RESUMO
Detection of DNA copy number aberrations by shallow whole-genome sequencing (WGS) faces many challenges, including lack of completion and errors in the human reference genome, repetitive sequences, polymorphisms, variable sample quality, and biases in the sequencing procedures. Formalin-fixed paraffin-embedded (FFPE) archival material, the analysis of which is important for studies of cancer, presents particular analytical difficulties due to degradation of the DNA and frequent lack of matched reference samples. We present a robust, cost-effective WGS method for DNA copy number analysis that addresses these challenges more successfully than currently available procedures. In practice, very useful profiles can be obtained with â¼0.1× genome coverage. We improve on previous methods by first implementing a combined correction for sequence mappability and GC content, and second, by applying this procedure to sequence data from the 1000 Genomes Project in order to develop a blacklist of problematic genome regions. A small subset of these blacklisted regions was previously identified by ENCODE, but the vast majority are novel unappreciated problematic regions. Our procedures are implemented in a pipeline called QDNAseq. We have analyzed over 1000 samples, most of which were obtained from the fixed tissue archives of more than 25 institutions. We demonstrate that for most samples our sequencing and analysis procedures yield genome profiles with noise levels near the statistical limit imposed by read counting. The described procedures also provide better correction of artifacts introduced by low DNA quality than prior approaches and better copy number data than high-resolution microarrays at a substantially lower cost.
Assuntos
Biologia Computacional , Variações do Número de Cópias de DNA , Genoma Humano , Sequenciamento de Nucleotídeos em Larga Escala , Algoritmos , Composição de Bases , Linhagem Celular Tumoral , Hibridização Genômica Comparativa , Biologia Computacional/métodos , Genômica/métodos , Humanos , Neoplasias/genética , SoftwareRESUMO
PURPOSE: Problems in management of oral cancers or precancers include identification of patients at risk for metastasis, tumor recurrence, and second primary tumors or risk for progression of precancers (dysplasia) to cancer. Thus, the objective of this study was to clarify the role of genomic aberrations in oral cancer progression and metastasis. EXPERIMENTAL DESIGN: The spectrum of copy number alterations in oral dysplasia and squamous cell carcinomas (SCC) was determined by array comparative genomic hybridization. Associations with clinical characteristics were studied and results confirmed in an independent cohort. RESULTS: The presence of one or more of the chromosomal aberrations +3q24-qter, -8pter-p23.1, +8q12-q24.2, and +20 distinguishes a major subgroup (70%-80% of lesions, termed 3q8pq20 subtype) from the remainder (20%-30% of lesions, non-3q8pq20). The 3q8pq20 subtype is associated with chromosomal instability and differential methylation in the most chromosomally unstable tumors. The two subtypes differ significantly in clinical outcome with risk for cervical (neck) lymph node metastasis almost exclusively associated with the 3q8pq20 subtype in two independent oral SCC cohorts. CONCLUSIONS: Two subtypes of oral lesions indicative of at least two pathways for oral cancer development were distinguished that differ in chromosomal instability and risk for metastasis, suggesting that +3q,-8p, +8q, and +20 constitute a biomarker with clinical utility for identifying patients at risk for metastasis. Moreover, although increased numbers of genomic alterations can be harbingers of progression to cancer, dysplastic lesions lacking copy number changes cannot be considered benign as they are potential precursors to non-3q8pq20 locally invasive, yet not metastatic oral SCC.
Assuntos
Carcinoma de Células Escamosas/genética , Carcinoma de Células Escamosas/patologia , Variações do Número de Cópias de DNA , Instabilidade Genômica , Neoplasias de Cabeça e Pescoço/secundário , Neoplasias Bucais/genética , Neoplasias Bucais/patologia , Estudos de Coortes , Hibridização Genômica Comparativa , Progressão da Doença , Feminino , Humanos , Metástase Linfática , Masculino , Pessoa de Meia-Idade , Lesões Pré-Cancerosas/genética , Lesões Pré-Cancerosas/patologia , RiscoRESUMO
We describe a contact printing approach for microarrays that uses fused-silica capillary tubes with tapered tips for printing pins and a pressure/vacuum system to control pin loading, printing, and cleaning. The printing process is insensitive to variable environmental factors such as humidity, and the small diameter of the pins allows routine printing from 1536 well source plates. Pin load capacity, 0.2 microL in the current system, is adjustable by controlling pin length. More than 2000 spots can be printed per 0.2-microL pin load (<100 pl/spot), and densities of >12,000 spots/cm(2) are readily achievable. Solutions with a wide range of viscosities and chemical properties can be printed. The system can print tens of thousands of different solutions at high speed, due to the ability to use large numbers of pins simultaneously, and can produce a large number of replicate arrays since all of the solution picked up by the pins is available for deposition.
