Novel Regions of Allelic Imbalance Identified by Genome-Wide Analysis of Neuroblastoma1

Home , CORO1C

[CANCER RESEARCH 62, 1761–1767, March 15, 2002] Novel Regions of Allelic Imbalance Identified by Genome-wide Analysis of Neuroblastoma1

Jaume Mora,2 Nai-Kong V. Cheung, Sandra Oplanich, Lishi Chen, and William L. Gerald Departments of Pathology [J. M., S. O., L. C., W. G.] and Pediatrics [N-K. V. C.), Memorial Sloan-Kettering Cancer Center, New York, New York 10021

ABSTRACT high density, genome-wide allelic study. Only the series of Takita et al. (18) analyzed all chromosomes. This study used 35 RFLP probes Several nonrandom chromosomal abnormalities have been associated and eight microsatellite markers, with only one or two probes for most with neuroblastoma (NB). However, the relationship of each genetic event of the chromosomes. to the clinical course of disease is not firmly established. We have performed a genome-wide allelic scan of NB to identify regions with frequent To provide a comprehensive analysis of AI in NB, we performed a allelic imbalance (AI) and correlate the allelotype with clinical features of genome-wide scan using 217 fluorescently labeled microsatellite disease. Nineteen tumors from patients across the spectrum of NB were markers with two aims: (a) to identify new areas of AI; and (b)to used. Genome-wide allelotype was performed using 169 fluorescently correlate allelotype patterns with clinical subtypes of NB. labeled microsatellite markers from the Weber 9a human screening set (Research Genetics, Huntsville, AL) and 48 independent markers for high-density analysis of selected regions. Eleven chromosomal regions had MATERIALS AND METHODS AI in >25% of tumors including loci known previously to be frequently Nineteen frozen tumor specimens each with Ͼ75% tumor cell content altered such as 1p36 (10 of 19; 52%), 2p (9 of 19; 47%), 17q (8 of 19; 42%), obtained from 10 patients with stage 4 NB [according to the INSS (19)], 8 11q23 (8 of 19; 42%), 14q32 (7 of 19; 37%), 19q (6 of 19; 31%), 7q (6 of patients with LR NB (INSS stages 1, 2, and 3) and one patient with INSS stage 19; 31%), 9p21 (5 of 19; 26%), and three novel regions of frequent AI at 4s disease were studied. Human tissues were used for biological studies 10p11-p15 (7 of 19; 40%), 12q24.1 (5 of 19; 26%), and 8qcen–q24 (5 of 19; according to the guidelines of the institutional review board. 26%). AI of four regions (8q, 10p, 19q, and 12q) allowed the distinction of Clinical and biological characteristics for all cases are summarized in Table two genetic groups that matched clinical significant subgroups of NB. AI 1. High-risk LR NB is defined as disease locally progressing and requiring at 12q24 and 19q13 was found exclusively in high-risk local-regional cytotoxic therapy or progression to stage 4. High-risk stage 4 NB is defined by tumors, whereas AI at 10p11 and 8q appeared to be specific for stage 4 MYCN amplification. tumors with MCYN amplification. Spontaneously remitting or quiescent Genome-wide allelotyping was performed using the Weber 9a panel of 169 tumors were intact at all of the regions described above. polymorphic microsatellite markers (Research Genetics, Huntsville, AL) evenly distributed with an average of 20-cM genetic distance. The 169 markers INTRODUCTION were combined into 21 panels containing six to nine markers each of different sizes and dyes (6-carboxyfluorescein, hexachlorafluorescein, tetrachlorafluorescein). In the early 1980s, the first karyotypic reports of NB3 cell lines and The products for each panel were pooled and loaded into a 48-tube tray with stage 4 tumors revealed several nonrandom chromosomal abnormal- 6-carboxytetramethylrhodamine size standard. One run of the 48-tube tray (24 h) ities associated with the disease including losses on chromosomes 1p is therefore sufficient to analyze each pair sample of tumor and normal DNA for and 11q, gains on chromosomes 17q and 1q, the presence of homozy- all 169 markers. Alleles were measured using an ABI model 310 automated gous staining regions and double minutes, and changes in the normal fluorescent DNA sequencer/genotyper (Applied Biosystems, Foster City, CA). Data were analyzed with GeneScan v3.1 and Genotyper v3.6 NT software diploid chromosomal content (1–5). Amplification of the proto-onco- (Applied Biosystems, Foster City, CA). Each allele assignment was also con- gene MYCN was subsequently identified in the homozygous staining firmed manually. Forty-eight additional markers for region-specific analyses of regions and double minutes (6). In the 1990s, PCR-based LOH and chromosomes 1p36, 1p22, 11q23, 14q32, 9p21, 17q, and 19q13 were obtained FISH analyses showed alteration of subchromosomal regions not from the genome database (www.gdb.org) and used as published previously identified previously by karyotyping including losses at 3p, 4p, 9p, (20–22). and 14q and gains at 5q and 18q in 20–40% of NB tumors of all risk In comparison to CGH or FISH analyses, use of fluorescent DNA primers categories (7–13). CGH has been used to provide an entire genome for quantitation of PCR products does not readily distinguish gain from loss survey of NB (14–16). These studies confirmed previous data and (23). The term AI is used, but in some cases previous karyotypic, FISH, or CGH with multicolor FISH has been used to characterize the multiple CGH data are available to determine whether it represents gain or loss. AI was chromosomal alterations in NB cell lines (17). Despite the identifica- determined by comparison of the allelic ratio between the normal and tumor specimen in heterozygous samples as described previously (24). AI was tion of numerous chromosomal regions that are consistently altered in defined as ratios Ͼ1.5 for loss of the shortest allele or Ͻ0.5 for the largest in NB, MYCN is the only gene corresponding to these regions identified cases of diploid tumor content. For near-triploid tumors, ratios of Ͻ0.35 and to date. Ͼ2 were used to match the AI criteria for diploid tumors (20). This formula Several regions in NB (such as 1p36) have received detailed PCR- establishes AI as a Ͼ50% reduction in allele intensity and accounts for based allelic analysis; however, there has not been a comprehensive, preferential amplification of the shortest allele (25).

