diff --git a/conf/subtypes.yml b/conf/subtypes.yml index a8f8d81..3cd6967 100644 --- a/conf/subtypes.yml +++ b/conf/subtypes.yml @@ -1,6 +1,6 @@ base: &base aneuploidy: - - hyperdiploid + - high hyperdiploid - low hyperdiploid - iAMP21 ph-group: @@ -29,11 +29,10 @@ base: &base - NUTM1-r Control: - Control - dnam: <<: *base aneuploidy: - - hyperdiploid + - high hyperdiploid - low hyperdiploid - iAMP21 - hypodiploid diff --git a/data/signatures/signature_cpgs_v3.csv b/data/signatures/signature_cpgs_v3.csv index 944a386..a367ed7 100644 --- a/data/signatures/signature_cpgs_v3.csv +++ b/data/signatures/signature_cpgs_v3.csv @@ -15,40 +15,40 @@ aneuploidy,14.5,cg22787468,0.0035416452499653778,0.9617316784506511,0.9614220416 aneuploidy,14.5,cg23715732,0.0004908724704964784,0.9617316784506511,0.9614220416217418,0.9617541156175394,17.0,RPTOR;RPTOR, RPTOR aneuploidy,14.5,cg24467190,0.0009690699532818086,0.9617316784506511,0.9614220416217418,0.9617541156175394,2.0,DNAJB2;DNAJB2, DNAJB2 aneuploidy,14.5,cg24968629,0.0032293394475320864,0.9617316784506511,0.9614220416217418,0.9617541156175394,22.0,CELSR1, CELSR1 -hyperdiploid,4.0,cg01791669,0.0006933870801414055,0.9844372677935618,0.9821678898565079,0.9852845664177959,12.0,SSH1;SSH1;SSH1, SSH1 -hyperdiploid,4.0,cg02696971,0.0005063440118138447,0.9844372677935618,0.9821678898565079,0.9852845664177959,3.0,CBLB, CBLB -hyperdiploid,4.0,cg02846963,0.0016218278469571766,0.9844372677935618,0.9821678898565079,0.9852845664177959,4.0,NA, -hyperdiploid,4.0,cg03001048,0.0011067685000126835,0.9844372677935618,0.9821678898565079,0.9852845664177959,1.0,NOS1AP;NOS1AP, NOS1AP -hyperdiploid,4.0,cg03976877,0.001559897828863304,0.9844372677935618,0.9821678898565079,0.9852845664177959,7.0,VIPR2;VIPR2, VIPR2 -hyperdiploid,4.0,cg04970438,0.0005839686710663772,0.9844372677935618,0.9821678898565079,0.9852845664177959,10.0,TAF3, TAF3 -hyperdiploid,4.0,cg05184729,0.0006880496500216584,0.9844372677935618,0.9821678898565079,0.9852845664177959,5.0,NA, -hyperdiploid,4.0,cg06834427,0.0008560436678741736,0.9844372677935618,0.9821678898565079,0.9852845664177959,2.0,NA, -hyperdiploid,4.0,cg07543883,0.0004591176505960928,0.9844372677935618,0.9821678898565079,0.9852845664177959,19.0,ANGPTL6;ANGPTL6, ANGPTL6 -hyperdiploid,4.0,cg08202165,0.0011356967583671107,0.9844372677935618,0.9821678898565079,0.9852845664177959,6.0,NA, -hyperdiploid,4.0,cg08376828,0.000863090676883757,0.9844372677935618,0.9821678898565079,0.9852845664177959,10.0,NA, -hyperdiploid,4.0,cg08882216,0.001445133815026023,0.9844372677935618,0.9821678898565079,0.9852845664177959,7.0,EPHB6, EPHB6 -hyperdiploid,4.0,cg09719124,0.0007201004771551343,0.9844372677935618,0.9821678898565079,0.9852845664177959,3.0,LMCD1, LMCD1 -hyperdiploid,4.0,cg09894698,0.0006092814319926413,0.9844372677935618,0.9821678898565079,0.9852845664177959,11.0,ASCL2, ASCL2 -hyperdiploid,4.0,cg10063047,0.0009468274925516919,0.9844372677935618,0.9821678898565079,0.9852845664177959,21.0,FTCD;FTCD, FTCD -hyperdiploid,4.0,cg10206933,0.001218846081311591,0.9844372677935618,0.9821678898565079,0.9852845664177959,10.0,BNIP3, BNIP3 -hyperdiploid,4.0,cg10362869,0.0005226053639846602,0.9844372677935618,0.9821678898565079,0.9852845664177959,2.0,NCKAP5;NCKAP5, NCKAP5 -hyperdiploid,4.0,cg10619342,0.001171910087945308,0.9844372677935618,0.9821678898565079,0.9852845664177959,15.0,LOC390594, LOC390594 -hyperdiploid,4.0,cg11189837,0.0007595868220523441,0.9844372677935618,0.9821678898565079,0.9852845664177959,21.0,ADAMTS1, ADAMTS1 -hyperdiploid,4.0,cg11199770,0.002369956189339993,0.9844372677935618,0.9821678898565079,0.9852845664177959,19.0,TSHZ3, TSHZ3 -hyperdiploid,4.0,cg13794530,0.0008076628352490202,0.9844372677935618,0.9821678898565079,0.9852845664177959,7.0,VIPR2;VIPR2, VIPR2 -hyperdiploid,4.0,cg15057852,0.00038785328278000277,0.9844372677935618,0.9821678898565079,0.9852845664177959,20.0,KIF16B, KIF16B -hyperdiploid,4.0,cg16200531,0.0009490587015759679,0.9844372677935618,0.9821678898565079,0.9852845664177959,2.0,NA, -hyperdiploid,4.0,cg17090401,0.0004038314176245101,0.9844372677935618,0.9821678898565079,0.9852845664177959,4.0,FAT1, FAT1 -hyperdiploid,4.0,cg17716765,0.002846892887401596,0.9844372677935618,0.9821678898565079,0.9852845664177959,15.0,APBA2;APBA2, APBA2 -hyperdiploid,4.0,cg20663432,0.0016308789793530857,0.9844372677935618,0.9821678898565079,0.9852845664177959,12.0,ANO2, ANO2 -hyperdiploid,4.0,cg20719675,0.0004429979070884313,0.9844372677935618,0.9821678898565079,0.9852845664177959,2.0,CHRNA1;CHRNA1, CHRNA1 -hyperdiploid,4.0,cg23320499,0.0016139095838665,0.9844372677935618,0.9821678898565079,0.9852845664177959,12.0,DUSP16, DUSP16 -hyperdiploid,4.0,cg23584087,0.0019535452447866724,0.9844372677935618,0.9821678898565079,0.9852845664177959,13.0,KL, KL -hyperdiploid,4.0,cg25857569,0.0010910210025555317,0.9844372677935618,0.9821678898565079,0.9852845664177959,3.0,PPM1L, PPM1L -hyperdiploid,4.0,cg26071526,0.0021039922435095292,0.9844372677935618,0.9821678898565079,0.9852845664177959,10.0,TACC2;TACC2;TACC2;TACC2;TACC2;TACC2, TACC2 -hyperdiploid,4.0,cg26282731,0.0019345048216024875,0.9844372677935618,0.9821678898565079,0.9852845664177959,4.0,ARHGAP10, ARHGAP10 -hyperdiploid,4.0,cg26645082,0.0009572601819929528,0.9844372677935618,0.9821678898565079,0.9852845664177959,11.0,SHANK2, SHANK2 -hyperdiploid,4.0,cg27180671,0.0012327209124322126,0.9844372677935618,0.9821678898565079,0.9852845664177959,17.0,PITPNC1;PITPNC1, PITPNC1 +high hyperdiploid,4.0,cg01791669,0.0006933870801414055,0.9844372677935618,0.9821678898565079,0.9852845664177959,12.0,SSH1;SSH1;SSH1, SSH1 +high