Assuntos
Análise em Microsséries/instrumentação , Dióxido de Silício/química , Cromossomos Artificiais Bacterianos/química , Cromossomos Artificiais Bacterianos/genética , DNA/genética , DNA/isolamento & purificação , Humanos , Análise em Microsséries/métodos , Análise de Sequência com Séries de Oligonucleotídeos/instrumentação , Análise de Sequência com Séries de Oligonucleotídeos/métodos , Oligonucleotídeos/química , Oligonucleotídeos/genética , VácuoRESUMO
BACKGROUND: In melanoma, morphology-based classification systems have not been able to provide relevant information for selecting treatments for patients whose tumors have metastasized. The recent identification of causative genetic alterations has revealed mutations in signaling pathways that offer targets for therapy. Identifying morphologic surrogates that can identify patients whose tumors express such alterations (or functionally equivalent alterations) would be clinically useful for therapy stratification and for retrospective analysis of clinical trial data. METHODOLOGY/PRINCIPAL FINDINGS: We defined and assessed a panel of histomorphologic measures and correlated them with the mutation status of the oncogenes BRAF and NRAS in a cohort of 302 archival tissues of primary cutaneous melanomas from an academic comprehensive cancer center. Melanomas with BRAF mutations showed distinct morphological features such as increased upward migration and nest formation of intraepidermal melanocytes, thickening of the involved epidermis, and sharper demarcation to the surrounding skin; and they had larger, rounder, and more pigmented tumor cells (all p-values below 0.0001). By contrast, melanomas with NRAS mutations could not be distinguished based on these morphological features. Using simple combinations of features, BRAF mutation status could be predicted with up to 90.8% accuracy in the entire cohort as well as within the categories of the current World Health Organization (WHO) classification. Among the variables routinely recorded in cancer registries, we identified age < 55 y as the single most predictive factor of BRAF mutation in our cohort. Using age < 55 y as a surrogate for BRAF mutation in an independent cohort of 4,785 patients of the Southern German Tumor Registry, we found a significant survival benefit (p < 0.0001) for patients who, based on their age, were predicted to have BRAF mutant melanomas in 69% of the cases. This group also showed a different pattern of metastasis, more frequently involving regional lymph nodes, compared to the patients predicted to have no BRAF mutation and who more frequently displayed satellite, in-transit metastasis, and visceral metastasis (p < 0.0001). CONCLUSIONS: Refined morphological classification of primary melanomas can be used to improve existing melanoma classifications by forming subgroups that are genetically more homogeneous and likely to differ in important clinical variables such as outcome and pattern of metastasis. We expect this information to improve classification and facilitate stratification for therapy as well as retrospective analysis of existing trial data.
Assuntos
DNA de Neoplasias/genética , Melanócitos/patologia , Melanoma/classificação , Mutação , Proteínas Proto-Oncogênicas B-raf/genética , Neoplasias Cutâneas/classificação , Proteínas ras/genética , Idoso , Biópsia , Análise Mutacional de DNA , Feminino , Seguimentos , Humanos , Masculino , Melanoma/genética , Melanoma/patologia , Pessoa de Meia-Idade , Fenótipo , Neoplasias Cutâneas/genética , Neoplasias Cutâneas/patologiaRESUMO
Primary melanoma can recur at the excision site if not excised with a safety margin of surrounding uninvolved skin. To characterize the nature of residual melanoma in the skin surrounding primary tumors targeted by safety margins, we used array comparative genomic hybridization and fluorescent in situ hybridization to detect and spatially map aberrations in the skin adjacent to acral melanomas. Melanocytic cells with genetic amplifications in histopathologically normal skin (field cells) were detected exclusively in the epidermis in 84% of 19 cases, with a mean extension of 6.1 mm (in situ melanomas) and 4.5 mm (invasive melanomas) beyond the histopathological margin. Genetic profiling of these field cells indicated that they represent an early phase of disease preceding melanoma in situ. The extent of field cells did not correlate with tumor depth or diameter, indicating that tumor depth is not suited to predict the extent of field cells. These results demonstrate that, on acral sites, melanoma field cells extend significantly into seemingly normal skin. These field cells provide a plausible explanation for the tendency of certain melanoma types to recur locally despite apparently having undergone complete excision.
