Patterns Of Genomic Alterations Research Articles

Abstract A53: Genome-wide profile of somatic copy number alterations in Wilms tumor: Comparison between samples derived from patients with and without relapse

Abstract Wilms tumor (WT) is the most common kidney malignancy of childhood; nevertheless, its pathogenesis remains largely unknown. Although the majority of the WT occur sporadically, a strong genetic component is present at least in the many cases which are related to underlying syndromes. Tumor relapse occurs at a rate of approximately 15%, and molecular studies are focused in identifying markers to define the minimal therapy for limiting the late effects of treatment while maintaining high survival rate. Loss of heterozygosity of both 1p and 16q was already associated to an increased risk of relapse and death although detected in a very small subset of WT patients, making this feature a less sensitive prognostic factor. Somatic DNA copy number alterations (CNAs) are common genetic mutations in cancer, and often define key pathogenic events. This study was designed to assess the genome profile of CNAs in WT, aiming to identify genetic markers associated to relapse that could be of clinical and prognostic importance. We performed an array-CGH based survey of 48 WT samples, mainly tumors in stages III and IV, derived from patients with (17) and without (31) relapse in at least three years. Data was obtained using a high resolution oligoarray platform (180K - Agilent), with an average resolution >70 Kb, and analysis was performed on the software Nexus 6 (Biodiscovery). The analysis revealed high frequency of arm/whole chromosome alterations at 1q, 7q, and chromosomes 6 and 12 (gains), while losses were recurrent at 7p, 11 q, and 16q chromosome regions. WT derived from patients with relapse exhibited a distinctive pattern of genomic alterations, mainly characterized for an increased frequency of proximal 1q gain and low amplitude gain of chromosome 6. Additionally, analysis of small regions affected by recurrent focal alterations disclosed new genes that can be relevant for Wilms tumorigenesis and relapse. Financial support: FAPESP/CNPq Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the Second AACR International Conference on Frontiers in Basic Cancer Research; 2011 Sep 14-18; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2011;71(18 Suppl):Abstract nr A53.

Genomic distance entrained clustering and regression modelling highlights interacting genomic regions contributing to proliferation in breast cancer

BackgroundGenomic copy number changes and regional alterations in epigenetic states have been linked to grade in breast cancer. However, the relative contribution of specific alterations to the pathology of different breast cancer subtypes remains unclear. The heterogeneity and interplay of genomic and epigenetic variations means that large datasets and statistical data mining methods are required to uncover recurrent patterns that are likely to be important in cancer progression.ResultsWe employed ridge regression to model the relationship between regional changes in gene expression and proliferation. Regional features were extracted from tumour gene expression data using a novel clustering method, called genomic distance entrained agglomerative (GDEC) clustering. Using gene expression data in this way provides a simple means of integrating the phenotypic effects of both copy number aberrations and alterations in chromatin state. We show that regional metagenes derived from GDEC clustering are representative of recurrent regions of epigenetic regulation or copy number aberrations in breast cancer. Furthermore, detected patterns of genomic alterations are conserved across independent oestrogen receptor positive breast cancer datasets. Sequential competitive metagene selection was used to reveal the relative importance of genomic regions in predicting proliferation rate. The predictive model suggested additive interactions between the most informative regions such as 8p22-12 and 8q13-22.ConclusionsData-mining of large-scale microarray gene expression datasets can reveal regional clusters of co-ordinate gene expression, independent of cause. By correlating these clusters with tumour proliferation we have identified a number of genomic regions that act together to promote proliferation in ER+ breast cancer. Identification of such regions should enable prioritisation of genomic regions for combinatorial functional studies to pinpoint the key genes and interactions contributing to tumourigenicity.

