Clinical whole-genome sequencing from routine formalin-fixed, paraffin-embedded specimens: pilot study for the 100,000 Genomes Project

Pauline Robbe; Niko Popitsch; Samantha J L Knight; Pavlos Antoniou; Jennifer Becq; Miao He; Alexander Kanapin; Anastasia Samsonova; Dimitrios V Vavoulis; Mark T Ross; Zoya Kingsbury; Maite Cabes; Sara D C Ramos; Suzanne Page; Helene Dreau; Kate Ridout; Louise J Jones; Alice Tuff-Lacey; Shirley Henderson; Joanne Mason; Francesca M Buffa; Clare Verrill; David Maldonado-Perez; Ioannis Roxanis; Elena Collantes; Lisa Browning; Sunanda Dhar; Stephen Damato; Susan Davies; Mark Caulfield; David R Bentley; Jenny C Taylor; Clare Turnbull; Anna Schuh; 100,000 Genomes Project

doi:10.1038/gim.2017.241

Clinical whole-genome sequencing from routine formalin-fixed, paraffin-embedded specimens: pilot study for the 100,000 Genomes Project

Genet Med. 2018 Oct;20(10):1196-1205. doi: 10.1038/gim.2017.241. Epub 2018 Feb 1.

Authors

Pauline Robbe¹, Niko Popitsch², Samantha J L Knight², Pavlos Antoniou³, Jennifer Becq⁴, Miao He⁴, Alexander Kanapin⁵, Anastasia Samsonova⁵, Dimitrios V Vavoulis³, Mark T Ross⁴, Zoya Kingsbury⁴, Maite Cabes⁶, Sara D C Ramos⁶, Suzanne Page⁶, Helene Dreau⁶, Kate Ridout³, Louise J Jones⁷, Alice Tuff-Lacey⁷, Shirley Henderson⁶, Joanne Mason⁷, Francesca M Buffa⁸, Clare Verrill⁹, David Maldonado-Perez¹⁰, Ioannis Roxanis¹⁰, Elena Collantes¹⁰, Lisa Browning¹⁰, Sunanda Dhar¹⁰, Stephen Damato¹⁰, Susan Davies¹⁰, Mark Caulfield^{7

11}, David R Bentley⁴, Jenny C Taylor^{2

12}, Clare Turnbull^{7

10

13}, Anna Schuh^{6

12

14}; 100,000 Genomes Project

Affiliations

¹ Oxford Molecular Diagnostics Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, UK. [email protected].
² Wellcome Trust Centre of Human Genetics, University of Oxford, Old Road Campus Research Building, Oxford, UK.
³ Oxford Molecular Diagnostics Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
⁴ Illumina Cambridge Ltd., Chesterford Research Park, Saffron Walden, UK.
⁵ Department of Oncology, University of Oxford, Oxford, UK.
⁶ Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK.
⁷ Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK.
⁸ Computational Biology and Integrative Genomics, Department of Oncology, University of Oxford, Oxford, UK.
⁹ Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford, UK.
¹⁰ Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK.
¹¹ NIHR Biomedical Research Centre at Barts Health NHS Trust, London, UK.
¹² NIHR Comprehensive Biomedical Research Centre, Oxford, UK.
¹³ Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK.
¹⁴ Oxford Molecular Diagnostics Centre, Department of Oncology, University of Oxford, Oxford, UK.

Abstract

Purpose: Fresh-frozen (FF) tissue is the optimal source of DNA for whole-genome sequencing (WGS) of cancer patients. However, it is not always available, limiting the widespread application of WGS in clinical practice. We explored the viability of using formalin-fixed, paraffin-embedded (FFPE) tissues, available routinely for cancer patients, as a source of DNA for clinical WGS.

Methods: We conducted a prospective study using DNAs from matched FF, FFPE, and peripheral blood germ-line specimens collected from 52 cancer patients (156 samples) following routine diagnostic protocols. We compared somatic variants detected in FFPE and matching FF samples.

Results: We found the single-nucleotide variant agreement reached 71% across the genome and somatic copy-number alterations (CNAs) detection from FFPE samples was suboptimal (0.44 median correlation with FF) due to nonuniform coverage. CNA detection was improved significantly with lower reverse crosslinking temperature in FFPE DNA extraction (80 °C or 65 °C depending on the methods). Our final data showed somatic variant detection from FFPE for clinical decision making is possible. We detected 98% of clinically actionable variants (including 30/31 CNAs).

Conclusion: We present the first prospective WGS study of cancer patients using FFPE specimens collected in a routine clinical environment proving WGS can be applied in the clinic.

Keywords: clinical variant reporting; copy-number alteration; formalin-fixed, paraffin-embedded (FFPE); somatic variants; whole-genome sequencing.

Publication types

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

MeSH terms

DNA Copy Number Variations / genetics*
Decision Making
Female
Genome, Human / genetics*
Humans
Male
Neoplasms / blood
Neoplasms / genetics*
Neoplasms / pathology
Paraffin Embedding
Polymorphism, Single Nucleotide / genetics
Whole Genome Sequencing / methods*

Abstract

Publication types

MeSH terms

Grants and funding