Assuntos
Carcinoma in Situ/patologia , Melanoma/patologia , Recidiva Local de Neoplasia/prevenção & controle , Neoplasias Cutâneas/patologia , Adulto , Idoso , Idoso de 80 Anos ou mais , Carcinoma in Situ/cirurgia , Feminino , Humanos , Hibridização in Situ Fluorescente , Masculino , Melanoma/cirurgia , Pessoa de Meia-Idade , Invasividade Neoplásica/patologia , Estudos Retrospectivos , Neoplasias Cutâneas/cirurgiaRESUMO
Investigators representing all major melanoma research areas present an overview of the most important challenges for the field. Four major research areas are covered plus the training of new investigators. For each area we first describe the present status, its strengths and weaknesses, and then outline specific recommendations. In basic research of melanoma, we outline the pertinent issues for melanoma classification, understanding melanocyte development and transformation, melanoma resistance, tumor microenvironment, metastasis, animal models, immune response, and blood and tissue diagnostics. In clinical research we provide an overview of the current challenges and the strategies for characterization, monitoring, and therapy. It will be important to develop strong research and clinical infrastructures by establishing tumor banks, identifying and validating biomarkers, developing new imaging techniques, and increasing multidisciplinary collaboration and communication. To strengthen the field we need to recruit both young and established investigators and foster career development plans that cover all disciplines. Recent research advances provide significant opportunities to have a major impact on this devastating disease. This group provides recommendations for both short- and long-term strategies that build on research strengths and opportunities established by the many members of the research community.
Assuntos
Melanoma , Pesquisa , Neoplasias Cutâneas , Humanos , Melanoma/patologia , Melanoma/terapia , Neoplasias Cutâneas/patologia , Neoplasias Cutâneas/terapiaRESUMO
The adaptation of a population to a new environment is a result of selection operating on a suite of stochastically occurring mutations. This article presents an analytical approach to understanding the population dynamics during adaptation, specifically addressing a system in which periods of growth are separated by selection in bottlenecks. The analysis derives simple expressions for the average properties of the evolving population, including a quantitative description of progressive narrowing of the range of selection coefficients of the predominant mutant cells and of the proportion of mutant cells as a function of time. A complete statistical description of the bottlenecks is also presented, leading to a description of the stochastic behavior of the population in terms of effective mutation times. The effective mutation times are related to the actual mutation times by calculable probability distributions, similar to the selection coefficients being highly restricted in their probable values. This analytical approach is used to model recently published experimental data from a bacterial coculture experiment, and the results are compared to those of a numerical model published in conjunction with the data. Finally, experimental designs that may improve measurements of fitness distributions are suggested.
Assuntos
Genética Populacional , Mutação , Dinâmica Populacional , Reprodução Assexuada , Bactérias/genética , Modelos Genéticos , Modelos EstatísticosRESUMO
BACKGROUND: Amplifications, regions of focal high-level copy number change, lead to overexpression of oncogenes or drug resistance genes in tumors. Their presence is often associated with poor prognosis; however, the use of amplification as a mechanism for overexpression of a particular gene in tumors varies. To investigate the influence of genome position on propensity to amplify, we integrated a mutant form of the gene encoding dihydrofolate reductase into different positions in the human genome, challenged cells with methotrexate and then studied the genomic alterations arising in drug resistant cells. RESULTS: We observed site-specific differences in methotrexate sensitivity, amplicon organization and amplification frequency. One site was uniquely associated with a significantly enhanced propensity to amplify and recurrent amplicon boundaries, possibly implicating a rare folate-sensitive fragile site in initiating amplification. Hierarchical clustering of gene expression patterns and subsequent gene enrichment analysis revealed two clusters differing significantly in expression of MYC target genes independent of integration site. CONCLUSION: These studies suggest that genome context together with the particular challenges to genome stability experienced during the progression to cancer contribute to the propensity to amplify a specific oncogene or drug resistance gene, whereas the overall functional response to drug (or other) challenge may be independent of the genomic location of an oncogene.