Genomic profiling of adult acute lymphoblastic leukemia by single nucleotide polymorphism oligonucleotide microarray and comparison to pediatric acute lymphoblastic leukemia

Differences in survival have been reported between pediatric and adult acute lymphoblastic leukemia. The inferior prognosis in adult acute lymphoblastic leukemia is not fully understood but could be attributed, in part, to differences in genomic alterations found in adult as compared to in pediatric acute lymphoblastic leukemia. We compared two different sets of high-density single nucleotide polymorphism array genotyping data from 75 new diagnostic adult and 399 previously published diagnostic pediatric acute lymphoblastic leukemia samples. The patients' samples were randomly acquired from among Caucasian and Asian populations and hybridized to either Affymetrix 50K or 250K single nucleotide polymorphism arrays. The array data were investigated with Copy Number Analysis for GeneChips (CNAG) software for allele-specific copy number analysis. The high density single nucleotide polymorphism array analysis of 75 samples of adult acute lymphoblastic leukemia led to the identification of numerous cryptic and submicroscopic genomic lesions with a mean of 7.6 genomic alterations per sample. The patterns and frequencies of lesions detected in the adult samples largely reproduced known genomic hallmarks detected in previous single nucleotide polymorphism-array studies of pediatric acute lymphoblastic leukemia, such as common deletions of 3p14.2 (FHIT), 5q33.3 (EBF), 6q, 9p21.3 (CDKN2A/B), 9p13.2 (PAX5), 13q14.2 (RB1) and 17q11.2 (NF1). Some differences between adult and pediatric acute lymphoblastic leukemia were identified when the pediatric data set was partitioned into hyperdiploid and non-hyperdiploid cases and then compared to the nearly exclusively non-hyperdiploid adult samples. In this analysis, adult samples had a higher rate of deletions of chromosome 17p (TP53) and duplication of 17q. Our analysis of adult acute lymphoblastic leukemia cases led to the identification of new potential target lesions relevant for the pathogenesis of acute lymphoblastic leukemia. However, no unequivocal pattern of submicroscopic genomic alterations was found to separate adult acute lymphoblastic leukemia from pediatric acute lymphoblastic leukemia. Therefore, apart from different therapy regimen, differences of prognosis between adult and pediatric acute lymphoblastic leukemia are probably based on genetic subgroups according to cytogenetically detectable lesions but not focal genomic copy number microlesions.

Abstract PL1-1: Genomic architecture characterizes tumor progression paths and fate in breast cancer patients

Abstract Breast cancer is a heterogeneous disease as reflected by histopathology, molecular alterations and clinical behavior. In order to relate cellular and sub-cellular features to clinical parameters and outcome, substantial effort has been exerted towards identifying tumor groups with distinct molecular features. The gene expression based classification that we proposed ten years ago identified five different subgroups with difference in survival; two Luminal-cell related groups (Luminal A and luminal B), a myoepithelial-cell related group (Basal-like), a HER2 enriched, and a Normal-like group. The Basal-like and Luminal carcinomas have different etiologies and for most purposes may be considered as distinct diseases. This is also reflected in the genomic portraits defined by aCGH (array Comparative Genomic Hybridization), and it seems evident that the history of the molecular subgroups is written in the DNA alterations. We have developed two platform independent algorithms to explore genomic architectural distortion using aCGH data to measure whole arm gains and losses (WAAI) and complex rearrangements (CAAI). By applying CAAI and WAAI to data from 595 breast cancer patients we were able to separate the cases into eight subgroups with different distribution of genomic distortion. Within each subgroup data from expression analyses, sequencing and ploidy indicated that progression occurs along separate paths into more complex genotypes. Several of the CGH based subgroups were enriched for either luminal related or basal related tumors, and showed distinct patterns of genomic alterations. In particular, basal related tumors were separated into genomic classes with distinct patterns of alterations emphasizing genomic heterogeneity also in this expression subclass. Histological grade had prognostic impact only in the Luminal related groups while the complexity identified by CAAI had an overall independent prognostic power. These results emphasizes the relationship between structural genomic alterations, expression subtypes and clinical behavior, and provides a score of genomic complexity as a new tool for prognostication in breast cancer. Using SNP arrays and a novel bioinformatic approach, ASCAT (Allele-Specific Copy number Analysis of Tumors), we have performed genome wide allele-specific copy number analysis of 112 breast cancer genomes. We were able to accurately dissect the allele-specific copy number in each tumor, simultaneously estimating and adjusting for both tumor ploidy and non-aberrant cell admixture, allowing calculation of “Tumor Profiles” (genome-wide allele-specific copy-number profiles) from which gains, losses, copy-number-neutral events and LOH could be determined. The tumors had on average a non-aberrant cell admixture of 49%, and 45% of them were aneuploid (>2.7n). By aggregation of Tumor Profiles across the sample set a genome-wide view of LOH and copy-number-neutral events was obtained. The Tumor Profiles also revealed differences in aberrant tumor cell fraction, ploidy, gains, losses, LOH and copy-number-neutral events between the five expression subtypes. Basal-like breast carcinomas have a significantly higher frequency of LOH compared to other subtypes, and their Tumor Profiles show large-scale loss of genomic material during tumor development, followed by a whole-genome duplication, resulting in near-triploid genomes. From the Tumor Profiles we could also construct a genome-wide map of allelic skewness, indicating loci where one allele is preferentially lost while the other allele is preferentially gained. We hypothesize that these alternative alleles have a different influence on breast carcinoma development. Citation Information: Clin Cancer Res 2010;16(7 Suppl):PL1-1