hyperdiploid,4.0,cg02696971,0.0005063440118138447,0.9844372677935618,0.9821678898565079,0.9852845664177959,3.0,CBLB, CBLB +high hyperdiploid,4.0,cg02846963,0.0016218278469571766,0.9844372677935618,0.9821678898565079,0.9852845664177959,4.0,NA, +high hyperdiploid,4.0,cg03001048,0.0011067685000126835,0.9844372677935618,0.9821678898565079,0.9852845664177959,1.0,NOS1AP;NOS1AP, NOS1AP +high hyperdiploid,4.0,cg03976877,0.001559897828863304,0.9844372677935618,0.9821678898565079,0.9852845664177959,7.0,VIPR2;VIPR2, VIPR2 +high hyperdiploid,4.0,cg04970438,0.0005839686710663772,0.9844372677935618,0.9821678898565079,0.9852845664177959,10.0,TAF3, TAF3 +high hyperdiploid,4.0,cg05184729,0.0006880496500216584,0.9844372677935618,0.9821678898565079,0.9852845664177959,5.0,NA, +high hyperdiploid,4.0,cg06834427,0.0008560436678741736,0.9844372677935618,0.9821678898565079,0.9852845664177959,2.0,NA, +high hyperdiploid,4.0,cg07543883,0.0004591176505960928,0.9844372677935618,0.9821678898565079,0.9852845664177959,19.0,ANGPTL6;ANGPTL6, ANGPTL6 +high hyperdiploid,4.0,cg08202165,0.0011356967583671107,0.9844372677935618,0.9821678898565079,0.9852845664177959,6.0,NA, +high hyperdiploid,4.0,cg08376828,0.000863090676883757,0.9844372677935618,0.9821678898565079,0.9852845664177959,10.0,NA, +high hyperdiploid,4.0,cg08882216,0.001445133815026023,0.9844372677935618,0.9821678898565079,0.9852845664177959,7.0,EPHB6, EPHB6 +high hyperdiploid,4.0,cg09719124,0.0007201004771551343,0.9844372677935618,0.9821678898565079,0.9852845664177959,3.0,LMCD1, LMCD1 +high hyperdiploid,4.0,cg09894698,0.0006092814319926413,0.9844372677935618,0.9821678898565079,0.9852845664177959,11.0,ASCL2, ASCL2 +high hyperdiploid,4.0,cg10063047,0.0009468274925516919,0.9844372677935618,0.9821678898565079,0.9852845664177959,21.0,FTCD;FTCD, FTCD +high hyperdiploid,4.0,cg10206933,0.001218846081311591,0.9844372677935618,0.9821678898565079,0.9852845664177959,10.0,BNIP3, BNIP3 +high hyperdiploid,4.0,cg10362869,0.0005226053639846602,0.9844372677935618,0.9821678898565079,0.9852845664177959,2.0,NCKAP5;NCKAP5, NCKAP5 +high hyperdiploid,4.0,cg10619342,0.001171910087945308,0.9844372677935618,0.9821678898565079,0.9852845664177959,15.0,LOC390594, LOC390594 +high hyperdiploid,4.0,cg11189837,0.0007595868220523441,0.9844372677935618,0.9821678898565079,0.9852845664177959,21.0,ADAMTS1, ADAMTS1 +high hyperdiploid,4.0,cg11199770,0.002369956189339993,0.9844372677935618,0.9821678898565079,0.9852845664177959,19.0,TSHZ3, TSHZ3 +high hyperdiploid,4.0,cg13794530,0.0008076628352490202,0.9844372677935618,0.9821678898565079,0.9852845664177959,7.0,VIPR2;VIPR2, VIPR2 +high hyperdiploid,4.0,cg15057852,0.00038785328278000277,0.9844372677935618,0.9821678898565079,0.9852845664177959,20.0,KIF16B, KIF16B +high hyperdiploid,4.0,cg16200531,0.0009490587015759679,0.9844372677935618,0.9821678898565079,0.9852845664177959,2.0,NA, +high hyperdiploid,4.0,cg17090401,0.0004038314176245101,0.9844372677935618,0.9821678898565079,0.9852845664177959,4.0,FAT1, FAT1 +high hyperdiploid,4.0,cg17716765,0.002846892887401596,0.9844372677935618,0.9821678898565079,0.9852845664177959,15.0,APBA2;APBA2, APBA2 +high hyperdiploid,4.0,cg20663432,0.0016308789793530857,0.9844372677935618,0.9821678898565079,0.9852845664177959,12.0,ANO2, ANO2 +high hyperdiploid,4.0,cg20719675,0.0004429979070884313,0.9844372677935618,0.9821678898565079,0.9852845664177959,2.0,CHRNA1;CHRNA1, CHRNA1 +high hyperdiploid,4.0,cg23320499,0.0016139095838665,0.9844372677935618,0.9821678898565079,0.9852845664177959,12.0,DUSP16, DUSP16 +high hyperdiploid,4.0,cg23584087,0.0019535452447866724,0.9844372677935618,0.9821678898565079,0.9852845664177959,13.0,KL, KL +high hyperdiploid,4.0,cg25857569,0.0010910210025555317,0.9844372677935618,0.9821678898565079,0.9852845664177959,3.0,PPM1L, PPM1L +high hyperdiploid,4.0,cg26071526,0.0021039922435095292,0.9844372677935618,0.9821678898565079,0.9852845664177959,10.0,TACC2;TACC2;TACC2;TACC2;TACC2;TACC2, TACC2 +high hyperdiploid,4.0,cg26282731,0.0019345048216024875,0.9844372677935618,0.9821678898565079,0.9852845664177959,4.0,ARHGAP10, ARHGAP10 +high hyperdiploid,4.0,cg26645082,0.0009572601819929528,0.9844372677935618,0.9821678898565079,0.9852845664177959,11.0,SHANK2, SHANK2 +high hyperdiploid,4.0,cg27180671,0.0012327209124322126,0.9844372677935618,0.9821678898565079,0.9852845664177959,17.0,PITPNC1;PITPNC1, PITPNC1 low hyperdiploid,2.5,cg01154505,9.455060155697214e-05,0.9915208775654637,0.9917459636767609,0.991105173693409,2.0,FBLN7;FBLN7, FBLN7 low hyperdiploid,2.5,cg02068356,0.0002994102382637451,0.9915208775654637,0.9917459636767609,0.991105173693409,1.0,NA, low hyperdiploid,2.5,cg02610360,0.0016338162854547388,0.9915208775654637,0.9917459636767609,0.991105173693409,11.0,TMEM136, TMEM136 diff --git a/data/signatures/signature_genes_v3.csv b/data/signatures/signature_genes_v3.csv index 280a7e8..897a54b 100644 --- a/data/signatures/signature_genes_v3.csv +++ b/data/signatures/signature_genes_v3.csv @@ -28,34 +28,34 @@ aneuploidy,5.0,ENSG00000205755,0.0025031964905207105,0.977088736104192,0.9759283 aneuploidy,5.0,ENSG00000213416,0.0017475780730277766,0.977088736104192,0.9759283074382226,0.9760419496930308,KRTAP4-12,17 aneuploidy,5.0,ENSG00000267206,0.0004019097167064514,0.977088736104192,0.9759283074382226,0.9760419496930308,LCN6,9 aneuploidy,5.0,ENSG00000274443,0.0008024923887781239,0.977088736104192,0.9759283074382226,0.9760419496930308,C8orf89,8 -hyperdiploidy,3.0,ENSG00000057019,0.0011226551226551252,1.0,0.9952955044955044,0.9965021645021644,DCBLD2,3 -hyperdiploidy,3.0,ENSG00000095585,0.0004939682539682551,1.0,0.9952955044955044,0.9965021645021644,BLNK,10 -hyperdiploidy,3.0,ENSG00000110077,0.0007634054834054851,1.0,0.9952955044955044,0.9965021645021644,MS4A6A,11 -hyperdiploidy,3.0,ENSG00000115457,0.013471861471861501,1.0,0.9952955044955044,0.9965021645021644,IGFBP2,2 -hyperdiploidy,3.0,ENSG00000124491,0.006991364764268001,1.0,0.9952955044955044,0.9965021645021644,F13A1,6 -hyperdiploidy,3.0,ENSG00000132465,0.004217449074223276,1.0,0.9952955044955044,0.9965021645021644,JCHAIN,4 -hyperdiploidy,3.0,ENSG00000133067,0.0015268109668109702,1.0,0.9952955044955044,0.9965021645021644,LGR6,1 -hyperdiploidy,3.0,ENSG00000143036,0.00035924963924964005,1.0,0.9952955044955044,0.9965021645021644,SLC44A3,1 -hyperdiploidy,3.0,ENSG00000145087,0.00044906204906205007,1.0,0.9952955044955044,0.9965021645021644,STXBP5L,3 -hyperdiploidy,3.0,ENSG00000147180,0.009144995506285843,1.0,0.9952955044955044,0.9965021645021644,ZNF711,X -hyperdiploidy,3.0,ENSG00000164938,0.004442913645494298,1.0,0.9952955044955044,0.9965021645021644,TP53INP1,8 -hyperdiploidy,3.0,ENSG00000166503,0.014460827487924276,1.0,0.9952955044955044,0.9965021645021644,HDGFL3,15 -hyperdiploidy,3.0,ENSG00000168671,0.010982415720480254,1.0,0.9952955044955044,0.9965021645021644,UGT3A2,5 -hyperdiploidy,3.0,ENSG00000170561,0.007409523809523826,1.0,0.9952955044955044,0.9965021645021644,IRX2,5 -hyperdiploidy,3.0,ENSG00000174059,0.0023351226551226604,1.0,0.9952955044955044,0.9965021645021644,CD34,1 -hyperdiploidy,3.0,ENSG00000179862,0.002827223815610918,1.0,0.9952955044955044,0.9965021645021644,CITED4,1 -hyperdiploidy,3.0,ENSG00000182272,0.0025128803812674828,1.0,0.9952955044955044,0.9965021645021644,B4GALNT4,11 -hyperdiploidy,3.0,ENSG00000196653,0.007903492063492081,1.0,0.9952955044955044,0.9965021645021644,ZNF502,3 -hyperdiploidy,3.0,ENSG00000283977,0.0006286868686868701,1.0,0.9952955044955044,0.9965021645021644,AC084337.2,11 -low hyperdiploidy,2.5,ENSG00000147183,0.0007412924424972647,1.0,0.9673202614379086,0.9731601731601731,CPXCR1,X -low hyperdiploidy,2.5,ENSG00000167768,0.0007824753559693349,1.0,0.9673202614379086,0.9731601731601731,KRT1,12 -low hyperdiploidy,2.5,ENSG00000171643,0.0005353778751369134,1.0,0.9673202614379086,0.9731601731601731,S100Z,5 -low hyperdiploidy,2.5,ENSG00000198157,0.0005353778751369134,1.0,0.9673202614379086,0.9731601731601731,HMGN5,X -low hyperdiploidy,2.5,ENSG00000235272,0.0007824753559693349,1.0,0.9673202614379086,0.9731601731601731,RAMACL,6 -low hyperdiploidy,2.5,ENSG00000265118,0.004035925520262885,1.0,0.9673202614379086,0.9731601731601731,AC134669.1,17 -low hyperdiploidy,2.5,ENSG00000266076,0.0017708652792990211,1.0,0.9673202614379086,0.9731601731601731,AC004805.1,17 -low hyperdiploidy,2.5,ENSG00000269897,0.005271412924424993,1.0,0.9673202614379086,0.9731601731601731,COMMD3-BMI1,10 -low hyperdiploidy,2.5,ENSG00000285283,0.0011531215772179672,1.0,0.9673202614379086,0.9731601731601731,AL035078.4,11 +high hyperdiploid,3.0,ENSG00000057019,0.0011226551226551252,1.0,0.9952955044955044,0.9965021645021644,DCBLD2,3 +high hyperdiploid,3.0,ENSG00000095585,0.0004939682539682551,1.0,0.9952955044955044,0.9965021645021644,BLNK,10 +high hyperdiploid,3.0,ENSG00000110077,0.0007634054834054851,1.0,0.9952955044955044,0.9965021645021644,MS4A6A,11 +high hyperdiploid,3.0,ENSG00000115457,0.013471861471861501,1.0,0.9952955044955044,0.9965021645021644,IGFBP2,2 +high hyperdiploid,3.0,ENSG00000124491,0.006991364764268001,1.0,0.9952955044955044,0.9965021645021644,F13A1,6 +high hyperdiploid,3.0,ENSG00000132465,0.004217449074223276,1.0,0.9952955044955044,0.9965021645021644,JCHAIN,4 +high hyperdiploid,3.0,ENSG00000133067,0.0015268109668109702,1.0,0.9952955044955044,0.9965021645021644,LGR6,1 +high hyperdiploid,3.0,ENSG00000143036,0.00035924963924964005,1.0,0.9952955044955044,0.9965021645021644,SLC44A3,1 +high hyperdiploid,3.0,ENSG00000145087,0.00044906204906205007,1.0,0.9952955044955044,0.9965021645021644,STXBP5L,3 +high hyperdiploid,3.0,ENSG00000147180,0.009144995506285843,1.0,0.9952955044955044,0.9965021645021644,ZNF711,X +high hyperdiploid,3.0,ENSG00000164938,0.004442913645494298,1.0,0.9952955044955044,0.9965021645021644,TP53INP1,8 +high hyperdiploid,3.0,ENSG00000166503,0.014460827487924276,1.0,0.9952955044955044,0.9965021645021644,HDGFL3,15 +high hyperdiploid,3.0,ENSG00000168671,0.010982415720480254,1.0,0.9952955044955044,0.9965021645021644,UGT3A2,5 +high hyperdiploid,3.0,ENSG00000170561,0.007409523809523826,1.0,0.9952955044955044,0.9965021645021644,IRX2,5 +high hyperdiploid,3.0,ENSG00000174059,0.0023351226551226604,1.0,0.9952955044955044,0.9965021645021644,CD34,1 +high hyperdiploid,3.0,ENSG00000179862,0.002827223815610918,1.0,0.9952955044955044,0.9965021645021644,CITED4,1 +high hyperdiploid,3.0,ENSG00000182272,0.0025128803812674828,1.0,0.9952955044955044,0.9965021645021644,B4GALNT4,11 +high hyperdiploid,3.0,ENSG00000196653,0.007903492063492081,1.0,0.9952955044955044,0.9965021645021644,ZNF502,3 +high hyperdiploid,3.0,ENSG00000283977,0.0006286868686868701,1.0,0.9952955044955044,0.9965021645021644,AC084337.2,11 +low hyperdiploid,2.5,ENSG00000147183,0.0007412924424972647,1.0,0.9673202614379086,0.9731601731601731,CPXCR1,X +low hyperdiploid,2.5,ENSG00000167768,0.0007824753559693349,1.0,0.9673202614379086,0.9731601731601731,KRT1,12 +low hyperdiploid,2.5,ENSG00000171643,0.0005353778751369134,1.0,0.9673202614379086,0.9731601731601731,S100Z,5 +low hyperdiploid,2.5,ENSG00000198157,0.0005353778751369134,1.0,0.9673202614379086,0.9731601731601731,HMGN5,X +low hyperdiploid,2.5,ENSG00000235272,0.0007824753559693349,1.0,0.9673202614379086,0.9731601731601731,RAMACL,6 +low hyperdiploid,2.5,ENSG00000265118,0.004035925520262885,1.0,0.9673202614379086,0.9731601731601731,AC134669.1,17 +low hyperdiploid,2.5,ENSG00000266076,0.0017708652792990211,1.0,0.9673202614379086,0.9731601731601731,AC004805.1,17 +low hyperdiploid,2.5,ENSG00000269897,0.005271412924424993,1.0,0.9673202614379086,0.9731601731601731,COMMD3-BMI1,10 +low hyperdiploid,2.5,ENSG00000285283,0.0011531215772179672,1.0,0.9673202614379086,0.9731601731601731,AL035078.4,11 iAMP21,2.8,ENSG00000022556,0.005127931769722824,1.0,0.9939202841602841,0.9961069518716578,NLRP2,19 iAMP21,2.8,ENSG00000101493,0.020234541577825203,1.0,0.9939202841602841,0.9961069518716578,ZNF516,18 iAMP21,2.8,ENSG00000105642,0.019911158493248083,1.0,0.9939202841602841,0.9961069518716578,KCNN1,19 diff --git a/data/test_data/dnam/pheno.csv b/data/test_data/dnam/pheno.csv index 733f3a7..7e58830 100644 --- a/data/test_data/dnam/pheno.csv +++ b/data/test_data/dnam/pheno.csv @@ -1,129 +1,129 @@ public_id,tissue,subjects,age,gender,cytogenetics,Subtype_updated -0121C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2,F,hyperdiploid,HeH -0419C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.5,M,hyperdiploid,HeH -0544C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),5.2,F,hyperdiploid,HeH -0592C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.5,F,hyperdiploid,HeH -0166C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.4,M,hyperdiploid,HeH -0376C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),7.8,M,hyperdiploid,HeH -0429C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),6.2,M,hyperdiploid,HeH -0957C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.1,M,hyperdiploid,HeH -0610C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),6,F,hyperdiploid,HeH -0689C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),1.1,F,hyperdiploid,HeH -0363C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.7,M,hyperdiploid,HeH -0286C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),7.2,M,hyperdiploid,HeH -0556C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4,M,hyperdiploid,HeH -0684C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.8,M,hyperdiploid,HeH -0247C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3,F,hyperdiploid,HeH -0186C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.2,M,hyperdiploid,HeH -0371C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.6,F,hyperdiploid,HeH -0506C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),6.2,M,hyperdiploid,HeH -0427C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.3,F,hyperdiploid,HeH -0891C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.4,F,hyperdiploid,HeH -1663C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2,M,hyperdiploid,HeH -0269C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.8,M,hyperdiploid,HeH -0244C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.6,M,hyperdiploid,HeH -0401C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),5.3,F,hyperdiploid,HeH -0364C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),8.5,M,hyperdiploid,HeH -0490C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),6.1,M,hyperdiploid,HeH -0488C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.4,M,hyperdiploid,HeH -0354C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),1.5,F,hyperdiploid,HeH -0388C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),13,F,hyperdiploid,HeH -1662C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.1,F,hyperdiploid,HeH -0240C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.7,M,hyperdiploid,HeH -0519C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),5,M,hyperdiploid,HeH -0448C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.2,M,hyperdiploid,HeH -0591C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),7.4,F,hyperdiploid,HeH -0580C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),5.9,F,hyperdiploid,HeH -0798C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),11,F,hyperdiploid,HeH -1184C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.4,M,hyperdiploid,HeH -0568C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),0.5,F,hyperdiploid,HeH -0802C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.4,M,hyperdiploid,HeH -1261C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.6,M,hyperdiploid,HeH -1592C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.8,F,hyperdiploid,HeH -1073C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),5.8,M,hyperdiploid,HeH -0779C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),6.1,M,hyperdiploid,HeH -1270C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),1.6,M,hyperdiploid,HeH -0778C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.7,F,hyperdiploid,HeH -0770C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),9,F,hyperdiploid,HeH -0741C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),1,F,hyperdiploid,HeH -1556C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.6,M,hyperdiploid,HeH -0774C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),5.6,M,hyperdiploid,HeH -0916C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.5,F,hyperdiploid,HeH -0794C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3,M,hyperdiploid,HeH -1099C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.1,F,hyperdiploid,HeH -0862C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.6,F,hyperdiploid,HeH -0953C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),1.5,M,hyperdiploid,HeH -0907C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),9.6,M,hyperdiploid,HeH -0697C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),12,F,hyperdiploid,HeH -1115C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.6,F,hyperdiploid,HeH -0676C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),10,F,hyperdiploid,HeH -0985C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),6,F,hyperdiploid,HeH -1370C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),6.6,F,hyperdiploid,HeH -0870C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),5.1,M,hyperdiploid,HeH -0620C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),7.4,F,hyperdiploid,HeH -0993C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4,F,hyperdiploid,HeH -1285C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.8,F,hyperdiploid,HeH -0990C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.1,M,hyperdiploid,HeH -0873C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.8,F,hyperdiploid,HeH -0857C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.1,M,hyperdiploid,HeH -1272C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2,M,hyperdiploid,HeH -1481C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.9,F,hyperdiploid,HeH -1473C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),7.9,M,hyperdiploid,HeH -1029C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.6,M,hyperdiploid,HeH -0670C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),14,M,hyperdiploid,HeH -0409C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.5,F,hyperdiploid,HeH -0060C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.6,F,ETV6/RUNX1,t(12;21) -0431C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.4,M,ETV6/RUNX1,t(12;21) -0439C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),5.7,M,ETV6/RUNX1,t(12;21) -0558C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.8,M,ETV6/RUNX1,t(12;21) -0370C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),1.5,M,ETV6/RUNX1,t(12;21) -0372C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.3,M,ETV6/RUNX1,t(12;21) -0444C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.4,M,ETV6/RUNX1,t(12;21) -0399C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.9,F,ETV6/RUNX1,t(12;21) -1656C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.6,M,ETV6/RUNX1,t(12;21) -0393C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.4,F,ETV6/RUNX1,t(12;21) -0423C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),8.5,M,ETV6/RUNX1,t(12;21) -0403C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.8,M,ETV6/RUNX1,t(12;21) -1636C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),6.9,F,ETV6/RUNX1,t(12;21) -0532C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),6.6,M,ETV6/RUNX1,t(12;21) -1595C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.7,M,ETV6/RUNX1,t(12;21) -0565C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.7,M,ETV6/RUNX1,t(12;21) -0543C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4,F,ETV6/RUNX1,t(12;21) -0163C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.7,F,ETV6/RUNX1,t(12;21) -1669C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),5.7,F,ETV6/RUNX1,t(12;21) -0587C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),5.7,F,ETV6/RUNX1,t(12;21) -1046C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),1,M,ETV6/RUNX1,t(12;21) -0727C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.9,M,ETV6/RUNX1,t(12;21) -0718C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.8,M,ETV6/RUNX1,t(12;21) -0824C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.1,M,ETV6/RUNX1,t(12;21) -0940C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.6,M,ETV6/RUNX1,t(12;21) -1489C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),6,F,ETV6/RUNX1,t(12;21) -1447C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4,F,ETV6/RUNX1,t(12;21) -1579C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.9,F,ETV6/RUNX1,t(12;21) -0809C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.9,M,ETV6/RUNX1,t(12;21) -1041C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),6.8,M,ETV6/RUNX1,t(12;21) -0690C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.4,F,ETV6/RUNX1,t(12;21) -0925C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),5.3,M,ETV6/RUNX1,t(12;21) -1477C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),6.5,F,ETV6/RUNX1,t(12;21) -1436C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.8,F,ETV6/RUNX1,t(12;21) -1544C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2,M,ETV6/RUNX1,t(12;21) -1094C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.9,F,ETV6/RUNX1,t(12;21) -0708C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.5,F,ETV6/RUNX1,t(12;21) -0829C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.6,F,ETV6/RUNX1,t(12;21) -1294C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),1.7,F,ETV6/RUNX1,t(12;21) -1213C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.4,M,ETV6/RUNX1,t(12;21) -1558C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.9,M,ETV6/RUNX1,t(12;21) -1517C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),9,F,ETV6/RUNX1,t(12;21) -1539C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.6,M,ETV6/RUNX1,t(12;21) -1120C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),1.6,M,ETV6/RUNX1,t(12;21) -1372C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.5,F,ETV6/RUNX1,t(12;21) -1286C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.3,M,ETV6/RUNX1,t(12;21) -0952C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.3,M,ETV6/RUNX1,t(12;21) -0995C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.2,M,ETV6/RUNX1,t(12;21) -1344C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.7,M,ETV6/RUNX1,t(12;21) -0946C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),8.9,M,ETV6/RUNX1,t(12;21) -1086C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),7.4,M,ETV6/RUNX1,t(12;21) -1074C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),1.9,M,ETV6/RUNX1,t(12;21) +0121C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2,F,hyperdiploid,high