To identify genetic changes related to tumor progression and find out diagnostic and prognostic genetic markers in gastrointestinal stromal tumors (GISTs), 95 tumor samples (24 benign GISTs, 36 malignant primary GISTs, and 35 GIST-metastases) from 60 patients were studied using comparative genomic hybridization. DNA copy number changes were detected in all samples. Benign GISTs had a mean of 2.6 aberrations/sample (losses:gains, 5:1) and significantly fewer DNA copy number changes and fewer gains than malignant primary and metastatic GISTs (P < 0.01). High-level amplifications were not seen in benign GISTs. Malignant primary GISTs had a mean of 7.5 aberrations/tumor (losses:gains, 1.6:1), whereas the mean number of aberrations/metastatic GIST was 9 (losses:gains, 1.8:1). Frequent changes observed in all GIST groups included losses in chromosome arms 1p (51%), 14q (74%), and 22q (53%). Gains and high-level amplifications at 8q and 17q were significantly more frequent in metastatic GISTs (57 and 43%) than in benign GISTs (8 and 0%; P < 0.001) and malignant primary GISTs (33 and 25%; P < 0.05). Gains and high-level amplifications at 20q were only seen in malignant primary and metastatic GISTs (P < 0.01), and gains at 5p were not detected in benign GISTs(P < 0.01). Losses in chromosome arm 9p were never seen in benign tumors (P < 0.001), and they were more frequent in metastatic GISTs than in malignant primary GISTs (63 and 36%; P < 0.05). Losses in 13q were less frequent in benign GISTs than in malignant primary (P < 0.05) and metastatic (P < 0.01) GISTs. Our results show that several DNA copy number changes are related to the behavior of GISTs and can be used as prognostic markers for tumor progression.

GISTs3, classified previously as smooth muscle tumors, constitute the most important group of primary mesenchymal tumors of the gastrointestinal tract. These tumors occur at all levels of the gastrointestinal tract and usually present between the sixth and eighth decades. Immunohistochemically, GISTs are usually positive for KIT (CD117) and CD34, variably positive for smooth muscle actin, and usually negative for desmin, in contrast to true smooth muscle tumors. GISTs are negative for S100 protein, in contrast to schwannomas (1, 2).

Clinically and pathologically, GISTs represent a spectrum of tumors including benign and malignant variants, the latter of which are generally identified by mitotic activity (>1 mitosis/10 high-power field). In some cases, the prediction of biological potential is difficult, because larger tumors with lower mitotic activity may also occasionally metastasize.

CGH enables screening of entire tumor genomes for gains and losses of DNA copy number and consequent mapping of aberrations to chromosomal subregions (reviewed in Refs. 3 and 4). Recently, we reported using CGH that loss of genetic material at chromosome arm 14q is the most frequently occurring aberration in both benign and malignant primary GISTs (5). The DNA copy number changes seen in GISTs were not detected in leiomyomas and leiomyosarcomas (6). Therefore, the immunophenotypic characteristics and the genetic profile of GISTs have clearly placed it as a separate tumor entity different from other mesenchymal tumors of the gastrointestinal tract. However, the prognostic evaluation of GISTs remained a difficult issue, requiring a complex multiparametric approach.

This study was performed to analyze the CGH changes in benign and malignant primary GISTs and to investigate whether progressive DNA copy number changes occur in recurrent and metastatic GISTs. We also investigated whether any DNA copy number change has prognostic significance for GISTs.

Tumors.

Ninety-five GIST samples from 60 patients were included in the study. The samples consisted of 24 benign GISTs, 36 malignant primary GISTs,and 35 GIST metastases that were available from 15 of the malignant primary GISTs. Immunohistochemically identified leiomyomas and leiomyosarcomas (desmin-positive, CD117-negative) and schwannomas(S100-protein positive, CD117-negative) were excluded from the study. Most GISTs were CD117 and CD34 positive (92 and 72%, respectively). The categorization of GISTs into benign and malignant tumors was based on mitotic counts. Benign GISTs had <2 mitoses/10 high-power field. Malignant or potentially malignant GISTs had >1 mitosis/10 high-power fields. Follow-up data for 6–209 months (mean, 41 months) were available for all patients except four (nos. 25, 26, 29, and 48). None of the patients with benign tumors showed recurrence or metastases.

CGH.

Because CGH sensitivity requires at least 50% of tumor material within a sample, paraffin-embedded tissue sections were dissected to obtain at least 70% of tumor cells. DNA from paraffin-embedded tissue sections was extracted as described earlier (7).

CGH was performed according to standard procedures with a modification using a mixture of fluorochromes conjugated to dCTP and dUTP nucleotides for nick translation (8). Hybridizations,washings, and ISIS digital image analysis (Metasystems GmbH,Altlussheim, Germany) were performed as described elsewhere(5).

Controls.

In each CGH experiment, a negative control (peripheral blood DNA from a healthy donor) and a positive control were included. The positive control was a gastric tumor with known DNA copy number changes. On the basis of our earlier reports and the control results, we used 1.17 and 0.85 as cutoff levels for gains and losses, respectively. All of the CGH results were confirmed using a 99% confidence interval.

Statistical Analysis.

All of the CGH results were confirmed using a 99% confidence interval. Briefly, intra-experiment SDs for all positions in the CGH ratio profiles were calculated from the variation of the ratio values of all homologous chromosomes within the experiment. Confidence intervals for the ratio profiles were then computed by combining them with an empirical inter-experiment SD and by estimating error probabilities based on the t distribution. For the analysis of the frequencies of DNA copy number changes in primary and metastatic GISTs,we used Fisher’s exact two-tailed test. Ps <0.05 were considered significant.

