Biomedical subjects

Jane Fridlyand

Publications and source records attributed to Jane Fridlyand.

30 records · Page 2Linked to original sources

PubMed2004

High-resolution analysis of DNA copy number alterations in colorectal cancer by array-based comparative genomic hybridization.

Array-based comparative genomic hybridization (CGH) allows for the simultaneous examination of thousands of genomic loci at 1-2 Mb resolution. Copy number alterations detected by array-based CGH can aid in the identification and localization of cancer causing genes. Here we report the results of array-based CGH in a set of 125 primary colorectal tumors hybridized onto an array consisting of 2463 bacterial artificial chromosome clones. On average, 17.3% of the entire genome was altered in our samples (8.5 +/- 6.7% gained and 8.8 +/- 7.3% lost). Losses involving 8p, 17p, 18p or 18q occurred in 37, 46, 49 and 60% of cases, respectively. Gains involving 8q or 20q were observed 42 and 65% of the time, respectively. A transition from loss to gain occurred on chromosome 8 between 41 and 48 Mb, with 25% of cases demonstrating a gain of 8p11 (45-53 Mb). Chromosome 8 also contained four distinct loci demonstrating high-level amplifications, centering at 44.9, 60, 92.7 and 144.7 Mb. On 20q multiple high-level amplifications were observed, centering at 32.3, 37.8, 45.4, 54.7, 59.4 and 65 Mb. Few differences in DNA copy number alterations were associated with tumor stage, location, age and sex of the patient. Microsatellite stable and unstable (MSI-H) tumors differed significantly with respect to the frequency of alterations (20 versus 5%, respectively, P < 0.01). Interestingly, MSI-H tumors were also observed to have DNA copy number alterations, most commonly involving 8q. This high-resolution analysis of DNA copy number alterations in colorectal cancer by array-based CGH allowed for the identification of many small, previously uncharacterized, genomic regions, such as on chromosomes 8 and 20. Array-based CGH was also able to identify DNA copy number changes in MSI-H tumors.

Chromosome Mapping↗

PubMed2004

Mechanisms of cell-cycle arrest in Spitz nevi with constitutive activation of the MAP-kinase pathway.

Spitz nevi are benign melanocytic nevi that overlap histopathologically with melanoma. We previously found copy number increases of chromosome 11p frequently paralleled by mutations in the HRAS oncogene mapping to this region. In this study, we explored mechanisms that inhibit proliferation in the presence of HRAS activation. We analyzed MAP-kinase activation using immunohistochemistry for phospho-ERK, cyclin D1, and microphthalmia transcription factor expression in 17 Spitz nevi with and 18 Spitz nevi without 11p copy number increase. We found relatively high levels of phospho-ERK and cyclin D1 expression suggesting MAP-kinase pathway activation in both groups of Spitz nevi. However, Spitz nevi with 11p copy number increases showed significantly higher levels of cyclin D1 expression and lower levels of microphthalmia transcription factor expression suggesting stronger MAP-kinase pathway activation in this group. Contrasting this apparent activation, the proliferation rate as assessed by Mib1 expression was low in both groups. An analysis of cell-cycle inhibitory proteins including p16, p21, and p27 showed that the majority of Spitz nevus cells expressed high levels of p16, with cells of the cases that had increased copy number of 11p expressing significantly higher levels than those of Spitz nevi with normal copy number of 11p. We propose that in benign nevi with constitutive activation of the MAP-kinase pathway, p16 functions as an essential mediator of oncogene-induced senescence preventing progression to melanoma.

Calibration↗

PubMed2003

Determinants of BRAF mutations in primary melanomas.