Assuntos
Amplificação de Genes , Regulação Neoplásica da Expressão Gênica , Linhagem Celular Tumoral , Amplificação de Genes/efeitos dos fármacos , Humanos , Metotrexato/farmacologia , Tetra-Hidrofolato Desidrogenase/genéticaRESUMO
Constitutional submicroscopic DNA copy number alterations have been shown to cause numerous medical genetic syndromes, and are suspected to occur in a portion of cases for which the causal events remain undiscovered. Array comparative genomic hybridization (array CGH) allows high-throughput, high-resolution genome scanning for DNA dosage aberrations and thus offers an attractive approach for both clinical diagnosis and discovery efforts. Here we assess this capability by applying array CGH to the analysis of copy number alterations in 44 patients with a phenotype of the 22q11.2 deletion syndrome. Twenty-five patients had the deletion on chromosome 22 characteristic of this syndrome as determined by fluorescence in situ hybridization (FISH). The array measurements were in complete concordance with the FISH analysis, supporting their diagnostic utility. These data show that a genome-scanning microarray has the level of sensitivity and specificity required to prospectively interrogate and identify single copy number aberrations in a clinical setting. We demonstrate that such technology is ideally suited for microdeletion syndromes such as 22q11.2.
Assuntos
Deleção Cromossômica , Cromossomos Humanos Par 22 , Síndrome de DiGeorge/diagnóstico , Síndrome de DiGeorge/genética , Hibridização de Ácido Nucleico/métodos , Mapeamento Cromossômico/métodos , Cromossomos Artificiais Bacterianos , Cromossomos Humanos , Clonagem Molecular , Dosagem de Genes , Humanos , Sensibilidade e EspecificidadeRESUMO
Despite the recent consensus on the eligibility of adjuvant systemic therapy in patients with lymph node-negative breast cancer (NNBC) based on clinicopathologic criteria, specific biological markers are needed to predict sensitivity to the different available therapeutic options. We examined the feasibility of developing a genomic predictor of chemotherapy response and recurrence risk in 185 patients with NNBC using assembled arrays containing 2,460 bacterial artificial chromosome clones for scanning the genome for DNA copy number changes. After surgery, 90 patients received anthracycline-based chemotherapy, whereas 95 did not. Tamoxifen was administered to patients with hormone receptor-positive tumors. The association of genomic and clinicopathologic data and outcome was computed using Cox proportional hazard models and multiple testing adjustment procedures. Analysis of NNBC genomes revealed a common genomic signature. Specific DNA copy number aberrations were associated with hormonal receptor status, but not with other clinicopathologic variables. In patients treated with chemotherapy, none of the genomic changes were significantly correlated with recurrence. In patients not receiving chemotherapy, deletion of eight bacterial artificial chromosome clones clustered to chromosome 11q was independently associated with relapse (disease-free survival at 10 years+/-SE, 40%+/-14% versus 86%+/-6%; P<0.0001). The 54 patients with deletion of 11q (29%) did not present more aggressive clinicopathologic features than those without 11q loss. The adverse influence of 11q deletion on clinical outcome was confirmed in an independent validation series of 88 patients with NNBC. Our data suggests that patients with NNBC with the 11q deletion might benefit from anthracycline-based chemotherapy despite other clinical, pathologic, or genetic features. However, these initial findings should be evaluated in randomized clinical trials.