Changes in DNA copy numbers were detected in all samples. DNA copy number changes were seen in all chromosomes in malignant primary and metastatic GISTs, whereas fewer chromosomes were involved in benign GISTs (Figs. 1 and 2 ). Benign GISTs had a mean of 2.6 aberrations/case (losses:gains, 5:1)and contained significantly fewer DNA copy number changes and fewer gains than malignant primary and metastatic GISTs(P < 0.01). High-level amplifications were not seen in benign GISTs. In malignant primary GISTs, the mean number of aberrations/case was 7.5 (losses:gains, 1.6:1), whereas the mean was 9 in metastatic GISTs (losses:gains, 1.8:1). The CGH profiles in metastatic GISTs and malignant primary tumors were similar, but metastatic GISTs showed a larger number of high-level amplifications. There was no correlation between the location and any specific DNA copy number changes.

Changes that were frequently detected in all GISTs with no statistical differences between benign, malignant primary, and metastatic tumors included losses in chromosome arms 1p (51%), 14q (74%), and 22q(53%).

Gains and high-level amplifications at 8q and 17q were significantly more often detected in metastatic GISTs (57 and 43%) than in benign GISTs (8 and 0%; P < 0.001) and malignant primary GISTs (33 and 25%; P < 0.05). Gains and high-level amplifications at 20q were only seen in malignant primary and metastatic GISTs (P < 0.01), and gains at 5p were not detected in benign GISTs (P < 0.01). Losses in 9p were never seen in benign tumors(P < 0.001), and they were more frequent in metastatic GISTs than in malignant primary tumors (63 and 36%; P < 0.05). The losses in 13q were less frequent in benign GISTs than in malignant primary(P < 0.05) and metastatic(P < 0.01) GISTs. In addition, several other changes were seen more frequently in malignant primary and metastatic GISTs than in benign GISTs. The details of DNA copy number changes are shown in Table 1 and Fig. 1. Fig. 2 shows the relative frequencies of the aberrations in all GISTs, and Table 2 summarizes the significant DNA copy number changes.

On the basis of a large series of clinically benign and malignant GISTs and their metastases, we investigated the possible value of CGH to identify genetic markers of tumor behavior. The observation that benign tumors, almost exclusively, contain losses rather than gains,whereas malignant primary GISTs and their metastases contain gains and high-level amplifications, presents an apparently clear criterion for categorization of these tumors. Accordingly, losses are more likely related to the development of GISTs, whereas accumulation of additional genetic alterations, especially gains/amplicons, is required for malignant transformation and metastatic behavior in GISTs. Absence of gains correlated with benign GISTs with verified good prognosis,whereas presence of gains was more frequent in malignant primary GISTs and their metastases (P < 0.01). Therefore,absence of gains can be considered as a good prognostic parameter,which can be used as a new complementary diagnostic criterion for characterization of GISTs.

Gains and high-level amplifications at 5p, 8q, 17q, and 20q and losses in 9p, 13q, 15q, and 19q correlated with malignant primary GISTs and metastatic GISTs. Moreover, the gains at 8q, 17q, and 20q and the losses in 9p were more frequent in metastatic GISTs than in malignant primary GISTs (P < 0.05). Therefore, clones with this genetic make-up have a potential capability of developing metastases.

Losses in 1p, 14q, and 22q seen in benign GISTs seem to be unique because they have been reported rarely in other tumors at frequencies as high as observed in GISTs (9). These changes were frequently seen in benign GISTs, indicating that they may be early events in GIST development. The fact that these losses were maintained with tumor progression suggests that they are required for the maintenance of GIST phenotype. The present extended study also supports the notion that these changes may be unique for GIST development. Recently, we reported high-resolution deletion mapping of chromosome 14 in GISTs and identified two possible tumor suppressor loci in 14q11.2 and 14q23 (10).

The gains/high-level amplifications at 5p, 8q, 17q, and 20q as well as the losses in 9p, 13q, 15q, and 19q were detected in many malignant GISTs and their metastases. Such changes have also been reported in several other tumors, such as carcinomas of lung, breast, and ovary,and in squamous cell carcinomas of the head with variable frequencies(reviewed in Refs. 3 and 4). Gains and high-level amplifications at 8q22–q24 and 17q21–qter have been implicated as poor prognostic indicators in breast cancer, ovarian cancer, osteosarcomas, and neuroblastomas (11–14). The gains and high-level amplifications at 8q and 20q correlate with invasiveness in breast cancer (15, 16).

Although these chromosomal regions are known to contain several oncogenes, such as CMYC at 8q and ERBB2 at 17q,the possibility of yet undiscovered oncogenes cannot be ruled out(14). At 20q, several genes have been implicated in breast cancer, and the region is known to harbor specific amplified genes(AIB1, AIB3, and AIB4; Ref. 17). Several candidate genes are located at 20q, e.g., the PTP1B/PTPN1 gene (20q12), which is involved in growth regulation, and the MYBL2 gene (20q13), which plays an important role in cell cycle progression. Moreover, the human cellular apoptosis susceptibility (CAS) gene has been mapped to this same region (18). There are no known oncogenes that map to 5p.

Losses in 9p were associated with recurrences and unfavorable outcome in squamous cell carcinoma of the head and neck (19) and in astrocytic tumors (20). Losses in 13q12–q13 are associated with poor prognosis in familial and sporadic breast cancer(21). Losses in 15q have been observed rarely upon CGH. LOH studies have suggested the presence of a putative tumor suppressor gene in 15q in small cell lung cancer (22). However, there are no data related to its potential prognostic significance or identified tumor suppressor genes.

In summary, our results show that genetic changes can be used as a complementary diagnostic tool for the prognostication of GISTs and for the differentiation between benign and malignant tumors. The increased number of changes and/or increased number of gains correlate with malignant behavior. Furthermore, the genetic changes seen as gains at 5p, 8q, 17q, and 20q and losses in 9p, 13q, 15q, and 19q are new prognostic parameters for GISTs.

Fig. 1.

Summary of DNA copy number gains and losses detected by CGH in 60 GIST patients. Each bar represents one patient, regardless of the number of samples available, and the minimal common overlapping regions are presented. Gains are on the right hand side, losses on the left. Green broken lines, benign tumors; green continuous lines, malignant primary tumors that had no metastases samples. Blue lines, the aberration was seen in the malignant primary tumor and in at least one metastatic sample from the same patient. Red lines, changes that were seen on metastatic samples but not in their primary tumors for the same patient.