The RAS/mitogen-activated protein kinase pathway sends external growth-promoting signals to the nucleus. BRAF, a critical serine/threonine kinase in this pathway, is frequently activated by somatic mutation in melanoma. Using a cohort of 115 patients with primary invasive melanomas, we show that BRAF mutations are statistically significantly more common in melanomas occurring on skin subject to intermittent sun exposure than elsewhere (23 of 43 patients; P<.001, two-sided Fisher's exact test). By contrast, BRAF mutations in melanomas on chronically sun-damaged skin (1 of 12 patients) and melanomas on skin relatively or completely unexposed to sun, such as palms, soles, subungual sites (6 of 39 patients), and mucosal membranes (2 of 21 patients) are rare. We found no association of mutation status with clinical outcome or with the presence of an associated melanocytic nevus. The mutated BRAF allele was frequently found at an elevated copy number, implicating BRAF as one of the factors driving selection for the frequent copy number increases of chromosome 7q in melanoma. In summary, the uneven distribution of BRAF mutations strongly suggests distinct genetic pathways leading to melanoma. The high mutation frequency in melanomas arising on intermittently sun-exposed skin suggests a complex causative role of such exposure that mandates further evaluation.

Adult↗

PubMed2003

Differentiation of lobular versus ductal breast carcinomas by expression microarray analysis.

Invasive lobular and ductal breast tumors have distinct histologies and clinical presentation. Other than altered expression of E-cadherin, little is known about the underlying biology that distinguishes the tumor subtypes. We used cDNA microarrays to identify genes differentially expressed between lobular and ductal tumors. Unsupervised clustering of tumors failed to distinguish between the two subtypes. Prediction analysis for microarrays (PAM) was able to predict tumor type with an accuracy of 93.7%. Genes that were significantly differentially expressed between the two groups were identified by MaxT permutation analysis using t tests (20 cDNA clones and 10 unique genes), significance analysis for microarrays (33 cDNA clones and 15 genes, at an estimated false discovery rate of 2%), and PAM (31 cDNAs and 15 genes). There were 8 genes identified by all three of these related methods (E-cadherin, survivin, cathepsin B, TPI1, SPRY1, SCYA14, TFAP2B, and thrombospondin 4), and an additional 3 that were identified by significance analysis for microarrays and PAM (osteopontin, HLA-G, and CHC1). To validate the differential expression of these genes, 7 of them were tested by real-time quantitative PCR, which verified that they were differentially expressed in lobular versus ductal tumors. In conclusion, specific changes in gene expression distinguish lobular from ductal breast carcinomas. These genes may be important in understanding the basis of phenotypic differences among breast cancers.

Breast Neoplasms↗

PubMed2003

Genome-wide array CGH analysis of murine neuroblastoma reveals distinct genomic aberrations which parallel those in human tumors.

Neuroblastoma, the third most common tumor of childhood, is a complex disease in which few genetic mutations have been identified.Mice expressing a human MYCN oncogene driven by the rat tyrosine hydroxylase promoter (TH-MYCN) represent an animal model for this disorder. We performed microarray-based comparative genomic hybridization analysis on murine tumors, identifying gains on chromosomes 1, 3, 11, 14, 17, and 18 and losses on chromosomes 5, 9, and 16. Fluorescence in situ hybridization analysis confirmed an amplicon on chromosome 18 as the site of TH-MYCN transgene integration. Selected tumors with localized gains of chromosome 11 delineate a 15-Mb region orthologous to human chromosome 17q and help to narrow the minimal region gained in human tumors. We observed clustered loss of chromosomes 5, 9, and 16, orthologous to a similar pattern of combined loss of chromosomes 3p, 4p, and 11q in human tumors. These data demonstrate conservation of many genetic changes in murine and human neuroblastoma and suggest that further delineation of genetic abnormalities in murine tumors may identify genes important in human disease.

Allelic Imbalance↗

PubMed2003

Shaping of tumor and drug-resistant genomes by instability and selection.

