alterations],
  [
    #set align(center + horizon)
    #double_boxes(
      auto,
      auto,
      [
        #set align(center + horizon)

        *Somatic intergenic alterations are responsible of the deregulation of
    oncogenes.*
        #image("./Images/bradner_cis_small.png", height: 50%)
      ],
      [Bradner JE, et al. Cancer. Cell. 2017 Feb9 ;168(4):629-643],
    )
  ],
)

#simple_dia(
  [🍹 Preliminary results],
  [
    #set align(center + horizon)
    #double_boxes(
      auto,
      auto,
      [
        - 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%)
      ],
      [Smith, C et al. “TAL1 activation in T-cell acute lymphoblastic leukemia: a novel
        oncogenic 3' neo-enhancer.” Haematologica vol. 108,5 1259-1271. 1 May. 2023],
    )
  ],
)

#simple_dia(
	[🎯 Goals],
	[
	#set align(center + horizon)
	#set text(22pt)
	#double_boxes(
		auto,
		auto,
		[
		#line-by-line[
			- *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.
			- *Discover* similar alterations deregulating genes not known to be oncogenes.
		]
		// #uncover(
		// 	(1, 2, 3, 4, 5),
		// 	[- *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(
		5,
		[
		#double_boxes(
			auto,
			auto,
			[
			#set align(center)
			*#sym.arrow.r.stroked* Implementation of the *Oxford Nanopore sequencing
			method* and integrate multi-omics data.
		],
			[],
		)
	],
	)
],
)

#simple_dia(
  [🖥️ Infrastucture],
  [
    #double_boxes(
      auto,
      auto,
      [
        *Computer A* for processing and analyzing the signal generated by the sequencer
        (MAD).
        - 2x Intel Xeon Platinum 8380 CPU 2.30GHz
        - 160 cores
        - 503 GB RAM
        - 4 nVidia A100 GPU
      ],
      [],
    )
    #image("./Images/promethions_stock.jpg", height: 35%)
    #uncover(
      2,
      [
        #double_boxes(
          auto,
          auto,
          [
            *Computer B* for data archiving and sharing.
            - 52 To fo HD in raidz1 mode (redundancy)
            - LTO: magnetic tape drive (raw data archiving)
          ],
          [],
        )
      ],
    )
  ],
)

#simple_dia(
  [🧪 Wet lab],
  [
    #set align(center + horizon)

    #double_boxes(
      auto,
      auto,
      [
        - Intermediate difficulty level.
        - 3 half-days of work.
      ],
      [],
    )

    #uncover(
      2,
      [
        #double_boxes(
          auto,
          auto,
          align(
            center,
            [
              1. Genomic DNA *shearing* Covaris g-TUBE (3µg, 8,000rpm, 1min)
              #image("./Images/covaris.png", height: 20%)
            ],
          ),
          [],
        )
      ],
    )
  ],
)

#simple_dia(
  [🧪 Wet lab],
  [
    #set align(center + horizon)
    #double_boxes(
      auto,
      70%,
      [
        #set align(center + horizon)
        2. *Preparation of the sequence library*
        DNA *repair* and end-prep #sym.arrow.r.stroked *barcode* ligation #sym.arrow.r.stroked *adapter* ligation
        #image("./Images/library_construction.png", height: 70%)
      ],
      [],
    )
  ],
)

#simple_dia(
  [🧪 Wet lab],
  [
    #set align(center + horizon)
    #double_boxes(
      auto,
      75%,
      [
        #set align(center + horizon)
        3. Flowcells *loading* and *sequencing run*
        #grid(
          columns: (auto, auto),
          gutter: 45pt,
          image("./Images/fc_loading.png", height: 65%),
          image("./Images/sequencing_principle.png", height: 75%),
        )
      ],
      [],
    )
  ],
)

#simple_dia(
  [💾 Bioinformatic Pipeline ],
  [
    #double_boxes(
      auto,
      auto,
      [
        1. *Base calling* and *Alignement* on hs1 (T2T).

