#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 #v(10pt) ], [], ) #double_boxes( auto, auto, [ #image("./Images/histo_ages.png") ], [Internal unpublished data], ) ], ) #simple_dia( [👨‍⚕️ Model --- T-ALL ], [ #double_boxes( auto, auto, [ #set align(center + horizon) #v(10pt) Acute lymphoblastic leukemia is a rare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 ], [], ), ) ], )