Fig. 1.

Summary of DNA copy number gains and losses detected by CGH in 60 GIST patients. Each bar represents one patient, regardless of the number of samples available, and the minimal common overlapping regions are presented. Gains are on the right hand side, losses on the left. Green broken lines, benign tumors; green continuous lines, malignant primary tumors that had no metastases samples. Blue lines, the aberration was seen in the malignant primary tumor and in at least one metastatic sample from the same patient. Red lines, changes that were seen on metastatic samples but not in their primary tumors for the same patient.

Close modal
Fig. 2.

Comparative frequencies of losses (left)and gains (right) detected in 24 benign GISTs(green), 36 malignant primary GISTs(blue), and 35 metastatic GISTs (red). Chromosomal numbers are shown in the middle, and the minimal common overlapping regions, when applicable, are added to each bar.

Fig. 2.

Comparative frequencies of losses (left)and gains (right) detected in 24 benign GISTs(green), 36 malignant primary GISTs(blue), and 35 metastatic GISTs (red). Chromosomal numbers are shown in the middle, and the minimal common overlapping regions, when applicable, are added to each bar.

Close modal

The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

Supported by grants from the Finnish Cancer Society and the University of Helsinki in Finland.

The abbreviations used are: GIST,gastrointestinal stromal tumor; CGH, comparative genomic hybridization.

Table 1

Clinical, histological, and CGH karyotype findings of 95 gastrointestinal stromal tumors obtained from 60 patients

Metastases from the same patient have the same number as the primary tumor but with a different letter, e.g. b, c, d.

