ARHGEF10L (55160) / Hs_ARHGEF10L_1_SG QuantiTect Primer Assay
CCNL2 (81669) / Hs_CCNL2_1_SG QuantiTect Primer Assay
NOTCH2 (4853) / Hs_NOTCH2_1_SG QuantiTect Primer Assay
ADORA3 (140) / Hs_ADORA3_1_SG QuantiTect Primer Assay
SNRP70 (6625) / Hs_SNRP70_SG QuantiTect Primer Assay
ZNF404 (342908) / Hs_ZNF404_SG QuantiTect Primer Assay
MKNK2 (2872) / Hs_MKNK2_SG QuantiTect Primer Assay
EGLN2 (112398) / Hs_EGLN2_SG QuantiTect Primer Assay
GAPDH (2597) / Hs_GAPDH _SG QuantiTect Primer Assay
Table 1S, Supplementary Material. Primer Pairs used in RT-PCR. (gene ID)
probe set / Gene Symbol / Entrez Gene / Gene Title / Chromosomal Location / Fold change / P value201721_s_at / LAPTM5 / 7805 / lysosomal associated multispanning membrane protein 5 / chr1p34 / 2.09 / 0.001164
202443_x_at / NOTCH2 / 4853 / Notch homolog 2 (Drosophila) / chr1p13-p11 / 1.84 / 7.00E-06
203722_at / ALDH4A1 / 8659 / aldehyde dehydrogenase 4 family, member A1 / chr1p36 / 2.2 / 0.001901
204320_at / COL11A1 / 1301 / collagen, type XI, alpha 1 / chr1p21 / 2.2 / 0.00479
206164_at / CLCA2 / 9635 / chloride channel, calcium activated, family member 2 / chr1p31-p22 / 2.39 / 0.005108
207107_at / RPE65 / 6121 / retinal pigment epithelium-specific protein 65kDa / chr1p31 / 2.93 / 0.002025
214511_x_at / FCGR1B / 2210 / Fc fragment of IgG, high affinity Ib, receptor (CD64) / chr1p11.2 / 2.56 / 0.000309
219103_at / DDEFL1 / 55616 / development and differentiation enhancing factor-like 1 / chr1p36.12 / 2.24 / 0.000125
221656_s_at / ARHGEF10L / 55160 / Rho guanine nucleotide exchange factor (GEF) 10-like / chr1p36.13 / 2.13 / 6.60E-05
222999_s_at / CCNL2 / 81669 / cyclin L2 / chr1p36.33 / 2.06 / 0.000145
223660_at / ADORA3 / 140 / adenosine A3 receptor / chr1p13.2 / 2.4 / 0.00156
235275_at / BMP8B / 656 / Bone morphogenetic protein 8b (osteogenic protein 2) / chr1p35-p32 / 2.39 / 0.000422
1552309_a_at / NEXN / 91624 / nexilin (F actin binding protein) / chr1p31.1 / 2.27 / 0.00531
Supplementary Material: Table 2S. Genes located at 1p chromosomal arm over-expressed in tumors presenting ROH.
probe set / Gene Symbol / Entrez Gene / Gene Title / Chromosomal Location / fold change / P value201221_s_at / SNRP70 / 6625 / small nuclear ribonucleoprotein 70kDa polypeptide / chr19q13.3 / 1.86 / 2.00E-06
201531_at / ZFP36 / 7538 / zinc finger protein 36, C3H type, homolog (mouse) / chr19q13.1 / 2.31 / 0.003805
204122_at / TYROBP / 7305 / TYRO protein tyrosine kinase binding protein / chr19q13.1 / 2.21 / 0.00105
205264_at / CD3EAP / 10849 / CD3e molecule, epsilon associated protein / chr19q13.3 / 2.48 / 0.004813
206520_x_at / SIGLEC6 / 946 / sialic acid binding Ig-like lectin 6 / chr19q13.3 / 2.21 / 0.005101
208106_x_at / PSG6 / 5675 / pregnancy specific beta-1-glycoprotein 6 / chr19q13.2 / 2.15 / 0.002903
215019_x_at / ZNF528 / 84436 / zinc finger protein 528 / chr19q13 / 3.97 / 0.007146
217133_x_at / CYP2B6 / 1555 / cytochrome P450, family 2, subfamily B, polypeptide 6 / chr19q13.2 / 2.86 / 0.002599
217541_x_at / ZNF816A / 125893 / zinc finger protein 816A / chr19q13.41 / 2.27 / 0.003468
218831_s_at / FCGRT / 2217 / Fc fragment of IgG, receptor, transporter, alpha / chr19q13.3 / 1.99 / 6.10E-05
219741_x_at / ZNF552 / 79818 / zinc finger protein 552 / chr19q13.43 / 3.27 / 0.005886
220440_at / LGALS13 / 29124 / lectin, galactoside-binding, soluble, 13 (galectin 13) / chr19q13.1 / 2.73 / 0.003321
220956_s_at / EGLN2 / 112398 / egl nine homolog 2 (C. elegans) / chr19q13.2 / 2.23 / 0.000102
221860_at / HNRPL / 3191 / heterogeneous nuclear ribonucleoprotein L / chr19q13.2 / 2.32 / 1.70E-05
221870_at / EHD2 / 30846 / EH-domain containing 2 / chr19q13.3 / 3.89 / 0.004003
223897_at / ZNF765 / 91661 / zinc finger protein 765 / chr19q13.41 / 2.53 / 0.00304
224673_at / LENG8 / 114823 / leukocyte receptor cluster (LRC) member 8 / chr19q13.42 / 1.96 / 0.000489
227327_at / MEGF8 / 1954 / multiple EGF-like-domains 8 / chr19q12 / 1.95 / 2.00E-06
233175_at / ZNF460 / 10794 / Zinc finger protein 460 / chr19q13.4 / 2.26 / 0.001913
239043_at / ZNF404 / 342908 / zinc finger protein 404 / chr19q13.31 / 2.07 / 0.000288
1552807_a_at / SIGLEC10 / 89790 / sialic acid binding Ig-like lectin 10 / chr19q13.3 / 2.14 / 2.20E-05
1554824_at / ZNF585A / 199704 / zinc finger protein 585A / chr19q13.12 / 2.57 / 0.003148
1569940_at / SLC6A16 / 28968 / Solute carrier family 6, member 16 / chr19q13.1-q13.4 / 2.28 / 0.000626
Supplementary Material: Table 3S.Genes located at 19q chromosomal arm over-expressed in tumors presenting ROH.