Received 7/16/01; accepted 1/17/02. RESULTS 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 Regions of Frequent AI among the Samples Studied 18 U.S.C. Section 1734 solely to indicate this fact. 1 This study was supported by Young Investigator Award YIA 2000 (to J. M.) from the American Society of Clinical Oncology. Presented in part at the 37th American Society One hundred sixty-nine fluorescent polymorphic markers were of Clinical Oncology annual meeting, San Francisco, May 2001. used spanning the entire human genome with an average intermarker 2 To whom requests for reprints should be addressed, at Department of Hematology distance of 20 cM. Information on 48 additional polymorphic markers and Oncology, Hospital Sant Joan de Deu de Barcelona, Passeig de Sant Joan de Deu num 2, 08950 Esplugues del Llobregat Barcelona, Spain. Phone: (34)-93-280-40-00, extension spanning known regions of AI for NB (1p36, 9p21, 11q23, 14q32, 2361; Fax: (34)-93-203-3959; E-mail: [email protected]. 17q, and 19q13) was available for all of the cases (20–22). Fig. 1 3 The abbreviations used are: NB, neuroblastoma; LOH, loss of heterozygosity; FISH, fluorescence in situ hybridization; CGH, comparative genomic hybridization; AI, allelic shows representative electropherogram output data from the ABI 310 imbalance; INSS, International Neuroblastoma Staging System; LR, local-regional. Genotyper Software. Multiple microsatellite markers are pooled, and 1761

Table 1 Clinical and biological characteristics for all patients studied Specimen Age INSS stage Histologyb Ploidy MYCN Therapy Outcomec F/ud Groupa 1 1388-Dx Liver 1.2 mo 4s FH 1 NAM SX A 50 2117-Dx LN 8 mo 4 UH 1,1 NAM N5 A 80 1940-Dx Retroperitoneum 13 mo 4 FH 1,27 NAM SX A 16 987-Dx Retroperitoneal T 11 mo 3 FH 1,44 NAM SX A 92 1646-Dx Adrenal 6 mo 4 FH 1 AM N7 A 35 Group 2 1163-Dx Mediastinum 17 mo 3 FH 1,55 NAM SXϩN5 D 66 1637-Dx Mediastinum 6 yr 3 UH 1,07 NAM SXϩN7 D 25 2116-Dx Jaw 5 yr 2 UH NAM N8 A 41 1837-Dx Retroperitoneal T 13 mo 3 FH 1,12 NAM CCG-3891 A 34 1841-Dx Adrenal 6 yr 1 UH 1 NAM N7 D 22 1591-Dx Adrenal 3 yr 3 UH 1 AM SXϩN7 A 26 1428-rel Abdominal T 4 yr 3 UH 1,14 NAM CCG3881/N7 D 41 Group 3 1586-Dx Adrenal 3.1 yr 4 UH AM N7 D 24 1381-Dx Retroperitoneal T 9.6 mo 4 UH 1 AM N7 D 8 1659-Dx Adrenal 5 yr 4 UH 2 AM N7 A 30 1379-Dx Neck mass 2.8 yr 4 UH AM N7 A 56 1377-Dx Adrenal 3 yr 4 UH 1,04 AM N7 A 57 1464-Dx Adrenal 1.3 yr 4 UH AM N7 A 47 2019-Dx Mediastinal T 2 mo 2 FH 1 NAM SX A 15 a Group, genetic groups according to the allelotype pattern; Dx, specimen taken at diagnosis; rel, specimen taken at relapse; LN, lymph node; T, tumor; NAM, nonamplified; AM, amplified (Ͼ10 copies/haploid genome); SX, surgery; N5, N6, N7, and N8, Memorial Sloan-Kettering Cancer Center multimodality protocols; CCG, Children’s Cancer Group protocols. b Histology according to the International Pathology classification system. FH, favorable histology; UH, unfavorable histology. c A, alive; D, dead. d F/u, follow-up in months. fluorescent intensity for each allele in both nonneoplastic (top panel) NB such as 2p and 7q (2, 15, 16). The 2p region most likely represents and tumor (bottom panel) tissue are analyzed automatically by the gain of genetic material at the MYCN locus. Overall, the AI frequency sequencer. for these known regions across all of the samples using the 217 Fig. 2 graphs the frequency of AI across all markers for each markers set was: 1p36 LOH, 52% (10 of 19); 2p gain, 47% (9 of 19); chromosomal arm with common AI of contiguous markers. The plot 17q arm gain, 42% (8 of 19); 11q23 LOH, 42% (8 of 19); 14q32 LOH, demonstrates that most (81%) have regions of Ͻ25% AI detected. We 37% (7 of 19); 19q LOH, 31% (6 of 19); 7q gain, 31% (6 of 19); and therefore chose to focus on regions with Ͼ25% AI frequency as 9p21 LOH, 26% (5 of 19). representative of commonly altered alleles in NB. Eleven regions, Three previously unrecognized regions of significant AI were iden- defined as contiguous AI over several markers (see Fig. 2) with Ͼ25% tified at 10p11–p15 (40%; 6 of 15), 12q24.1 (26%; 5 of 19), and frequency of AI were detected. These included regions of LOH 8qcen–q24 (26%; 5 of 19). Fig. 3 shows the results of the 11 characterized previously on chromosome arms 1p36, 17q, 11q23, chromosomal regions with Ͼ25% AI for all cases and details the 14q32, 19q13, and 9p21 and regions known to be altered by gains in markers defining the minimal areas of AI.

