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["Supplementary Data 1: Sample overview"]
[]
["Dictionary"]
["Sample_ID","Samples Ids used in the manuscript"]
["Histopathology","Categorical variable indicating the tumor classification defined by  histopathology : Atypical, Typical, LCNEC, LCNEC combined SCLC, LCNEC combined ADC, LCNEC combined SqCC, SCLC, Carcinoid"]
["Molecular.subtype.based.on.George.et.al.,2018","Categorical variable indicating molecular subtype of LCNEC samples defined in George et al. 2018, Nat commun. Values : Type 1 LCNEC or Type 2 LNEC"]
["Stage_UICC","Categorical variable indicating tumor stage given by histopatologists based on the TNM. Values : I, Ia, IA1, IA2, IA3, IB, II, IIA, IIB, III, IIIA, IIIb, IIIC, IV, IVA, and NA (not available)"]
["WGS/WES","Categorical variable indicating the type of sequencing performed on DNA. Values : WES for whole exome sequencing, WGS for whole genome sequencing, WES/WGS when both sequencing were performed, and no when sequencing was not available/performed"]
["RNAseq","Binary variable indicating if transcriptome sequencing was performed on RNA (RNA-seq). Values : yes, no"]
["Epic 850K","Binary variable indicating if methylation assay  was performed (Epic 850K arrays). Values : yes, no"]
["Age","Numerical value of the patient age at diagnosis"]
["Age_class","Class of the patient age at diagnosis. Values: (15,40] , (40,60] , (60,90] , NA"]
["Sex","Categorical variable indicating the patient sex. Values: M for male and F for female, and NA"]
["Sex_inferred","Categorical variable indicating the patient inferred-sex using molecular data. Values: M for male and F for female"]
["Smoking_status","Categorical variable indicating the smoking status of the patient. Values: Never, Current, Former, Passive, NA"]
["Professional_exposure","Categorical variable indicating reported professional exposure"]
["Survival_censor","Categorical variable indicating the vital status of the patients. Values : alive, dead, NA, 0 (note: values 0 are reported from George et al., 2018 and were considered NA in the present study)"]
["Survival_months","Numerical value of the time between diagnosis and the last vital status (survival_censor)"]
["cluster_LNET","Cluster membership of the LNET samples. Clusters were defined based on the MOFA analysis using only the LNET samples"]
["cluster_LNEN","Cluster membership of the LNEN samples. Clusters were defined based on the MOFA analysis using the LNEN samples"]
["Neutrophil-to-Lymphocyte_ratio","Neutrophil to lymphocyte ratio estimated from RNA-seq data"]
["WES/WGS_source","Categorical variable indicating the whole exome/genome sequencing data sources. Values: New for sequencing newly performed for this paper, otherwise the papers containing the data are mentioned"]
["RNAseq_source","Categorical variable indicating the transcripome sequencing data sources. Values: New for sequencing newly performed for this paper, otherwise the papers containing the data are mentioned"]
["Epic_850K_source","Categorical variable indicating the methylation data sources. Values: New for sequencing newly performed and NA for samples without methylation data available "]
["MOFA LNEN+SCLC","Latent factors coordinates associated with MOFA latent factors based on the LNEN and SCLC samples. Five latent factors are provided (LF1-LF5.LNEN_SCLC)"]
["MOFA LNEN","Latent factors coordinates associated with MOFA latent factors based on the LNEN. Five latent factors are provided (LF1-LF5.LNEN)"]
["MOFA LNET+SCLC","Latent factors coordinates associated with MOFA latent factors based on the LNET and SCLC samples. Five latent factors are provided (LF1-LF5.LNET_SCLC)"]
["MOFA LNET","Latent factors coordinates associated with MOFA latent factors based on the LNET. Five latent factors are provided (LF1-LF5.LNET)"]
["Immune cell quantification","Quantification of the immune cells from RNA-seq data. 11 categories are reported for each sample with RNASeq data:  B.cell, Macrophages.M1, Macrophages.M2, Monocytes, Neutrophils, NK.cells, T.cells.CD4, T.cells.CD8, Tregs, Dendritic.cells, and Other"]
["Methylation-ML","Class probabilities resulting from the ML model trained on LNEN samples and on methylation features only. Methylation-ML_Atypical_prob, Methylation-ML_Typical_prob and Methylation-ML_LCNEC_prob correspond to the probabilities of being atypical, typical or LCNEC  respectively."]