probe set / Gene Symbol / Entrez Gene / Gene Title / Chromosomal Location / fold change / P value201120_s_at / PGRMC1 / 10857 / progesterone receptor membrane component 1 / chrXq22-q24 / -2.19 / 0.000136
201309_x_at / C5orf13 / 9315 / chromosome 5 open reading frame 13 / chr5q22.1 / -2.07 / 2.50E-05
201742_x_at / SFRS1 / 6426 / splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) / chr17q21.3-q22 / -1.94 / 6.70E-05
203030_s_at / PTPRN2 / 5799 / protein tyrosine phosphatase, receptor type, N polypeptide 2 / chr7q36 / -1.9 / 7.20E-05
203267_s_at / DRG2 / 1819 / developmentally regulated GTP binding protein 2 / chr17p11.2 / -2.82 / 0.000313
203390_s_at / KIF3C / 3797 / kinesin family member 3C / chr2p23 / -1.83 / 2.20E-05
203680_at / PRKAR2B / 5577 / protein kinase, cAMP-dependent, regulatory, type II, beta / chr7q22 / -2.11 / 1.90E-05
204260_at / CHGB / 1114 / chromogranin B (secretogranin 1) / chr20pter-p12 / -3.69 / 0.000112
204493_at / BID / 637 / BH3 interacting domain death agonist / chr22q11.1 / -2.07 / 2.20E-05
204612_at / PKIA / 5569 / protein kinase (cAMP-dependent, catalytic) inhibitor alpha / chr8q21.12 / -2.33 / 8.90E-05
204995_at / CDK5R1 / 8851 / cyclin-dependent kinase 5, regulatory subunit 1 (p35) / chr17q11.2 / -2.05 / 0.00023
206013_s_at / ACTL6B / 51412 / actin-like 6B / chr7q22 / -2.03 / 0.000119
207183_at / GPR19 / 2842 / G protein-coupled receptor 19 / chr12p12.3 / -1.93 / 0.000296
208017_s_at / MCF2 / 4168 / MCF.2 cell line derived transforming sequence / chrXq27 / -2.81 / 0.000289
208698_s_at / NONO / 4841 / non-POU domain containing, octamer-binding / chrXq13.1 / -2.28 / 0.00016
208860_s_at / ATRX / alpha thalassemia/mental retardation syndrome X-linked (RAD54 homolog, S. cerevisiae) / chrXq13.1-q21.1 / -2.04 / 1.80E-05
209629_s_at / NXT2 / 55916 / nuclear transport factor 2-like export factor 2 / chrXq22.3 / -2.71 / 1.30E-05
211547_s_at / PAFAH1B1 / 5048 / platelet-activating factor acetylhydrolase, isoform Ib, alpha subunit 45kDa / chr17p13.3 / -1.99 / 0.000209
211559_s_at / CCNG2 / 901 / cyclin G2 / chr4q21.1 / -2.17 / 0.000129
213439_x_at / RPIP8 / 10900 / RaP2 interacting protein 8 / chr17q21.31 / -1.99 / 0.000258
214495_at / CACNG2 / 10369 / calcium channel, voltage-dependent, gamma subunit 2 / chr22q13.1 / -3.34 / 5.40E-05
214930_at / SLITRK5 / 26050 / SLIT and NTRK-like family, member 5 / chr13q31.2 / -1.94 / 0.000105
217196_s_at / CAMSAP1L1 / 23271 / calmodulin regulated spectrin-associated protein 1-like 1 / chr1q32.1 / -1.79 / 7.00E-06
218573_at / MAGEH1 / 28986 / melanoma antigen family H, 1 / chrXp11.21 / -1.8 / 4.00E-06
219685_at / TMEM35 / 59353 / transmembrane protein 35 / chrXq22.1 / -2.12 / 9.30E-05
220040_x_at / KIAA1166 / 55906 / KIAA1166 / chrXq11.1 / -1.99 / 0.00021
220345_at / LRRTM4 / 80059 / leucine rich repeat transmembrane neuronal 4 / chr2p12 / -3.73 / 0.000213
221586_s_at / E2F5 / 1875 / E2F transcription factor 5, p130-binding / chr8q21.2 / -1.87 / 0.000103
221618_s_at / LOC728198 / TAF9B RNA polymerase II, TATA box binding protein (TBP)-associated factor, 31kDa / chrXq13.1-q21.1 / -2.56 / 0.000173
222441_x_at / SLMO2 / 51012 / slowmo homolog 2 (Drosophila) / chr20q13.32 / -2.01 / 3.80E-05
222697_s_at / ABHD10 / 55347 / abhydrolase domain containing 10 / chr3q13.2 / -2.02 / 0.000134
225541_at / RPL22L1 / 200916 / ribosomal protein L22-like 1 / chr3q26.2 / -2.23 / 0.000146
226339_at / TRUB1 / 142940 / TruB pseudouridine (psi) synthase homolog 1 (E. coli) / chr10q25.3 / -1.86 / 0.000169
227453_at / UNC13A / 23025 / unc-13 homolog A (C. elegans) / chr19p13.11 / -2.03 / 0.000187
228695_at / C8orf46 / 254778 / chromosome 8 open reading frame 46 / chr8q13.1 / -2.36 / 0.000115
230030_at / HS6ST2 / 90161 / heparan sulfate 6-O-sulfotransferase 2 / chrXq26.2 / -2.26 / 0.000214
230272_at / LOC645323 / 645323 / Hypothetical LOC645323 / chr5q14.3 / -1.73 / 2.10E-05
230869_at / LOC728215 / similar to transmembrane protein 28 / chr13q33.3 / -2.38 / 0.000118
231202_at / ALDH1L2 / 160428 / aldehyde dehydrogenase 1 family, member L2 / chr12q23.3 / -2.43 / 0.000238
233051_at / SLITRK2 / 84631 / SLIT and NTRK-like family, member 2 / chrXq27.3 / -2.23 / 0.00019
235475_at / SERP1 / 27230 / Stress-associated endoplasmic reticulum protein 1 / chr3q25.1 / -1.84 / 0.000174
236771_at / C6orf159 / 134701 / chromosome 6 open reading frame 159 / chr6q14.2 / -2.13 / 0.000136
237304_at / SYCE2 / 256126 / synaptonemal complex central element protein 2 / chr19p13.13 / -2.78 / 0.000155
238516_at / BMPR2 / 659 / bone morphogenetic protein receptor, type II (serine/threonine kinase) / chr2q33-q34 / -2.42 / 4.50E-05
241682_at / KLHL23 / 151230 / kelch-like 23 (Drosophila) / chr2q31.1 / -1.84 / 5.00E-06
1552752_a_at / CADM2 / 253559 / cell adhesion molecule 2 / chr3p12.1 / -1.87 / 6.10E-05
1555460_a_at / SLC39A6 / 25800 / solute carrier family 39 (zinc transporter), member 6 / chr18q12.2 / -2.07 / 0.000158
1556627_at / DRP2 / 1821 / dystrophin related protein 2 / chrXq22 / -2.07 / 5.10E-05
1556641_at / FLJ37228 / 285264 / hypothetical protein FLJ37228 / chr3q26.2 / -2.58 / 0.000273
1557910_at / HSP90AB1 / 3326 / heat shock protein 90kDa alpha (cytosolic), class B member 1 / chr6p12 / -2.83 / 1.00E-06
Supplementary material, Table 4S. A set of50Genes over-expressed in tumors with combined loss of heterozigosity at 1p-19q and with the lowest p-value.
