Papers.md
... ...
@@ -57,85 +57,37 @@ bibliography: 'morinlab.bib'
57 57
58 58
|Entity|Method|Paired samples|Unpaired samples|Cell lines|Example gene|Study|
59 59
|:-:|:-:|:-:|:-:|:-:|:-:|:-------:|
60
-|DLBCL|Sanger|0|5|0|BCL2|[@tanakaFrequentIncidenceSomatic1992](papers/tanakaFrequentIncidenceSomatic1992.md)|
61
-|BL|Sanger|0|0|9|MYC|[@johnstonCmycHypermutationBurkitt1992](papers/johnstonCmycHypermutationBurkitt1992.md)|
62
-|DLBCL|Sanger|11|28|0|MYC|[@pasqualucciHypermutationMultipleProtooncogenes2001](papers/pasqualucciHypermutationMultipleProtooncogenes2001.md)|
63
-|BL|Sanger|0|24|0|TP53|[@wildaInactivationARFMDM2p53Pathway2004](papers/wildaInactivationARFMDM2p53Pathway2004.md)|
64
-|DLBCL|Sanger|134|0|20|PRDM1|[@pasqualucciInactivationPRDM1BLIMP12006](papers/pasqualucciInactivationPRDM1BLIMP12006.md)|
65 60
|PMBL|Sanger||||GPR126|[@wenigerMutationsTumorSuppressor2006](papers/wenigerMutationsTumorSuppressor2006.md)|
66
-|DLBCL|Sanger||||FAS|[@schollMutationsRegionFAS2007](papers/schollMutationsRegionFAS2007.md)|
67
-|DLBCL|Sanger|6|217|21|CARD11|[@lenzOncogenicCARD11Mutations2008](papers/lenzOncogenicCARD11Mutations2008.md)|
68
-|DLBCL|Sanger||||NFKBIA|[@lakeMutationsNFKBIAEncoding2009](papers/lakeMutationsNFKBIAEncoding2009.md)|
69
-|DLBCL|Sanger|0|101||TNFAIP3|[@compagnoMutationsMultipleGenes2009](papers/compagnoMutationsMultipleGenes2009.md)|
70 61
|PMBL|Sanger||||STAT6|[@ritzRecurrentMutationsSTAT62009](papers/ritzRecurrentMutationsSTAT62009.md)|
71 62
|PMBL|Sanger||||TNFAIP3|[@schmitzTNFAIP3A20Tumor2009](papers/schmitzTNFAIP3A20Tumor2009.md)|
72
-|FL|Sanger|11|251|0|TNFRSF14|[@cheungAcquiredTNFRSF14Mutations2010](papers/cheungAcquiredTNFRSF14Mutations2010.md)|
73
-|DLBCL/FL|RNA-seq/WGS|1|31|7|EZH2|[@morinSomaticMutationsAltering2010](papers/morinSomaticMutationsAltering2010.md)|
74
-|DLBCL|Sanger|0|382|20|MYD88|[@ngoOncogenicallyActiveMYD882011](papers/ngoOncogenicallyActiveMYD882011.md)|
75
-|DLBCL|RNA-seq/WGS|14|103|10|B2M|[@morinFrequentMutationHistonemodifying2011](papers/morinFrequentMutationHistonemodifying2011.md)|
76
-|DLBCL|exome|6|92|23|CD36|[@pasqualucciAnalysisCodingGenome2011](papers/pasqualucciAnalysisCodingGenome2011.md)|
77
-|DLBCL/FL|exome|7|134|0|CREBBP|[@pasqualucciInactivatingMutationsAcetyltransferase2011](papers/pasqualucciInactivatingMutationsAcetyltransferase2011.md)|
78
-|DLBCL|exome/Sanger||||BRAF|[@tiacciBRAFMutationsHairycell2011](papers/tiacciBRAFMutationsHairycell2011.md)|
79 63
|MZL|Sanger||||BIRC3|[@rossiAlterationBIRC3Multiple2011](papers/rossiAlterationBIRC3Multiple2011.md)|
80 64
|MZL|exome||||ARID1A|[@rossiCodingGenomeSplenic2012](papers/rossiCodingGenomeSplenic2012.md)|
81
-|BL|RNA-seq/WGS/exome||53||CCND3|[@richterRecurrentMutationID32012](papers/richterRecurrentMutationID32012.md)|
82
-|DLBCL|Sanger||||MIR142|[@kwanhianMicroRNA142Mutated202012](papers/kwanhianMicroRNA142Mutated202012.md)|
83
-|DLBCL|WGS|40|0|0|CXCR4|[@khodabakhshiRecurrentTargetsAberrant2012](papers/khodabakhshiRecurrentTargetsAberrant2012.md)|
84 65
|PMBL|Array/Sanger||||MAP3K14|[@ottoGeneticLesionsTRAF32012](papers/ottoGeneticLesionsTRAF32012.md)|
85
-|DLBCL|exome|55|0|0|ACTB|[@lohrDiscoveryPrioritizationSomatic2012](papers/lohrDiscoveryPrioritizationSomatic2012.md)|