Fig. 1. Electropherogram output data from the Genotyper software. Panel 11 from normal (top) and tumor (bottom) pair are shown. Each allele peak is automatically labeled with map-pair number in the panel, bp size, and peak height. The table details the calculations originated from the genotyper software. Category, microsatellite marker; Mker, marker of each panel; Pk1, peak 1 or allele one bp size; Ht1, height off the first peak or allele; Pk2, peak 2 or allele two bp size; Ht2, height off the second peak or allele; PkHtRatio, ratio between allele 2 versus allele 1 heights for each sample; T/NRatio, ratio between PkHt from the normal versus the tumor; Assess, assessment according to predetermined cutoffs. 1762

One patient had multiply recurrent, chemoresistant LR disease that evolved into metastatic disease to the bone marrow after 5 years (T#1163, Table 2). Two patients with INSS stage 3 disease at diagnosis (T#1637 and 1837) evolved to stage 4N disease within 1 year with distant lymph node metastasis but no bone or bone marrow involvement. One patient presented with INSS stage 1 tumor (T#1841, Table 2) managed without cytotoxic therapy but developed metastatic disease in liver and lungs 11 months later. One case (T#2116, Table 2) presented with INSS stage 2 disease managed without cytotoxic therapy and relapsed 2 years later with bone and lymph node metastasis. One case (T#1428, Table 2) with INSS stage 3 had multiply recurrent, refractory LR disease over the course of 3 years that eventually killed the patient. One case (T#1591) presented as INSS stage 3 and was MYCN amplified. Because of the MYCN status, this patient was treated with high-dose multimodality therapy from the beginning and did well. Genetic group 2 is composed predominantly of patients presenting with LR NB disease that is progressive and associated with poor survival. Group 3. All tumors in this group had AI at 8qcen–q24 or 10p11- p15 or both. Furthermore, all tumors had an intact 19q13, and all but Fig. 2. Frequency plot of AI for all of the consistent hot spots on each chromosomal one were also intact at 12q24.1 regions altered frequently in group 2 arms defined across the samples studied. The frequency of altered hot spot regions found in the study are graphed and colored in the chromosomal arms encountered. (Table 2). These patients predominantly presented with stage 4 disease and MYCN amplification (Ͼ10 copies/haploid genome; 6 of 7), Three Distinct Genetic Profiles Distinguish Clinically Relevant a classically lethal form of NB. Only one case (T#2019) did not match Subgroups of NB the clinical pattern, although the tumor had 8q AI characteristic of this group. This patient presented at very young age, 3 months, with a LR The profile of AI for four chromosomal regions (8q, 10p, 19q, and tumor in the chest that was treated surgically. MYCN was not ampli- 12q) allowed the distinction of three genetic groups (Tables 1 and 2 fied. No cytotoxic therapy was given, and residual local [131I]me- and Fig. 3). After review of the clinical characteristics and outcome taiodobenzylguanidine-positive lymph nodes continued to improve. for all cases in each genetic group, distinguishable clinical patterns This patient is alive and well 18 months from diagnosis. Genetic appeared to correlate with these three genetic profiles (see below). group 3 seems to be a profile associated with stage 4, MYCN- Table 2 shows the status of regions with frequent (Ͼ25%) AI for the amplified NB. three groups. Color codes highlight the genetic characteristics of each group. DISCUSSION Group 1. These tumors were characterized genetically by a gen- erally low frequency of AI and more specifically by retained heterozy- Genome-wide allelotype analysis of tumor DNA was first per- gosity in regions of LOH defining groups 2 and 3 (see Table 2 and formed for colorectal cancer (26). Since then this approach has been Fig. 3). The patients were all very young (all presented at Ͻ13 months used to study carcinomas of the lung (27, 28), nasopharynx (29), of age) with spontaneously remitting or quiescent tumors. One patient esophagus (30, 31), cervix (32), endometrium (33), kidney (34), breast with an INSS stage 4s diploid tumor (T#1388, Table 2) had one cycle (35, 36), pheochromocytomas and medullary thyroid carcinomas (37), of chemotherapy during infancy but persistent disease managed with- pituitary tumors (38), childhood brain tumors (39), and acute lym- out cytotoxic therapy, finally undergoing definitive resection of viable phoblastic leukemia (40, 41) and has successfully contributed to the tumor at 3 years of age. One INSS stage 4 infant (T#2117, Table 2) isolation of several tumor suppressor genes (42, 43). The recent was managed with multimodality therapy and has residual but non- development of semiautomated techniques using fluorescent-labeled progressing tumor 6 years after diagnosis and 4 years since last primers for the genotyping of microsatellites has allowed high-reso- chemotherapy. One patient presented at 13 months of age with ab- lution screening. dominal primary and distant lymph node metastasis (INSS stage 4), Previous allelotypic analyses of NB have been restricted primarily which was managed without cytotoxic therapy and spontaneously to particular chromosomal regions or arms (7–13, 20–22, 44, 45). Our regressed (T#1940, Table 2). One 11-month-old with INSS stage 3, results thus represent, to date, the highest resolution genome-wide NB triploid NB was completely resected, managed with surgery alone, allelotyping and allow for the determination of loci interactions. It was and doing well 7 years after diagnosis (T#987, Table 2). One infant shown previously that chromosome arm 1p (multiple sites) and 17q stage 4 was MYCN amplified (T#1646, Table 2) and was managed have the most frequent AI (loss and gain, respectively) in NB (1–3, with N7-type multimodality therapy (25). This patient is alive and 15). Our results agree with and extend these findings. Overall, we well, free of disease 3 years from diagnosis. Genetic group 1 therefore found 11 different sites of frequent AI, 3 of them (8q, 10p, and 12q) seems to distinguish a nonlethal form of NB (i.e., long-term survival). not described previously in NB. Group 2. This group had AI at 12q24 and/or 19q13 LOH. These A new region of AI on chromosome 8q was found consistently genetic markers appear to be highly specific for this group because centered around the microsatellite marker D8S1119 (ATA19G07; see only one tumor (T#1379) from group 3 showed AI at 12q24 (in red, Fig. 3). This marker4 has been well characterized cytogenetically at Table 2). All tumors in this group were intact at chromosomal arm 8q21.3 and in the draft sequence comprises the chromosome 8: 8qcen–q24, a marker with high frequency of AI in group 3 tumors 99020313–99040347 base positions. One uncharacterized gene map- (see below). Patients in this group presented with LR disease, refractory to multimodality therapy. Most slowly progressed over time into 4 MIT chromosome 8 genetic map: http://carbon.wi.mit.edu and http://genome.ucsc. lethal stage 4 disease. edu/goldenPath/hgTracks.htmland. 1763