probe set
/Gene Symbol
/Entrez Gene
/Gene Title
/Chromosomal Location
/fold change
/P value
201289_at / CYR61 / 3491 / cysteine-rich, angiogenic inducer, 61 / chr1p31-p22 / 2.52 / 0.007174201336_at / VAMP3 / 9341 / vesicle-associated membrane protein 3 (cellubrevin) / chr1p36.23 / 1.96 / 4.00E-06
201721_s_at / LAPTM5 / 7805 / lysosomal associated multispanning membrane protein 5 / chr1p34 / 2.27 / 0.00027
202443_x_at / NOTCH2 / 4853 / Notch homolog 2 (Drosophila) / chr1p13-p11 / 1.86 / 2.90E-05
202481_at / DHRS3 / 9249 / dehydrogenase/reductase (SDR family) member 3 / chr1p36.1 / 2.26 / 9.80E-05
202953_at / C1QB / 713 / complement component 1, q subcomponent, B chain / chr1p36.12 / 2.61 / 0.000145
203068_at / KLHL21 / 9903 / kelch-like 21 (Drosophila) / chr1p36.31 / 1.97 / 0.000153
203379_at / RPS6KA1 / 6195 / ribosomal protein S6 kinase, 90kDa, polypeptide 1 / chr1p / 2.27 / 6.00E-06
203416_at / CD53 / 963 / CD53 molecule / chr1p13 / 2.21 / 0.00022
203508_at / TNFRSF1B / 7133 / tumor necrosis factor receptor superfamily, member 1B / chr1p36.3-p36.2 / 2.22 / 2.40E-05
203722_at / ALDH4A1 / 8659 / aldehyde dehydrogenase 4 family, member A1 / chr1p36 / 2.57 / 0.000247
203725_at / GADD45A / 1647 / growth arrest and DNA-damage-inducible, alpha / chr1p31.2-p31.1 / 2.86 / 0.009327
204430_s_at / SLC2A5 / 6518 / solute carrier family 2 (facilitated glucose/fructose transporter) / chr1p36.2 / 2.27 / 0.000217
205234_at / SLC16A4 / 9122 / solute carrier family 16, member 4 / chr1p13.3 / 2.5 / 0.001128
207107_at / RPE65 / 6121 / retinal pigment epithelium-specific protein 65kDa / chr1p31 / 3.75 / 0.000233
207541_s_at / EXOSC10 / 5394 / exosome component 10 / chr1p36.22 / 1.79 / 1.00E-05
208634_s_at / MACF1 / 23499 / microtubule-actin crosslinking factor 1 / chr1p32-p31 / 1.85 / 1.00E-06
209791_at / PADI2 / 11240 / peptidyl arginine deiminase, type II / chr1p36.13 / 3.1 / 0.000787
212294_at / GNG12 / 55970 / guanine nucleotide binding protein (G protein), gamma 12 / chr1p31.3 / 3.05 / 1.00E-06
213382_at / MST1 / macrophage stimulating 1 (hepatocyte growth factor-like) / chr1p36.13 / 2.25 / 0.002943
214016_s_at / SFPQ / 6421 / splicing factor proline/glutamine-rich / chr1p34.3 / 1.9 / 3.60E-05
214180_at / MAN1C1 / 57134 / mannosidase, alpha, class 1C, member 1 / chr1p35 / 2.64 / 0.001381
214511_x_at / FCGR1B / 2210 / Fc fragment of IgG, high affinity Ib, receptor (CD64) / chr1p11.2 / 2.83 / 0.0001
214529_at / TSHB / 7252 / thyroid stimulating hormone, beta / chr1p13 / 2.43 / 0.002013
215017_s_at / FNBP1L / 54874 / formin binding protein 1-like / chr1p22.1 / 2.16 / 0.000314
215268_at / KIAA0754 / 643314 / hypothetical LOC643314 / chr1p34.2 / 2.33 / 0.001489
217877_s_at / GPBP1L1 / 60313 / GC-rich promoter binding protein 1-like 1 / chr1p34.1 / 1.75 / 0
218232_at / C1QA / 712 / complement component 1, q subcomponent, A chain / chr1p36.12 / 2.49 / 0.000157
218552_at / ECHDC2 / 55268 / enoyl Coenzyme A hydratase domain containing 2 / chr1p32.3 / 2.53 / 0.000247
219103_at / DDEFL1 / 55616 / development and differentiation enhancing factor-like 1 / chr1p36.12 / 2.22 / 0.000112
221656_s_at / ARHGEF10L / 55160 / Rho guanine nucleotide exchange factor (GEF) 10-like / chr1p36.13 / 2.01 / 0.00018
221958_s_at / GPR177 / 79971 / G protein-coupled receptor 177 / chr1p31.3 / 2.02 / 5.00E-06
57163_at / ELOVL1 / 64834 / elongation of very long chain fatty acids -like 1 / chr1p34.2 / 2.16 / 0.000142
222999_s_at / CCNL2 / cyclin L2 / chr1p36.33 / 2.1 / 0.000384
223660_at / ADORA3 / 140 / adenosine A3 receptor / chr1p13.2 / 2.82 / 0.000188
224562_at / WASF2 / 10163 / WAS protein family, member 2 / chr1p36.11-p34.3 / 2.24 / 1.00E-06
224706_at / KIAA2013 / 90231 / KIAA2013 / chr1p36.22 / 1.87 / 6.00E-06