Feedback Circuit among INK4 Tumor Suppressors Constrains Human Glioblastoma Development

SummaryWe have developed a nonheuristic genome topography scan (GTS) algorithm to characterize the patterns of genomic alterations in human glioblastoma (GBM), identifying frequent p18INK4C and p16INK4A codeletion. Functional reconstitution of p18INK4C in GBM cells null for both p16INK4A and p18INK4C resulted in impaired cell-cycle progression and tumorigenic potential. Conversely, RNAi-mediated depletion of p18INK4C in p16INK4A-deficient primary astrocytes or established GBM cells enhanced tumorigenicity in vitro and in vivo. Furthermore, acute suppression of p16INK4A in primary astrocytes induced a concomitant increase in p18INK4C. Together, these findings uncover a feedback regulatory circuit in the astrocytic lineage and demonstrate a bona fide tumor suppressor role for p18INK4C in human GBM wherein it functions cooperatively with other INK4 family members to constrain inappropriate proliferation.

Marked Genomic Differences Characterize Primary and Secondary Glioblastoma Subtypes and Identify Two Distinct Molecular and Clinical Secondary Glioblastoma Entities

Glioblastoma is classified into two subtypes on the basis of clinical history: "primary glioblastoma" arising de novo without detectable antecedent disease and "secondary glioblastoma" evolving from a low-grade astrocytoma. Despite their distinctive clinical courses, they arrive at an indistinguishable clinical and pathologic end point highlighted by widespread invasion and resistance to therapy and, as such, are managed clinically as if they are one disease entity. Because the life history of a cancer cell is often reflected in the pattern of genomic alterations, we sought to determine whether primary and secondary glioblastomas evolve through similar or different molecular pathogenetic routes. Clinically annotated primary and secondary glioblastoma samples were subjected to high-resolution copy number analysis using oligonucleotide-based array comparative genomic hybridization. Unsupervised classification using genomic nonnegative matrix factorization methods identified three distinct genomic subclasses. Whereas one corresponded to clinically defined primary glioblastomas, the remaining two stratified secondary glioblastoma into two genetically distinct cohorts. Thus, this global genomic analysis showed wide-scale differences between primary and secondary glioblastomas that were previously unappreciated, and has shown for the first time that secondary glioblastoma is heterogeneous in its molecular pathogenesis. Consistent with these findings, analysis of regional recurrent copy number alterations revealed many more events unique to these subclasses than shared. The pathobiological significance of these shared and subtype-specific copy number alterations is reinforced by their frequent occurrence, resident genes with clear links to cancer, recurrence in diverse cancer types, and apparent association with clinical outcome. We conclude that glioblastoma is composed of at least three distinct molecular subtypes, including novel subgroups of secondary glioblastoma, which may benefit from different therapeutic strategies.