Fig. 3. Summary results for all cases of the 11 chromosomal regions (chromosome column on the left indicates chromosome number) with Ͼ25% AI. The microsatellite markers are listed on the left in order from p telomere to q telomere for each chromosome. Cases are listed horizontally as tumor numbers. The markers defining the minimal areas of AI [shortest Green (or ϩ), intact; gray (or 1), homozygote; red .[ء regions of overlap (SRO) or hot spots for each chromosome are labeled on the right-hand side of each chromosome list with a (or Ϫ), AI. Cases are grouped in three clinically relevant groups of NB: group 1 (left), characterized by their general low frequency of AI and more specifically by intact regions defining groups 2 and 3. Clinically, this group is composed of young patients (all infants except one diagnosed at 13 months of age) with spontaneously remitting or quiescent tumors; group 1764

Table 2 Summary of the allelotype pattern for each of the 11 chromosomal arms lung, ovary, and skin (49). Furthermore, in melanomas and gliomas, showing significant (Ͼ25%) AIa monosomy of chromosome 10 is an indicator of poor clinical prognosis (50, 51). In these tumor types, two regions at 10p15 and 10q have been described. Three tumor suppressor genes have been identified in the long arm of chromosome 10, PTEN (52), DBMT1 (53), and LGI1 (54) but none in the short arm. Very few genes have been isolated in this region but include IDI1, AKR1C3, DDH1, NET1A, PRKCQ, and the GATA-binding protein 3. In our study, LOH at chromosome 10 was found exclusively at 10p11.23–p15.1 and was associated with MYCN-amplified stage 4 tumors. The new region of AI on chromosome 12 is defined by the con- sensus marker D12S395 (or CHLC.GATA4H01.523) cytogenetically mapping at 12q24.23 according to the draft sequence.5 The mapping position at chromosome 12 is 137873902–138074246r. 12q24 is a common breakpoint region for balanced and unbalanced transloca- tions in many hematological malignancies6 and the site of genes involved in neurological disorders like spinocerebellar ataxia type 2 (ataxin-2) and phenylketonuria (phenylalanine hydroxylase gene); genes involved in signaling transduction and differentiation such as DTX1, CORO1C, and H11 genes; and the critical region for the Noonan syndrome (55–59). Our results show 12q24.23 AI together with 19q13 LOH, as specific markers for high-risk LR NB. NB is a heterogeneous disease with three clinically relevant categories derived from the natural history of the disease: (a) infants with widespread disease that can spontaneously regress without medical intervention (stage 4s); (b) LR disease that may recur but does not metastasize to bone or bone marrow (stages 1, 2, and 3); and (c) systemic disease with a Ϫ, intact region; ϩ, AI; green areas, characteristic negative AI regions for each widespread metastasis that responds to cytotoxic therapy but frequently group; yellow areas, characteristic AI regions for each group; red boxes, exceptions. becomes resistant to medical treatment (stage 4). Efforts for a genetic classification of NB have been attempted in the past (60); however, the ping in the region is AC084128.2 in the chromosome 8 clone CTD- resulting groups did not entirely coincide with the risk categories used in 3118D11. Nearby areas at 8q24 have been implicated in tumorigen- clinical trials (i.e., COG), and they did not match with the natural history esis. 8qcen–q24 gains have been described in Wilms’ tumors (46), groups of disease either because metastatic (INSS stage 4) and nonmeta- hepatoblastomas (47), and germ cell tumors (48). Furthermore, 8q static tumors (INSS stage 3) were grouped together. Many commonly gain was found to be of poor prognostic significance in a series of altered regions, such as 1p36 LOH, 11q23 LOH, 14q32 LOH and 17q hepatoblastomas (47). A few genes have been identified in this region gain, can be detected in all risk categories of NB, as shown in this and including growth-related genes FGFR1; RAB4, a member of the RAS previous reports (20, 22). oncogene family; LYN, an v-yes-1 Yamaguchi sarcoma viral related Experience in the last decade in our institution supports the hypoth- gene; and others, TAGLN2, CYP7A1, SDCBP, and NSMAF, a sphin- esis that the natural history of disease defines relevant clinical groups gomyelinase activator factor. The results of our study show a high of NB and that there exist distinct molecular genetic profiles for each association between MYCN-amplified stage 4 tumors and 8q21.3 AI. pattern of disease (20–22). Therapeutic approaches can therefore be Future investigations with higher resolution will therefore be crucial tailored for each group (61–63). The results in this study identified to narrow down the smallest common region of AI, and analysis novel regions of AI specifically associated with three distinct clinical should determine whether 8q21.3 AI corresponds to gain of genetic patterns. This correlation illustrates the fundamental importance of material as described previously in other childhood tumor types. having precise and complete clinical information in refining the The new region of AI for NB on chromosome 10 is defined by three genetic profiling of human cancers. markers (see Fig. 3): (a) D10S1435 (or CHCL GATA88F09) at Two patients provided clinical exceptions to the genetic groups 10p15.1 and situated at chromosome 10 2607874–2627906; (b) defined here and are worth further discussion. One case (tumor #2019) D10S1430 (or CHCL GATA84C01) at 10p13, chromosome 10: had some of the genetic characteristics of stage 4, MYCN-amplified 13308340–13508486. This marker has three nearby genes in the draft tumors, i.e., 8q21.3 AI. This patient presented as a young infant with sequence, AL 512284.15, AC 026221.8, and AL 512783.16, all of LR tumor, MYCN nonamplified, and is doing well with surgery alone, unknown function; and (c) D10S1426 (or CHLC.GATA73E11) at 1 year after diagnosis. The other case was also an infant with stage 4, 10p11.23, chromosome 10: 32735722–32936077 bp position. This MYCN-amplified disease (tumor #1646) managed with multimodality new region is therefore a vast area from 10p11.23 to 10p15.1.5 Loss therapy because of the well-established risk factor, MYCN. The tumor, of an entire copy of chromosome 10 is common in tumors of the brain, however, did not have the genetic characteristics of stage 4, MYCN-