["Expression-ML","Class probabilities resulting from the ML model trained on LNEN samples and on expression features only. Expression-ML_Atypical_prob, Expression-ML_Typical_prob and Expression-ML_LCNEC_prob correspond to the probabilities of being atypical, typical or LCNEC  respectively."]
["MKI67-ML","Class probabilities resulting from the ML model trained on LNEN samples and on MKI67 expression only. MKI67-ML_Atypical_prob, MKI67-ML_Typical_prob and MKI67-ML_LCNEC_prob correspond to the probabilities of being atypical, typical or LCNEC  respectively."]
["MOFA-ML","Class probabilities resulting from the ML model trained on LNEN samples and the MOFA latent factors. MOFA-ML_Atypical_prob, MOFA-ML_Typical_prob and MOFA-ML_LCNEC_prob correspond to the probabilities of being atypical, typical or LCNEC,  respectively."]
["ExpressionMethylation-ML","Class probabilities resulting from the ML model trained on LNEN samples and on both expression and methylation features. ExpressionMethylation-ML_Atypical_prob, ExpressionMethylation-ML_Typical_prob and ExpressionMethylation-ML_LCNEC_prob correspond to the probabilities of being atypical, typical or LCNEC  respectively."]
["ExpressionPC-ML","Class probabilities resulting from the ML model trained on LNEN samples and on the principal components computed based on expression data. ExpressionPC-ML_Atypical_prob, ExpressionPC-ML_Typical_prob and ExpressionPC-ML_LCNEC_prob:  probabilities of being atypical, typical or LCNEC,  respectively."]
["MethylationPC-ML","Class probabilities resulting from the ML model trained on LNEN samples and on methylation features only. MethylationPC-ML_Atypical_prob, MethylationPC-ML_Typical_prob and MethylationPC-ML_LCNEC_prob:  probabilities of being atypical, typical or LCNEC , respectively."]
[]
[]
[]
[{"$nulls":21},"MOFA LNEN+SCLC",{"$nulls":4},"MOFA LNEN",{"$nulls":4},"MOFA LNET+SCLC",{"$nulls":4},"MOFA LNET",{"$nulls":4},"Immune cell quantification",{"$nulls":10},"Methylation-ML",null,null,"Expression-ML",null,null,"MKI67-ML",null,null,"MOFA-ML",null,null,"ExpressionMethylation-ML",null,null,"ExpressionPC-ML",null,null,"MethylationPC-ML"]
["Sample_ID","Histopathology","Molecular.subtype.based.on.George.et.al.,2018","Stage_UICC","WGS/WES","RNAseq","Epic 850K","Age","Age_class","Sex","Sex_inferred","Smoking_status","Professional_exposure","Survival_censor","Survival_months","cluster_LNET","cluster_LNEN","Neutrophil-to-Lymphocyte_ratio","WES/WGS_source","RNAseq_source","Epic_850K_source","LF1.LNEN_SCLC","LF2.LNEN_SCLC","LF3.LNEN_SCLC","LF4.LNEN_SCLC","LF5.LNEN_SCLC","LF1.LNEN","LF2.LNEN","LF3.LNEN","LF4.LNEN","LF5.LNEN","LF1.LNET_SCLC","LF2.LNET_SCLC","LF3.LNET_SCLC","LF4.LNET_SCLC","LF5.LNET_SCLC","LF1.LNET","LF2.LNET","LF3.LNET","LF4.LNET","LF5.LNET","B.cells","Macrophages.M1","Macrophages.M2","Monocytes","Neutrophils","NK.cells","T.cells.CD4","T.cells.CD8","Tregs","Dendritic.cells","Other