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Detection of structural variants in circulating cell-free DNA from sarcoma patients using next generation sequencing

Circulating tumour DNA (ctDNA) analysis using next generation sequencing (NGS) is being implemented in clinical practice for treatment stratification and disease monitoring. However, using ctDNA to detect structural variants, a common occurrence in sarcoma, can be challenging. Here, we use a sarcoma...

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Main Authors: McConnell, Lauren (Author) , Gazdova, Jana (Author) , Beck-Ringger, Katja (Author) , Srivastava, Shambhavi (Author) , Harewood, Louise (Author) , Stewart, Peter (Author) , Hübschmann, Daniel (Author) , Stenzinger, Albrecht (Author) , Glimm, Hanno (Author) , Heilig, Christoph E. (Author) , Fröhling, Stefan (Author) , Gonzalez, David (Author)
Format: Article (Journal)
Language:English
Published: 3 December 2020
In: Cancer research
Year: 2020, Volume: 12, Issue: 12, Pages: 1-9
ISSN:1538-7445
DOI:10.3390/cancers12123627
Online Access:Verlag, lizenzpflichtig, Volltext: https://doi.org/10.3390/cancers12123627
Verlag, lizenzpflichtig, Volltext: https://www.mdpi.com/2072-6694/12/12/3627
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Author Notes:Lauren Mc Connell, Jana Gazdova, Katja Beck, Shambhavi Srivastava, Louise Harewood, JP Stewart, Daniel Hübschmann, Albrecht Stenzinger, Hanno Glimm, Christoph E. Heilig, Stefan Fröhling and David Gonzalez
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Summary:Circulating tumour DNA (ctDNA) analysis using next generation sequencing (NGS) is being implemented in clinical practice for treatment stratification and disease monitoring. However, using ctDNA to detect structural variants, a common occurrence in sarcoma, can be challenging. Here, we use a sarcoma-specific targeted NGS panel to identify translocations and copy number variants in a cohort of 12 tissue specimens and matched circulating cell-free DNA (cfDNA) from soft tissue sarcoma patients, including alveolar rhabdomyosarcoma (n = 2), Ewing’s Sarcoma (n = 2), synovial sarcoma (n = 2), extraskeletal myxoid chondrosarcoma (n = 1), clear cell sarcoma (n = 1), undifferentiated round cell sarcoma (n = 1), myxoid liposarcoma (n = 1), alveolar soft part cell sarcoma (n = 1) and dedifferentiated liposarcoma (n = 1). Structural variants were detected in 11/12 (91.6%) and 6/12 (50%) of tissue and plasma samples, respectively. Structural variants were detected in cfDNA at variant allele frequencies >0.2% with an average sequencing depth of 1026×. The results from this cohort show clinical potential for using NGS in ctDNA to aid in the diagnosis and clinical monitoring of sarcomas and warrant additional studies in larger cohorts.
Item Description:Gesehen am 03.03.2022
Physical Description:Online Resource
ISSN:1538-7445
DOI:10.3390/cancers12123627

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