        Latest version of Dorado 0.8.1 with latest AI model of 5mC 5hmC modified
        basecalling (v5.0).

        #set align(center + horizon)
        #grid(
          columns: (0.6fr, 0.1fr, 1fr),
          gutter: 15pt,
          image("./Images/pod5_signal.png", height: 30%),
          [$#sym.arrow.r.long$],
          text(
            10pt,
            raw(
              "059b2db8-416c-4fdf-b7eb-3cdd3390a3bd 0 chr1 2 1 1075S5M1D8M1D36M1D4M1D116M1D111M1I485M3I595M...69M1I12M1I16M1D48M1641S * 0 0 AAGGTTAAAACCAAGACTCGCTGTGC 8;88;;<<<:::98...87877676645654456798997 qs:i:22 du:f:14.
               137 ns:i:70685 ts:i:904 mx:i:2 ch:i:1307 st:Z:2023-12-14T18:30:59.187+00:00 rn:i:36917 fn:Z:PAS34492_pass_barcode
               09_2e65ae3a_a7dfa7d7_4228.pod5 sm:f:-764.172 sd:f:0.00798761 sv:Z:pa dx:i:0 RG:Z:a7dfa7d727c0e04ecb6e9c5c3dac8080fe7cffaa_dna_r10.4.1_e8.2_400bps_sup@v4.3.0 MN:i:5392 MM:Z:C+h.,1,0,1,0,0,4,5,117,36,0,93,99,56,0,65...; ML:B:C,152,3,5,3,3,1,...; NM:i:1
               71 ms:i:4485 AS:i:4438 nn:i:0 de:f:0.0502045 tp:A:P cm:i:11 s1:i:82 s2:i:148 MD:Z:5^A8^C36^C4^A116^C...; rl:i
               :3576 SA:Z:chr8,146252402,-,1604M1D3788S,36,10;",
              block: true,
            ),
          ),
        )

      ],
      [],
    )

    #uncover(
      2,
      double_boxes(
        auto,
        auto,
        [2. *Variant calling*
            #set text(13pt)
            - DeepVariant (Google v1.6.1) on constit and tumoral BAMs.
            - ClairS (HK-UBAL v0.1.7) takes both constit and tumoral BAMs.
            - #strike[Sniffles (Fritz Sedlazeck v2.2) on constit and tumoral BAMs.]
            - NanoMonSV (Yuichi Shiraishi v0.7.2) takes both constit and tumoral BAMs.
            - Exogene (Z. Stephens v15) viral integration.
        ],
        [],
      ),
    )
  ],
)

#simple_dia(
  [💾 Bioinformatic Pipeline --- Aggregation],
  [
    #set align(center + horizon)
    #grid(
      columns: (40%, 40%),
      gutter: 8%,
      double_boxes(
        auto,
        auto,
        [1. VCF filter #align(center + horizon, image("./Images/first_pass_flow.png", height: 90%)) ],
        [],
      ),
      uncover(
        2,
        double_boxes(
          auto,
          auto,
          [2. BAM filter #align(center + horizon, image("./Images/second_pass_flow.png", height: 90%)) ],
          [],
        ),
      ),
    )
  ],
)

#simple_dia(
	[📈 Results --- Number of somatic alterations],
	[
	#set align(center + horizon)
	#set text(16pt)
	#double_boxes(
		auto,
		75%,
		[
		#set align(center + horizon)
		#image("./Images/n_somatic.png", height: 90%)
	],
		[],
	)
],
)

#simple_dia(
  [💾 Bioinformatic Pipeline --- Annotation],
  [
    #double_boxes(
      auto,
      auto,
      [
        3. Annotations
        - VEP for variant consequence prediction (ensembl v112)
        - Cosmic DB (latest)
        - dbSNP
        - NCBI genomic regions (latest)
      ],
      [],
    )
    #image("./Images/vep_consequences.svg", height: 60%)
  ],
)