224818_at / SORT1 / 6272 / sortilin 1 / chr1p21.3-p13.1 / 2.02 / 2.90E-05
225353_s_at / C1QC / 714 / complement component 1, q subcomponent, C chain / chr1p36.11 / 2.1 / 0.002603
226103_at / NEXN / 91624 / nexilin (F actin binding protein) / chr1p31.1 / 2.66 / 0.002728
234369_at / OR4F16 / olfactory receptor, family 4, subfamily F, member 3 / chr1p36.33 / 2.5 / 0.003459
234703_at / HHLA3 / 11147 / HERV-H LTR-associating 3 / chr1p31.1 / 2.61 / 0.00088
235275_at / BMP8B / 656 / Bone morphogenetic protein 8b (osteogenic protein 2) / chr1p35-p32 / 2.41 / 0.000824
237470_at / DOCK7 / 85440 / dedicator of cytokinesis 7 / chr1p31.3 / 2.41 / 0.000129
240868_at / CTTNBP2NL / 55917 / CTTNBP2 N-terminal like / chr1p13.2 / 1.89 / 5.10E-05
243256_at / MKNK1 / 8569 / MAP kinase interacting serine/threonine kinase 1 / chr1p33 / 2.52 / 0.000929
244261_at / IL28RA / 163702 / interleukin 28 receptor, alpha (interferon, lambda receptor) / chr1p36.11 / 2.94 / 1.70E-05
Supplementary Material, Table 5S. Genes located at 1p chromosomal arm over-expressed in tumors presenting ROH at 1p-19q. Represent 17% of over-expressed genes.
probe set
/Gene Symbol
/Entrez Gene
/Gene Title
/Chromosomal Location
/fold change
/P value
201531_at / ZFP36 / 7538 / zinc finger protein 36, C3H type, homolog (mouse) / chr19q13.1 / 2.52 / 0.001614204039_at / CEBPA / 1050 / CCAAT/enhancer binding protein (C/EBP), alpha / chr19q13.1 / 2.22 / 7.30E-05
204122_at / TYROBP / 7305 / TYRO protein tyrosine kinase binding protein / chr19q13.1 / 2.72 / 2.10E-05
205119_s_at / FPR1 / 2357 / formyl peptide receptor 1 / chr19q13.4 / 2.43 / 0.002146
207857_at / LILRA2 / 11027 / leukocyte immunoglobulin-like receptor, / chr19q13.4 / 2.32 / 1.00E-05
210644_s_at / LAIR1 / 3903 / leukocyte-associated immunoglobulin-like receptor 1 / chr19q13.4 / 2.09 / 3.80E-05
213076_at / ITPKC / 80271 / inositol 1,4,5-trisphosphate 3-kinase C / chr19q13.1 / 2.01 / 0.00077
213553_x_at / APOC1 / 341 / apolipoprotein C-I / chr19q13.2 / 2.21 / 0.001119
217133_x_at / CYP2B6 / 1555 / cytochrome P450, family 2, subfamily B, polypeptide 6 / chr19q13.2 / 2.71 / 0.003824
217541_x_at / LOC731901 / zinc finger protein 816A / chr19q13.41 / 2.32 / 0.002502
218831_s_at / FCGRT / 2217 / Fc fragment of IgG, receptor, transporter, alpha / chr19q13.3 / 2.07 / 2.40E-05
219415_at / TTYH1 / 57348 / tweety homolog 1 (Drosophila) / chr19q13.4 / 1.93 / 0.000108
219741_x_at / ZNF552 / 79818 / zinc finger protein 552 / chr19q13.43 / 3.02 / 0.008078
220088_at / C5AR1 / 728 / complement component 5a receptor 1 / chr19q13.3-q13.4 / 2.8 / 0.000439
220440_at / LGALS13 / 29124 / lectin, galactoside-binding, soluble, 13 (galectin 13) / chr19q13.1 / 2.47 / 0.006724
220956_s_at / EGLN2 / 112398 / egl nine homolog 2 (C. elegans) / chr19q13.2 / 2.6 / 5.00E-06
221860_at / HNRPL / 3191 / heterogeneous nuclear ribonucleoprotein L / chr19q13.2 / 2.12 / 0.000118
224252_s_at / FXYD5 / 53827 / FXYD domain containing ion transport regulator 5 / chr19q12-q13.1 / 2.08 / 0.001546
227196_at / RHPN2 / 85415 / rhophilin, Rho GTPase binding protein 2 / chr19q13.11 / 2.25 / 0.001796
227327_at / MEGF8 / 1954 / multiple EGF-like-domains 8 / chr19q12 / 1.95 / 4.00E-06
236664_at / AKT2 / 208 / v-akt murine thymoma viral oncogene homolog 2 / chr19q13.1-q13.2 / 2.31 / 0.000975
1552807_a_at / SIGLEC10 / 89790 / sialic acid binding Ig-like lectin 10 / chr19q13.3 / 2.22 / 2.50E-05
1558256_at / LOC148189 / 148189 / hypothetical protein LOC148189 / chr19q12 / 1.96 / 0.000306
1569940_at / SLC6A16 / 28968 / Solute carrier family 6, member 16 / chr19q13.1-q13.4 / 2.15 / 0.00144
Supplementary Material, Table 6S. 24 Genes located at 19q chromosomal arm over-expressed in tumors presenting ROH at 1p-19q. This group represents 9% of over-expressed genes.