6 5 Internet address: http://genome.ucsc.edu/goldenPath/hgTracks.htmland. Internet address: http://cgap.nci.nih.gov/Chromosomes.

2(center), AI at 12q24 and/or 19q13 LOH and intact at chromosomal arm 8qcen–q24, a marker with high frequency of AI in group 3 tumors. Clinically, this group presented as LR disease, with refractory primary tumors despite multimodality therapy; group 3 (right), AI at 8qcen–q24 or 10p11-p15 or both and intact at 19q13 and 12q24.1 regions frequently altered in group 2. Clinically, this group is composed primarily of cases with stage 4 disease at diagnosis and MYCN amplification. 1765

Downloaded from cancerres.aacrjournals.org on September 26, 2021. © 2002 American Association for Cancer Research. NEUROBLASTOMA ALLELOTYPE amplified tumors (group 3) but displayed features resembling that of tional Criteria for neuroblastoma diagnosis, staging, and response to treatment. group 1 tumors, the nonlethal form of NB. The patient is alive and J. Clin. Oncol., 11: 1466–1477, 1993. 20. Mora, J., Cheung, N. K., Kushner, B. H., LaQuaglia, M. P., Kramer, K., Fazzari, M., well 3 years from diagnosis. It is likely that the clinical course of Heller, G., Chen, L., and Gerald, W. L. Clinical categories of neuroblastoma are disease for NB is complex and dependent on many more factors than associated with different patterns of loss of heterozygosity on chromosome arm 1p. J. Mol. Diag., 2: 1–9, 2000. simply AI status. These factors are likely to include genetic alter- 21. Mora, J., Cheung, N. K., Chen, L., Qin, J., and Gerald, W. Loss of heterozygosity at ations, age, and therapeutic approach. These exceptions to the genetic 19q13.3 is associated with locally aggressive neuroblastoma. Clin. Cancer Res., 7: classification based on AI status raise the issue of cooperating factors 1358–1361, 2001. 22. Mora, J., Cheung, N. K., Chen, L., Qin, J., and Gerald, W. Survival analysis of and the effect of therapeutic intervention on the natural history of clinical, pathologic and genetic features in neuroblastoma presenting as local-regional disease. disease. Cancer (Phila.), 91: 435–442, 2001. The role of the new regions of AI as clinical markers for high-risk 23. Cher, M. L., MacGrogan, D., Bookstein, R., Brown, J. A., Jenkins, R. B., and Jensen, R. H. Comparative genomic hybridization, allelic imbalance, and fluorescence in situ tumors needs to be confirmed in a larger cohort of patients. Further hybridization on chromosome 8 in prostate cancer. Genes Chromosomes Cancer, 11: studies to identify the relevant genes in each region may contribute to 153–162, 1994. 24. Cawkwell, L., Bell, S. M., Lewis, F. A., Dixon, M. F., Taylor, G. R., and Quirke, P. an understanding of the basic biology that underlies the clinical Rapid detection of allele loss in colorectal tumours using microsatellites and fluores- complexity of NB. cent DNA technology. Br. J. Cancer, 67: 1262–1267, 1993. 25. Walsh, P. S., Erlich, H. A., and Higuchi, R. Preferential PCR amplification of alleles: mechanisms and solutions. PCR Methods Appl., 1: 241, 1998. 26. Vogelstein, B., Fearon, E. R., Kern, S. E., Hamilton, S. R., Preisinger, A. C., REFERENCES Nakamura, Y., and White, R. Allelotype of colorectal carcinomas. Science (Wash. 1. Brodeur, G. M., Sekhon, G. S., and Goldstein, M. N. Chromosomal aberrations in DC), 244: 207–211, 1989. human neuroblastomas. Cancer (Phila.), 40: 2256–2263, 1977. 27. Sanchez-Cespedes, M., Ahrendt, S. A., Piantadosi, S., Rosell, R., Monzo, M., Wu, L., 2. Brodeur, G. M., Green, A. A., Hayes, F. A., Williams, K. J., Williams, D. L., and Westra, W. H., Yang, S. C., Jen, J., and Sidransky, D. Chromosomal alterations in Tsiatis, A. A. Cytogenetic features of human neuroblastomas and cell lines. Cancer lung adenocarcinoma from smokers and nonsmokers. Cancer Res., 61: 1309–1313, Res., 41: 4678–4686, 1981. 2001. 