The identification of chromosome abnormalities associated with the invasive phenotype of uveal melanoma in vitro

Cross, Neil; Rennie, I G; Murray, AK; Sisley, Karen

doi:10.1007/s10585-005-5142-2

Cited by 5 publications

(4 citation statements)

References 18 publications

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“…28,29 However, immunohistochemistry for BAP1 does not correlate in all cases with the BAP1 mutational status in UM and is therefore not a perfect surrogate. 28 In the present series, partial deletions of chromosome 3 were found in 4.0% of cases, which is comparable with some previous series [30][31][32] but lower than others. 17,33,34 Recruitment bias may explain part of this discrepancy, but it is probably explained by the variety of technologies and the different classifications that were used.…”

Section: Discussionsupporting

confidence: 90%

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Association of Partial Chromosome 3 Deletion in Uveal Melanomas With Metastasis-Free Survival

Rodrigues

Salviat

et al. 2020

JAMA Ophthalmol

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IMPORTANCE Studies on uveal melanomas (UMs) have demonstrated the prognostic value of 8q gain and monosomy 3, but the prognosis of UMs with partial deletion of chromosome 3 remains to be defined.OBJECTIVE To examine the association of partial chromosome 3 deletion in UMs with metastasis-free survival. DESIGN, SETTING, AND PARTICIPANTSThis retrospective cohort study of 1088 consecutive comparative genomic hybridization arrays performed from May 1, 2006, to July 31, 2015, assessed patients presenting with UMs with and without partial loss of chromosome 3 at a referral center. Data analysis was performed from September 1, 2017, to November 30, 2017.EXPOSURE Uveal melanoma with or without partial loss of chromosome 3. MAIN OUTCOMES AND MEASURESMetastasis-free survival and overall survival at 60 months. RESULTSOf the 1088 consecutive comparative genomic hybridization arrays that were performed, 43 UMs (4.0%) in 43 patients (median age, 58 years [range, 12-79 years]; 22 [51%] female) carried partial deletions of chromosome 3. Median follow-up was 66 months (range, 1.2-126.2 months). Metastasis-free survival at 60 months was 33.6% (95% CI, 15.8%-71.4%) for UMs that carried a deletion of the BAP1 (BRCA1 associated protein 1) locus (BAP1del; 24 tumors) and 80.5% (95% CI, 64.8%-100%) for UMs without the loss of the BAP1 locus (BAP1 normal [BAP1nl]; 19 tumors) (log-rank P = .001). Overall survival at 60 months was 64.5% (95% CI, 43.5%-95.8%) in the BAP1del group vs 84.1% (95% CI, 69.0%-100%) in the BAP1nl group (log-rank P < .001). In these 43 cases, metastasis-free survival at 60 months was 100% for UMs without loss of the BAP1 locus or 8q gain, 70.0% (95% CI, 50.5%-96.9%) for UMs that carried 1 of these alterations, and 12.5% (95% CI, 2.1%-73.7%) for those that carried both (log-rank P < .001). Similarly, overall survival at 60 months was 100% for UMs without loss of the BAP1 locus or 8q gain, 80.8% (95% CI, 63.3%-100%) for UMs that carried 1 of these alterations, and 46.7% (95% CI, 23.3%-93.6%) for those that carried both (log-rank P < .001). CONCLUSIONS AND RELEVANCEThese findings suggest that partial deletion of chromosome 3 encompassing the BAP1 locus is associated with poor prognosis. A cytogenetic classification of UMs could be proposed based on the status of the BAP1 locus instead of the chromosome 3 locus, while also taking chromosome 8q into account.