probe set / Gene Symbol / Entrez Gene / Gene Title / Chromosomal Location / fold change / P value200791_s_at / IQGAP1 / 8826 / IQ motif containing GTPase activating protein 1 / chr15q26.1 / 2.94 / 0.000172
200931_s_at / VCL / 7414 / vinculin / chr10q22.1-q23 / 2.09 / 0
201141_at / GPNMB / 10457 / glycoprotein (transmembrane) nmb / chr7p15 / 3.45 / 4.80E-05
201324_at / EMP1 / 2012 / epithelial membrane protein 1 / chr12p12.3 / 4.82 / 8.20E-05
201887_at / IL13RA1 / 3597 / interleukin 13 receptor, alpha 1 / chrXq24 / 2.61 / 2.00E-06
201954_at / ARPC1B / actin related protein 2/3 complex, subunit 1B, 41kDa / chr7q22.1 / 1.84 / 1.60E-05
202122_s_at / M6PRBP1 / 10226 / mannose-6-phosphate receptor binding protein 1 / chr19p13.3 / 2.16 / 1.60E-05
202133_at / WWTR1 / 25937 / WW domain containing transcription regulator 1 / chr3q23-q24 / 2.57 / 3.10E-05
202803_s_at / ITGB2 / 3689 / integrin, beta 2 (complement component 3 receptor 3 and 4 subunit) / chr21q22.3 / 3.01 / 6.60E-05
202947_s_at / GYPC / 2995 / glycophorin C (Gerbich blood group) / chr2q14-q21 / 2.61 / 2.10E-05
202957_at / HCLS1 / 3059 / hematopoietic cell-specific Lyn substrate 1 / chr3q13 / 2.55 / 5.30E-05
203045_at / NINJ1 / 4814 / ninjurin 1 / chr9q22 / 2.21 / 1.40E-05
203052_at / C2 / 717 / complement component 2 / chr6p21.3 / 2.2 / 0.00017
203104_at / CSF1R / 1436 / colony stimulating factor 1 receptor / chr5q33-q35 / 2.65 / 5.20E-05
203236_s_at / LGALS9 / 3965 / lectin, galactoside-binding, soluble, 9 (galectin 9) / chr17q11.1 / 2.08 / 9.10E-05
203547_at / CD4 / 920 / CD4 molecule / chr12pter-p12 / 1.99 / 0.000227
203665_at / HMOX1 / 3162 / heme oxygenase (decycling) 1 / chr22q12|22q13.1 / 2.04 / 0.000214
204319_s_at / RGS10 / 6001 / regulator of G-protein signalling 10 / chr10q25 / 2.14 / 8.60E-05
204787_at / VSIG4 / 11326 / V-set and immunoglobulin domain containing 4 / chrXq12-q13.3 / 3.22 / 0.000247
204924_at / TLR2 / 7097 / toll-like receptor 2 / chr4q32 / 2.96 / 0.000156
205111_s_at / PLCE1 / 51196 / phospholipase C, epsilon 1 / chr10q23 / 2.16 / 0.000273
205130_at / RAGE / 5891 / renal tumor antigen / chr14q32 / 2.14 / 7.10E-05
205168_at / DDR2 / 4921 / discoidin domain receptor family, member 2 / chr1q12-q23 / 2.47 / 0.000289
207030_s_at / CSRP2 / 1466 / cysteine and glycine-rich protein 2 / chr12q21.1 / 2.26 / 0.000333
208130_s_at / TBXAS1 / 6916 / thromboxane A synthase 1 (platelet, cytochrome P450, family 5, subfamily A) / chr7q34-q35 / 2.42 / 6.00E-06
208789_at / PTRF / 284119 / polymerase I and transcript release factor / chr17q21.31 / 2.19 / 0.000253
209619_at / CD74 / 972 / CD74 molecule, major histocompatibility complex, class II invariant chain / chr5q32 / 2.73 / 0.000222
209875_s_at / SPP1 / 6696 / secreted phosphoprotein 1 / chr4q21-q25 / 4.1 / 1.70E-05
210166_at / TLR5 / 7100 / toll-like receptor 5 / chr1q41-q42 / 2.46 / 2.50E-05
212185_x_at / MT2A / 4502 / metallothionein 2A / chr16q13 / 2.05 / 0.00034
212501_at / CEBPB / 1051 / CCAAT/enhancer binding protein (C/EBP), beta / chr20q13.1 / 1.89 / 1.40E-05
212658_at / LHFPL2 / 10184 / lipoma HMGIC fusion partner-like 2 / chr5q14.1 / 2.01 / 7.90E-05
213110_s_at / COL4A5 / 1287 / collagen, type IV, alpha 5 (Alport syndrome) / chrXq22 / 2.42 / 9.20E-05
217757_at / A2M / 2 / alpha-2-macroglobulin / chr12p13.3-p12.3 / 1.87 / 7.00E-05
218205_s_at / MKNK2 / 2872 / MAP kinase interacting serine/threonine kinase 2 / chr19p13.3 / 1.94 / 9.30E-05
219202_at / RHBDF2 / 79651 / rhomboid 5 homolog 2 (Drosophila) / chr17q25.1 / 2.72 / 0
219725_at / TREM2 / 54209 / triggering receptor expressed on myeloid cells 2 / chr6p21.1 / 2.83 / 0.000267
222496_s_at / FLJ20273 / 54502 / RNA-binding protein / chr4p13-p12 / 2.39 / 8.00E-06
224606_at / KLF6 / 1316 / Kruppel-like factor 6 / chr10p15 / 1.79 / 4.00E-06
225803_at / FBXO32 / 114907 / F-box protein 32 / chr8q24.13 / 2.12 / 0.000253
226017_at / CMTM7 / 112616 / CKLF-like MARVEL transmembrane domain containing 7 / chr3p22.3 / 1.97 / 0.000117
226068_at / SYK / 6850 / Spleen tyrosine kinase / chr9q22 / 2.29 / 0.00024
226592_at / ZNF618 / 114991 / zinc finger protein 618 / chr9q32 / 1.97 / 0.000201
226909_at / KIAA1729 / 85460 / KIAA1729 protein / chr4p16.1 / 2.64 / 2.70E-05
227276_at / PLXDC2 / 84898 / plexin domain containing 2 / chr10p12.32 / 2.14 / 4.10E-05
229273_at / SALL1 / 6299 / sal-like 1 (Drosophila) / chr16q12.1 / 2.12 / 0.000188
229435_at / GLIS3 / 169792 / GLIS family zinc finger 3 / chr9p24.2 / 3.27 / 1.40E-05
238444_at / ZNF618 / 114991 / zinc finger protein 618 / chr9q32 / 2.17 / 0.000112
244840_x_at / DOCK4 / 9732 / dedicator of cytokinesis 4 / chr7q31.1 / 2.09 / 0.00032
1553906_s_at / FGD2 / 221472 / FYVE, RhoGEF and PH domain containing 2 / chr6p21.2 / 2.07 / 4.00E-06
Supplementary Material, Table 7S. A subset of 50Genes over-expressed in tumors with ROH at 1p-19q, with the lowest p-value and not located in the deleted chromosomal arms.
