Supplementary results:
Independent cohort validation of MYC and TNFRSF11B at 8q24
An independent validation cohort of 413 cases was used to validate the association between gains of MYC , TNFRSF11B , ESRP1 , MMP9 , and CSE1L and patient prognosis.
The general conditions of the patients in the training and validation cohorts are comparable. Patients with a gain of either MYC or TNFRSF11B presented a shorter median overall survival than those without gain ( MYC : median survival: 23.24 months vs. 42.77 months, P = 0.034; TNFRSF11B : median survival: 26.36 months vs. 30.06 months, P = 0.047, Supplementary Figures A and 1B), whereas there was no significant difference in survival between the patients with a gain of MMP9 , CSE1L , or ESRP1 and those without gain (data not shown).
Moreover, the GC patients with a high copy number gain (copy number > 4) of MYC or TNFRSF11B exhibited an even poorer overall survival than those with a copy number gain (2 < copy number ≤ 4) and those with no gain (
MYC : median survival: 12.26 months vs. 26.56 months vs. 42.77 months, P < 0.001; TNFRSF11B : median survival:
17.98 months vs. 26.66 months vs. 36.06 months, P = 0.015, Supplementary Figures C and D).
Association of 8q24 gain with survival and clinicopathological features
The survival-related genes MYC and TNFRSF11B are found within a wide range of amplified regions in 8q24, which spans approximately 20 million base pairs. We found that the patient group with gains of both MYC and TNFRSF11B was markedly

segregated from non-gain group. The co-gain group presented a significantly lower five-year survival rate than the non-gain group (median survival: 23.24 months vs.
45.14 months, P = 0.019, Supplementary Figure E). The statistical analysis showed that the co-gain of MYC and TNFRSF11B was strongly associated with the depth of wall invasion and TNM stage in both the training and validation cohorts (supplementary
Table 4).

Table 1S. Probe information.
Chromosome Symbol chr20 CSE1L chr8 chr8
DNA srand
+
TNFRSF11B -
ESRP1 +
Probe set region Chromosome region
108-672
656-1260
8160-8805
47096244-47146892
120004976-120033563
95722575-95788869 chr20 chr8 chr8 chr20
MMP9
MYC
CCNE2
SRC
+
+
-
+
1171-1782
674-1182
13207-13777
27895-28533
44070953-44078606
128817497-128822855
95961627-95976659
35406501-35467234

Table 2S. Representative amplified genomic loci and genes by aCGH analysis.
Chromosome Region Location chr20
Representative Genes p13 p12.3
0-5M
5-6M
TCF15, PSMF1, SNRPB, TMC2, NOP56, EBF4, PTPRA, GNRH2,
MRPS26, OXT, AVP, UBOX5, FASTKD5, GFRA4, ADAM33, CENPB,
CDC25B, ANK2, SMOX, ADRA1D, PRND, PRNT, RASSF2, SLC23A2,
PCNA, CDS2
PROKR2, CHGB, TRMT6, MCM8, CRLS1, LRRN4, FERMT1 p12.2 p12.1
10-11M JAG1, BTBD3
16-17M SNRPB2, OTOR, BFSP1, DSTN, RRBP1, BANF2, SNX5, SNORD17,
OVOL2 p11.21-23 20-25M CD93, NXT1, GZF1, NAPB, CST11, CST8, CST2, CST5, CST7, ACSS1,
VSX1, ENTPD6, PYGB, NLP q11-q13 29-62M BCL2L1, PLAGL2, SNTA1, E2F1, TP53INP2, NCOA6, HMGB3L1,
MMP24, UQCC, CEP250, SRC, NNAT, STK4, TP53TG5, MMP9, NCOA5,
CD40, CDH22, TP53RK, NCOA3, B4GALT5, SNAI1, CEBPB, PTPN1,
BCAS4, ATP9A, BCAS1, BMP7, PTK6, SRMS, TNFRSF6B, SAMD10 chr8 chr7 chr13 p11.22 39M ADAM5, ADAM3A q21.13q24.3
80M-
146M
ESRP1, CCNE2, TP53INP1, UQCRB, RPL30, SNORA72, STK3, COX6C,
YWHAZ, SAMD12, TNFRSF11B, MYC, TG, SLA, PTK2, GPR20,
LYPD2, CYP11B1, CYP11B2, MAPK15, EPPK1, PARP10 p14-p22.3 0-30M MMD2, RNF216L, RBAK, WIPI2, SLC29A4, RPA3, CDCA7L, IL6,
CCDC126, STK31, NPY, MPP6, DFNA5, OSBPL3, CYCS, C7orf31, NPVF, q22.1 100M
NFE2L3, CBX3, SNX10, SKAP2, CREB5, CPVL, CHN2, PRR15 , NOD1
LRCH4, FBXO24, PCOLCE, MOSPD3, TFR2, GNB2, GIGYF1, POP7,
EPO, ZAN q14.11 40-41M KIAA0564 q21.33 72-73M C13orf34, DIS3, PIBF1, KLF5, KLF12 q22-q31 74-95M LMO7, KCTD12, BTF3L1, CLN5, FBXL3, MYCBP2, SCEL, SLAIN1, q32
EDNRB, POU4F1, RBM26, SPRY2, GPR180
95-104M STK24, SLC15A1, UBAC2, GPR18, GPR183, FKSG29, TM9SF2, CLYBL,
PCCA, TMTC4 q33-q34 109-115M CARKD, CARS2, ING1, SOX1, ATP11A, F10, ATP4B, GRK1, GAS6,
RASA3, CDC16 chr5 chr19 chr17 chr11 chr1 p15.33 0-1M CEP72, TPPP, ZDHHC11 p13.3-p12 31-45M CDH6, PDZD2, SPEF2, IL7R, CAPSL, SKP2, GDNF, EGFLAM, LIFR,
DAB2, SEPP1, HMGCS1, CCL28, NNT q13.11 32-35M UQCRFS1, POP4, CCNE1 q13.12-33 35-49M PDCD5, ANKRD27, SLC7A9, CCDC123, CEBPA, CEBPG, PEPD, GPI,
PDCD2L, WTIP, SCGBL, BCL3, CBLC q12 q25.3 p11.2 q11 q13.3 q21.2q21.3
34-36M STARD3, PNMT, PERLD1, ERBB2, GRB7, PSMD3, CSF3, MSL1, CASC3,
CDC6, RARA, GFBP4, TNS4
77M ANAPC11, NPB, SIRT7, MAFG, LOC92659, PYCR1, NOTUM
45M PHF21A
55M OR4C11,OR4P4,OR4S2,OR4C6
68M-69M MRPL21, GHMBP2, CCND1, ORAOV1, FGF19, FGF4, FGF3, ANO1,
149M-
151M
FADD
SEMA6C, PSMB4, SNX27, TNRC4, MRPL9, OAZ3, LINGO4, RORC,
THEM5, LCE3C, LCE1D chr3 chr15 chr22 chr18 chr6 q26.2q26.31
170M MDS1, TERC, SAMD7, SEC62, GPR160, PHC3, PRKCI, SKIL, CLDN11,
SLC7A14 q11.1 18-19M CXADRP2, POTEB, OR4M2, OR4N4 q11.21 22M GSTT1, LOC391322, GSTTP2 q11.1 17-18M MIB1, GATA6, CTAGE1 p21.33 32M HLA-DRB5