#simple_dia(
  [📈 Results --- Number of somatic missense alterations],
  [
    #set align(center + horizon)
    #set text(16pt)
    #double_boxes(
      auto,
      75%,
      [
        #set align(center + horizon)
        #image("./Images/n_somatic_missenses.png", height: 90%)
      ],
      [],
    )
  ],
)


#simple_dia(
  [🏎️ Performances --- Substitution calling],
  [
    #set align(center + horizon)
    #set text(16pt)
    #double_boxes(
      auto,
      70%,
      [
        #set align(center + horizon)
        #image("./Images/perf.png", height: 90%)
      ],
      [],
    )
  ],
)

#simple_dia(
  [💾 Bioinformatic Pipeline --- _de novo_],
  [

    #double_boxes(
      auto,
      auto,
      [
        Implementation of _de novo assemblage_ for LRS: \
        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 resulting consensus sequence (Blast, minimap2).
      ],
      [],
    )

    #align(
      center,
      double_boxes(
        auto,
        70%,
        image("./Images/sc-finder.png", height: 55%),
        [],
      ),
    )
  ],
)

#simple_dia(
	[📈 Results --- Number of somatic SV],
	[
	#set align(center + horizon)
	#set text(16pt)
	#double_boxes(
		auto,
		75%,
		[
		#set align(center + horizon)
		#image("./Images/n_somatic_SV.png", height: 90%)
	],
		[],
	)
],
)

#simple_dia(
  [🔬 Visualization and interpretation of results],
  [
    #set align(center + horizon)
    #set text(22pt)
    #double_boxes(
      auto,
      auto,
      [
        #set align(center + horizon)

        Development of a web service (HTMX + Bun) for *sharing, visualization, and
        interpretation of the results*.

        #link("http://localhost")[*DEMO*] (C.... ex.: _PHF6_ et _AEBP2_)
      ],
      [],
    )
  ],
)

#simple_dia(
  [📝 Reporting],
  [
    #set align(center + horizon)
    #double_boxes(
      auto,
      80%,
      [
        #set align(center + horizon)
        After the manual interpretation of the results and the redaction of a conclusion.
      ],
      [],
    )

    #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
        ],
        [],
      ),
    )

    #uncover(
      3,
      double_boxes(
        auto,
        25%,
        align(
          center,
          link("http://localhost/data/longreads_basic_pipe/CHAMPION/diag/report/CHAMPION_report.pdf")[Example...],
        ),
        [],
      ),
    )
  ],
)

#simple_dia(
  [👥 Cohorts],
  [
    #set align(center + horizon)
    #set text(22pt)

    #double_boxes(
      auto,
      auto,
      [
        Initially, to investigate our hypothesis, we decided to sequence T-ALLs
        harboring deregulation of the expression of known frequent oncogenes in T-ALL:
        - *_TAL1_* (cis-deregulated),
        - *_HOXA9_* (RT-MLPA neg),
        - * _TLX1_* deregulated without genetic explanation (FISH neg and NGS panel neg).
      ],
      [],
    )

    #uncover(
      2,
      [
        #double_boxes(
          auto,
          auto,
          [
            We also decided to sequence a cohort of pediatric T-ALLs and an adult one with
            deregulation of _TLX3_ (Pediac/Manon project). As well as a cohort of T-ALLs *<
            3 years*.
          ],
          [],
        )
      ],
    )
  ],
)

#simple_dia(
  [👥 Bilan des flowcells],
	image("./Images/Bilan_Nanopore_20241030.png")
)

#simple_dia(
  [👥 Cohort _HOXA_ --- n = 14],
  [
    #set align(center + horizon)
    #set text(16pt)
    #double_boxes(
      auto,
      auto,
      [
        #table(
          columns: (1fr, auto, auto, auto, auto),
			inset: 5pt,
          align: (auto, center, center, center, center),
          stroke: colors.indigo,
          [*id*],
          [*X*],
          [*mécanisme*],
					[*interpretation*],
          [*info*],

