Identification of small gains and losses in single cells after whole genome amplification on tiling oligo arrays

Geigl, Jochen B.; Obenauf, Anna C.; Waldispuehl-Geigl, Julie; Hoffmann, Eva Maria; Auer, Martina; Hörmann, Martina; Fischer, Maria; Trajanoski, Zlatko; Schenk, Michael A.; Baumbusch, Lars Oliver; Speicher, Michael R.

doi:10.1093/nar/gkp526

Cited by 65 publications

(63 citation statements)

References 20 publications

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“…10 As shown previously, no major artifacts were induced by whole-genome amplification and a similar signal-to-noise ratio of the aCGH profile was observed when using amplified or non-amplified DNA. 11 aCGH was performed in all cases in which DNA was available. Briefly, 250 ng unamplified or amplified DNA was labeled using the Bioprime Array CGH Genomic Labeling Kit according to the manufacturer's instructions (Invitrogen, Carlsberg, CA, USA).…”

Section: Dna Extraction and Acghmentioning

confidence: 99%

Histological and genetic evidence for a variant of superficial spreading melanoma composed predominantly of large nests

et al. 2012

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Cutaneous melanomas are characterized by a range of histological appearances, and several morphological variants have been described. In this study, we report a variant of superficial spreading melanoma that is characterized by large, irregular junctional melanocytic nests. The junctional nests varied in shape and size, showed focal tendency to confluence, and were often surrounded by a cuff of epidermal keratinocytes. The melanocytes comprising the nests showed variable cytological atypia. In most of the cases, scant intraepidermal or junctional single melanocytes were seen, and other well-documented diagnostic criteria for melanoma were lacking, and as a result, histological recognition of these tumors as melanoma was difficult. Some cases were associated with an invasive dermal component or showed evidence of sun damage. To provide supporting evidence for malignancy, we analyzed these tumors for genomic aberrations. Using array comparative genomic hybridization (aCGH), we identified multiple genomic aberrations in all analyzed cases. A similar pattern of genomic aberrations was seen in a control group of bona fide superficial spreading melanomas, suggesting that these 'melanomas composed exclusively or predominantly of large nests' are indeed variants of superficial spreading melanoma. Fluorescence in-situ hybridization (FISH) was positive in 40% of the cases. However, using aCGH, the FISH-negative cases showed multiple genomic aberrations in regions that are not covered by FISH. The low sensitivity of the FISH test can be explained by the fact that FISH only evaluates four genomic loci for aberrations, whereas aCGH surveys the entire genome. In summary, we present histological and molecular genetic evidence for a morphological variant of superficial spreading melanoma. Awareness of the histological features will aid in their correct diagnosis as melanoma, and in difficult cases, judicious application of ancillary tests such as aCGH (rather than FISH) will assist accurate diagnosis. Modern Pathology (2012) 25, 838-845; doi:10.1038/modpathol.2012; published online 2 March 2012 Keywords: chromosomal aberrations; comparative genomic hybridization; fluorescence in-situ hybridization; melanocytic tumors; melanoma Cutaneous melanomas are characterized by a diverse range of histological appearances, and several morphological variants have been described. The most common subtypes in histological classification systems are superficial spreading melanoma, nodular melanoma, lentigo maligna melanoma, and acral lentiginous melanoma. 1 Although histological evaluation is a reliable means of accurately classifying melanocytic tumors as benign

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Section: Dna Extraction and Acghmentioning

confidence: 99%

Histological and genetic evidence for a variant of superficial spreading melanoma composed predominantly of large nests

et al. 2012

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“…Intratumor heterogeneity studies profiling or sequencing DNA from individual tumor cells require whole-genome amplification (WGA). By using commercially available methods for WGA, it is possible to amplify DNA from a single cell to a level where it can be profiled by microarrays, but these studies have been challenged by technical difficulty and limited reproducibility (75)(76)(77)(78). Analyzing WGA fragments from single cells using targeted approaches such as DNA microarrays is problematic because fragments are randomly amplified from a small fraction (<10%) of the genome, and thus many fail to hybridize to their target probes.…”

Section: Figurementioning

confidence: 99%

Insight into the heterogeneity of breast cancer through next-generation sequencing

Russnes¹,

Navin²,

Hicks³

et al. 2011

J. Clin. Invest.

222

154

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Rapid and sophisticated improvements in molecular analysis have allowed us to sequence whole human genomes as well as cancer genomes, and the findings suggest that we may be approaching the ability to individualize the diagnosis and treatment of cancer. This paradigmatic shift in approach will require clinicians and researchers to overcome several challenges including the huge spectrum of tumor types within a given cancer, as well as the cellto-cell variations observed within tumors. This review discusses how next-generation sequencing of breast cancer genomes already reveals insight into tumor heterogeneity and how it can contribute to future breast cancer classification and management.

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“…15 To obtain a high purity of tumor DNA, only areas with a tumor cell infiltration of over 90% were microdissected for DNA isolation using the QIAamp DNA formalin-fixed, paraffinembedded tissue kit (Qiagen, Hilden, Germany). Samples were labeled with a bioprime array CGH genomic labeling kit according to the manufacturer's instructions (Invitrogen, Carlsberg, CA, USA).…”

Section: Array Cghmentioning

confidence: 99%

Classifying ambiguous melanocytic lesions with FISH and correlation with clinical long-term follow up

et al. 2010

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Recently, initial studies describing the use of multicolor fluorescence in situ hybridization (FISH) for classifying melanocytic skin lesions have been published demonstrating a high sensitivity and specificity in discriminating melanomas from nevi. However, the majority of these studies included neither histologically ambiguous lesions nor a clinical long-term follow up. This study was undertaken to validate a special multicolor FISH test in histologically ambiguous melanocytic skin lesions with known clinical long-term follow up. FISH was scored by three independent pathologists in a series of 22 melanocytic skin lesions, including 12 ambiguous cases using four probes targeting chromosome 6p25, centromere 6, 6q23, and 11q13. The FISH results were compared with array comparative genomic hybridization data and correlated to the clinical long-term follow up (mean: 65 months). Pair-wise comparison between the interpretations of the observers showed a moderate to substantial agreement (j 0.47-0.61). Comparing the FISH results with the clinical behavior reached an overall sensitivity of 60% and a specificity of 50% (v 2 ¼ 0.25; P ¼ 0.61) for later development of metastases. Comparison of array comparative genomic hybridization data with FISH analyses did not yield significant results but array comparative genomic hybridization data demonstrated that melanocytic skin lesions with the development of metastases showed significantly more chromosomal aberrations (Po0.01) compared with melanocytic skin lesions without the development of metastases. The FISH technique with its present composition of locus-specific probes for RREB1/MYB and CCND1 did not achieve a clinically useful sensitivity and specificity. However, a reassessment of the probes and better standardization of the method may lead to a valuable diagnostic tool.

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Identification of small gains and losses in single cells after whole genome amplification on tiling oligo arrays

Cited by 65 publications

References 20 publications

Histological and genetic evidence for a variant of superficial spreading melanoma composed predominantly of large nests

Histological and genetic evidence for a variant of superficial spreading melanoma composed predominantly of large nests

Insight into the heterogeneity of breast cancer through next-generation sequencing

Classifying ambiguous melanocytic lesions with FISH and correlation with clinical long-term follow up

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