Genomic analysis of a case of multifocal adenocarcinoma in ulcerative colitis

Long-standing ulcerative colitis is associated with an elevated risk of developing colonic adenocarcinoma. A very limited group of patients present with multiple synchronous cancers. This could be due to either a multifocal presentation of the same neoplastic clone or different tumors arising in a large area of polyclonal dysplastic colonic mucosa ("field cancerization"). Here, we describe a patient with long-standing colitis and three different tumors in the rectosigmoid part of the large bowel. Clonal evaluation of the lesions was performed by array-based comparative genomic hybridization. These three neoplasms showed a comparable pattern of genomic alterations characterized by gains of chromosomes 12, 13, and 20. Noteworthy, dysplastic mucosa distal to the three cancers displayed a completely different pattern of genomic changes indicating that different cell lineages were present. In addition, all three carcinomas were microsatellite stable and revealed identical immunoprofiles for several cancer-associated genes. We conclude that these three multifocal tumors must have originated from the same preneoplastic lineage.

Inferring a Tumor Progression Model for Neuroblastoma From Genomic Data

The knowledge of the key genomic events that are causal to cancer development and progression not only is invaluable for our understanding of cancer biology but also may have a direct clinical impact. The task of deciphering a model of tumor progression by requiring that it explains (or at least does not contradict) known clinical and molecular evidence can be very demanding, particularly for cancers with complex patterns of clinical and molecular evidence. We formalize the process of model inference and show how a progression model for neuroblastoma (NB) can be inferred from genomic data. The core idea of our method is to translate the model of clonal cancer evolution to mathematical testable rules of inheritance. Seventy-eight NB samples in stages 1, 4S, and 4 were analyzed with array-based comparative genomic hybridization. The pattern of recurrent genomic alterations in NB is strongly stage dependent and it is possible to identify traces of tumor progression in this type of data. A tumor progression model for neuroblastoma is inferred, which is in agreement with clinical evidence, explains part of the heterogeneity of the clinical behavior observed for NB, and is compatible with existing empirical models of NB progression.

Genome‐wide array‐based comparative genomic hybridization of natural killer cell lymphoma/leukemia: Different genomic alteration patterns of aggressive NK‐cell leukemia and extranodal Nk/T‐cell lymphoma, nasal type

Natural killer (NK) cell lymphomas/leukemias are highly aggressive lymphoid malignancies, but little is known about their genomic alterations, and thus there is an urgent need for identification and analysis of NK cell lymphomas/leukemias. Recently, we developed our own array-based comparative genomic hybridization (array CGH) with an average resolution of 1.3 Mb. We performed an array CGH analysis for 27 NK-cell lymphoma/leukemia cases that were classified into two disease groups based on the World Health Organization Classification (10 aggressive NK-cell leukemia cases and 17 extranodal NK/T-cell [NK/T] lymphomas, nasal type). We identified the differences in the genomic alteration patterns of the two groups. The recurrent regions characteristic of the aggressive NK-cell leukemia group compared with those of the extranodal NK/T lymphoma, nasal-type group, were gain of 1q and loss of 7p15.1-p22.3 and 17p13.1. In particular, gain of 1q23.1-24.2 (P = 0.041) and 1q31.3-q44 (P = 0.003-0.047), and loss of 7p15.1-p22.3 (P = 0.012-0.041) and 17p13.1 (P = 0.012) occurred significantly more frequently in the former than in the latter group. Recurrent regions characteristic of the extranodal NK/T lymphoma, nasal-type group, compared with those of the other group were gain of 2q, and loss of 6q16.1-q27, 11q22.3-q23.3, 5p14.1-p14.3, 5q34-q35.3, 1p36.23-p36.33, 2p16.1-p16.3, 4q12, and 4q31.3-q32.1. Our results can be expected to provide further insights into the genetic basis of lymphomagenesis and the clinicopathologic features of NK-cell lymphomas/leukemias.