Tumors with defects in mismatch repair (MMR) show fewer chromosomal changes by cytogenetic analyses than most solid tumors, suggesting that a greater proportion of the alterations required for malignancy occur in genes with nucleotide sequences susceptible to errors normally corrected by MMR. Here, we used genome-wide microarray comparative genomic hybridization to carry out a higher resolution evaluation of the effect of MMR competence on genomic alterations occurring in 20 cell lines and to determine if characteristic aberrations arise in MMR-proficient and -deficient HCT116 cells undergoing selection for methotrexate resistance. We observed different spectra of aberrations in MMR-proficient compared to -deficient cell lines, as well as among cell lines with different types of MMR-deficiency. We also observed different genetic routes to drug resistance. Resistant MMR-deficient cells most frequently displayed no copy number alterations (16/29 cell pools), whereas all MMR-proficient cells had unique abnormalities involving chromosome 5, including amplicons centered on the target gene, DHFR and/or a neighboring novel locus (7/13 pools). These observations support the concept that tumor genomes are shaped by selection for alterations that promote survival and growth advantage, as well as by the particular dysfunctions in genes responsible for maintenance of genetic integrity.

Base Pair Mismatch↗

PubMed2003

Genome-wide-array-based comparative genomic hybridization reveals genetic homogeneity and frequent copy number increases encompassing CCNE1 in fallopian tube carcinoma.

Fallopian tube carcinoma (FTC) is a rare, poorly studied and aggressive cancer, associated with poor survival. Since tumorigenesis is related to the acquisition of genetic changes, we used genome-wide array comparative genomic hybridization to analyse copy number aberrations occurring in FTC in order to obtain a better understanding of FTC carcinogenesis and to identify prognostic events and targets for therapy. We used arrays of 2464 genomic clones, providing approximately 1.4 Mb resolution across the genome to map genomic DNA copy number aberrations quantitatively from 14 FTC onto the human genome sequence. All tumors showed a high frequency of copy number aberrations with recurrent gains on 3q, 6p, 7q, 8q, 12p, 17q, 19 and 20q, and losses involving chromosomes 4, 5q, 8p, 16q, 17p, 18q and X. Recurrent regions of amplification included 1p34, 8p11-q11, 8q24, 12p, 17p13, 17q12-q21, 19p13, 19q12-q13 and 19q13. Candidate, known oncogenes mapping to these amplicons included CMYC (8q24), CCNE1 (19q12-q21) and AKT2 (19q13), whereas PIK3CA and KRAS, previously suggested to be candidate driver genes for amplification, mapped outside copy number maxima on 3q and 12p, respectively. The FTC were remarkably homogeneous, with some recurrent aberrations occurring in more than 70% of samples, which suggests a stereotyped pattern of tumor evolution.

Carcinoma↗

PubMed2003

Bagging to improve the accuracy of a clustering procedure.

MOTIVATION: The microarray technology is increasingly being applied in biological and medical research to address a wide range of problems such as the classification of tumors. An important statistical question associated with tumor classification is the identification of new tumor classes using gene expression profiles. Essential aspects of this clustering problem include identifying accurate partitions of the tumor samples into clusters and assessing the confidence of cluster assignments for individual samples. RESULTS: Two new resampling methods, inspired from bagging in prediction, are proposed to improve and assess the accuracy of a given clustering procedure. In these ensemble methods, a partitioning clustering procedure is applied to bootstrap learning sets and the resulting multiple partitions are combined by voting or the creation of a new dissimilarity matrix. As in prediction, the motivation behind bagging is to reduce variability in the partitioning results via averaging. The performances of the new and existing methods were compared using simulated data and gene expression data from two recently published cancer microarray studies. The bagged clustering procedures were in general at least as accurate and often substantially more accurate than a single application of the partitioning clustering procedure. A valuable by-product of bagged clustering are the cluster votes which can be used to assess the confidence of cluster assignments for individual observations. SUPPLEMENTARY INFORMATION: For supplementary information on datasets, analyses, and software, consult http://www.stat.berkeley.edu/~sandrine and http://www.bioconductor.org.

Algorithms↗

PubMed2003

Array-based comparative genomic hybridization for genome-wide screening of DNA copy number in bladder tumors.