Assuntos
Protocolos de Quimioterapia Combinada Antineoplásica/uso terapêutico , Neoplasias da Mama/tratamento farmacológico , Neoplasias da Mama/genética , Deleção Cromossômica , Cromossomos Humanos Par 11 , Recidiva Local de Neoplasia/genética , Adulto , Antraciclinas/administração & dosagem , Neoplasias da Mama/metabolismo , Neoplasias da Mama/patologia , Feminino , Dosagem de Genes , Predisposição Genética para Doença , Humanos , Hibridização in Situ Fluorescente , Metástase Linfática , Pessoa de Meia-Idade , Hibridização de Ácido Nucleico , Valor Preditivo dos Testes , Receptores de Estrogênio/biossíntese , Receptores de Progesterona/biossínteseRESUMO
Integrative genomic and gene-expression analyses have identified amplified oncogenes in B-cell non-Hodgkin lymphoma (B-NHL), but the capability of such technologies to localize tumor suppressor genes within homozygous deletions remains unexplored. Array-based comparative genomic hybridization (CGH) and gene-expression microarray analysis of 48 cell lines derived from patients with different B-NHLs delineated 20 homozygous deletions at 7 chromosome areas, all of which contained tumor suppressor gene targets. Further investigation revealed that only a fraction of primary biopsies presented inactivation of these genes by point mutation or intragenic deletion, but instead some of them were frequently silenced by epigenetic mechanisms. Notably, the pattern of genetic and epigenetic inactivation differed among B-NHL subtypes. Thus, the P53-inducible PIG7/LITAF was silenced by homozygous deletion in primary mediastinal B-cell lymphoma and by promoter hypermethylation in germinal center lymphoma, the proapoptotic BIM gene presented homozygous deletion in mantle cell lymphoma and promoter hypermethylation in Burkitt lymphoma, the proapoptotic BH3-only NOXA was mutated and preferentially silenced in diffuse large B-cell lymphoma, and INK4c/P18 was silenced by biallelic mutation in mantle-cell lymphoma. Our microarray strategy has identified novel candidate tumor suppressor genes inactivated by genetic and epigenetic mechanisms that substantially vary among the B-NHL subtypes.
Assuntos
Proteínas Reguladoras de Apoptose/genética , Proteínas de Transporte/genética , Inibidor de Quinase Dependente de Ciclina p18/genética , Genes Supressores de Tumor , Proteínas de Homeodomínio/genética , Linfoma de Células B/genética , Proteínas de Membrana/genética , Proteínas Nucleares/genética , Proteínas Proto-Oncogênicas c-bcl-2/genética , Proteínas Proto-Oncogênicas/genética , Deleção de Sequência , Fatores de Transcrição/genética , Proteínas de Transporte Vesicular/genética , Proteínas Adaptadoras de Transdução de Sinal , Apoptose/genética , Proteína 11 Semelhante a Bcl-2 , Biópsia , Linhagem Celular Tumoral , Mapeamento Cromossômico , Cromossomos Humanos/genética , Cromossomos Humanos/ultraestrutura , Metilação de DNA , Análise Mutacional de DNA , DNA de Neoplasias/genética , Epigênese Genética , Dosagem de Genes , Regulação Neoplásica da Expressão Gênica , Inativação Gênica , Homozigoto , Humanos , Linfoma de Células B/classificação , Linfoma de Células B/imunologia , Linfoma de Células B/patologia , Hibridização de Ácido Nucleico , Análise de Sequência com Séries de Oligonucleotídeos , Mutação Puntual , Regiões Promotoras Genéticas/genética , Proteínas de Ligação a RNA , Nexinas de ClassificaçãoRESUMO
Angioimmunoblastic T-cell lymphoma (AILT) is a histopathologically well-defined entity. However, despite a number of cytogenetic studies, the genetic basis of this lymphoma entity is not clear. Moreover, there is an overlap to some cases of peripheral T-cell lymphoma unspecified (PTCL-u) in respect to morphological and genetic features. We used array-based comparative genomic hybridization (CGH) to study genetic imbalances in 39 AILT and 20 PTCL-u. Array-based CGH revealed complex genetic imbalances in both AILT and PTCL-u. Chromosomal imbalances were more frequent in PTCL-u than in AILT and gains exceeded the losses. The most recurrent changes in AILT were gains of 22q, 19, and 11p11-q14 (11q13) and losses of 13q. The most frequent changes in PTCL-u were gains of 17 (17q11-q25), 8 (involving the MYC locus at 8q24), and 22q and losses of 13q and 9 (9p21-q33). Interestingly, gains of 4q (4q28-q31 and 4q34-qtel), 8q24, and 17 were significantly more frequent in PTCL-u than in AILT. The regions 6q (6q16-q22) and 11p11 were predominantly lost in PTCL-u. Moreover, we could identify a recurrent gain of 11q13 in both AILT and PTCL-u, which has previously not been described in AILT. Trisomies 3 and 5, which have been described as typical aberrations in AILT, were identified only in a small number of cases. In conclusion, CGH revealed common genetic events in peripheral T-cell lymphomas as well as peculiar differences between AILT and PTCL-u.