86 66
|MZL|Panel||||CARD11|[@yanBCRTLRSignaling2012](papers/yanBCRTLRSignaling2012.md)|
87
-|BL|exome|| ||ACAD9|[@loveGeneticLandscapeMutations2012](papers/loveGeneticLandscapeMutations2012.md)|
88
-|BL|RNA-seq||||C16orf48|[@schmitzBurkittLymphomaPathogenesis2012](papers/schmitzBurkittLymphomaPathogenesis2012.md)|
89 67
|MZL|Array/Sanger||||ATM|[@braggioGenomicAnalysisMarginal2012](papers/braggioGenomicAnalysisMarginal2012.md)|
90 68
|MCL|WGS/exome||||ABCA3|[@beaLandscapeSomaticMutations2013](papers/beaLandscapeSomaticMutations2013.md)|
91
-|DLBCL|exome|34|39| 21|ARID1A|[@zhangGeneticHeterogeneityDiffuse2013](papers/zhangGeneticHeterogeneityDiffuse2013.md)|
92
-|DLBCL|Sanger|0|0| 6|EBF1|[@bohleRoleEarlyBcell2013](papers/bohleRoleEarlyBcell2013.md)|
93
-|DLBCL|WGS|40|0|13|ABI3BP|[@morinMutationalStructuralAnalysis2013](papers/morinMutationalStructuralAnalysis2013.md)|
94 69
|MZL|exome||||AMOTL1|[@parryWholeExomeSequencing2013](papers/parryWholeExomeSequencing2013.md)|
95 70
|MCL|exome||||ANK2|[@zhangGenomicLandscapeMantle2014](papers/zhangGenomicLandscapeMantle2014.md)|
96 71
|PMBL|WGS/Sanger||||PTPN1|[@gunawardanaRecurrentSomaticMutations2014](papers/gunawardanaRecurrentSomaticMutations2014.md)|
97
-|BL|Sanger||||ARHGEF1|[@muppidiLossSignalingGa132014](papers/muppidiLossSignalingGa132014.md)|
98
-|BL|RNA-seq|0|20 |0|CCNF|[@abateDistinctViralMutational2015](papers/abateDistinctViralMutational2015.md)|
99
-|DLBCL|Sanger|24|0|0 |STAT6|[@yildizActivatingSTAT6Mutations2015](papers/yildizActivatingSTAT6Mutations2015.md)|
100 72
|PMBL|Sanger||||CIITA|[@mottokGenomicAlterationsCIITA2015](papers/mottokGenomicAlterationsCIITA2015.md)|
101 73
|PMBL|Sanger||||CD58|[@schneiderAlterationsCD58Gene2015](papers/schneiderAlterationsCD58Gene2015.md)|
102 74
|PMBL|exome||||ARIH2|[@reichelFlowSortingExome2015](papers/reichelFlowSortingExome2015.md)|
103
-|DLBCL|Sanger||||MAP2K1|[@shinBRAFV600EMAP2K12015](papers/shinBRAFV600EMAP2K12015.md)|
104 75
|MZL|exome|| ||KLHL6|[@ganapathiGeneticLandscapeDural2016](papers/ganapathiGeneticLandscapeDural2016.md)|
105
-|DLBCL|exome|14|0|0|XPO1|[@mareschalWholeExomeSequencing2016](papers/mareschalWholeExomeSequencing2016.md)|
106
-|FL|WGS|3|3| (100.0)|ATP6AP1|[@okosunRecurrentMTORC1activatingRRAGC2016](papers/okosunRecurrentMTORC1activatingRRAGC2016.md)|
107 76
|PMBL|Sanger|1|1| (100.0)|XPO1|[@jardinRecurrentMutationsExportin2016](papers/jardinRecurrentMutationsExportin2016.md)|
108 77
|PMBL|exome/Sanger|1|1| (100.0)|NFKBIE|[@mansouriFrequentNFKBIEDeletions2016](papers/mansouriFrequentNFKBIEDeletions2016.md)|
109
-|FL|exome|1|1 |(100.0)|MAP2K1|[@louissaintPediatrictypeNodalFollicular2016](papers/louissaintPediatrictypeNodalFollicular2016.md)|
110 78
|MZL|exome/panel|31|8| (25.8)|ABCA13|[@spinaGeneticsNodalMarginal2016](papers/spinaGeneticsNodalMarginal2016.md)|
111 79
|MCL|exome|1|1 |(100.0)|CARD11|[@wuGeneticHeterogeneityPrimary2016](papers/wuGeneticHeterogeneityPrimary2016.md)|
112
-|DLBCL|exome|2|2| (100.0)|NFKBIE|[@morinGeneticLandscapesRelapsed2016](papers/morinGeneticLandscapesRelapsed2016.md)|
113 80
|MZL|panel|2|0| (0.0)|CD9B|[@vandenbrandRecurrentMutationsGenes2017](papers/vandenbrandRecurrentMutationsGenes2017.md)|
114 81