","Methylation-ML_Atypical_prob","Methylation-ML_Typical_prob","Methylation-ML_LCNEC_prob","Expression-ML_Atypical_prob","Expression-ML_Typical_prob","Expression-ML_LCNEC_prob","MKI67-ML_Atypical_prob","MKI67-ML_Typical_prob","MKI67-ML_LCNEC_prob","Mofa-ML_Atypical_prob","Mofa-ML_Typical_prob","Mofa-ML_LCNEC_prob","ExpressionMethylation-ML_Atypical_prob","ExpressionMethylation-ML_Typical_prob","ExpressionMethylation-ML_LCNEC_prob","ExpressionPC-ML_Atypical_prob","ExpressionPC-ML_Typical_prob","ExpressionPC-ML_LCNEC_prob","MethylationPC-ML_Atypical_prob","MethylationPC-ML_Typical_prob","MethylationPC-ML_LCNEC_prob"]
["LNEN002","Atypical","NA","IA1","WES","yes","yes",49,"(40,60]","M","M","Never","NA","alive",287.7,"Ca B","Ca B",0.5848228337,"new","new","new",0.719769257779114,0.631103633463735,-1.8367572058782,0.479062255327335,-0.887664677103489,-0.903407118217485,1.52744466464861,-0.38415834919951,0.935011403602169,-0.374202842251779,1.32384320927333,-0.542479489077765,0.411354724408043,0.510375480886921,0.213368134316617,-1.42084938235852,-0.0172648344699804,-2.42577663366783,-0.155566537430677,1.17413504274469,0.0135795334103834,0,0.0319096575060876,0.0188782104146515,0.0443697216058593,0.0198953550426932,0.00636877119646703,0.00347840556720627,0.0325465894383938,0,0.828973755818258,0.368,0.592,0.04,0.528,0.46,0.012,0.054,0.946,0,0.276,0.724,0,0.552,0.384,0.064,0.742,0.256,0.002,0.232,0.76,0.008]
["LNEN003","Atypical","NA","IA1","WES","yes","yes",17,"(15,40]","M","M","Never","NA","dead",100,"Ca A2","Ca A",0.2849128917,"new","new","new",0.515467440093072,0.83240047689809,0.587220283868343,1.26225237710726,-0.216151007742394,-0.768599248277947,-0.496340432994792,-1.11287811282095,0.314755939452238,-0.570778435607578,-0.352125007819716,-0.677568149084066,0.937557901423396,0.131637340463233,-0.0958072913790164,0.23239236885215,0.946003555629581,-0.498951271601527,0.109764071083437,-0.250218075377531,0.00742335499435669,0,0.0371179912279099,0,0.0328729013254799,0.014939969149255,0.00152307130389668,0.00584853424657885,0.0856438484437768,0.00844817645128478,0.806182152857461,0.304,0.694,0.002,0.218,0.778,0.004,0.132,0.868,0,0.268,0.73,0.002,0.296,0.692,0.012,0.26,0.73,0.01,0.294,0.704,0.002]
["LNEN004","Atypical","NA","IB","WES","yes","yes",18,"(15,40]","M","M","Current","NA","alive",163.2,"Ca A2","Ca A",0.4042901599,"new","new","new",0.675836290162986,0.763466463561932,0.676429080337072,1.46947353807026,-0.109775775360312,-0.867596158154929,-0.550324932514279,-1.21747988774307,0.206255515913336,-0.391980618452154,-0.441384495950489,-0.632212044004216,1.16388079593747,0.0975486306521119,-0.139719888071083,0.310065390550476,1.09802944205061,-0.298400674624299,0.084402232142359,-0.243300573132204,0.00433611208923216,0,0.032169846372906,0,0.0271138086476076,0.00862397877768001,0.00126263016912637,0.0167870609689079,0.0360554383204115,0.017430563116739,0.856220561537389,0.264,0.732,0.004,0.218,0.778,0.004,0.944,0.056,0,0.102,0.898,0,0.322,0.676,0.002,0.202,0.796,0.002,0.486,0.514,0]