Clinicopathologic significance and prognostic value of chromosomal imbalances in diffuse large B-cell lymphomas.

To determine the clinicopathologic significance and prognostic value of chromosomal imbalances in diffuse large B-cell lymphomas (DLBCL). We have examined 64 tumors at diagnosis using comparative genomic hybridization and real-time quantitative polymerase chain reaction (PCR), single-stranded conformational polymorphism, and DNA sequencing for the analysis of several potential target genes. The most recurrent alterations were gains of 18q (20%), Xq (15%), 2p, 7q, and 12p (14%), and losses of 6q and 17p (14%). Frequent high-level DNA amplifications were detected at 2p13-p16 and 18q21 loci. Real-time quantitative PCR detected REL and BCL11A gene amplifications in the nine patients with gains at 2p13-p16 and only in one additional patient with normal chromosome 2. Similarly, the BCL-2 gene was amplified in the 12 tumors with gains of 18q21 but in none of 39 patients with normal 18q profile. p53 gene inactivation was detected in nine of 58 (16%) tumors and was commonly associated with 17p losses. Tumors with 18q gains were significantly associated with a high number of chromosomal imbalances, primary nodal presentation, high serum lactate dehydrogenase levels, high International Prognostic Index, shorter cause-specific survival, and a high risk of relapse. Losses of 17p and p53 gene alterations were associated with an absence of complete response achievement. These results suggest that DLBCLs have a characteristic pattern of genomic alterations; 18q gains or amplifications and 17p losses are associated with particular clinicopathological features and aggressive clinical behavior. Additional studies are needed to confirm these observations in larger series of patients.

Klinik, Histopathologie und Molekularbiologie des Tubenkarzinoms

Das Tubenkarzinom ist das seltenste aller gynäkologischen Malignome. Seine geringe Inzidenz verhinderte bislang die Durchführung aussagekräftiger Untersuchungen, so dass kein zulänglich definiertes Therapiekonzept für dieses Krankheitsbild existiert. In Zeiten der evidenzbasierten Medizin stellt daher die Behandlung des Tubenkarzinoms ein Dilemma für jeden Kliniker dar. Notgedrungen orientiert sich die Behandlung an den Resultaten aus kleineren retrospektiven Untersuchungen mit langen Datenerhebungsperioden und aus den Erkenntnissen aus größeren Untersuchungen beim Ovarialkarzinom. Beide Entitäten weisen einige charakteristische Unterschiede auf, teilen aber auch viele Gemeinsamkeiten. Das Tubenkarzinom weist im Vergleich zum Ovarialkarzinom eine frühere klinische Symptomatik, eine höhere Prävalenz der Frühstadien und metastatische Beteiligung retroperitonealer Lymphknoten auf. Bis heute ist nicht geklärt, ob spezifische tumorbiologische Faktoren eine Rolle in diesem Zusammenhang spielen. Neuere Untersuchungen decken jedoch zunehmend klinische und tumorbiologische Gemeinsamkeiten zwischen beiden Tumorentitäten auf, die über den gemeinsamen Müller'schen Ursprung hinausgehen. So bestätigen jüngste Ergebnisse aus retrospektiven Untersuchungen die Bedeutung der zytoreduktiven Chirurgie und die hohe Chemosensibilität gegenüber Platinderivaten analog zum Therapiekonzept beim Ovarialkarzinom. Zudem lassen neue Erkenntnisse über Häufigkeiten und Muster genetischer Alterationen eine gemeinsame molekulargenetische Pathogenese vermuten. Die Prävalenz von BRCA1- und BRCA2-Mutationen beim Tubenkarzinom gleicht den bisherigen Ergebnissen zufolge der beim Ovarialkarzinom, und komparative Genomhybridisierungen zeigen vergleichbare genomische Alterationen beider Tumorentitäten.