probe set / Gene Symbol / Entrez Gene / Gene Title / Chromosomal Location / fold change / P value204850_s_at / DCX / 1641 / doublecortex; lissencephaly, X-linked (doublecortin) / chrXq22.3-q23 / -2.24 / 0.002409
204995_at / CDK5R1 / 8851 / cyclin-dependent kinase 5, regulatory subunit 1 (p35) / chr17q11.2 / -2.05 / 0.00023
205165_at / CELSR3 / 1951 / cadherin, EGF LAG seven-pass G-type receptor 3 / chr3p24.1-p21.2 / -2.57 / 0.003744
205289_at / BMP2 / 650 / bone morphogenetic protein 2 / chr20p12 / -3.53 / 0.000728
208017_s_at / MCF2 / 4168 / MCF.2 cell line derived transforming sequence / chrXq27 / -2.81 / 0.000289
208850_s_at / THY1 / 7070 / Thy-1 cell surface antigen / chr11q22.3-q23 / -2.24 / 0.005629
210015_s_at / MAP2 / 4133 / microtubule-associated protein 2 / chr2q34-q35 / -2.01 / 0.000433
211547_s_at / PAFAH1B1 / 5048 / platelet-activating factor acetylhydrolase, isoform Ib / chr17p13.3 / -1.99 / 0.000209
213683_at / ACSL6 / 23305 / acyl-CoA synthetase long-chain family member 6 / chr5q31 / -2.27 / 0.00404
214930_at / SLITRK5 / 26050 / SLIT and NTRK-like family, member 5 / chr13q31.2 / -1.94 / 0.000105
214953_s_at / APP / 351 / amyloid beta (A4) precursor protein / chr21q21.2|21q21.3 / -1.97 / 0.000723
233051_at / SLITRK2 / 84631 / SLIT and NTRK-like family, member 2 / chrXq27.3 / -2.23 / 0.00019
233051_at / CEBPB / 1051 / CCAAT/enhancer binding protein (C/EBP), beta / chr20q13.1 / 1.89 / 0.000014
Supplementary Material, Table 8S. Genes differentially expressed between tumors with ROH and LOH at 1p-19q involved in neurogenesis according to GO level 6.
Genes with FC negative value were over-expressed in tumors with LOH at 1p-19q, while positive FC value indicated over-expression in the ROH group. Notably, only one gene over-expressed in the ROH group, CEBPB, participates in neurogenesis.
robe set / Gene Symbol / Entrez Gene / Gene Title / Chromosomal Location / fold change / P value203854_at / CFI * / 3426 / complement factor I / chr4q25 / 3.56 / 0.007028
204924_at / TLR2 * / 7097 / toll-like receptor 2 / chr4q32 / 2.96 / 0.000156
203508_at / TNFRSF1B / 7133 / tumor necrosis factor receptor superfamily, member 1B / chr1p36.3-p36.2 / 2.22 / 2.40E-05
210166_at / TLR5 * / 7100 / toll-like receptor 5 / chr1q41-q42 / 2.46 / 2.50E-05
203645_s_at / CD163 * / 9332 / CD163 molecule / chr12p13.3 / 8.66 / 0.004264
201743_at / CD14 * / 929 / CD14 molecule / chr5q22-q32|5q31.1 / 2.96 / 0.00953
204232_at / FCER1G * / 2207 / Fc fragment of IgE, high affinity I, receptor for; gamma polypeptide / chr1q23 / 2.17 / 0.000373
215051_x_at / AIF1 / 199 / allograft inflammatory factor 1 / chr6p21.3 / 2.33 / 0.001458
209906_at / C3AR1 / 719 / complement component 3a receptor 1 / chr12p13.31 / 2.61 / 0.000368
205859_at / LY86 * / 9450 / lymphocyte antigen 86 / chr6p25.1 / 2.26 / 0.000502
202376_at / SERPINA3 / 12 / serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin) / chr14q32.1 / 7.53 / 0.008055
208747_s_at / C1S * / 716 / complement component 1, s subcomponent / chr12p13 / 2.56 / 0.002663
212501_at / CEBPB * / 1051 / CCAAT/enhancer binding protein (C/EBP), beta / chr20q13.1 / 1.89 / 1.40E-05
203923_s_at / CYBB * / 1536 / cytochrome b-245, beta polypeptide (chronic granulomatous disease) / chrXp21.1 / 2.13 / 0.00053
209875_s_at / SPP1 * / 6696 / secreted phosphoprotein 1 / chr4q21-q25 / 4.1 / 1.70E-05
202953_at / C1QB * / 713 / complement component 1, q subcomponent, B chain / chr1p36.12 / 2.61 / 0.000145
205668_at / LY75 * / 4065 / lymphocyte antigen 75 / chr2q24 / 2.09 / 0.000612
207643_s_at / TNFRSF1A / 7132 / tumor necrosis factor receptor superfamily, member 1A / chr12p13.2 / 2.33 / 0.000746
225353_s_at / C1QC * / 714 / complement component 1, q subcomponent, C chain / chr1p36.11 / 2.1 / 0.002603
202803_s_at / ITGB2 * / 3689 / integrin, beta 2 (complement component 3 receptor 3 and 4 subunit) / chr21q22.3 / 3.01 / 6.60E-05
205098_at / CCR1 * / 1230 / chemokine (C-C motif) receptor 1 / chr3p21 / 2.42 / 0.000566
201531_at / ZFP36 / 7538 / zinc finger protein 36, C3H type, homolog (mouse) / chr19q13.1 / 2.52 / 0.001614
200986_at / SERPING1 * / 710 / serpin peptidase inhibitor, clade G (C1 inhibitor), member 1, / chr11q12-q13.1 / 2.57 / 0.005892
203052_at / C2 * / 717 / complement component 2 / chr6p21.3 / 2.2 / 0.00017
205119_s_at / FPR1 / 2357 / formyl peptide receptor 1 / chr19q13.4 / 2.43 / 0.002146
223660_at / ADORA3 / 140 / adenosine A3 receptor / chr1p13.2 / 2.82 / 0.000188
218232_at / C1QA * / 712 / complement component 1, q subcomponent, A chain / chr1p36.12 / 2.49 / 0.000157
211852_s_at / ATRN / 8455 / attractin / chr20p13 / -2.01 / 0.000456
Supplementary Material, Table 9S.Genes differentially expressed between tumors with ROH and LOH at 1p-19q involved in inflammatory response according to GO level 5. Genes with FC negative value were over-expressed in tumors with LOH at 1p-19q, while positive FC value indicated over-expression in the ROH group. Genes marked with * are also involved in the immune response according to GO level 4 (detailed in table 10S). ATRN was the only gene involved in inflammatory processes that was over-expressed in tumors with LOH.