Assuntos
Aberrações Cromossômicas , Linfoma de Células T Periférico/genética , Linfoma de Células T/genética , Análise de Sequência com Séries de Oligonucleotídeos , Humanos , Hibridização in Situ Fluorescente , Linfoma de Células T/patologia , Linfoma de Células T Periférico/patologiaRESUMO
Recent studies suggest that thousands of genes may contribute to breast cancer pathophysiologies when deregulated by genomic or epigenomic events. Here, we describe a model "system" to appraise the functional contributions of these genes to breast cancer subsets. In general, the recurrent genomic and transcriptional characteristics of 51 breast cancer cell lines mirror those of 145 primary breast tumors, although some significant differences are documented. The cell lines that comprise the system also exhibit the substantial genomic, transcriptional, and biological heterogeneity found in primary tumors. We show, using Trastuzumab (Herceptin) monotherapy as an example, that the system can be used to identify molecular features that predict or indicate response to targeted therapies or other physiological perturbations.
Assuntos
Neoplasias da Mama/classificação , Neoplasias da Mama/genética , Neoplasias da Mama/patologia , Neoplasias da Mama/terapia , Linhagem Celular Tumoral , Feminino , Perfilação da Expressão Gênica , Regulação Neoplásica da Expressão Gênica , Genômica , Humanos , Proteínas de Neoplasias/análiseRESUMO
This study explores the roles of genome copy number abnormalities (CNAs) in breast cancer pathophysiology by identifying associations between recurrent CNAs, gene expression, and clinical outcome in a set of aggressively treated early-stage breast tumors. It shows that the recurrent CNAs differ between tumor subtypes defined by expression pattern and that stratification of patients according to outcome can be improved by measuring both expression and copy number, especially high-level amplification. Sixty-six genes deregulated by the high-level amplifications are potential therapeutic targets. Nine of these (FGFR1, IKBKB, ERBB2, PROCC, ADAM9, FNTA, ACACA, PNMT, and NR1D1) are considered druggable. Low-level CNAs appear to contribute to cancer progression by altering RNA and cellular metabolism.
Assuntos
Neoplasias da Mama/genética , Genômica , Transcrição Gênica , Neoplasias da Mama/etiologia , Neoplasias da Mama/patologia , Neoplasias da Mama/terapia , Aberrações Cromossômicas , Feminino , Amplificação de Genes , Dosagem de Genes , Perfilação da Expressão Gênica , HumanosRESUMO
Genetic and epigenetic alterations have been identified that lead to transcriptional deregulation in cancers. Genetic mechanisms may affect single genes or regions containing several neighboring genes, as has been shown for DNA copy number changes. It was recently reported that epigenetic suppression of gene expression can also extend to a whole region; this is known as long-range epigenetic silencing. Various techniques are available for identifying regional genetic alterations, but no large-scale analysis has yet been carried out to obtain an overview of regional epigenetic alterations. We carried out an exhaustive search for regions susceptible to such mechanisms using a combination of transcriptome correlation map analysis and array CGH data for a series of bladder carcinomas. We validated one candidate region experimentally, demonstrating histone methylation leading to the loss of expression of neighboring genes without DNA methylation.