					[ALLEMAND],	text(fill: red)[11],	[Multiples mutations de _MLLT3_ + hotspot _CSF3R_], [❓], [],
					[BELARBI],	text(fill: yellow)[13],	[Altération de _GATA3_ + _KMT2C_], [❓], [],
					[BERNIER], text(fill: green)[15],	[DPP10::SET], [✅], [],
					[BOUDJELTHIA], text(fill: yellow)[13],	[_KMT2E_ ter], [❓], [JAK/STAT],
					[GARAGNON], text(fill: green)[13],	[TRB::HOXA *inv7*], [✅], [JAK/STAT],
					[HATTAB],	text(fill: red)[11], [AFDN::KMT2A *t(6;11)*], [✅], [],
					[KENNOUCHE],	[_en cours_],	[], [], [],
					[LAVIDALE],	[_en cours_],	[], [], [],
					[MANCUSO],	text(fill: red)[10], [TNRC18::KMT2A], [✅], [],
					[MERY],	text(fill: green)[16], [TRB::HOXA *inv7*], [✅], [JAK/STAT],
					[MICHELAS],	[_en cours_],	[], [], [],
					[MIGAUD],	text(fill: green)[26], [mutation _EN1_ (homeobox)], [❓], [],
					[MORIN],	text(fill: green)[22], [TRB::HOXA *inv7*], [✅], [JAK/STAT],
					[SAUTRE],	text(fill: green)[28], [AFDN::KMT2A *t(6;11)*], [✅], []
        )
      ],
      [],
    )
  ],
)


// #simple_dia(
//   [👥 Cohorts],
//   [
//     #set align(center + horizon)
//     #set text(16pt)
//     #double_boxes(
//       auto,
//       auto,
//       [
//         #table(
//           columns: (1fr, auto, auto, auto, auto, auto, auto),
//           align: (auto, center, center, center, center, center, center),
//           inset: 10pt,
//           stroke: colors.indigo,
//           [*Projet*],
//           [*Demandés*],
//           [*#sym.emptyset MRD*],
//           [*Possibles*],
//           [*En attente*],
//           [*Séquencés ($1/2$)*],
//           [*> 10X*],
//
//           [*_HOXA_ + / RT-MLPA #sym.emptyset*],
//           [30],
//           [23],
//           [7],
//           [2],
//           [2 (3)],
//           [2],
//
//           [*_HOXA_ + / RT-MLPA -*], [29], [20], [9], [2], [3 (4)], [3],
//           [*_TAL1_ + / mono-alléliques*], [10], [3], [7], [0], [5 (2)], [5],
//           [*_TLX1_ + / FISH -*], [14], [6], [8], [5], [1 (2)], [1],
//           [*< 3 ans*], [24], [8], [16], [5], [6 (5)], [6],
//           [*_TLX3_ + adultes*], [21], [9], [12], [4], [3 (5)], [3],
//           [*_TLX3_ + pédiatriques*], [14], [1], [13], [2], [5 (6)], [5],
//         )
//       ],
//       [],
//     )
//
//     #uncover(
//       2,
//       [
//         #set text(20pt)
//         #double_boxes(
//           auto,
//           auto,
//           [
//             - Samples remaining: 62
//             - Remaining flow cells for 58 samples.
//           ],
//           [],
//         )
//       ],
//     )
//   ],
// )
//

// #simple_dia([Results --- Number of somatic alterations], [
//   #set align(center + horizon)
//
//   #double_boxes(auto, auto, [
//     Callers overlapps
//     #image("./Images/hist_callers.png")
//   ], [])
// ])