Genomic imbalances in ovarian borderline serous and mucinous tumors

We analyzed 25 ovarian borderline tumors (13 serous and 12 mucinous tumors) by comparative genomic hybridization (CGH). Genomic imbalance was detected in 85% of serous tumors and 75% of mucinous tumors. Different patterns of genomic alterations were identified in serous and mucinous tumors. Gain of the X chromosome was common in both serous (30%) and mucinous (42%) tumors. However, gain of chromosome 8 was detected exclusively in 38% of serous and mixed sero-mucinous tumors, but not in any pure mucinous tumors. According to the present and previous studies, gain of chromosome 8 is the most common abnormality in borderline serous tumors. Gain of the same chromosome is also common in high grade and advanced stage serous carcinomas, but uncommon in early stage serous carcinomas. In addition gain of chromosome X is common in borderline serous and mucinous tumors, while loss of chromosome X is predominant in invasive carcinomas. These findings do not support the multi-step progression theory from borderline tumor to high-grade, advanced stage carcinoma, but indicate that the borderline ovarian tumor is a distinct entity. Genes in chromosome 8 may be critical for the development and the differentiation of borderline serous tumors.

Risk assignment in childhood brain tumors: The emerging role of molecular and biologic classification

Brain tumors as a group are the most common solid tumors of childhood and currently have the highest mortality rate. A major emphasis has historically been placed on stratifying therapy for these tumors based on histologic and clinical prognostic factors. However, with the increasing application of molecular approaches to refine the categorization of these tumors, it has become apparent that histologically comparable lesions may exhibit diverse patterns of gene expression and genomic alterations, which may correspond with important prognostic distinctions. This paper summarizes these observations and discusses how they are being applied in a preliminary fashion as a foundation for risk-adapted stratification of childhood brain tumor therapy.

Patterns of specific genomic alterations associated with poor prognosis in high-grade renal cell carcinomas

A series of 13 sporadic renal cell carcinomas was analyzed for the specific chromosome rearrangements after serial xenografting into immunodeficient mice. Seven tumors displayed genetic traits of the conventional subtype and 5 showed genetic features of the papillary subtype. In all the xenografted conventional tumors, we observed loss of 3p, as well as loss of the 9p21 region and of the long arm of chromosome 14, both considered as markers of a poor prognosis. In the xenografted papillary tumors, a duplication of chromosome arm 8q was observed concomitant with the duplication of the 7q31 region. The association of the 7q31 and 8q22∼qter duplicated regions was also observed for one conventional tumor. The latency of tumor take was found to be reduced and the median time to passage statistically shorter for all tumors which presented the associated duplication of the 7q31 and 8q22∼qter regions. The proto-oncogene NOV (nephroblastoma overexpressed gene) maps to 8q24.1 and is overexpressed in some Wilms tumors. It could be an interesting candidate gene, since its level of expression and release in the culture medium was found to be increased in all of the fast growing tumors analyzed.