probe set / Gene Symbol / Entrez Gene / Gene Title / Chromosomal Location / fold change / P value205285_s_at / FYB / 2533 / FYN binding protein (FYB-120/130) / chr5p13.1 / 2.17 / 0.001282
210889_s_at / FCGR2B / 2213 / Fc fragment of IgG, low affinity IIb, receptor (CD32) / chr1q23 / 2.75 / 0.003235
226068_at / SYK / 6850 / Spleen tyrosine kinase / chr9q22 / 2.29 / 0.00024
232617_at / CTSS / 1520 / cathepsin S / chr1q21 / 2.19 / 0.001297
209619_at / CD74 / 972 / CD74 molecule, major histocompatibility complex, class II invariant chain / chr5q32 / 2.73 / 0.000222
201487_at / CTSC / 1075 / cathepsin C / chr11q14.1-q14.3 / 2.5 / 0.000468
218831_s_at / FCGRT / 2217 / Fc fragment of IgG, receptor, transporter, alpha / chr19q13.3 / 2.07 / 2.40E-05
221698_s_at / CLEC7A / 64581 / C-type lectin domain family 7, member A / chr12p13.2 / 2.45 / 0.000467
203104_at / CSF1R / 1436 / colony stimulating factor 1 receptor / chr5q33-q35 / 2.65 / 5.20E-05
219725_at / TREM2 / 54209 / triggering receptor expressed on myeloid cells 2 / chr6p21.1 / 2.83 / 0.000267
201601_x_at / IFITM1 / 8519 / interferon induced transmembrane protein 1 (9-27) / chr11p15.5 / 2.36 / 0.007481
210644_s_at / LAIR1 / 3903 / leukocyte-associated immunoglobulin-like receptor 1 / chr19q13.4 / 2.09 / 3.80E-05
204319_s_at / RGS10 / 6001 / regulator of G-protein signalling 10 / chr10q25 / 2.14 / 8.60E-05
203416_at / CD53 / 963 / CD53 molecule / chr1p13 / 2.21 / 0.00022
214511_x_at / FCGR1B / 2210 / Fc fragment of IgG, high affinity Ib, receptor (CD64) / chr1p11.2 / 2.83 / 0.0001
206295_at / IL18 / 3606 / interleukin 18 (interferon-gamma-inducing factor) / chr11q22.2-q22.3 / 2.65 / 0.0046
203561_at / FCGR2A / 2212 / Fc fragment of IgG, low affinity IIa, receptor (CD32) / chr1q23 / 2.08 / 0.001114
204994_at / MX2 / 4600 / myxovirus (influenza virus) resistance 2 (mouse) / chr21q22.3 / 2.21 / 0.001006
200986_at / SERPING1 / 710 / serpin peptidase inhibitor, clade G (C1 inhibitor), member 1, (angioedema, hereditary) / chr11q12-q13.1 / 2.57 / 0.005892
203547_at / CD4 / 920 / CD4 molecule / chr12pter-p12 / 1.99 / 0.000227
220088_at / C5AR1 / 728 / complement component 5a receptor 1 / chr19q13.3-q13.4 / 2.8 / 0.000439
207857_at / LILRA2 / 11027 / leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 2 / chr19q13.4 / 2.32 / 1.00E-05
212587_s_at / PTPRC / 5788 / protein tyrosine phosphatase, receptor type, C / chr1q31-q32 / 2.62 / 0.001806
211990_at / HLA-DPA1 / 3113 / major histocompatibility complex, class II, DP alpha 1 / chr6p21.3 / 2.74 / 0.005371
208850_s_at / THY1 / 7070 / Thy-1 cell surface antigen / chr11q22.3-q23 / -2.24 / 0.005629
224833_at / ETS1 / 2113 / v-ets erythroblastosis virus E26 oncogene homolog 1 (avian) / chr11q23.3 / -2.3 / 0.004544
208650_s_at / CD24 / 934 / CD24 molecule / chr6q21 / -3.32 / 0.000476
Supplementary Material, Table 10S.Genes differentially expressed between tumors with ROH and LOH at 1p-19q involved in immune response according to GO level 4. Genes with FC negative value were over-expressed in tumors with LOH at 1p-19q, while positive FC value indicated over-expression in the ROH group. A group of genes marked with * in table 9S have to be added to this list and seem to have a dual function.