Genome-wide copy number profiles were characterized in 41 primary bladder tumors using array-based comparative genomic hybridization (array CGH). In addition to previously identified alterations in large chromosomal regions, alterations were identified in many small genomic regions, some with high-level amplifications or homozygous deletions. High-level amplifications were detected for 192 genomic clones, most frequently at 6p22.3 (E2F3), 8p12 (FGFR1), 8q22.2 (CMYC), 11q13 (CCND1, EMS1, INT2), and 19q13.1 (CCNE). Homozygous deletions were detected in 51 genomic clones, with four showing deletions in more than one case: two clones mapping to 9p21.3 (CDKN2A/p16, in nine cases), one at 8p23.1 (three cases), and one at 11p13 (two cases). Significant correlations were observed between copy number gain of clones containing CCNE1 and gain of ERBB2, and between gain of CCND1 and deletion of TP53. In addition, there was a significant complementary association between gain of CCND1 and gain of E2F3. Although there was no significant relationship between copy number changes and tumor stage or grade, the linked behavior among genomic loci suggests that array CGH will be increasingly important in understanding pathways critical to bladder tumor biology.

Chromosomes, Human, Pair 9↗

PubMed2003

High-resolution analysis of paraffin-embedded and formalin-fixed prostate tumors using comparative genomic hybridization to genomic microarrays.

We have used prostate cancer, the most commonly diagnosed noncutaneous neoplasm among men, to investigate the feasibility of performing genomic array analyses of archival tissue. Prostate-specific antigen and a biopsy Gleason grade have not proven to be accurate in predicting clinical outcome, yet they remain the only accepted biomarkers for prostate cancer. It is likely that distinct spectra of genomic alterations underlie these phenotypic differences, and that once identified, may be used to differentiate between indolent and aggressive tumors. Array comparative genomic hybridization allows quantitative detection and mapping of copy number aberrations in tumors and subsequent associations to be made with clinical outcome. Archived tissues are needed to have patients with sufficient clinical follow-up. In this report, 20 formalin-fixed and paraffin-embedded prostate cancer samples originating from 1986 to 1996 were studied. We present a straightforward protocol and demonstrate the utility of archived tissue for array comparative genomic hybridization with a 2400 element BAC array that provides high-resolution detection of both deletions and amplifications.

Chromosome Aberrations↗

PubMed2002

Multiple genetic loci modify susceptibility to plasmacytoma-related morbidity in E(mu)-v-abl transgenic mice.

There is a great difference in susceptibility to v-abl transgene-induced plasmacytoma between the BALB/cAn and the relatively resistant C57BL/6J mouse strains. We have used the Mapmaker/SURVIVOR algorithm to analyze genome-wide scans on over 800 transgenic F2 hybrid mice, and have mapped at least six loci on chromosomes 2, 4, 11, 17, and 18 that modify tumor-related morbidity. As in human multiple myeloma, males were found to be more prone to plasmacytomagenesis. Different loci influence tumor susceptibility in male and female mice. Survival in females may be largely controlled by a pair of interacting loci on chromosomes 2 and 17.

Algorithms↗

PubMed2002

A prediction-based resampling method for estimating the number of clusters in a dataset.

BACKGROUND: Microarray technology is increasingly being applied in biological and medical research to address a wide range of problems, such as the classification of tumors. An important statistical problem associated with tumor classification is the identification of new tumor classes using gene-expression profiles. Two essential aspects of this clustering problem are: to estimate the number of clusters, if any, in a dataset; and to allocate tumor samples to these clusters, and assess the confidence of cluster assignments for individual samples. Here we address the first of these problems. RESULTS: We have developed a new prediction-based resampling method, Clest, to estimate the number of clusters in a dataset. The performance of the new and existing methods were compared using simulated data and gene-expression data from four recently published cancer microarray studies. Clest was generally found to be more accurate and robust than the six existing methods considered in the study. CONCLUSIONS: Focusing on prediction accuracy in conjunction with resampling produces accurate and robust estimates of the number of clusters.

Algorithms↗