3. Gilbert, F., Feder, M., Balaban, G., et al. Human neuroblastomas and abnormalities 28. Girard, L., Zochbauer-Muller, S., Virmani, A. K., Gazdar, A. F., and Minna, J. D. of chromosomes 1 and 17. Cancer Res., 44: 5444–5449, 1984. Genome-wide allelotyping of lung cancer identifies new regions of allelic loss, 4. Haag, M. M., Soukup, S. W., and Neely, J. E. Chromosome analysis of a human differences between small cell lung cancer and non-small cell lung cancer, and loci neuroblastoma. Cancer Res., 41: 2995–2999, 1981. clustering. Cancer Res., 60: 4894–4906, 2000. 5. Biedler, J. L., and Spengler, B. A. Human neuroblastoma cytogenetics. In: A. E. 29. Lo, K. W., Teo, P. M., Hui, A. B., To, K. F., Tsang, Y. S., Chan, S. Y., Mak, K. F., Evans (ed.), Advances in Neuroblastoma Research, pp. 81–96. New York: Raven Lee, J. C., and Huang, D. P. High resolution allelotype of microdissected primary Press, 1980. nasopharyngeal carcinoma. Cancer Res., 60: 3348–3353, 2000. 6. Brodeur, G. M., Seeger, R. C., Schwab, M., Varmus, H. E., and Bishop, J. M. 30. Dolan, K., Garde, J., Gosney, J., Sissons, M., Wright, T., Kingsnorth, A. N., Walker, Amplification of N-myc in untreated human neuroblastomas correlates with advanced S. J., Sutton, R., Meltzer, S. J., and Field, J. K. Allelotype analysis of oesophageal stage disease. Science (Wash. DC), 224: 1121–1124, 1984. adenocarcinoma: loss of heterozygosity occurs at multiple sites. Br. J. Cancer, 78: 7. Fong, C. T., White, P. S., Peterson, K., Sapienza, C., Cavenee, W. K., Kern, S. E., 950–957, 1998. Vogelstein, B., Cantor, A. B., Look, A. T., and Brodeur, G. M. Loss of heterozygosity 31. Hu, N., Roth, M. J., Polymeropolous, M., Tang, Z. Z., Emmert-Buck, M. R., Wang, for chromosomes 1 or 14 defines subsets of advanced neuroblastomas. Cancer Res., Q. H., Goldstein, A. M., Feng, S. S., Dawsey, S. M., Ding, T., Zhuang, Z. P., Han, 52: 1780–1785, 1992. X. Y., Ried, T., Giffen, C., and Taylor, P. R. Identification of novel regions of allelic 8. Ejeskar, K., Aburatani, H., Abrahamsson, J., Kogner, P., and Martinsson, T. Loss of loss from a genomewide scan of esophageal squamous-cell carcinoma in a high-risk heterozygosity of 3p markers in neuroblastoma tumours implicate a tumor-suppressor Chinese population. Genes Chromosomes Cancer, 27: 217–228, 2000. locus distal to the FHIT gene. Br. J. Cancer, 77: 1787–1791, 1998. 32. Mitra, A. B., Murty, V. V., Li, R. G., Pratap, M., Luthra, U. K., and Chaganti, R. S. 9. Caron, H., van Sluis, P., Buschman, R., Pereira do Tanque, R., Maes, P., Beks, L., de Allelotype analysis of cervical carcinoma. Cancer Res., 54: 4481–4487, 1994. Kraker, J., Voute, P. A., Vergnaud, G., Westerveld, A., Slater, R., and Versteeg, R. 33. Fujino, T., Risinger, J. I., Collins, N. K., Liu, F. S., Nishii, H., Takahashi, H., Allelic loss of the short arm of chromosome 4 in neuroblastoma suggests a novel Westphal, E. M., Barrett, J. C., Sasaki, H., Kohler, M. F., Berchuck, A., and Boyd, J. tumor suppressor gene locus. Hum. Genet., 97: 834–837, 1996. Allelotype of endometrial carcinoma. Cancer Res., 54: 4294–4298, 1994. 10. Marshall, B., Isidro, G., Martins, A. G., and Boavida, M. G. Loss of heterozygosity 34. Thrash-Bingham, C. A., Greenberg, R. E., Howard, S., Bruzel, A., Bremer, M., Goll, at chromosome 9p21 in primary neuroblastomas: evidence for two deleted regions. A., Salazar, H., Freed, J. J., and Tartof, K. D. Comprehensive allelotyping of human Cancer Genet. Cytogenet., 96: 134–139, 1997. renal cell carcinomas using microsatellite DNA probes. Proc. Natl. Acad. Sci. USA, 11. Weiss, M. J., Guo, C., Shusterman, S., Hii, G., Mirensky, T. L., White, P. S., Hogarty, 92: 2854–2858, 1995. M. D., Rebbeck, T. R., Teare, D., Urbanek, M., Brodeur, G. M., and Maris, J. M. 35. Kerangueven, F., Noguchi, T., Coulier, F., Allione, F., Wargniez, V., Simony- Localization of a hereditary neuroblastoma predisposition gene to 16p12–p13. Med. Lafontaine, J., Longy, M., Jacquemier, J., Sobol, H., Eisinger, F., and Birnbaum, D. Pediatr. Oncol., 35: 526–530, 2000. Genome-wide search for loss of heterozygosity shows extensive genetic diversity of 12. Meltzer, S. J., O’Doherty, S. P., Frantz, C. N., Smolinski, K., Yin, J., Cantor, A. B., human breast carcinomas. Cancer Res., 57: 5469–5474, 1997. Liu, J., Valentine, M., Brodeur, G. M., and Berg, P. E. Allelic imbalance on 36. Osborne, R. J., and Hamshere, M. G. A genome-wide map showing common regions chromosome 5q predicts long-term survival in neuroblastoma. Br. J. Cancer, 74: of loss of heterozygosity/allelic imbalance in breast cancer. Cancer Res., 60: 3706– 1855–1861, 1996. 