["LNEN005","Atypical","NA","IB","WES","yes","yes",80,"(60,90]","M","M","Former","Asbestos (fibres)","alive",144.6,"Ca A1","LCNEC",5.1071444758,"new","new","new",-1.51751075272366,0.0888499065641471,-0.252646882600827,-0.0219122968889354,0.634338550553083,1.33971221609828,0.157535963123452,-0.103464259974107,-0.602934867476274,-2.60855759173935,0.248274104315019,0.119709278471109,-0.774860912948155,-0.2293807222235,3.26266858364005,-0.152528170176307,-0.697455409367199,0.788747601705724,-3.79658831934917,-2.39064462690764,0.0113438226756701,0.0143578856801024,0.038973855046084,0,0.168459308430444,0.00379313990742514,0,0.00424975499482203,0.0135983113806901,0,0.745223921884763,0.17,0.056,0.774,0.378,0.17,0.452,0.43,0,0.57,0.096,0,0.904,0.19,0.134,0.676,0.04,0.01,0.95,0.372,0.064,0.564]
["LNEN006","Atypical","NA","IB","WES","yes","yes",58,"(40,60]","F","F","Never","NA","alive",166.3,"Ca A2","Ca A",0.1768211325,"new","new","new",0.563452019085657,0.584753169926641,0.11865594653276,0.870346149733487,0.467904318455691,-0.666653208567382,-0.134023147926902,-0.830309190844229,-0.439988201423312,-0.083994079341475,-0.194557803065368,-0.481833176140919,0.866704719239904,-0.105514287270557,0.433882961413759,0.128217192357008,0.657046157329334,0.401901665931852,-0.733895938339971,0.258134031409656,0.00465926135568438,6.65072035820823E-005,0.0360404131084233,0.0314407864533728,0.013102949986797,0.0117019014599666,0.0308731479594029,0.00432455294045855,0.022543986997465,0.00615318453955614,0.839093307995291,0.358,0.636,0.006,0.414,0.57,0.016,0.006,0.994,0,0.676,0.312,0.012,0.394,0.58,0.026,0.632,0.366,0.002,0.312,0.658,0.03]
["LNEN007","Atypical","NA","IIIA","WES","yes","yes",66,"(60,90]","M","M","Never","NA","dead",50.7,"Ca B","Ca B",0.6449616904,"new","new","new",0.608829605448104,0.76005908756212,-3.32883153461062,0.335791015309484,0.156304566346692,-0.846947354265902,2.68256269222004,-0.299491102290113,-0.253069987337354,-0.489407603004811,2.10001957681303,-0.529659061452942,0.376080591308693,-0.20955982082758,-1.04993249872917,-1.98822163676241,0.223908577496739,1.2968783393813,1.1397627352981,-0.324508466689057,0.00778886057049232,0,0.0303661207317146,0,0.0497913130712414,0.0143340453643537,0,0.00523264395565372,0.0498448696294263,0.00802270220714934,0.834619444469969,0.762,0.224,0.014,0.558,0.43,0.012,0.95,0.05,0,0.788,0.212,0,0.838,0.144,0.018,0.702,0.286,0.012,0.964,0.028,0.008]