Comparative Genomic Hybridization Identifies Loss of 18q22-qter as an Early and Specific Event in Tumorigenesis of Midgut Carcinoids

Carcinoid tumors are rare neuroendocrine tumors occurring in the lung or in the digestive tract where they are further subclassified as foregut, midgut, or hindgut carcinoids. To gain a better understanding of the genetic basis of the different types of carcinoid tumors, we have characterized numerical imbalances in a series of midgut carcinoids, and compared the results to previous findings in carcinoids from the lung. Numerical imbalances were revealed in 16 of the 18 tumors, and the most commonly detected aberrations were losses of 18q22-qter (67%), 11q22-q23 (33%), and 16q21-qter (22%), and gain of 4p14-qter (22%). The total number of alterations found in the metastases was significantly higher than in the primary tumors, indicating the accumulation of acquired genetic changes in the tumor progression. Losses of 18q and 11q were present both in primary tumors and metastases, whereas loss of 16q and gain of 4 were only detected in metastases. Furthermore, the pattern of comparative genomic hybridization alterations varied depending on the total number of detected alterations. Taken together, the findings would suggest a progression of numerical imbalances, in which loss of 18q and 11q represent early events, and loss of 16q and gain of 4p are late events in the tumor progression of midgut carcinoids. When compared to previously published comparative genomic hybridization abnormalities in lung carcinoids, loss of 11q was found to occur in both tumor types, whereas loss of 18q and 16q and gain of 4 were not revealed in lung carcinoids. The results indicate that inactivation of a putative tumor suppressor gene in 18q22-qter represents a frequent and early event that is specific for the development of midgut carcinoids.

Genomic deletion and p53 inactivation in cervical carcinoma.

The tumor-suppressor gene p53 acts as "the guardian of the genome", sensing DNA damage and initiating protective responses. To examine the hypothesis that p53 abnormality leads to increased genomic alterations in primary tumor cells, our study utilized 51 primary tumors of cervical carcinoma and 10 microsatellite markers. These markers were mapped to the short arms of chromosomes 3 and 5, covering the regions 3p13-25 and 5p15.1-15.3. Genomic deletion on 3p and 5p was correlated with genetic or epigenetic p53 inactivation pathways, including p53 mutation, genetic deletion of p53 and cervical infection with human papillomavirus. The proportion of abnormal p53 was found to be significantly higher in the cases exhibiting loss of heterozygosity (LOH) on 5p (p < 0.001), supporting the hypothesis of the presence of a p53-dependent pathway to cervical tumorigenesis. In contrast, however, LOH on 3p was found to be independent of p53 inactivation. A common deletion region, 3p22-24, was identified in 44% of informative cases, and genomic loss at this specific region was correlated with early tumorigenic onset and poor grade of tumor differentiation. Diversity within the patterns of genomic alteration in the same form of cancer suggests different sets of risk/tumorigenic profiles, molecular pathogenesis, as well as prognosis and outcome.

Subsets of glioblastoma multiforme defined by molecular genetic analysis.

Glioblastoma multiforme is a clinically and histologically heterogeneous lesion; however, to date, it has not been possible to subdivide glioblastomas on a clinical, histopathological or biological basis. Previous studies have demonstrated that loss of portions of chromosomes 10 and 17 and amplification of the epidermal growth factor receptor (EGFR) gene are the most frequent genetic alterations in glioblastoma. We therefore examined 74 glioblastomas from 67 patients for loss of heterozygosity on chromosomes 10 and 17, and for amplification of the epidermal growth factor receptor gene, to determine whether glioblastomas can be subtyped on a genetic basis. Using Southern blot analysis we were able to detect different patterns of genomic alterations. Eighteen of 67 informative patients were characterized by a loss of heterozygosity on the short arm of chromosome 17 in the tumor tissue. Forty-five of 64 informative patients showed a loss of heterozygosity on chromosome 10. Amplification of the epidermal growth factor receptor gene was noted in 25 of 67 patients and was restricted to those glioblastomas that had lost portions of chromosome 10. Epidermal growth factor receptor gene amplification occurred significantly more often in patients without chromosome 17p loss than in patients with chromosome 17p loss (p = 0.01). In addition, those glioblastomas with a loss of chromosome 17p occurred in patients significantly younger than those with glioblastomas characterized by EGFR gene amplification (p = 0.001). These data emphasize the genetic heterogeneity of glioblastoma and suggest the division of glioblastoma into genetic subsets.