Table 3S Representative deleted genes in loss regions by aCGH analysis.
Chromosome Region Location chr19 chr14 chr22 chr11 chr1 chr9 chr4 chr6 chr16 chr17 chr18 chr3 q13.42
q13.42
q13.43
56M
59M
60M
Representative Genes
SIGLEC14
LILRA3, KIR3DP1
KIR2DL4
KIR2DL2, KIR2DL5A,
p13.3 q11.2
0-1M
19M
KIR2DL5B, KIR3DS1
OR4Q3, OR4M1, OR4N2, OR4K2,
OR4K5, OR4K1
HEATR4
q24.2 q11.22
q13.1 p15.4
p15.4 q44
p31.1
73M
22M
37M
5M
55M
LOC391322, GSTT1, GSTTP2
APOBEC3A, APOBEC3B
OR52N5
OR4C11, OR4P4, OR4S2,OR4C6
246M OR2T10, OR2T11, OR2T34
71M NEGR1 p24.1
p21.3
8M
21M
PTPRD
C9orf53, CDKN2A p14.1 69M UGT2B17
p26.31
172M GALNTL6 p21.33 32M
p25.2
3M q12.2
q23.1
54M
76M
HLA-DRB5
HLA-DRB6
CES4
WWOX q21.31 41M q21.1 46M p14.2 59M
KIAA1267
SMAD4
FHIT

Table 4S. Association of co-gain of MYC and TNFRSF11B with clinicopathological parameters in gastric cancer patients
Characteristic
Original cohort
No. of patient
Age at surgery-year
Sex
Male
Female
Tumor stage
I+II
III+IV
T stage
1+2
3+4
N stage
Negative
Positive
Differentiation
Moderately differentiated
Poorly differentiated
Vascular invasion
V(-)
V(+)
Location
Cardia
Non-cardia
Validation cohort
No. of patient
Age at surgery-year
Sex
Male
Non-gain Signature Co-gain Signature P Value
20
57.05±9.71
21
62.43±8.55 0.032
12
8
8
12
8
12
34
84
5
15
10
8
5
15
131
59.64±11.62
86
45
17
4
1
20
1
20
27
129
4
17
7
14
7
14
168
61.05±10.24
121
47
0.232
0.022
0.764
0.022
0.023
0.886
0.378
0.236
<0.001
Female
Tumor stage
I+II
III+IV
T stage
1+2
3+4
N stage
Negative
Positive
Differentiation
Moderately differentiated
Poorly differentiated
46
85
24
107
35
96
34
92
37
131
13
155
30
138
40
122
0.012
0.006
0.065
0.659
Vascular invasion
V(-)
V(+)
Location
Cardia
Non-cardia
51
71
31
100
56
101
54
114
0.296
0.107

Table 5S Characteristic parameters analysis in two cohorts
Characteristic aCGH cohort
Original cohort
No. of patient (%)
Age at surgery
Sex
Male
Female
Tumor stage
I+II
III+IV
Differentiation
Well-moderately differentiated
Poorly differentiated
Vascular invasion
V(-)
V(+)
Location
Cardia
Non-cardia
129
60.5
94
35
39
90
39
90
50
72
39
90
QGP cohort
384
58.4
264
120
122
262
99
273
145
215
112
272
P Value
0.081
0.378
<0.001
0.886
0.891
0.818