["LNEN008","Atypical","NA","IB","no","yes","no",64,"(60,90]","M","M","Current","NA","alive",204.3,"Ca B","Ca B",0.293289923,"NA","new","NA",0.885112277410916,0.774840211354115,-2.88329539700873,0.191563126718029,0.790031981586098,-1.19973623817646,2.29145059617623,-0.314345489739475,-0.900254353425298,-0.0826132962908636,1.80172485868206,-0.610581413822592,-0.00108897447701225,0.62713193129,0.0151375448273932,-1.773094684112,0.225757683689519,-2.36491149994869,0.605498409025245,1.14659178825795,0.00407606647514217,0,0.028962521432024,0.0393565449623302,0.0215166570790657,0.0357385558386649,0,0.00516764978586984,0.0283808249284377,0,0.836801179498465,"NA","NA","NA",0.408,0.572,0.02,0,1,0,0.312,0.688,0,"NA","NA","NA",0.622,0.378,0,"NA","NA","NA"]
["LNEN009","Atypical","NA","IV","WES","yes","yes",49,"(40,60]","M","M","NA","NA","dead",5.3,"Ca B","Ca B",0.2837067541,"new","new","new",-0.0681764326970687,0.31663580762296,-2.2725475145004,0.933545195992278,0.808710577481821,-0.00921778103813931,1.79563332159611,-0.849712143603344,-0.821237778183005,1.8718197138507,1.37998978987033,-0.158591291773228,0.85978425339545,-0.446106911127582,0.380450794259568,-1.29446549120461,-0.159916028790186,1.47699038927053,-1.40833676549132,2.50275282976401,0.0127758132922986,0.0120648821773896,0.0593770811379066,0,0.0244392719332356,0.0281156198432945,0,0.0151874150646311,0.0300638734081575,0.000652207779331705,0.817323835363755,0.58,0.27,0.15,0.724,0.198,0.078,0.338,0.662,0,0.638,0.242,0.12,0.618,0.184,0.198,0.74,0.194,0.066,0.598,0.384,0.018]
["LNEN010","Atypical","NA","IB","WES","yes","yes",58,"(40,60]","M","M","Never","NA","dead",84,"Ca B","Ca B",0.0773103024,"new","new","new",0.59072877055222,0.608164122056944,-3.77371907396866,0.279156197590127,0.218238616258737,-0.777044127453109,3.06441523181592,-0.190256390779947,-0.313552707326517,-0.124664757261481,2.36552683168145,-0.417357475524563,0.345718425945648,-0.25208840088103,-0.856485430544231,-2.23768453054852,0.0786898622781333,1.48064792481689,1.00720346078104,-0.199118603751702,0.0148599302692181,0,0.0199933496556115,0.051814016062694,0.0097929789854345,0.0222176846681611,0,0.0106643426398769,0.0789291156881429,0,0.791728582030861,0.72,0.266,0.014,0.76,0.23,0.01,0.744,0,0.256,0.938,0.062,0,0.892,0.098,0.01,0.976,0.024,0,0.896,0.1,0.004]
["LNEN011","Atypical","NA","IIB","WES","yes","yes",52,"(40,60]","F","F","NA","NA","alive",236,"Ca A2","Ca A",0.5017306439,"new","new","new",0.803454771190405,0.705018478924451,0.925202355721793,1.24941195950821,0.105946659273393,-0.944551634767152,-0.764461254148755,-1.08032847456255,-0.00999565165148081,-0.159762650387983,-0.669225209278786,-0.604158817722694,1.12744582889424,0.0724957038023422,0.0657088938839521,0.526703834828315,1.01822538151552,-0.270295769096292,-0.143702381494267,0.146916466553751,0.00256335718031581,0,0.0415823077060024,0,0.0355582129856469,0.0139838915704166,0.0443530528654285,0.000858235065993833,0.00911258394048032,0.0406806964585856,0.81130766222713,0.23,0.77,0,0.12,0.876,0.004,0,1,0,0,1,0,0.298,0.694,0.008,0.108,0.89,0.002,0.056,0.944,0]