3712, 2000. 13. Takita, J., Hayashi, Y., Takei, K., Yamaguchi, N., Hanada, R., Yamamoto, K., and 37. Khosla, S., Patel, V. M., Hay, I. D., Schaid, D. J., Grant, C. S., van Heerden, J. A., Yokota, J. Allelic imbalance on chromosome 18 in neuroblastoma. Eur. J. Cancer, 36: and Thibodeau, S. N. Loss of heterozygosity suggests multiple genetic alterations in 508–513, 2000. pheochromocytomas and medullary thyroid carcinomas. J. Clin. Investig., 87: 1691– 14. Van Roy, N., Jauch, A., Van Gele, M., Laureys, G., Versteeg, R., De Paepe, A., 1699, 1991. Cremer, T., and Speleman, F. Comparative genomic hybridization analysis of human 38. Clayton, R. N., Pfeifer, M., Atkinson, A. B., Belchetz, P., Wass, J. A., Kyrodimou, E., neuroblastomas: detection of distal 1p deletions and further molecular genetic char- Vanderpump, M., Simpson, D., Bicknell, J., and Farrell, W. E. Different patterns of acterization of neuroblastoma cell lines. Cancer Genet. Cytogenet., 97: 135–142, allelic loss (loss of heterozygosity) in recurrent human pituitary tumors provide 1997. evidence for multiclonal origins. Clin. Cancer Res., 6: 3973–3982, 2000. 15. Plantaz, D., Mohapatra, G., Matthay, K. K., Pellarin, M., Seeger, R. C., and Feuer- 39. Blaeker, H., Rasheed, B. K., McLendon, R. E., Friedman, H. S., Batra, S. K., Fuchs, stein, B. G. Gain of chromosome 17 is the most frequent abnormality detected in H. E., and Bigner, S. H. Microsatellite analysis of childhood brain tumors. Genes neuroblastoma by comparative genomic hybridization. Am. J. Pathol., 150: 81–89, Chromosomes Cancer, 15: 54–63, 1996. 1997. 40. Takeuchi, S., Bartram, C. R., Wada, M., Reiter, A., Hatta, Y., Seriu, T., Lee, E., 16. Lo Cunsolo, C., Bicocchi, M. P., Petti, A. R., and Tonini, G. P. Numerical and Miller, C. W., Miyoshi, I., and Koeffler, H. P. Allelotype analysis of childhood acute structural aberrations in advanced neuroblastoma tumours by CGH analysis: survival lymphoblastic leukemia. Cancer Res., 55: 5377–5382, 1995. correlates with chromosome 17 status. Br. J. Cancer, 83: 1295–1300, 2000. 41. Chambon-Pautas, C., Cave, H., Gerard, B., Guidal-Giroux, C., Duval, M., Vilmer, E., 17. Van Roy, N., Van Limbergen, H., Vandesompele, J., Van Gele, M., Poppe, B., and Grandchamp, B. High-resolution allelotype analysis of childhood B-lineage acute Salwen, H., Laureys, G., Manoel, N., De Paepe, A., and Speleman, F Combined lymphoblastic leukemia. Leukemia (Baltimore), 12: 1107–1113, 1998. M-FISH and CGH analysis allows comprehensive description of genetic alterations in 42. Hahn, S. A., Schutte, M., Hoque, A. T., Moskaluk, C. A., da Costa, L. T., Rozenblum, neuroblastoma cell lines. Genes Chromosomes Cancer, 32: 126–135, 2001. E., Weinstein, C. L., Fischer, A., Yeo, C. J., Hruban, R. H., and Kern, S. E. DPC4, 18. Takita, J., Hayashi, Y., Kohno, T., Shiseki, M., Yamaguchi, N., Hanada, R., a candidate tumor suppressor gene at human chromosome 18q21.1. Science (Wash. Yamamoto, K., and Yokota, J. Allelotype of neuroblastoma. Oncogene, 11: 1829– DC), 271: 350–353, 1996. 1834, 1995. 43. Steck, P. A., Pershouse, M. A., Jasser, S. A., Yung, W. K., Lin, H., Ligon, A. H., 19. Brodeur, G. M., Pritchard, J., Berthold, F., Carlsen, N. L., Castel, V., Castelberry, Langford, L. A., Baumgard, M. L., Hattier, T., Davis, T., Frye, C., Hu, R., Swedlund, R. P., De Bernardi, B., Evans, A. E., Favrot, M., Hedborg, F., Kaneko, M., Kemshead, B., Teng, D. H., Tavtigian, S. V. Identification of a candidate tumour suppressor gene, J., Lampert, F., Lee, R. E. J., Look, T., Pearson, A. D. J., Philip, T., Roald, B., MMAC1, at chromosome 10q23.3 that is mutated in multiple advanced cancers. Nat. Sawada, T., Seeger, R. C., Tsuchida, Y., and Voute, P. A. Revisions of the Interna- Genet., 15: 356–362, 1997. 1766