No.Age/sex/codeHistologySiteaSizebFollow-up in monthsCGH karyotypea
LossesGains and high-level amplifications
59/m G1 Benign Jejunum 5, 5 NED, 51 1p, 15, 18, 22  
45/m G2 Benign Stomach 4, 5 NED, 45 14  
50/m G12 Benign Stomach 3, 3 NED, 38 1p, 14 8q 
75/m G25 Benign Stomach NED, 87 14, 22  
63/m G9 Benign Stomach 3, 5 NED, 41 14q11–q13, 14q23–qter, 22  
61/f G10 Benign Stomach NED, 40 1p, 14  
81/m G13 Benign Stomach 5, 5 NED, 110 15  
80/m G14 Benign Stomach NED, 124 14  
9/73/f G18 Benign Stomach 3, 5 NED, 81 11p, 14 5q22–qter 
10 63/f G19 Benign Jejunum NED, 31 1p, 11, 14, 15, 21 1q, 5, 7p, 18q 
11 58/m G21 Benign Stomach NED, 210 14q13–qter, 22  
12 49/f G23 Benign Stomach 16 NED, 209 22q12–qter  
13 65/f G24 Benign Stomach NED, 28 14, Xq  
14 73/m G26 Benign Stomach NED, 82 14, 15, 21, 22  
15 79/f G29 Benign Stomach NED, 133 22q12–qter  
16 78/m G32 Benign Stomach 2, 5 NED, 75 14, 22  
17 80/m G35 Benign Jejunum 4, 5 NED, 24 1p, 6q, 13q21–qter, 14 19 
18 85/m G38 Benign Stomach NED, 21 14, 22  
19 69/m G41 Benign Jejunum NED, 14 1p, 11p, 13, 14q11–q12, 15, 22  
20 67/f G44 Benign Stomach NED, 6 14  
21 53/m G48 Benign Stomach NED, 31 14  
22 34/m G49 Benign Stomach 6, 5 NED, 32  7, 8, 11 
23 41/m G52 Benign Jejunum NED, 13 1p31.2–pter, 6q, 22  
24 68/m G60 Benign Stomach NED, 33 14  
25 74/f G15 Malignant Stomach NA NA 14q13–qter, 15q15–qter, 18 16, 17 
26 60/f G22 Malignant Stomach NA 10q 3q, 5, 7, 12, 13, 18 
27 59/m G47 Malignant Colon 18 NED, 12 1p, 6q, 8p22–pter, 10, 11q14–qter, 12, 14, 15, 18q11–q23 2q22–qter 
28 52/m G6 Malignant Stomach 15 DOD, 5 3cen–p21, 14 1q32–qter, 3p22–pter, 3q (3q26–q29) 8p12–qter 
29 72/m G17 Malignant Jejunum 15 NA 2q31–qter, 3p, 9p  
30 60/m G20 Malignant Jejunum 10 DOD, 9 1p, 13, 14cen–q23, 15, 21, 22 3q, 8, 16p, 17 
31 68/f G27 Malignant Stomach 15 DOD, 71 1cen–p31, 3p, 14q21–q23, 15q21–qter 2q34–q37 
32 88/f G31 Malignant Stomach DOD, 26 1cen–p31, 8p, 9q, 10p15–q22, 22, X 1p32–pter, 5p, 9p, 17q21–q25 
33 63/m G36 Malignant Colon 16 NED, 24 8p21–pter, 10pter–q22, 14q21–q32 1p, 5, 7p, 8q22–qter, 9q, 19, 20 
34 63/m G11 Malignant Rectum NED, 39 8p, 9, 13q21–qter, 14, 15q15–q22, 22 3, 5, 8q, 11, 12, 17, 18, X 
35 86/f G16 Malignant Small intestine 6, 5 DOD, 19 1p, 2p, 15  
36 43/f G28 Malignant Jejunum NED, 78 1cen–p31, 13q21–qter, 15q15–qter, 18q 4, 17, 18p, 19 
37 69/m G30 Malignant Stomach 11 DOD, 32  11q14–q22, 19, X 
38 41/m G42 Malignant Stomach 18 NED, 12 1p, 2p13–pter, 9p, 14, 15, 22 11q 
39 44/m G43 Malignant Stomach 17 NED, 9 22 5, 7 
40 73/f G45 Malignant Stomach NED, 8  5, 6p, 7 
41 71/f G46 Malignant Jejunum NED, 27 1p, 4, 10, 15, 22  
42 73/f G50 Malignant Jejunum Alive, 9 1p, 2q, 9p, 13, 14, 15, 18q, 22 5p14–pter 
43 59/m G58 Malignant Stomach 12 NED, 27 9, 14 4p, 5, 7 
44 37/f PR28 Malignant Small intestine NA DOD, 50 1p, 8p, 9p, 11p, 14, 18q, 22 1q11–q31, 8q, 9q, 16q, 19p, 20q 
45 73/f G65 Malignant Duodenum 6, 5 NED, 24 1p, 6q21–qter, 9p, 11, 13, 14, 15 
46 46/f K1 Malignant Stomach 10 Alive, 35 7p15–p22, 7q32–qter, 9p21.2–pter, 14, 15, 18p, 22q13 2q, 4q, 8q23–qter 
46b K2 Metastases Omentum   7p15–p22, 7q32–qter, 9p21.2–pter, 13q13–qter, 14, 15, 19q13.2–qter, 22q13 2q, 6p, 8q23–qter, 17q 
46c K3 Metastases Colon mesentry   7p15–pter, 7q32–qter, 9p21.2–pter, 14, 15, 19q13.2–qter, 22q13 2q, 4q, 8q23–qter, 17q 
46d K4 Metastases Omentum   4p, 7p15–p22, 7q32–qter, 9p21.2–pter, 10, 11, 13q13–qter, 14, 15, 19q13.2–qter, 22q13 8q23–qter, 17q 
46e K5 Metastases Liver   4p, 7p15–p22, 7q32–qter, 9p21.2–pter, 11p, 13q13–qter, 14, 15, 19q13.2–qter, 22q13 2q, 8q23–qter, 17q 
46f K6 Metastases Liver   1p34.3–pter, 4, 6q14–qter, 7p15–p22, 7q32–qter, 9, 14, 18, 22q13 1q, 5 