["LNEN012","Atypical","NA","IIIC","no","yes","no",70,"(60,90]","F","F","NA","NA","alive",111.7,"Ca A1","LCNEC",0.9622631233,"NA","new","NA",-1.0268018054386,-0.0161024395169236,-0.591052141997206,0.130015908239271,-0.600524153170457,0.766014166878896,0.437351263247362,0.194855121938484,0.385592205337576,-2.29354990139908,0.585014711432919,0.230208748668304,0.273796720672517,-3.15113726823387,0.928783293492842,-0.41819346423602,-0.640639093333467,4.10654256224063,-2.63964447111112,-4.54081828225011,0.0154587010705939,0.0194519497387763,0.04575543552215,0,0.0517423835775814,0.0133125710326435,0,0.0169370353996774,0.00806324657974677,0.0255940683842226,0.803684608694608,"NA","NA","NA",0.206,0.076,0.718,0.204,0,0.796,0.028,0.04,0.932,"NA","NA","NA",0.084,0.016,0.9,"NA","NA","NA"]
["LNEN013","Atypical","NA","IV","WES","yes","yes",58,"(40,60]","F","F","Never","NA","alive",117.8,"Ca A1","Ca A",0,"new","new","new",0.336810967401652,0.211572640817694,0.85503129851048,-2.13839255006834,0.376354654084765,-0.331725742782869,-0.788723286723024,1.5426808313742,-0.419386243964225,0.579481432547964,-0.60000955683388,-0.016763327308731,-1.62167353228693,-0.116457222205284,-0.0162427516748195,0.753942942509594,-1.26430541759981,0.318502547062583,-0.0699259384539573,0.589650116597771,0.00746500373353338,0.00384105111685003,0.0173277328821898,0,0,0.0349486340286136,0.0395368292811769,0.0118026797241504,0.0361324323533555,0.0731193780152197,0.775826258864911,0.34,0.596,0.064,0.372,0.528,0.1,1,0,0,0.212,0.746,0.042,0.204,0.654,0.142,0.542,0.222,0.236,0.168,0.828,0.004]
["LNEN014","Atypical","NA","IB","WES","yes","yes",58,"(40,60]","F","F","Never","NA","alive",90.5,"Ca B","Ca B",0,"new","new","new",0.708466001711187,0.609475050060637,-3.11436371482978,0.148661239630782,0.0497008265242617,-0.874415808098988,2.52412710324521,-0.123203724074417,-0.10960914256844,-0.14938524081974,2.00134186569356,-0.459763336751632,0.273756297631934,-0.0653328437890094,-0.571429510442004,-1.91534592454555,0.0258236531853607,0.587272763229755,0.787373276906119,0.175489494898739,0.00164260656594027,0,0,0.165731367307547,0,0.0398677596965361,0,0.0083787193126297,0.036731175192287,0,0.74764837192506,0.672,0.318,0.01,0.75,0.226,0.024,0,1,0,0.744,0.256,0,0.806,0.174,0.02,0.856,0.144,0,0.508,0.474,0.018]
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["S00613","LCNEC combined SCLC","Type 2 LCNEC","IV","no","yes","no",47,"(40,60]","M","M","Current","NA","dead",38,"NA","LCNEC",0.3529382847,"NA","George et al., 2018","NA",-0.984753683474898,-0.274308202167223,-0.214654366898534,0.208650426039991,-1.48400941375655,0.946063351360937,0.197538232954865,0.281264281109394,1.82768109562522,-1.20751456924731,"NA","NA","NA","NA","NA","NA","NA","NA","NA","NA",0.00189489042939492,0.00950597748409091,0.0141907694092194,0,0.0516291531185975,0.0460999751657806,0.0787151823012902,0.00424748052443289,0.0153262706434114,0.0509449378675228,0.72744536305626,"NA","NA","NA",0.074,0.018,0.908,0,0,1,0.006,0,0.994,"NA","NA","NA",0.11,0.002,0.888,"NA","NA","NA"]
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