hyperdiploid +0419C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.5,M,hyperdiploid,high hyperdiploid +0544C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),5.2,F,hyperdiploid,high hyperdiploid +0592C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.5,F,hyperdiploid,high hyperdiploid +0166C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.4,M,hyperdiploid,high hyperdiploid +0376C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),7.8,M,hyperdiploid,high hyperdiploid +0429C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),6.2,M,hyperdiploid,high hyperdiploid +0957C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.1,M,hyperdiploid,high hyperdiploid +0610C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),6,F,hyperdiploid,high hyperdiploid +0689C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),1.1,F,hyperdiploid,high hyperdiploid +0363C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.7,M,hyperdiploid,high hyperdiploid +0286C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),7.2,M,hyperdiploid,high hyperdiploid +0556C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4,M,hyperdiploid,high hyperdiploid +0684C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.8,M,hyperdiploid,high hyperdiploid +0247C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3,F,hyperdiploid,high hyperdiploid +0186C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.2,M,hyperdiploid,high hyperdiploid +0371C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.6,F,hyperdiploid,high hyperdiploid +0506C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),6.2,M,hyperdiploid,high hyperdiploid +0427C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.3,F,hyperdiploid,high hyperdiploid +0891C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.4,F,hyperdiploid,high hyperdiploid +1663C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2,M,hyperdiploid,high hyperdiploid +0269C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.8,M,hyperdiploid,high hyperdiploid +0244C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.6,M,hyperdiploid,high hyperdiploid +0401C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),5.3,F,hyperdiploid,high hyperdiploid +0364C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),8.5,M,hyperdiploid,high hyperdiploid +0490C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),6.1,M,hyperdiploid,high hyperdiploid +0488C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.4,M,hyperdiploid,high hyperdiploid +0354C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),1.5,F,hyperdiploid,high hyperdiploid +0388C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),13,F,hyperdiploid,high hyperdiploid +1662C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.1,F,hyperdiploid,high hyperdiploid +0240C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.7,M,hyperdiploid,high hyperdiploid +0519C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),5,M,hyperdiploid,high hyperdiploid +0448C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.2,M,hyperdiploid,high hyperdiploid +0591C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),7.4,F,hyperdiploid,high hyperdiploid +0580C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),5.9,F,hyperdiploid,high hyperdiploid +0798C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),11,F,hyperdiploid,high hyperdiploid +1184C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.4,M,hyperdiploid,high hyperdiploid +0568C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),0.5,F,hyperdiploid,high hyperdiploid +0802C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.4,M,hyperdiploid,high hyperdiploid +1261C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.6,M,hyperdiploid,high hyperdiploid +1592C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.8,F,hyperdiploid,high hyperdiploid +1073C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),5.8,M,hyperdiploid,high hyperdiploid +0779C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),6.1,M,hyperdiploid,high hyperdiploid +1270C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),1.6,M,hyperdiploid,high hyperdiploid +0778C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.7,F,hyperdiploid,high hyperdiploid +0770C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),9,F,hyperdiploid,high hyperdiploid +0741C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),1,F,hyperdiploid,high hyperdiploid +1556C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.6,M,hyperdiploid,high hyperdiploid +0774C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),5.6,M,hyperdiploid,high hyperdiploid +0916C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.5,F,hyperdiploid,high hyperdiploid +0794C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3,M,hyperdiploid,high hyperdiploid +1099C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.1,F,hyperdiploid,high hyperdiploid +0862C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.6,F,hyperdiploid,high hyperdiploid +0953C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),1.5,M,hyperdiploid,high hyperdiploid +0907C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),9.6,M,hyperdiploid,high hyperdiploid +0697C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),12,F,hyperdiploid,high hyperdiploid +1115C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.6,F,hyperdiploid,high hyperdiploid +0676C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),10,F,hyperdiploid,high