// #simple_dia(
//   [Results --- Number of somatic alterations],
//   [
//     #set align(center + horizon)
//     #double_boxes(
//       auto,
//       60%,
//       [
//         #set align(center + horizon)
//         Variants consequences
//         #image("./Images/hist_consequences.png", height: 90%)
//       ],
//       [],
//     )
//   ],
// )
//
// #simple_dia(
//   [Results --- Number of somatic alterations],
//   [
//     #set align(center + horizon)
//     #double_boxes(
//       auto,
//       90%,
//       [
//         #set align(center + horizon)
//         Variants in NCBI regions
//         #image("./Images/hist_regions.png", height: 90%)
//       ],
//       [],
//     )
//   ],
// )



// #simple_dia(
//   [Performances --- Phasing],
//   [
//     #set align(center + horizon)
//     #set text(16pt)
//     #double_boxes(
//       auto,
//       auto,
//       [
//         #set align(center + horizon)
//         #image("./Images/phasing_sch.png", height: 90%)
//       ],
//       [],
//     )
//   ],
// )
//
// #simple_dia(
//   [Performances --- Phasing],
//   [
//     #set align(center + horizon)
//     #set text(16pt)
//     #double_boxes(
//       auto,
//       70%,
//       [
//         #set align(center + horizon)
//         #image("./Images/phases.png", height: 90%)
//       ],
//       [],
//     )
//   ],
// )
//
// #simple_dia(
//   [🤖 SV calling -- inv7 case -- bp chromosome order],
//   [
//     #set align(center + horizon)
//     #set text(16pt)
//     #double_boxes(
//       auto,
//       auto,
//       [
//         #set align(center + horizon)
//         #image("./Images/graphviz_01.svg", height: 90%)
//       ],
//       [],
//     )
//   ],
// )
//
// #simple_dia(
//   [🤖 SV calling -- inv7 case -- paths visiting max bp],
//   [
//     #set align(center + horizon)
//     #set text(16pt)
//     #double_boxes(
//       auto,
//       auto,
//       [
//         #set align(center + horizon)
//         #image("./Images/graphviz_02.svg", height: 90%)
//       ],
//       [],
//     )
//   ],
// )
//
// #simple_dia(
//   [🤖 SV calling -- inv7 case -- simplification],
//   [
//     #set align(center + horizon)
//     #set text(16pt)
//     #double_boxes(
//       auto,
//       auto,
//       [
//         #set align(center + horizon)
//         #image("./Images/graphviz_03.svg", height: 90%)
//       ],
//       [],
//     )
//   ],
// )

#simple_dia(
  [🧬 Interesting results --- _HOXA9_],
  [
    #set align(center + horizon)

    #uncover(
      1,
      [
        #grid(
          columns: (60%, auto),
          gutter: 15pt,
          double_boxes(
            auto,
            auto,
            [
              #align(center, [*ME*])
              #v(12pt)
              - *Inv(7)(p15q34)* TRB/HOXA10
              - #raw("chr7:27,287,813_delins[ATGGGGGGGG_chr7:144,128,326inv]")
              - #raw("chr7:27,313,165_delins[GATGG_chr7:144,161,537inv]")
            ],
            [],
          ),
          double_boxes(
            auto,
            auto,
            figure(
              image("./Images/inv7.png", height: 60%),
              numbering: none,
              caption: [
                #set text(14pt)

                Résultats FISH break apart.

                #set text(10pt)
                Speleman, F et al. “A new recurrent inversion, inv(7)(p15q34), leads to
                transcriptional activation of HOXA10 and HOXA11 in a subset of T-cell acute
                lymphoblastic leukemias.” Leukemia vol. 19,3 (2005): 358-66.
              ],
            ),
            [],
          ),
        )
      ],
    )
  ],
)

#simple_dia(
  [🧬 Interesting results --- _HOXA9_],
  [
    #double_boxes(
      auto,
      auto,
      [
        #align(center, [*MA*])
        #v(12pt)

        - t(7;11)(p22;q23) likely *_KMT2A::TNRC18_*
        - #raw("chr11:118,503,451(KMT2A)_delins[CCCC_chr7:5476973(TNRC18)]")
        - Known fusion transcript (2 pediatric cases / 759 LAL. Meyer, C et al.
          Leukemia 2009)
        - RT-MLPA probes w/o TNRC18
      ],
      [],
    )