46g K7 Metastases Colon mesentry   7p15–p22, 7q32–qter, 9p21.2–pter, 14, 15, 18p, 19q13.2–qter, 22q13 2q, 4q, 8q23–qter, 17q 
46h K8 Metastases Colon mesentry   7p15–p22, 7q32–qter, 9p21.2–pter, 13q13–qter, 14, 15, 19q13.2–qter, 22q13 2pter–q13, 4q, 8q22–qter, 17q 
46l K9 Metastases Colon mesentry   1p, 7p15–p22, 7q32–qter, 9p21.2–pter, 11, 13q, 14, 15, 19q13.2–qter, 22q13, X 2q, 4q, 8q22–qter (8q23–qter), 17q 
46j K10 Metastases Colon mesentry   7p15–p22, 7q32–qter, 9p21.2–pter, 13q13–qter, 14, 15, 19q13.2–qter, 22q13 2pter–q13, 4q, 8q22–qter, 17q 
46k K11 Metastases Ovary   7p15–p22, 7q32–qter, 9p21.2–pter, 11, 13, 14, 15, 19q13.2–qter, 22q13, X 2q, 4q, 8q22–qter, 17q 
46l K12 Metastases Colon mesentry   7p15–p22, 7q32–qter, 9p21.2–pter, 13q13–qter, 14, 15, 19q13.2–qter, 22q13 2pter–q13, 8q23–qter, 17q 
46m K14 Metastases Colon mesentry   6q14–qter, 7p11–p15, 7q32–qter, 9pter–q34.1, 14, X  
47 67/m PR1 Malignant Jejunum DOD, 35 1p, 2, 11, 13, 14, 15, 18  
47b PR2 Metastases Abdomen   1p, 2, 11, 13, 14, 15 1q, 3, 5, 6p, 7, 8, 9 
47c PR48 Metastases Abdomen   1p, 2, 11, 13, 14, 15, 18 1q11–q24, 3p14–p22, 6p, 7, 8 
47d PR3 Metastases Abdomen   1p, 2p22–pter, 11, 13, 14, 15, 18 1q, 3, 6p, 7, 8, 9 
48 44/m G8 Malignant Stomach 17 NA 1q32–qter, 14 8q22–qter 
48b PR5 Metastases Abdomen   1p, 2q, 5p14.3–pter, 12q15–qter, 14, 19q 
49 64/m PR6 Malignant Small intestine 12 Alive, 24 1p, 6q, 13, 14, 15, 18, 22 5p, 6p, 7, 12q 
49b PR7 Metastases Liver   1p, 6q, 13, 14, 15, 18, 22 5p, 6p, 7, 12q 
50 59/f PR8 Malignant Stomach 15 Alive, 96 9pter–q31, 10p, 13, 14, 19q13.3–qter, X 2p14–pter, 4p15–pter, 6p, 8, 9q32–qter, 10q, 12, 17q, 19pter–q13.2, 20q 
50b PR9 Metastases Liver   9pter–q31, 10p, 13, 14, 19q13.3–qter, X 2p14–pter, 7, 8, 12, 17, 19pter–q13.2, 20q 
No.Age/sex/codeHistologySiteaSizebFollow-up in monthsCGH karyotypea
LossesGains and high-level amplifications
59/m G1 Benign Jejunum 5, 5 NED, 51 1p, 15, 18, 22  
45/m G2 Benign Stomach 4, 5 NED, 45 14  
50/m G12 Benign Stomach 3, 3 NED, 38 1p, 14 8q 
75/m G25 Benign Stomach NED, 87 14, 22  
63/m G9 Benign Stomach 3, 5 NED, 41 14q11–q13, 14q23–qter, 22  
61/f G10 Benign Stomach NED, 40 1p, 14  
81/m G13 Benign Stomach 5, 5 NED, 110 15  
80/m G14 Benign Stomach NED, 124 14  
9/73/f G18 Benign Stomach 3, 5 NED, 81 11p, 14 5q22–qter 
10 63/f G19 Benign Jejunum NED, 31 1p, 11, 14, 15, 21 1q, 5, 7p, 18q 
11 58/m G21 Benign Stomach NED, 210 14q13–qter, 22  
12 49/f G23 Benign Stomach 16 NED, 209 22q12–qter  
13 65/f G24 Benign Stomach NED, 28 14, Xq  
14 73/m G26 Benign Stomach NED, 82 14, 15, 21, 22  
15 79/f G29 Benign Stomach NED, 133 22q12–qter  
16 78/m G32 Benign Stomach 2, 5 NED, 75 14, 22  
17 80/m G35 Benign Jejunum 4, 5 NED, 24 1p, 6q, 13q21–qter, 14 19 
18 85/m G38 Benign Stomach NED, 21 14, 22  
19 69/m G41 Benign Jejunum NED, 14 1p, 11p, 13, 14q11–q12, 15, 22  
20 67/f G44 Benign Stomach NED, 6 14  
21 53/m G48 Benign Stomach NED, 31 14  
22 34/m G49 Benign Stomach 6, 5 NED, 32  7, 8, 11 
23 41/m G52 Benign Jejunum NED, 13 1p31.2–pter, 6q, 22  
24 68/m G60 Benign Stomach NED, 33 14  
25 74/f G15 Malignant Stomach NA NA 14q13–qter, 15q15–qter, 18 16, 17 
26 60/f G22 Malignant Stomach NA 10q 3q, 5, 7, 12, 13, 18 
27 59/m G47 Malignant Colon 18 NED, 12 1p, 6q, 8p22–pter, 10, 11q14–qter, 12, 14, 15, 18q11–q23 2q22–qter 
28 52/m G6 Malignant Stomach 15 DOD, 5 3cen–p21, 14 1q32–qter, 3p22–pter, 3q (3q26–q29) 8p12–qter 
29 72/m G17 Malignant Jejunum 15 NA 2q31–qter, 3p, 9p  
30 60/m G20 Malignant Jejunum 10 DOD, 9 1p, 13, 14cen–q23, 15, 21, 22 3q, 8, 16p, 17 