Assuntos
Dosagem de Genes , Transcrição Gênica , Neoplasias da Bexiga Urinária/genética , Linhagem Celular Tumoral , Cromossomos Humanos Par 3/genética , Metilação de DNA , DNA de Neoplasias/genética , DNA de Neoplasias/metabolismo , Epigênese Genética , Regulação Neoplásica da Expressão Gênica , Humanos , Análise de Sequência com Séries de OligonucleotídeosRESUMO
PURPOSE: Melanomas on mucosal membranes, acral skin (soles, palms, and nail bed), and skin with chronic sun-induced damage have infrequent mutations in BRAF and NRAS, genes within the mitogen-activated protein (MAP) kinase pathway commonly mutated in melanomas on intermittently sun-exposed skin. This raises the question of whether other aberrations are occurring in the MAP kinase cascade in the melanoma types with infrequent mutations of BRAF and NRAS. PATIENTS AND METHODS: We analyzed array comparative genomic hybridization data from 102 primary melanomas (38 from mucosa, 28 from acral skin, and 18 from skin with and 18 from skin without chronic sun-induced damage) for DNA copy number aberrations specific to melanoma subtypes where mutations in BRAF and NRAS are infrequent. A narrow amplification on 4q12 was found, and candidate genes within it were analyzed. RESULTS: Oncogenic mutations in KIT were found in three of seven tumors with amplifications. Examination of all 102 primary melanomas found mutations and/or copy number increases of KIT in 39% of mucosal, 36% of acral, and 28% of melanomas on chronically sun-damaged skin, but not in any (0%) melanomas on skin without chronic sun damage. Seventy-nine percent of tumors with mutations and 53% of tumors with multiple copies of KIT demonstrated increased KIT protein levels. CONCLUSION: KIT is an important oncogene in melanoma. Because the majority of the KIT mutations we found in melanoma also occur in imatinib-responsive cancers of other types, imatinib may offer an immediate therapeutic benefit for a significant proportion of the global melanoma burden.
Assuntos
Biomarcadores Tumorais/metabolismo , Melanoma/metabolismo , Proteínas Proto-Oncogênicas c-kit/metabolismo , Neoplasias Cutâneas/metabolismo , Adulto , Idoso , Antineoplásicos/uso terapêutico , Benzamidas , Feminino , Regulação Neoplásica da Expressão Gênica , Humanos , Mesilato de Imatinib , Imuno-Histoquímica , Masculino , Melanoma/tratamento farmacológico , Melanoma/genética , Análise em Microsséries , Pessoa de Meia-Idade , Hibridização de Ácido Nucleico , Piperazinas/uso terapêutico , Pirimidinas/uso terapêutico , Neoplasias Cutâneas/tratamento farmacológico , Neoplasias Cutâneas/genéticaRESUMO
Genomic disorders are characterized by the presence of flanking segmental duplications that predispose these regions to recurrent rearrangement. Based on the duplication architecture of the genome, we investigated 130 regions that we hypothesized as candidates for previously undescribed genomic disorders. We tested 290 individuals with mental retardation by BAC array comparative genomic hybridization and identified 16 pathogenic rearrangements, including de novo microdeletions of 17q21.31 found in four individuals. Using oligonucleotide arrays, we refined the breakpoints of this microdeletion, defining a 478-kb critical region containing six genes that were deleted in all four individuals. We mapped the breakpoints of this deletion and of four other pathogenic rearrangements in 1q21.1, 15q13, 15q24 and 17q12 to flanking segmental duplications, suggesting that these are also sites of recurrent rearrangement. In common with the 17q21.31 deletion, these breakpoint regions are sites of copy number polymorphism in controls, indicating that these may be inherently unstable genomic regions.
Assuntos
Duplicação Gênica , Genoma Humano , Deficiência Intelectual/genética , Quebra Cromossômica , Deleção Cromossômica , Cromossomos Artificiais Bacterianos , Cromossomos Humanos Par 17 , Dosagem de Genes , Rearranjo Gênico , Heterozigoto , Humanos , Hibridização in Situ Fluorescente , Mosaicismo , Hibridização de Ácido Nucleico , Análise de Sequência com Séries de Oligonucleotídeos , Mapeamento Físico do Cromossomo , Polimorfismo GenéticoRESUMO
Germline variants in MC1R, the gene encoding the melanocortin-1 receptor, and sun exposure increase risk for melanoma in Caucasians. The majority of melanomas that occur on skin with little evidence of chronic sun-induced damage (non-CSD melanoma) have mutations in the BRAF oncogene, whereas in melanomas on skin with marked CSD (CSD melanoma) these mutations are less frequent. In two independent Caucasian populations, we show that MC1R variants are strongly associated with BRAF mutations in non-CSD melanomas. In this tumor subtype, the risk for melanoma associated with MC1R is due to an increase in risk of developing melanomas with BRAF mutations.