    #image("./Images/MANCUS_7_11.svg")
  ],
)

#simple_dia(
  [🧬 Interesting results --- _HOXA9_],
  [
    #double_boxes(
      auto,
      auto,
      [
        #align(center, [*BE*])
        #v(12pt)

        - Translocation t(2;9)(q14.1;q34.11) likely fusion transcript *_SET::DPP10_*
        - #raw("chr9:140,901,114(SET)_delins[GAACATAAAGAAAAAAA_chr2:116,043,899(DPP10)]")
        - *New fusion transcript in T-ALL* (only described one time in CRC: Xia, Li C et al.
          “Identification of large rearrangements in cancer genomes with barcode linked
          reads.” Nucleic acids research vol. 46,4 2018)
      ],
      [],
    )

    #image("./Images/bernier_set.svg")
  ],
)

#simple_dia(
  [👥 Cohort _TAL1_ --- n = 12],
  [
    #set align(center + horizon)
    #set text(16pt)
    #double_boxes(
      auto,
      auto,
      [
        #table(
          columns: (1fr, auto, auto, auto),
					inset: 5pt,
          align: (auto, center, center, center),
          stroke: colors.indigo,
          [*id*],
          [*X*],
          [*mécanisme*],
					[*interpretation*],

					[ACHITE],	text(fill: yellow)[12],	[TAL1::RPTOR t(1;17)], [✅],
					[BECERRA],	text(fill: yellow)[12],	[TCR::LMO2], [❓],
					[CAMARA], text(fill: green)[20], [insertion intronique _MYB_], [❓],
					[COLLE], text(fill: red)[7],	[], [],
					[DAHAN], text(fill: yellow)[13],	[duplication intronique en tandem _TAL1_ (ex2-3)], [❓],
					[DOUYERE],	text(fill: yellow)[22 pas mrd], [(BCL11B::TLX3)], [❓],
					[FALLE],	[_en cours_],	[], [],
					[GILLOUX],	text(fill: yellow)[15 pas mrd],	[pas d'altération locus _TAL1_], [❓],
					[HENAUX],	text(fill: yellow)[12], [insertion intronique de 9nt dans _TAL1_ (ex3-4)], [❓],
					[JEANSELME], text(fill: yellow)[14], [duplication inversée intronique de 19nt dans _DAB1_], [❓],
					[ROBIN],	text(fill: yellow)[14],	[LMO2::RAG1 del 11q], [❓],
					[SCHOLZ],	text(fill: yellow)[18 pas mrd], [Probable dup inversée chr2:26,269,840-32,135,324], [❓],
        )
      ],
      [],
    )
  ],
)

#simple_dia(
  [🧬 Interesting results --- _TAL1_],
  [
    #align(
      center + horizon,
      grid(
        columns: (auto, auto),
        gutter: 10pt,
        double_boxes(
          auto,
          auto,
          [
            #align(center, [*DAH*])
            #v(12pt)

            - Mono-allelic surexpression of TAL1.
            - Somatic tandem duplication between exon 2 and 3 of TAL1.
            - Also observed in ChIP-seq data showing broad H3K4me3 coverage.
          ],
          [],
        ),
        double_boxes(
          auto,
          auto,
          image("./Images/DAH_TAL1_ins.png", height: 75%),
          [],
        ),
      ),
    )
  ],
)

// #simple_dia(
//   [🧬 Interesting results: _TAL1_],
//   align(
//     center + horizon,
//     double_boxes(
//       auto,
//       60%,
//       align(center)[🌐 show CAMA MYB insertion on line…],
//
//       [],
//     ),
//   ),
// )

