title: Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue.
abstract: Unlocking clinically translatable genomic information, including copy number alterations (CNA), from formalin-fixed paraffin-embedded (FFPE) tissue is challenging due to low yields and degraded DNA. We describe a robust, cost-effective low-coverage whole genome sequencing (LC WGS) method for CNA detection using 5 ng of FFPE-derived DNA. CN profiles using 100 ng or 5 ng input DNA were highly concordant and comparable with molecular inversion probe (MIP) array profiles. LC WGS improved CN profiles of samples that performed poorly using MIP arrays. Our technique enables identification of driver and prognostic CNAs in archival patient samples previously deemed unsuitable for genomic analysis due to DNA limitations.
authors.affiliation: Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia.|The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.
authors.forename: Tanjina
authors.initials: T
authors.lastname: Kader
authors.affiliation: The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.|Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia.
authors.forename: David L
authors.initials: DL
authors.lastname: Goode
authors.affiliation: Molecular Biomarkers and Translational Genomics Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia.
authors.forename: Stephen Q
authors.initials: SQ
authors.lastname: Wong
authors.affiliation: Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia.
authors.forename: Jacquie
authors.initials: J
authors.lastname: Connaughton
authors.affiliation: Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia.
authors.forename: Simone M
authors.initials: SM
authors.lastname: Rowley
authors.affiliation: LifePool, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia.
authors.forename: Lisa
authors.initials: L
authors.lastname: Devereux
authors.affiliation: Pathology, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia.
authors.forename: David
authors.initials: D
authors.lastname: Byrne
authors.affiliation: Pathology, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia.
authors.forename: Stephen B
authors.initials: SB
authors.lastname: Fox
authors.affiliation: Molecular Genomics Core Facility, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia.
authors.forename: Gisela
authors.initials: G
authors.lastname: Mir Arnau
authors.affiliation: The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.|Molecular Imaging and Targeted Therapeutics Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia.|Department of Pathology, University of Melbourne, Parkville, VIC, Australia.
authors.forename: Richard W
authors.initials: RW
authors.lastname: Tothill
authors.affiliation: Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia.|The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.|Department of Pathology, University of Melbourne, Parkville, VIC, Australia.
authors.forename: Ian G
authors.initials: IG
authors.lastname: Campbell
authors.affiliation: Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia. kylie.gorringe@petermac.org.|The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia. kylie.gorringe@petermac.org.|Department of Pathology, University of Melbourne, Parkville, VIC, Australia. kylie.gorringe@petermac.org.
authors.forename: Kylie L
authors.initials: KL
authors.lastname: Gorringe
mesh_terms: D001943:Breast Neoplasms / Q000473:pathology; D015266:Carcinoma, Merkel Cell / Q000473:pathology; D045744:Cell Line, Tumor; D015331:Cohort Studies; D003362:Cost-Benefit Analysis; D004247:DNA / Q000032:analysis*; D056915:DNA Copy Number Variations; D004260:DNA Repair; D005260:Female; D005557:Formaldehyde / Q000737:chemistry*; D018628:Gene Dosage; D015723:Gene Library; D015894:Genome, Human; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D010232:Paraffin / Q000737:chemistry; D020641:Polymorphism, Single Nucleotide; D011379:Prognosis; D017422:Sequence Analysis, DNA
chemical_list: D005557:Formaldehyde; D010232:Paraffin; D004247:DNA
keywords: Copy number; Formalin-fixed paraffin-embedded (FFPE); Low coverage whole genome sequencing (LC WGS); Low-input DNA; Next generation sequencing