44. Janoueix-Lerosey, I., Penther, D., Thioux, M., de Cremoux, P., Derre, J., Ambros, P., 54. Chernova, O. B., Somerville, R. P., and Cowell, J. K. A novel gene, LGI1, from Vielh, P., Benard, J., Aurias, A., and Delattre, O. Molecular analysis of chromosome 10q24 is rearranged and downregulated in malignant brain tumors. Oncogene, 17: arm 17q gain in neuroblastoma. Genes Chromosomes Cancer, 28: 276–284, 2000. 2873–2881, 1998. 45. White, P., Maris, J. M., Beltinger, C., Sulman, E., Marshall, H. N., Fujimori, M., 55. Kenmochi, N., Yoshihama, M., Higa, S., and Tanaka, T. The human ribosomal Kaufman, B. A., Biegel, J. A., Allen, C., Hilliard, C., et al. A region of consistent protein L6 gene in a critical region for Noonan syndrome. J. Hum. Genet., 45: deletion in neuroblastoma maps within human chromosome 1p36.2–36.2. Proc. Natl. 290–293, 2000. Acad. Sci. USA, 92: 5520–5524, 1995. 56. Lee, L., Dowhanick-Morrissette, J., Katz, A., Jukofsky, L., and Krantz, I. D. Chro- 46. Getman, M. E., Houseal, T. W., Miller, G. A., Grundy, P. E., Cowell, J. K., and mosomal localization, genomic characterization, and mapping to the Noonan syn- Landes, G. M. Comparative genomic hybridization and its application to Wilms’ drome critical region of the human Deltex (DTX1) gene. Hum. Genet., 107: 577–581, tumorigenesis. Cytogenet. Cell Genet., 82: 284–290, 1998. 2000. 47. Weber, R. G., Pietsch, T., von Schweinitz, D., and Lichter, P. Characterization of 57. Iizaka, M., Han, H. J., Akashi, H., Furukawa, Y., Nakajima, Y., Sugano, S., Ogawa, genomic alterations in hepatoblastomas. A role for gains on chromosomes 8q and 20 M., and Nakamura, Y. Isolation and chromosomal assignment of a novel human gene, as predictors of poor outcome. Am. J. Pathol., 157: 571–578, 2000. CORO1C, homologous to coronin-like actin-binding proteins. Cytogenet. Cell Genet., 48. Riopel, M. A., Spellerberg, A., Griffin, C. A., and Perlman, E. J. Genetic analysis of 88: 221–224, 2000. ovarian germ cell tumors by comparative genomic hybridization. Cancer Res., 58: 58. Matsuura, T., Sasaki, H., Yabe, I., Hamada, K., Hamada, T., Shitara, M., and Tashiro, 3105–3110, 1998. K. Mosaicism of unstable CAG repeats in the brain of spinocerebellar ataxia type 2. 49. Mertens, F., Johansson, B., Hoglund, M., and Mitelman, F. Chromosomal imbalance J. Neurol., 246: 835–839, 1999. maps of malignant solid tumors: a cytogenetic survey of 3185 neoplasms. Cancer 59. Erlandsen, H., and Stevens, R. C. The structural basis of phenylketonuria. Mol. Genet. Res., 57: 2765–2780, 1997. Metab., 68: 103–125, 1999. 50. Robertson, G. P., Herbst, R. A., Nagane, M., Huang, H. J., and Cavenee, W. K. The chromosome 10 monosomy common in human melanomas results from loss of two 60. Brodeur, G. M., Azar, C., Brother, M., Hiemstra, J., Kaufman, B., Marshall, H., separate tumor suppressor loci. Cancer Res., 59: 3596–35601, 1999. Moley, J., Nakagawara, A., Saylors, R., Scavarda, N., et al. Neuroblastoma: effect of 51. Balesaria, S., Brock, C., Bower, M., Clark, J., Nicholson, S. K., Lewis, P., de Sanctis, genetic factors on prognosis and treatment. Cancer (Phila.), 70: 1685–1694, 1992. S., Evans, H., Peterson, D., Mendoza, N., Glaser, M. G., Newlands, E. S., and Fisher, 61. Cheung, N. K. V., Kushner, B. H., LaQuaglia, M. P., Kramer, K., Gollamudi, S., R. A. Loss of chromosome 10 is an independent prognostic factor in high-grade Heller, G., Gerald, W., Yeh, S., Finn, R., Larson, S. M., Wuest, D., Byrnes, M., gliomas. Br. J. Cancer, 81: 1371–1377, 1999. Dantis, E., Mora, J., Cheung, I. Y., Rosenfield, H., Abramson, S., and O’Reilly, R. J. 52. Li, J., Yen, C., Liaw, D., Podsypanina, K., Bose, S., Wang, S. I., Puc, J., Miliaresis, N7: a novel multi-modality therapy of high risk neuroblastoma in children diagnosed C., Rodgers, L., McCombie, R., Bigner, S. H., Giovanella, B. C., Ittmann, M., Tycko, over 1 year of age. Med. Pediat. Oncol., 36: 227–230, 2001. B., Hibshoosh, H., Wigler, M. H., and Parsons, R. PTEN, a putative protein tyrosine 62. Cheung, N. K., Kushner, B. H., La Quaglia, M. P., Kramer, K., Ambros, P., phosphatase gene mutated in human brain, breast, and prostate cancer. Science Ambros, I., Ladanyi, M., Eddy, J., Bonilla, M. A., and Gerald, W. Survival from (Wash. DC), 275: 1943–1947, 1997. non-stage 4 neuroblastoma without cytotoxic therapy: an analysis of clinical and 53. Mollenhauer, J., Wiemann, S., Scheurlen, W., Korn, B., Hayashi, Y., Wilgenbus, biological markers. Eur. J. Cancer, 33: 2117–2119, 1997. K. K., von Deimling, A., and Poustka, A. DMBT1, a new member of the SRCR 63. Cheung, N. K. V., Kushner, B. H., and Kramer, K. Monoclonal antibody-based superfamily, on chromosome 10q25.3–26.1 is deleted in malignant brain tumours. therapy of neuroblastoma. In: M. Coppes and R. Arceci (eds.), Hematology/Oncology Nat. Genet., 17: 32–39, 1997. Clinics of North America, 15: 853–866, 2001.

1767

Downloaded from cancerres.aacrjournals.org on September 26, 2021. © 2002 American Association for Cancer Research. Novel Regions of Allelic Imbalance Identified by Genome-wide Analysis of Neuroblastoma

Jaume Mora, Nai-Kong V. Cheung, Sandra Oplanich, et al.

Cancer Res 2002;62:1761-1767.

Updated version Access the most recent version of this article at: http://cancerres.aacrjournals.org/content/62/6/1761

Cited articles This article cites 62 articles, 24 of which you can access for free at: http://cancerres.aacrjournals.org/content/62/6/1761.full#ref-list-1

Citing articles This article has been cited by 1 HighWire-hosted articles. Access the articles at: http://cancerres.aacrjournals.org/content/62/6/1761.full#related-urls

E-mail alerts Sign up to receive free email-alerts related to this article or journal.

Reprints and To order reprints of this article or to subscribe to the journal, contact the AACR Publications Subscriptions Department at [email protected].

Permissions To request permission to re-use all or part of this article, use this link http://cancerres.aacrjournals.org/content/62/6/1761. Click on "Request Permissions" which will take you to the Copyright Clearance Center's (CCC) Rightslink site.