31 68/f G27 Malignant Stomach 15 DOD, 71 1cen–p31, 3p, 14q21–q23, 15q21–qter 2q34–q37 
32 88/f G31 Malignant Stomach DOD, 26 1cen–p31, 8p, 9q, 10p15–q22, 22, X 1p32–pter, 5p, 9p, 17q21–q25 
33 63/m G36 Malignant Colon 16 NED, 24 8p21–pter, 10pter–q22, 14q21–q32 1p, 5, 7p, 8q22–qter, 9q, 19, 20 
34 63/m G11 Malignant Rectum NED, 39 8p, 9, 13q21–qter, 14, 15q15–q22, 22 3, 5, 8q, 11, 12, 17, 18, X 
35 86/f G16 Malignant Small intestine 6, 5 DOD, 19 1p, 2p, 15  
36 43/f G28 Malignant Jejunum NED, 78 1cen–p31, 13q21–qter, 15q15–qter, 18q 4, 17, 18p, 19 
37 69/m G30 Malignant Stomach 11 DOD, 32  11q14–q22, 19, X 
38 41/m G42 Malignant Stomach 18 NED, 12 1p, 2p13–pter, 9p, 14, 15, 22 11q 
39 44/m G43 Malignant Stomach 17 NED, 9 22 5, 7 
40 73/f G45 Malignant Stomach NED, 8  5, 6p, 7 
41 71/f G46 Malignant Jejunum NED, 27 1p, 4, 10, 15, 22  
42 73/f G50 Malignant Jejunum Alive, 9 1p, 2q, 9p, 13, 14, 15, 18q, 22 5p14–pter 
43 59/m G58 Malignant Stomach 12 NED, 27 9, 14 4p, 5, 7 
44 37/f PR28 Malignant Small intestine NA DOD, 50 1p, 8p, 9p, 11p, 14, 18q, 22 1q11–q31, 8q, 9q, 16q, 19p, 20q 
45 73/f G65 Malignant Duodenum 6, 5 NED, 24 1p, 6q21–qter, 9p, 11, 13, 14, 15 
46 46/f K1 Malignant Stomach 10 Alive, 35 7p15–p22, 7q32–qter, 9p21.2–pter, 14, 15, 18p, 22q13 2q, 4q, 8q23–qter 
46b K2 Metastases Omentum   7p15–p22, 7q32–qter, 9p21.2–pter, 13q13–qter, 14, 15, 19q13.2–qter, 22q13 2q, 6p, 8q23–qter, 17q 
46c K3 Metastases Colon mesentry   7p15–pter, 7q32–qter, 9p21.2–pter, 14, 15, 19q13.2–qter, 22q13 2q, 4q, 8q23–qter, 17q 
46d K4 Metastases Omentum   4p, 7p15–p22, 7q32–qter, 9p21.2–pter, 10, 11, 13q13–qter, 14, 15, 19q13.2–qter, 22q13 8q23–qter, 17q 
46e K5 Metastases Liver   4p, 7p15–p22, 7q32–qter, 9p21.2–pter, 11p, 13q13–qter, 14, 15, 19q13.2–qter, 22q13 2q, 8q23–qter, 17q 
46f K6 Metastases Liver   1p34.3–pter, 4, 6q14–qter, 7p15–p22, 7q32–qter, 9, 14, 18, 22q13 1q, 5 
46g K7 Metastases Colon mesentry   7p15–p22, 7q32–qter, 9p21.2–pter, 14, 15, 18p, 19q13.2–qter, 22q13 2q, 4q, 8q23–qter, 17q 
46h K8 Metastases Colon mesentry   7p15–p22, 7q32–qter, 9p21.2–pter, 13q13–qter, 14, 15, 19q13.2–qter, 22q13 2pter–q13, 4q, 8q22–qter, 17q 
46l K9 Metastases Colon mesentry   1p, 7p15–p22, 7q32–qter, 9p21.2–pter, 11, 13q, 14, 15, 19q13.2–qter, 22q13, X 2q, 4q, 8q22–qter (8q23–qter), 17q 
46j K10 Metastases Colon mesentry   7p15–p22, 7q32–qter, 9p21.2–pter, 13q13–qter, 14, 15, 19q13.2–qter, 22q13 2pter–q13, 4q, 8q22–qter, 17q 
46k K11 Metastases Ovary   7p15–p22, 7q32–qter, 9p21.2–pter, 11, 13, 14, 15, 19q13.2–qter, 22q13, X 2q, 4q, 8q22–qter, 17q 
46l K12 Metastases Colon mesentry   7p15–p22, 7q32–qter, 9p21.2–pter, 13q13–qter, 14, 15, 19q13.2–qter, 22q13 2pter–q13, 8q23–qter, 17q 
46m K14 Metastases Colon mesentry   6q14–qter, 7p11–p15, 7q32–qter, 9pter–q34.1, 14, X  
47 67/m PR1 Malignant Jejunum DOD, 35 1p, 2, 11, 13, 14, 15, 18  
47b PR2 Metastases Abdomen   1p, 2, 11, 13, 14, 15 1q, 3, 5, 6p, 7, 8, 9 
47c PR48 Metastases Abdomen   1p, 2, 11, 13, 14, 15, 18 1q11–q24, 3p14–p22, 6p, 7, 8 
47d PR3 Metastases Abdomen   1p, 2p22–pter, 11, 13, 14, 15, 18 1q, 3, 6p, 7, 8, 9 
48 44/m G8 Malignant Stomach 17 NA 1q32–qter, 14 8q22–qter 
48b PR5 Metastases Abdomen   1p, 2q, 5p14.3–pter, 12q15–qter, 14, 19q 
49 64/m PR6 Malignant Small intestine 12 Alive, 24 1p, 6q, 13, 14, 15, 18, 22 5p, 6p, 7, 12q 
49b PR7 Metastases Liver   1p, 6q, 13, 14, 15, 18, 22 5p, 6p, 7, 12q 
50 59/f PR8 Malignant Stomach 15 Alive, 96 9pter–q31, 10p, 13, 14, 19q13.3–qter, X 2p14–pter, 4p15–pter, 6p, 8, 9q32–qter, 10q, 12, 17q, 19pter–q13.2, 20q 
50b PR9 Metastases Liver   9pter–q31, 10p, 13, 14, 19q13.3–qter, X 2p14–pter, 7, 8, 12, 17, 19pter–q13.2, 20q 
Table 1A