|MZL|exome|28|2| (7.1)|ARHGAP20|[@jalladesExomeSequencingIdentifies2017](papers/jalladesExomeSequencingIdentifies2017.md)|
115
-|FL|exome|22|17 |(77.3)|ARID1A|[@krysiakRecurrentSomaticMutations2017](papers/krysiakRecurrentSomaticMutations2017.md)|
116
-|DLBCL|exome|3|3 |(100.0)|BTK|[@albuquerqueEnhancingKnowledgeDiscovery2017](papers/albuquerqueEnhancingKnowledgeDiscovery2017.md)|
117
-|DLBCL|exome|59|6 |(10.2)|ANKRD17|[@reddyGeneticFunctionalDrivers2017](papers/reddyGeneticFunctionalDrivers2017.md)|
118 82
|PMBL|exome|10|1 |(10.0)|AKAP6|[@tiacciPervasiveMutationsJAKSTAT2018](papers/tiacciPervasiveMutationsJAKSTAT2018.md)|
119
-|DLBCL|exome|19|2 |(10.5)|CCL4|[@chapuyMolecularSubtypesDiffuse2018](papers/chapuyMolecularSubtypesDiffuse2018.md)|
120 83
|PMBL|Sanger|1|1 |(100.0)|IL4R|[@viganoSomaticIL4RMutations2018](papers/viganoSomaticIL4RMutations2018.md)|
121
-|DLBCL|WGS|19|7| (36.8)|AICDA|[@arthurGenomewideDiscoverySomatic2018](papers/arthurGenomewideDiscoverySomatic2018.md)|
122
-|DLBCL|exome|16|7| (43.8)|CXCR5|[@schmitzGeneticsPathogenesisDiffuse2018](papers/schmitzGeneticsPathogenesisDiffuse2018.md)|
123 84
|PMBL|exome|7|4| (57.1)|ACTB|[@wienandGenomicAnalysesFlowsorted2019](papers/wienandGenomicAnalysesFlowsorted2019.md)|
124
-|BL|exome|1|0 |(0.0)|KMT2C|[@zhouSporadicEndemicBurkitt2019](papers/zhouSporadicEndemicBurkitt2019.md)|
125
-|BL|RNA-seq/exome|39|4| (10.3)|ALPK2|[@paneaWholeGenomeLandscape2019](papers/paneaWholeGenomeLandscape2019.md)|
126
-|BL|WGS|13|9| (69.2)|BACH2|[@grandeGenomewideDiscoverySomatic2019](papers/grandeGenomewideDiscoverySomatic2019.md)|
127 85
|PMBL|exome|21|6| (28.6)|CISH|[@mottokIntegrativeGenomicAnalysis2019](papers/mottokIntegrativeGenomicAnalysis2019.md)|
128 86
|MCL|WGS|5|3| (60.0)|BCOR|[@nadeuGenomicEpigenomicInsights2020](papers/nadeuGenomicEpigenomicInsights2020.md)|
129
-|FL|panel|1|1| (100.0)|CTSS|[@barariaCathepsinAlterationsInduce2020](papers/barariaCathepsinAlterationsInduce2020.md)|
130
-|DLBCL|exome/panel|1|1 |(100.0)|MS4A1|[@rushtonGeneticEvolutionaryPatterns2020](papers/rushtonGeneticEvolutionaryPatterns2020.md)|
131 87
|MCL|WGS/exome|7|6 |(85.7)|B2M|[@pararajalingamCodingNoncodingDrivers2020](papers/pararajalingamCodingNoncodingDrivers2020.md)|
132 88
|PMBL|panel|10|1 |(10.0)|ACTG1|[@deschGenotypingCirculatingTumor2020](papers/deschGenotypingCirculatingTumor2020.md)|
133
-|DLBCL|WGS|38|3 |(7.9)|ACTG1|[@hubschmannMutationalMechanismsShaping2021](papers/hubschmannMutationalMechanismsShaping2021.md)|
134 89
|PMBL|exome|11|5 |(45.5)|ABCA13|[@sarkozyMutationalLandscapeGray2021](papers/sarkozyMutationalLandscapeGray2021.md)|
135 90
|PMBL|exome|14|6 |(42.9)|BIRC3|[@dunsCharacterizationDLBCLPMBL2021](papers/dunsCharacterizationDLBCLPMBL2021.md)|
136
-|BL|panel|25|0| (0.0)|ADAMTS5|[@burkhardtClinicalRelevanceMolecular2022](papers/burkhardtClinicalRelevanceMolecular2022.md)|
137
-|BL|WGS|6|2| (33.3)|CDKN2C|[@thomasGeneticSubgroupsInform2023](papers/thomasGeneticSubgroupsInform2023.md)|
138
-|FL|exome|20|1| (5.0)|ABL2|[@russler-germainMutationsAssociatedProgression2023](papers/russler-germainMutationsAssociatedProgression2023.md)|
139 91
|PMBL|exome|7|2| (28.6)|ARID5B|[@gomezUltraDeepSequencingReveals2023](papers/gomezUltraDeepSequencingReveals2023.md)|
140 92
141 93