Shallow whole genome sequencing for robust copy number profiling of formalin-fixed paraffin-embedded breast cancers.

Pathology archives with linked clinical data are an invaluable resource for translational research, with the limitation that most cancer samples are formalin-fixed paraffin-embedded (FFPE) tissues. Therefore, FFPE tissues are an important resource for genomic profiling studies but are under-utilised...

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Detalles Bibliográficos
Autores: Chin, Suet-Feung, Santonja, Angela, Grzelak, Marta, Ahn, Soomin, Sammut, Stephen-John, Clifford, Harry, Rueda, Oscar M, Pugh, Michelle, Goldgraben, Mae A, Bardwell, Helen A, Cho, Eun Yoon, Provenzano, Elena, Rojo, Federico, Alba, Emilio, Caldas, Carlos
Tipo de recurso: artículo
Fecha de publicación:2018
País:España
Institución:Instituto de Salud Carlos III (ISCIII)
Repositorio:Repisalud
Idioma:inglés
OAI Identifier:oai:repisalud.isciii.es:20.500.12105/17584
Acceso en línea:http://hdl.handle.net/20.500.12105/17584
Access Level:acceso abierto
Palabra clave:Copy number (CN) and breast cancer
Formalin-fixed paraffin-embedded (FFPE)
Shallow whole genome sequencing (sWGS)
Biomarkers, Tumor
Breast Neoplasms
Case-Control Studies
DNA
DNA Copy Number Variations
Female
Formaldehyde
Gene Expression Profiling
Genomics
High-Throughput Nucleotide Sequencing
Humans
Neoplasm Invasiveness
Paraffin Embedding
Sequence Analysis, DNA
Tissue Fixation
Whole Genome Sequencing
Descripción
Sumario:Pathology archives with linked clinical data are an invaluable resource for translational research, with the limitation that most cancer samples are formalin-fixed paraffin-embedded (FFPE) tissues. Therefore, FFPE tissues are an important resource for genomic profiling studies but are under-utilised due to the low amount and quality of extracted nucleic acids. We profiled the copy number landscape of 356 breast cancer patients using DNA extracted FFPE tissues by shallow whole genome sequencing. We generated a total of 491 sequencing libraries from 2 kits and obtained data from 98.4% of libraries with 86.4% being of good quality. We generated libraries from as low as 3.8 ng of input DNA and found that the success was independent of input DNA amount and quality, processing site and age of the fixed tissues. Since copy number alterations (CNA) play a major role in breast cancer, it is imperative that we are able to use FFPE archives and we have shown in this study that sWGS is a robust method to do such profiling.

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