probe set / Gene Symbol / Entrez Gene / Gene Title / Chromosomal Location / Fold Change A/B1 / TesTAvsB1 / Fold Change B1/B2 / TesTB1vsB21553185_at / RASEF / 158158 / RAS and EF-hand domain containing / chr9q21.32 / 4.20 / 0.000278 / 2.29 / 0.004037
224012_at / ANKRD20A1 / ankyrin repeat domain 20 family, member A1 / chr9p11.2 / 6.34 / 0.000718 / 2.51 / 0.022708
206438_x_at / C12orf38 / 79867 / chromosome 12 open reading frame 38 / chr12q24.31 / 5.12 / 0.000018 / 2.40 / 0.004697
213835_x_at / GTPBP3 / 84705 / GTP binding protein 3 (mitochondrial) / chr19p13.11 / 4.38 / 0.000098 / 2.51 / 0.004197
223327_x_at / FLJ22795 / 80154 / hypothetical protein FLJ22795 / chr15q25.2 / 7.20 / 0.000224 / 3.14 / 0.004881
233810_x_at / PRO1268 / 29006 / PRO1268 protein / --- / 7.61 / 0.000224 / 3.09 / 0.005103
214205_x_at / TXNL2 / 10539 / thioredoxin-like 2 / chr10q26 / 8.99 / 0.000099 / 3.07 / 0.007160
206180_x_at / ZNF747 / 65988 / zinc finger protein 747 / chr16p11.2 / 8.44 / 0.000064 / 3.20 / 0.003730
233992_x_at / ZNF445 / 353274 / zinc finger protein 445 / chr3p21.32 / 8.66 / 0.000081 / 3.36 / 0.003037
222136_x_at / ZNF43 / 7594 / zinc finger protein 43 / chr19p13.1-p12 / 4.70 / 0.000047 / 2.30 / 0.007379
209057_x_at / CDC5L / 988 / CDC5 cell division cycle 5-like (S. pombe) / chr6p21 / 6.64 / 0.000055 / 2.52 / 0.010277
211697_x_at / PNO1 / 56902 / partner of NOB1 homolog (S. cerevisiae) / chr2p14 / 5.81 / 0.000055 / 2.53 / 0.005332
215582_x_at / MCM3AP / 8888 / minichromosome maintenance complex component 3 associated protein / chr21q22.3 / 7.07 / 0.000031 / 2.77 / 0.004353
203735_x_at / PPFIBP1 / 8496 / PTPRF interacting protein, binding protein 1 / chr12p11.23-p11.22 / 4.85 / 0.000019 / 2.50 / 0.002383
232644_x_at / OCIAD1 / 54940 / OCIA domain containing 1 / chr4p11 / 5.19 / 0.000027 / 2.34 / 0.005486
1563674_at / FCRL2 / 79368 / Fc receptor-like 2 / chr1q21 / 4.57 / 0.000097 / 1.96 / 0.053558
220232_at / SCD5 / 79966 / stearoyl-CoA desaturase 5 / chr4q21.22 / 3.90 / 0.000072 / 1.94 / 0.035676
220920_at / ATP10B / 23120 / ATPase, Class V, type 10B / chr5q34 / 4.20 / 0.000057 / 1.94 / 0.029905
244495_x_at / C18orf45 / 85019 / chromosome 18 open reading frame 45 / chr18q11.2 / 3.90 / 0.000018 / 2.07 / 0.007006
224159_x_at / TRIM4 / 89122 / tripartite motif-containing 4 / chr7q22-q31.1 / 4.12 / 0.000187 / 2.14 / 0.020014
1561894_at / LOC653739 / 653739 / hypothetical protein LOC653739 / chr7q33 / 4.37 / 0.000064 / 2.25 / 0.009900
Supplementary Material: Table 11S. Genes over-expressed in OT with Retention of Heterozigosity at 1p/19q defined as group B1 and down regulated in group A and B2.
MICROARRAYS / RT-PCRProbeset / Gene / Marker for / Fold Change expression microarray (T/C) / p-value / Normalized gene amount relative to Control Set
2-∆∆Ct / Normalized gene amount relative to Test Set
2-∆∆Ct
202443_x_at / NOTCH2 / 1p LOH (C) / 1.84 / 0.000007 / 1.0 [0.41, 2.39] / 2.4 [0.97,5.89]
223660_at / ADORA3 / 1p LOH (C) / 2.4 / 0.00156 / 1.0 [0.30, 2.99] / 3.38 [1.04,10.92]
221656_s_at / ARHGEF10L / 1p LOH (C) / 2.13 / 0.000066 / 1.0 [0.29, 3.41] / 1.44 [0.53,3.86]
222999_s_at / CCNL2 / 1p LOH (C) / 2.06 / 0.000145 / 1.0 [0.37, 2.63] / 0.84 [0.30,2.29]*
201221_s_at / SNRP70 / 19q LOH (C) / 1.86 / 0.000002 / 1.0 [0.30,3.24] / 6.02 [2.34,15.45]
239043_at / ZNF404 / 19q LOH (C) / 2.07 / 0.000288 / 1.0 [0.30,3.29] / 2.54 [0.97, 6.68]
220956_s_at / EGLN2 / 19q LOH (C) / 2.23 / 0.000102 / 1.0 [0.40, 2.47] / 3.09 [1.10,8.69]
218205_s_at / MKNK2 (19p) / 19p LOH (C) / 1.9 / 0.000185 / 1.0 [0.45, 2.20] / 1.61 [0.60,4.31]
Supplementary Material, Table 12S. Differential expression of most transcripts was confirmed by semi-quantitative RT-PCR. The Fold Change between Control (C) and Test set (T) remain similar on the array and by RT-PCR. 27 of the original 29 Oligodendroglial Tumors were used for the comparisons. Amplifications results obtained from SYBR-Green assay were normalized against GDAPH gene.
Sample / Molecular Status / Prediction Class / ProbabilityHo-160 / Unknown / 1 / 0,70
Ho-161 / Unknown / 2 / 1,00
Ho-167 / Unknown / 1 / 0,99
Ho-194 / Unknown / 2 / 1,00
Ho-196 / Unknown / 2 / 1,00
Ho-202 / Unknown / 1 / 0,76
Ho-203 / Unknown / 2 / 1,00
Ho-206 / Unknown / 1 / 0,92
Ho-207 / Unknown / 2 / 1,00
Ho-210 / Unknown / 2 / 0,61
Supplementary Material, Table 13S. Prediction Class assigned on Test Samples. Class1: Oligodendroglial Tumors with 1p/19q; Class 2: Oligodendroglial Tumors with ROH 1p/19q. Last column shows the probability to belong to the assigned class as inferred in dCHIP Analyzer.