Continued.

No.Age/sex/codeHistologySiteaSizebFollow-up in monthsCGH karyotypea
LossesGains and high-level amplifications
51 54/m PR10 Malignant Jejunum 15 Alive, 22 1p, 2, 7p, 11, 15, 18, 22 4q, 7q, 9p, 12q 
51b PR11 Metastases Abdomen   1p, 2, 4p, 11, 12p, 13, 15, 17p, 18, 22 5q, 7q, 8q, 9p, 21 
51c PR12 Metastases Abdomen   1p, 2p, 13, 15, 18, 22 5q, 10p 
52 59/m PR13 Malignant Small intestine 20 DOD, 49 1p, 8, 13, 14, 15, 22 1q, 2q22–qter, 4p, 5p, 17, 20p 
52b PR14 Metastases Abdomen   1p, 3pter–q13, 4q, 8, 9pter–q21, 10, 13, 14, 15, 22 1q, 2q22–qter, 4p, 5p, 17, 20p 
52c PR15 Metastases Abdomen   1p, 3pter–q13, 4q, 8, 9pter–q21, 13, 14, 15, 22 1q, 2q22–qter, 5p, 17, 20p 
53 62/f PR16 Malignant Stomach 15 Alive, 60 6, 9, 12pter–q22, 14, 22 17 
53b PR17G5 Metastases Abdomen  Alive 9, 14, 22 17q 
53c PR18 Metastases Abdomen   9, 14, 22 4, 17q, 20 
54 59/m PR19G3 Malignant Ileum 12 DOD, 14 13, 14q11–q12 5p 
54b PR20 Metastases Liver   12p, 14 5p, 8q 
55 38/f PR21 Malignant Jejunum 10 DOD, 59 1p, 11q14–qter, 13, 14, 15, 18, 22, X 1q, 5p, 8 
55b PR22 Metastases Abdomen   1p, 15, 18, 22q13 1q, X 
55c PR23 Metastases Abdomen   1p, 15, 18, 22q13 1q 
55d PR24 Metastases Abdomen   1p, 13, 15, 18, 22 1q 
56 52/f PR33 Malignant Small intestine 10 DOD, 12 1p, 14, 15 7, 8, 12q22–qter 
56b PR34 Metastases Abdomen   1p, 14, 15 7, 8, 12q22–qter 
57c PR35 Metastases Abdomen   1p, 14, 15 7, 8, 12q22–qter 
58 61/m PR36 Malignant Stomach 25 DOD, 19 1p, 11, 13, 14, 15 2q, 8q23–qter, 17q, X 
58b PR37 Metastases Abdomen   1p, 9 20 
58c PR38 Metastases Abdomen   1p, 9 17q22–qter, 20 
59 39/m PR39 Malignant Stomach 20 DOD, 14 4q27–q34, 9, 14, 22  
59b PR40 Metastases Abdomen   4q27–q34, 9, 14, 22  
59c 33/m PR42 Metastases Abdomen   1p11–p32, 4, 9pter–q33, 14 20q13.2–qter 
60 41/f PR45 Malignant Stomach Alive, 6 1p35–pter, 4, 9, 15, 22 5, 8p12–pter, 8q23–qter, 12q14–qter, 13, 18q 
60b PR46 Metastases Abdomen   1p35–pter, 4, 6q, 9, 14q11–q21, 15, 22 5, 8p12–pter, 8q23–qter, 12 (12q22–qter), 13, 18q, 20q 
60c PR47 Metastases Abdomen   1p35–pter, 4, 9, 10, 14, 15, 22 5p, 5q32–qter, 8p12–pter, 8q23–qter, 12 (12q22–qter), 13, 20q 
No.Age/sex/codeHistologySiteaSizebFollow-up in monthsCGH karyotypea
LossesGains and high-level amplifications
51 54/m PR10 Malignant Jejunum 15 Alive, 22 1p, 2, 7p, 11, 15, 18, 22 4q, 7q, 9p, 12q 
51b PR11 Metastases Abdomen   1p, 2, 4p, 11, 12p, 13, 15, 17p, 18, 22 5q, 7q, 8q, 9p, 21 
51c PR12 Metastases Abdomen   1p, 2p, 13, 15, 18, 22 5q, 10p 
52 59/m PR13 Malignant Small intestine 20 DOD, 49 1p, 8, 13, 14, 15, 22 1q, 2q22–qter, 4p, 5p, 17, 20p 
52b PR14 Metastases Abdomen   1p, 3pter–q13, 4q, 8, 9pter–q21, 10, 13, 14, 15, 22 1q, 2q22–qter, 4p, 5p, 17, 20p 
52c PR15 Metastases Abdomen   1p, 3pter–q13, 4q, 8, 9pter–q21, 13, 14, 15, 22 1q, 2q22–qter, 5p, 17, 20p 
53 62/f PR16 Malignant Stomach 15 Alive, 60 6, 9, 12pter–q22, 14, 22 17 
53b PR17G5 Metastases Abdomen  Alive 9, 14, 22 17q 
53c PR18 Metastases Abdomen   9, 14, 22 4, 17q, 20 
54 59/m PR19G3 Malignant Ileum 12 DOD, 14 13, 14q11–q12 5p 
54b PR20 Metastases Liver   12p, 14 5p, 8q 
55 38/f PR21 Malignant Jejunum 10 DOD, 59 1p, 11q14–qter, 13, 14, 15, 18, 22, X 1q, 5p, 8 
55b PR22 Metastases Abdomen   1p, 15, 18, 22q13 1q, X 
55c PR23 Metastases Abdomen   1p, 15, 18, 22q13 1q 
55d PR24 Metastases Abdomen   1p, 13, 15, 18, 22 1q 
56 52/f PR33 Malignant Small intestine 10 DOD, 12 1p, 14, 15 7, 8, 12q22–qter 
56b PR34 Metastases Abdomen   1p, 14, 15 7, 8, 12q22–qter 
57c PR35 Metastases Abdomen   1p, 14, 15 7, 8, 12q22–qter 
58 61/m PR36 Malignant Stomach 25 DOD, 19 1p, 11, 13, 14, 15 2q, 8q23–qter, 17q, X 
58b PR37 Metastases Abdomen   1p, 9 20 
58c PR38 Metastases Abdomen   1p, 9 17q22–qter, 20 
59 39/m PR39 Malignant Stomach 20 DOD, 14 4q27–q34, 9, 14, 22  
59b PR40 Metastases Abdomen   4q27–q34, 9, 14, 22  
59c 33/m PR42 Metastases Abdomen   1p11–p32, 4, 9pter–q33, 14 20q13.2–qter 
60 41/f PR45 Malignant Stomach Alive, 6 1p35–pter, 4, 9, 15, 22 5, 8p12–pter, 8q23–qter, 12q14–qter, 13, 18q 
60b PR46 Metastases Abdomen   1p35–pter, 4, 6q, 9, 14q11–q21, 15, 22 5, 8p12–pter, 8q23–qter, 12 (12q22–qter), 13, 18q, 20q 
60c PR47 Metastases Abdomen   1p35–pter, 4, 9, 10, 14, 15, 22 5p, 5q32–qter, 8p12–pter, 8q23–qter, 12 (12q22–qter), 13, 20q 

