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

Suet-Feung Chin; Angela Santonja; Marta Grzelak; Soomin Ahn; Stephen-John Sammut; Harry Clifford; Oscar M Rueda; Michelle Pugh; Mae A Goldgraben; Helen A Bardwell; Eun Yoon Cho; Elena Provenzano; Federico Rojo; Emilio Alba; Carlos Caldas

doi:10.1016/j.yexmp.2018.03.006

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

Exp Mol Pathol. 2018 Jun;104(3):161-169. doi: 10.1016/j.yexmp.2018.03.006. Epub 2018 Mar 31.

Authors

Affiliations

¹ Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK; Department of Oncology, University of Cambridge, Cambridge CB2 2QQ, UK; Cancer Research UK Cambridge Cancer Centre, Cambridge CB2 0QQ, UK. Electronic address: suet-feung.chin@cruk.cam.ac.uk.
² Medical Oncology Service, Hospital Universitario Regional y Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga (IBIMA), Málaga, Spain; Laboratorio de Biología Molecular del Cáncer, Centro de Investigaciones Médico-Sanitarias (CIMES), Universidad de Málaga, Málaga, Spain.
³ Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK.
⁴ Department of Pathology, Seoul National University Bundang Hospital, 82, Gumi-ro 173 Beon-gil, Bundang-gu, Seongnam, Gyeonggi 13620, Republic of Korea; Inivata, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
⁵ Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK; Department of Oncology, University of Cambridge, Cambridge CB2 2QQ, UK; Cancer Research UK Cambridge Cancer Centre, Cambridge CB2 0QQ, UK.
⁶ Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK; Cancer Research UK Cambridge Cancer Centre, Cambridge CB2 0QQ, UK.
⁷ Inivata UK, The Portway Building, Granta Park, Cambridge CB21 6GS, UK.
⁸ Department of Medical Genetics, University of Cambridge, Cambridge CB2 0QQ, UK.
⁹ Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, 50 Irwon-dong, Gangnam-gu, Seoul 135-710, Republic of Korea.
¹⁰ Cambridge Breast Unit, Addenbrooke's Hospital, Cambridge University Hospital NHS Foundation Trust, NIHR Cambridge Biomedical Research Centre, Cambridge CB2 2QQ, UK; Cancer Research UK Cambridge Cancer Centre, Cambridge CB2 0QQ, UK.
¹¹ Pathology Department, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain; GEICAM-Spanish Breast Cancer Research Group, Madrid, Spain.
¹² Medical Oncology Service, Hospital Universitario Regional y Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga (IBIMA), Málaga, Spain; GEICAM-Spanish Breast Cancer Research Group, Madrid, Spain; Laboratorio de Biología Molecular del Cáncer, Centro de Investigaciones Médico-Sanitarias (CIMES), Universidad de Málaga, Málaga, Spain.
¹³ Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK; Department of Oncology, University of Cambridge, Cambridge CB2 2QQ, UK; Cambridge Breast Unit, Addenbrooke's Hospital, Cambridge University Hospital NHS Foundation Trust, NIHR Cambridge Biomedical Research Centre, Cambridge CB2 2QQ, UK; Cancer Research UK Cambridge Cancer Centre, Cambridge CB2 0QQ, UK. Electronic address: carlos.caldas@cruk.cam.ac.uk.

Abstract

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.

Keywords: Copy number (CN) and breast cancer; Formalin-fixed paraffin-embedded (FFPE); Shallow whole genome sequencing (sWGS).

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Biomarkers, Tumor / genetics
Breast Neoplasms / genetics*
Breast Neoplasms / pathology
Case-Control Studies
DNA / analysis*
DNA / genetics
DNA Copy Number Variations*
Female
Formaldehyde / chemistry*
Gene Expression Profiling
Genomics
High-Throughput Nucleotide Sequencing / methods
Humans
Neoplasm Invasiveness
Paraffin Embedding / methods*
Sequence Analysis, DNA
Tissue Fixation / methods*
Whole Genome Sequencing / methods*

Substances

Biomarkers, Tumor
Formaldehyde
DNA

Abstract

Publication types

MeSH terms

Substances

Grants and funding