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Article

Large-scale analysis of whole genome sequencing data from formalin-fixed paraffin-embedded cancer specimens demonstrates preservation of clinical utility.

Nature communications - 4 Sept 2024

Basyuni Shadi, Heskin Laura, Degasperi Andrea, Black Daniella, Koh Gene C C, Chmelova Lucia, Rinaldi Giuseppe, Bell Steven, Grybowicz Louise, Elgar Greg, Memari Yasin, Robbe Pauline, Kingsbury Zoya, Caldas Carlos, Abraham Jean, Schuh Anna, Jones Louise, Tischkowitz Marc, Brown Matthew A, Davies Helen R, Nik-Zainal Serena

Abstract excerpt

Whole genome sequencing (WGS) provides comprehensive, individualised cancer genomic information. However, routine tumour biopsies are formalin-fixed and paraffin-embedded (FFPE), damaging DNA, historically limiting their use in WGS. Here we analyse FFPE cancer WGS datasets from England's 100,000 Genomes Project, comparing 578 FFPE samples with 11,014 fresh frozen (FF) samples across multiple tumour types. We use...

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Artifacts
Formaldehyde
Genome, Human
Genomics

Methodology Data sources Editorial policy Privacy About Contact Helena Bioinformatics

Paraffin Embedding

Tissue Fixation

Whole Genome Sequencing

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Identifiers

PMID: 39231944
DOI: 10.1038/s41467-024-51577-2
PMCID: PMC11374794

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