All metastases were intra-abdominal.

Maximum size in cm, high.

High-level amplifications are in bold; NED, no evidence of disease; NA, not available; DOD, died of disease.

Table 2

Summary of significant DNA copy number changes in GISTs

DNA copy number changes seen in primary malignant and metastatic tumors were compared to benign lesions. Ps are shown in parentheses. Ps shown in italics indicate comparison between metastatic and primary malignant tumors. Gains are indicated with + and losses with −.

Chromosomal regionBenign GISTMalignant GISTMetastatic GIST
8q+ 8% 33% (<0.001) 57% (<0.001), (<0.05) 
17q+ 25% (<0.05) 43% (<0.001), (<0.05) 
20q+ 11% (<0.001) 26% (<0.001), (<0.05) 
5p+ 31% (<0.001) 29% (<0.001) 
9p− 36% (<0.001) 63% (<0.001), (<0.05) 
13q− 8% 36% (<0.05) 46% (<0.001) 
Chromosomal regionBenign GISTMalignant GISTMetastatic GIST
8q+ 8% 33% (<0.001) 57% (<0.001), (<0.05) 
17q+ 25% (<0.05) 43% (<0.001), (<0.05) 
20q+ 11% (<0.001) 26% (<0.001), (<0.05) 
5p+ 31% (<0.001) 29% (<0.001) 
9p− 36% (<0.001) 63% (<0.001), (<0.05) 
13q− 8% 36% (<0.05) 46% (<0.001) 
1
Sarlomo-Rikala M., Kovatich A., Barusevicius A., Miettinen M. CD117: a sensitive marker for gastrointestinal stromal tumors that is more specific than CD34.
Mod. Pathol
,
11
:
728
-734,  
1998
.
2
Miettinen M., Sarlomo-Rikala M., Lasota J. Gastrointestinal stromal tumors: recent advances in understanding of their biology.
Hum. Pathol
,
30
:
1213
-1220,  
1999
.
3
Knuutila S., Björkqvist A-M., Autio K., Tarkkanen M., Wolf M., Monni O., Szymanska J., Larramendy M. L., Tapper J., Pere H., El-Rifai W., Hemmer S., Wasenius V-M., Vidgren V., Zhu Y. DNA copy number amplifications in human neoplasms.
Review of comparative genomic hybridization studies. Am. J. Pathol
,
152
:
1107
-1123,  
1998
.
4
Knuutila S., Aalto Y., Autio K., Björkqvist A-M., El-Rifai W., Hemmer S., Huhta T., Kettunen E., Kiuru-Kuhlefelt S., Larramendy M. L., Lushnikova T., Monni O., Pere H., Tapper J., Tarkkanen M., Varis A., Wasenius V-M., Wolf M., Zhu Y. DNA copy number losses in human neoplasms.
Am. J. Pathol
,
155
:
683
-694,  
1999
.
5
El-Rifai W., Sarlomo-Rikala M., Miettinen M., Knuutila S., Andersson L. C. DNA copy number losses in chromosome 14: an early change in gastrointestinal stromal tumors.
Cancer Res
,
56
:
3230
-3233,  
1996
.
6
El-Rifai W., Sarlomo-Rikala M., Knuutila S., Miettinen M. DNA copy number changes in development and progression in leiomyosarcoma of soft tissues.
Am. J. Pathol
,
153
:
985
-990,  
1998
.
7
Miller S. A., Dykes D. D., Polesky H. F. A simple salting out procedure for extracting DNA from human nucleated cells.
Nucleic Acids Res
,
16
:
1215
1988
.
8
El-Rifai W., Larramendy M. L., Björkqvist A-M., Hemmer S., Knuutila S. Optimization of comparative genomic hybridization using fluorochrome conjugated to dCTP and dUTP nucleotides.
Lab. Investig
,
77
:
699
-700,  
1997
.
9
Mitelman, F. Catalog of Chromosome Aberrations in Cancer, Ed. 4, 1987. New York: Wiley-Liss, Inc., 1991.
10
El-Rifai W., Sarlomo-Rikala M., Miettinen M., Andersson L. C., Knuutila S. High-resolution deletion mapping of chromosome 14 in stromal tumors of the gastrointestinal tract suggests two distinct tumor suppressor loci.
Genes Chromosomes Cancer
,
27
:
387
-391,  
2000
.
11
Bown N., Cotterill S., Lastowska M., O’Neill S., Pearson A. D., Plantaz D., Meddeb M., Danglot G., Brinkschmidt C., Christiansen H., Laureys G., Speleman F. Gain of chromosome arm 17q and adverse outcome in patients with neuroblastoma.
N. Engl. J. Med
,
340
:
1954
-1961,  
1999
.
12
Tarkkanen M., Elomaa I., Blomqvist C., Kivioja A. H., Kellokumpu-Lehtinen P., Bohling T., Valle J., Knuutila S. DNA sequence copy number increase at 8q: a potential new prognostic marker in high-grade osteosarcoma.
Int. J. Cancer
,
84
:
114
-121,  
1999
.
13
Arnold N., Hagele L., Walz L., Schempp W., Pfisterer J., Bauknecht T., Kiechle M. Overrepresentation of 3q and 8q material and loss of 18q material are recurrent findings in advanced human ovarian cancer.
Genes Chromosomes Cancer
,
16
:
46
-54,  
1996
.
14
Bärlund M., Tirkkonen M., Forozan F., Tanner M. M., Kallioniemi O., Kallioniemi A. Increased copy number at 17q22–q24 by CGH in breast cancer is due to high-level amplification of two separate regions.
Genes Chromosomes Cancer
,
20
:
372
-376,  
1997
.
15
Tanner M. M., Tirkkonen M., Kallioniemi A., Holli K., Collins C., Kowbel D., Gray J. W., Kallioniemi O. P., Isola J. Amplification of chromosomal region 20q13 in invasive breast cancer: prognostic implications.
Clin. Cancer Res
,
1
:
1455
-1461,  
1995
.
16
Isola J. J., Kallioniemi O. P., Chu L. W., Fuqua S. A., Hilsenbeck S. G., Osborne C. K., Waldman F. M. Genetic aberrations detected by comparative genomic hybridization predict outcome in node-negative breast cancer.
Am. J. Pathol
,
147
:
905
-911,  
1995
.
17
Tanner M. M., Tirkkonen M., Kallioniemi A., Isola J., Kuukasjärvi T., Collins C., Kowbel D., Guan X. Y., Trent J., Gray J. W., Meltzer P., Kallioniemi O. P. Independent amplification and frequent co-amplification of three nonsyntenic regions on the long arm of chromosome 20 in human breast cancer.
Cancer Res
,
56
:
3441
-3445,  
1996
.
18
Brinkmann U., Gallo M., Polymeropoulos M. H., Pastan I. The human CAS (cellular apoptosis susceptibility) gene mapping on chromosome 20q13 is amplified in BT474 breast cancer cells and part of aberrant chromosomes in breast and colon cancer cell lines.
Genome Res
,
6
:
187
-194,  
1996
.
19
Lydiatt W. M., Davidson B. J., Schantz S. P., Caruana S., Chaganti R. S. 9p21 deletion correlates with recurrence in head and neck cancer.
Head Neck
,
20
:
113
-118,  
1998
.
20
Maruno M., Yoshimine T., Muhammad A. K., Tokiyoshi K., Hayakawa T. Loss of heterozygosity of microsatellite loci on chromosome 9p in astrocytic tumors and its prognostic implications.
J. Neuro-Oncol
,
30
:
19
-24,  
1996
.
21
Eiriksdottir G., Johannesdottir G., Ingvarsson S., Bjornsdottir I. B., Jonasson J. G., Agnarsson B. A., Hallgrimsson J., Gudmundsson J., Egilsson V., Sigurdsson H., Barkardottir R. B. Mapping loss of heterozygosity at chromosome 13q: loss at 13q12–q13 is associated with breast tumour progression and poor prognosis.
Eur. J. Cancer
,
34
:
2076
-2081,  
1998
.
22
Stanton S. E., Shin S. W., Johnson B. E., Meyerson M. Recurrent allelic deletions of chromosome arms 15q and 16q in human small cell lung carcinomas.
Genes Chromosomes Cancer
,
27
:
323
-331,  
2000
.