hyperdiploid +0985C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),6,F,hyperdiploid,high hyperdiploid +1370C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),6.6,F,hyperdiploid,high hyperdiploid +0870C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),5.1,M,hyperdiploid,high hyperdiploid +0620C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),7.4,F,hyperdiploid,high hyperdiploid +0993C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4,F,hyperdiploid,high hyperdiploid +1285C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.8,F,hyperdiploid,high hyperdiploid +0990C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.1,M,hyperdiploid,high hyperdiploid +0873C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.8,F,hyperdiploid,high hyperdiploid +0857C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.1,M,hyperdiploid,high hyperdiploid +1272C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2,M,hyperdiploid,high hyperdiploid +1481C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.9,F,hyperdiploid,high hyperdiploid +1473C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),7.9,M,hyperdiploid,high hyperdiploid +1029C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.6,M,hyperdiploid,high hyperdiploid +0670C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),14,M,hyperdiploid,high hyperdiploid +0409C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.5,F,hyperdiploid,high hyperdiploid +0060C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.6,F,ETV6/RUNX1,ETV6::RUNX1 +0431C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.4,M,ETV6/RUNX1,ETV6::RUNX1 +0439C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),5.7,M,ETV6/RUNX1,ETV6::RUNX1 +0558C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.8,M,ETV6/RUNX1,ETV6::RUNX1 +0370C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),1.5,M,ETV6/RUNX1,ETV6::RUNX1 +0372C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.3,M,ETV6/RUNX1,ETV6::RUNX1 +0444C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.4,M,ETV6/RUNX1,ETV6::RUNX1 +0399C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.9,F,ETV6/RUNX1,ETV6::RUNX1 +1656C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.6,M,ETV6/RUNX1,ETV6::RUNX1 +0393C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.4,F,ETV6/RUNX1,ETV6::RUNX1 +0423C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),8.5,M,ETV6/RUNX1,ETV6::RUNX1 +0403C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.8,M,ETV6/RUNX1,ETV6::RUNX1 +1636C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),6.9,F,ETV6/RUNX1,ETV6::RUNX1 +0532C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),6.6,M,ETV6/RUNX1,ETV6::RUNX1 +1595C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.7,M,ETV6/RUNX1,ETV6::RUNX1 +0565C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.7,M,ETV6/RUNX1,ETV6::RUNX1 +0543C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4,F,ETV6/RUNX1,ETV6::RUNX1 +0163C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.7,F,ETV6/RUNX1,ETV6::RUNX1 +1669C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),5.7,F,ETV6/RUNX1,ETV6::RUNX1 +0587C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),5.7,F,ETV6/RUNX1,ETV6::RUNX1 +1046C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),1,M,ETV6/RUNX1,ETV6::RUNX1 +0727C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.9,M,ETV6/RUNX1,ETV6::RUNX1 +0718C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.8,M,ETV6/RUNX1,ETV6::RUNX1 +0824C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.1,M,ETV6/RUNX1,ETV6::RUNX1 +0940C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.6,M,ETV6/RUNX1,ETV6::RUNX1 +1489C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),6,F,ETV6/RUNX1,ETV6::RUNX1 +1447C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4,F,ETV6/RUNX1,ETV6::RUNX1 +1579C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.9,F,ETV6/RUNX1,ETV6::RUNX1 +0809C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.9,M,ETV6/RUNX1,ETV6::RUNX1 +1041C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),6.8,M,ETV6/RUNX1,ETV6::RUNX1 +0690C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.4,F,ETV6/RUNX1,ETV6::RUNX1 +0925C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),5.3,M,ETV6/RUNX1,ETV6::RUNX1 +1477C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),6.5,F,ETV6/RUNX1,ETV6::RUNX1 +1436C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.8,F,ETV6/RUNX1,ETV6::RUNX1 +1544C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2,M,ETV6/RUNX1,ETV6::RUNX1 +1094C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.9,F,ETV6/RUNX1,ETV6::RUNX1 +0708C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.5,F,ETV6/RUNX1,ETV6::RUNX1 +0829C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.6,F,ETV6/RUNX1,ETV6::RUNX1 +1294C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),1.7,F,ETV6/RUNX1,ETV6::RUNX1 +1213C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.4,M,ETV6/RUNX1,ETV6::RUNX1 +1558C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.9,M,ETV6/RUNX1,ETV6::RUNX1 +1517C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),9,F,ETV6/RUNX1,ETV6::RUNX1 +1539C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.6,M,ETV6/RUNX1,ETV6::RUNX1 +1120C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),1.6,M,ETV6/RUNX1,ETV6::RUNX1 +1372C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),2.5,F,ETV6/RUNX1,ETV6::RUNX1 +1286C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.3,M,ETV6/RUNX1,ETV6::RUNX1 +0952C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.3,M,ETV6/RUNX1,ETV6::RUNX1 +0995C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.2,M,ETV6/RUNX1,ETV6::RUNX1 +1344C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),4.7,M,ETV6/RUNX1,ETV6::RUNX1 +0946C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),8.9,M,ETV6/RUNX1,ETV6::RUNX1 +1086C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),7.4,M,ETV6/RUNX1,ETV6::RUNX1 +1074C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),1.9,M,ETV6/RUNX1,ETV6::RUNX1 0365C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),11,F,others,B-other 0425C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),1.3,M,others,B-other 0445C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),9.8,F,others,B-other @@ -197,14 +197,14 @@ public_id,tissue,subjects,age,gender,cytogenetics,Subtype_updated 0942C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),5,F,others,B-other 1292C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),10,F,others,B-other 1393C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),3.8,F,others,B-other -0398C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),1.7,F,TCF3/PBX1,t(1;19) -0851C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),12,M,TCF3/PBX1,t(1;19) -0416C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),11,F,TCF3/PBX1,t(1;19) -1397C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),1.8,F,TCF3/PBX1,t(1;19) -1026C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),1.6,M,TCF3/PBX1,t(1;19) -0711C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),7.7,F,TCF3/PBX1,t(1;19) -0441C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),0.3,F,MLL,11q23/MLL -0878C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),0.8,F,MLL,11q23/MLL +0398C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),1.7,F,TCF3/PBX1,TCF3::PBX1 +0851C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),12,M,TCF3/PBX1,TCF3::PBX1 +0416C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),11,F,TCF3/PBX1,TCF3::PBX1 +1397C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),1.8,F,TCF3/PBX1,TCF3::PBX1 +1026C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),1.6,M,TCF3/PBX1,TCF3::PBX1 +0711C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),7.7,F,TCF3/PBX1,TCF3::PBX1 +0441C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),0.3,F,MLL,KMT2A-r +0878C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),0.8,F,MLL,KMT2A-r U001C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),NA,NA,unknown,B-other U002C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),NA,NA,unknown,B-other U003C,bone marrow / peripheral blood,children with B-ALL (California Childhood Cancer Study),NA,NA,unknown,B-other diff --git a/tests/test_subtype.py b/tests/test_subtype.py index 966414f..002fa67 100644 --- a/tests/test_subtype.py +++ b/tests/test_subtype.py @@ -3,12 +3,12 @@ def test_list(): - legacy_dnam_subtype_groups = {'aneuploidy': ['hyperdiploid', 'low hyperdiploid', 'iAMP21', 'hypodiploid'], 'ph-group': ['BCR::ABL1', 'BCR::ABL1-like'], + legacy_dnam_subtype_groups = {'aneuploidy': ['high hyperdiploid', 'low hyperdiploid', 'iAMP21', 'hypodiploid'], 'ph-group': ['BCR::ABL1', 'BCR::ABL1-like'], 'ETV6-group': ['ETV6::RUNX1', 'ETV6::RUNX1-like'], 'T-ALL': ['T-ALL'], 'DUX4-r': ['DUX4-r'], 'PAX5alt': ['PAX5alt'], 'KMT2A-r': ['KMT2A-r'], 'ZNF384-r': ['ZNF384-r'], 'TCF3::PBX1': ['TCF3::PBX1'], 'MEF2D-r':['MEF2D-r'], 'PAX5 P80R': ['PAX5 P80R'], 'NUTM1-r': ['NUTM1-r'], 'Control': ['Control']} - legacy_gex_subtype_groups = {'aneuploidy': ['hyperdiploid', 'low hyperdiploid', 'iAMP21'], 'ph-group': ['BCR::ABL1', 'BCR::ABL1-like'], + legacy_gex_subtype_groups = {'aneuploidy': ['high hyperdiploid', 'low hyperdiploid', 'iAMP21'], 'ph-group': ['BCR::ABL1', 'BCR::ABL1-like'], 'ETV6-group': ['ETV6::RUNX1', 'ETV6::RUNX1-like'], 'T-ALL': ['T-ALL'], 'DUX4-r': ['DUX4-r'], 'PAX5alt': ['PAX5alt'], 'KMT2A-r': ['KMT2A-r'], 'ZNF384-r': ['ZNF384-r'], 'TCF3::PBX1': ['TCF3::PBX1'], 'MEF2D-r':['MEF2D-r'], 'PAX5 P80R': ['PAX5 P80R'], 'NUTM1-r': ['NUTM1-r'], 'Control': ['Control']} @@ -18,8 +18,8 @@ def test_list(): def test_group(): - assert Subtype.group('hyperdiploid', GEX) == 'aneuploidy' - assert Subtype.group('hyperdiploid', DNAM) == 'aneuploidy' + assert Subtype.group('high hyperdiploid', GEX) == 'aneuploidy' + assert Subtype.group('high hyperdiploid', DNAM) == 'aneuploidy' assert Subtype.group('BCR::ABL1', GEX) == 'ph-group' assert Subtype.group('BCR::ABL1', DNAM) == 'ph-group' assert Subtype.group('ETV6::RUNX1', GEX) == 'ETV6-group' @@ -49,5 +49,5 @@ def test_groups(): def test_subtypes(): - assert Subtype.subtypes(GEX) == ['hyperdiploid', 'low hyperdiploid', 'iAMP21', 'BCR::ABL1', 'BCR::ABL1-like', 'ETV6::RUNX1', 'ETV6::RUNX1-like', 'T-ALL', 'DUX4-r', 'PAX5alt', 'KMT2A-r', 'ZNF384-r', 'TCF3::PBX1', 'MEF2D-r', 'PAX5 P80R', 'NUTM1-r', 'Control'] - assert Subtype.subtypes(DNAM) == ['hyperdiploid', 'low hyperdiploid', 'iAMP21', 'hypodiploid', 'BCR::ABL1', 'BCR::ABL1-like', 'ETV6::RUNX1', 'ETV6::RUNX1-like', 'T-ALL', 'DUX4-r', 'PAX5alt', 'KMT2A-r', 'ZNF384-r', 'TCF3::PBX1', 'MEF2D-r', 'PAX5 P80R', 'NUTM1-r', 'Control'] + assert Subtype.subtypes(GEX) == ['high hyperdiploid', 'low hyperdiploid', 'iAMP21', 'BCR::ABL1', 'BCR::ABL1-like', 'ETV6::RUNX1', 'ETV6::RUNX1-like', 'T-ALL', 'DUX4-r', 'PAX5alt', 'KMT2A-r', 'ZNF384-r', 'TCF3::PBX1', 'MEF2D-r', 'PAX5 P80R', 'NUTM1-r', 'Control'] + assert Subtype.subtypes(DNAM) == ['high hyperdiploid', 'low hyperdiploid', 'iAMP21', 'hypodiploid', 'BCR::ABL1', 'BCR::ABL1-like', 'ETV6::RUNX1', 'ETV6::RUNX1-like', 'T-ALL', 'DUX4-r', 'PAX5alt', 'KMT2A-r', 'ZNF384-r', 'TCF3::PBX1', 'MEF2D-r', 'PAX5 P80R', 'NUTM1-r', 'Control']