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Section: Discussionsupporting

confidence: 90%

“…In the present series, partial deletions of chromosome 3 were found in 4.0% of cases, which is comparable with some previous series but lower than others . Recruitment bias may explain part of this discrepancy, but it is probably explained by the variety of technologies and the different classifications that were used.…”

Section: Discussionsupporting

confidence: 79%

Association of Partial Chromosome 3 Deletion in Uveal Melanomas With Metastasis-Free Survival

Rodrigues

Salviat

et al. 2020

JAMA Ophthalmol

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“…Although the distribution of driver genes shows a close correlation with the frequency and amplitude of CNV, most drivers do not demonstrate signal peaks nor overlap with the feature genes. Frequent duplications on chromosome 1 and deletions on chromosome 14 do not show direct correlations to common driver genes; however, a number of studies have shown the connection of CNAs on these regions to the progress and prognosis in these cancer types (Cross et al, 2005 ; Parsons et al, 2011 ; Mathieu et al, 2012 ; Boots-Sprenger et al, 2013 ; Cohen et al, 2015 ; Park et al, 2019 ).…”

Section: Resultsmentioning

confidence: 99%

Signatures of Discriminative Copy Number Aberrations in 31 Cancer Subtypes

Gao

Baudis

2021

Front. Genet.

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Copy number aberrations (CNA) are one of the most important classes of genomic mutations related to oncogenetic effects. In the past three decades, a vast amount of CNA data has been generated by molecular-cytogenetic and genome sequencing based methods. While this data has been instrumental in the identification of cancer-related genes and promoted research into the relation between CNA and histo-pathologically defined cancer types, the heterogeneity of source data and derived CNV profiles pose great challenges for data integration and comparative analysis. Furthermore, a majority of existing studies have been focused on the association of CNA to pre-selected “driver” genes with limited application to rare drivers and other genomic elements. In this study, we developed a bioinformatics pipeline to integrate a collection of 44,988 high-quality CNA profiles of high diversity. Using a hybrid model of neural networks and attention algorithm, we generated the CNA signatures of 31 cancer subtypes, depicting the uniqueness of their respective CNA landscapes. Finally, we constructed a multi-label classifier to identify the cancer type and the organ of origin from copy number profiling data. The investigation of the signatures suggested common patterns, not only of physiologically related cancer types but also of clinico-pathologically distant cancer types such as different cancers originating from the neural crest. Further experiments of classification models confirmed the effectiveness of the signatures in distinguishing different cancer types and demonstrated their potential in tumor classification.

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Section: Similarities Of Neural Crest Originated Subtypesmentioning

confidence: 99%

Signatures of Discriminative Copy Number Aberrations in 31 Cancer Subtypes

Gao

Baudis

2020

Preprint

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Copy number aberrations (CNA) are one of the most important classes of genomic mutations related to oncogenetic effects. In the past three decades, a vast amount of CNA data has been generated by molecular-cytogenetic and genome sequencing based methods. While this data has been instrumental in the identification of cancer-related genes and promoted research into the relation between CNA and histo-pathologically defined cancer types, the heterogeneity of source data and derived CNV profiles pose great challenges for data integration and comparative analysis. Furthermore, a majority of existing studies has been focused on the association of CNA to pre-selected “driver” genes with limited application to rare drivers and other genomic elements.In this study, we developed a bioinformatic pipeline to integrate a collection of 44,988 high-quality CNA profiles of high diversity. Using a hybrid model of neural networks and attention algorithm, we generated the CNA signatures of 31 cancer subtypes, depicting the uniqueness of their respective CNA landscapes. Finally, we constructed a multi-label classifier to identify the cancer type and the organ of origin from copy number profiling data. The investigation of the signatures suggested common patterns, not only of physiologically related cancer types but also of clinico-pathologically distant cancer types such as different cancers originating from the neural crest. Further experiments of classification models confirmed the effectiveness of the signatures in distinguishing different cancer types and demonstrated their potential in tumor classification.

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The identification of chromosome abnormalities associated with the invasive phenotype of uveal melanoma in vitro

Cited by 5 publications

References 18 publications

Association of Partial Chromosome 3 Deletion in Uveal Melanomas With Metastasis-Free Survival

Association of Partial Chromosome 3 Deletion in Uveal Melanomas With Metastasis-Free Survival

Signatures of Discriminative Copy Number Aberrations in 31 Cancer Subtypes

Signatures of Discriminative Copy Number Aberrations in 31 Cancer Subtypes

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