#simple_dia(
  [👥 Cohort _TLX1_ --- n = 8],
  [
    #set align(center + horizon)
    #set text(16pt)
    #double_boxes(
      auto,
      auto,
      [
        #table(
          columns: (1fr, auto, auto, auto),
					inset: 5pt,
          align: (auto, center, center, center),
          stroke: colors.indigo,
          [*id*],
          [*X*],
          [*mécanisme*],
					[*interpretation*],

					[AUBERT],	text(fill: green)[17],	[del 10q (10mb) ~ _TLX1_], [✅],
					[CHAMPION],	text(fill: green)[32],	[inv10], [✅],
					[LEVASSEUR], text(fill: green)[20], [inv10 (avec 5’ UTR ralongé)], [✅],
					[PARACHINI], text(fill: green)[17],	[t(10;14)], [✅],
					[PASSARD], text(fill: green)[18],	[chromothripsis du 10], [✅],
					[PAYSAN],	[_en cours_], [], [],
					[RIVOALEN],	text(fill: green)[19],	[inv10], [✅],
					[SALICETTO],	text(fill: yellow)[12 pas mrd],	[inv10], [✅],
        )
      ],
      [],
    )
  ],
)


#simple_dia(
  [🧬 Interesting results --- _TLX1_],
  [
    #align(
      center + horizon,
      grid(
        columns: (auto, auto),
        gutter: 10pt,
        [ #double_boxes(
            auto,
            auto,
            [
              #align(center, [*LEV*])
              #v(12pt)

              - Surexpression of TLX1.
              #uncover((2, 3), [- Inv10 ])
              #uncover(3, [- Modification of 3' UTR.])
            ],
            [],
          )
          #uncover(
            3,
            double_boxes(auto, auto, image("./Images/utr_tlx1.png"), []),
          )
        ],
        uncover(
          (2, 3),
          double_boxes(
            auto,
            auto,
            image("./Images/LEV_inv10_tlx1.png", height: 75%),
            [],
          ),
        ),
      ),
    )
  ],
)

#simple_dia(
  [🗣️ Discussion --- Poisson distribution & rare variants strategy]  ,
  double_boxes(auto, auto, align(center, image("./Images/freq_TRD_partners.png")), [])
)

#simple_dia(
  [🏁 Conclusions],
  [
    #set align(center + horizon)
    #double_boxes(
      auto,
      auto,
      [
        #align(center, [What is *done*])
        #v(12pt)
        #set list(marker: [✅])
        - The implementation of a robust and more informative whole-genome sequencing method.
        - The development of a pipeline for detecting somatic alterations (SNV, SV, viral insertion) as well as a simple way to visualize and interpret the results.
        - Compare missense/indels variant calling with NGS panel.
        - The integration, if available, of RNAseq / ChIPseq.
        - Develop a de novo assembly pipeline (better accuracy and visualization of SV).
        - Automate reporting.

      ],
      [],
    )
    #uncover(
      2,
      [
        #double_boxes(
          auto,
          auto,
          [
            #align(center, [*TODO*])
            #v(12pt)
            #set list(marker: [❌])
            - Functional experiments ?
            - Complete sequencing of cases (> 200).
            - Aggregate results by cohorts and tag recurrency (at gene and mutation levels).
          ],
          [],
        )
      ],
    )
  ],
)

#simple_dia(
  [💐 Remerciements],
  [
    #set align(center + horizon)
    #grid(
      columns: (auto, auto),
      double_boxes(
        auto,
        auto,
        [
          #set align(center + horizon)

          *The Necker team*

          Pr. Vahid Asnafi

          Dr. Patrick Villarese

          Dr. Agata Cieslak

          Coline Lefevre
        ],
        [],
      ),
      image("./Images/necker.svg"),
    )

    #grid(
      columns: (auto, auto),
      gutter: 10pt,
      image("./Images/amu.png", height: 33%),
      double_boxes(
        auto,
        auto,
        [
          #set align(center + horizon)

          *The TAGC team*

          Dr. Salvatore Spicuglia

          Dr. Guillaume Charbonnier

          Gaëlle Farah
        ],
        [],
      ),
    )
  ],
)