Absolute copy number fitting from shallow whole genome sequencing data

Abstract

Low-coverage or shallow whole genome sequencing (sWGS) approaches can efficiently detect somatic copy number aberrations (SCNAs) at low cost. This is clinically important for many cancers, in particular cancers with severe chromosomal instability (CIN) that frequently lack actionable point mutations and are characterised by poor disease outcome. Absolute copy number (ACN), measured in DNA copies per cancer cell, is required for meaningful comparisons between copy number states, but is challenging to estimate and in practice often requires manual curation. Using a total of 60 cancer cell lines, 148 patient-derived xenograft (PDX) and 142 clinical tissue samples, we evaluate the performance of available tools for obtaining ACN from sWGS. We provide a validated and refined tool called Rascal (relative to absolute copy number scaling) that provides improved fitting algorithms and enables interactive visualisation of copy number profiles. These approaches are highly applicable to both pre-clinical and translational research studies on SCNA-driven cancers and provide more robust ACN fits from sWGS data than currently available tools.

CNETML: Maximum likelihood inference of phylogeny from copy number profiles of spatio-temporal samples

“…In summary, it seems entirely feasible to recover the phylogeny directly from relative copy numbers, such as those from QDNAseq, when WGD is not clonal. For further validation of the inference, empirical information or methods to detect WGD [54] or call absolute copy numbers [27] from sWGS data may be used to estimate the presence of clonal WGD.…”

“…These longitudinal samples also contain temporal information that can be used to estimate node ages and mutation rates, which are important parameters in carcinogenesis. However, only a few reliable methods exist to detect CNAs from sWGS data, especially absolute copy numbers [27]. Most of the previous sample phylogeny inference methods are designed for absolute allele-specific integer copy numbers which are often called from SNP arrays and high-coverage NGS data, such as MEDICC [18], MEDICC2 [9], and PISCA [3].…”

Longitudinal monitoring of disease burden and response using ctDNA from dried blood spots in xenograft models

“…Given the high specificity and sensitivity of our approach, we were able to derive absolute copy number (ACN) data from as little as 500,000 human‐specific DBS reads using QDNAseq (Scheinin et al , 2014 ) followed by Rascal (Sauer et al , 2021 ) (Fig 1E ). The observed absolute somatic copy number aberrations (SCNAs) (Fig 1F ) and their extent were strongly correlated with sWGS of PDX tumour tissues from the same patient (Appendix Figs S2 and S3A–D ).…”

“…Tumour samples were processed following standardised operating protocols as outlined in the OV04 study design and as previously described (preprint: Sauer et al , 2021 ) before surgically engrafting into 6 to 8‐week‐old female NOD. Cg‐Prkdc scid Il2rg tm1WjI /SzJ (NSG) mice obtained from Charles River Laboratories.…”

“…All mouse work conducted was approved by and performed in accordance with the ethical regulations and guidelines of the Home Office UK and the CRUK CI Animal Welfare and Ethics Review Board (PPL number: PP7478310). Xenograft tissue processing and PDX passaging were performed as previously described (preprint: Sauer et al , 2021 ). In short, xenografting was performed either by subcutaneous surgical implantation (for first generation PDX mice) or subcutaneous injection of tumour cells from dissociated tumour tissues (for later PDX generations).…”