Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data

Gusnanto, Arief; Wood, Henry M.; Pawitan, Yudi; Rabbitts, Pamela; Berri, Stefano

doi:10.1093/bioinformatics/btr593

Cited by 157 publications

(165 citation statements)

References 22 publications

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“…Although the conducted validation steps indicate robustness of our observations, utilizing a maximum of parsimony approach has its limitations. Biology may behave differently than the simplest theorization (35), and in order to reduce the proportion of miscalled segments, we calibrated each observation to empirical data obtained from the infinium array (36). Complementary investigation using single-cell or in situ techniques could decrease the risk of false estimations and deduce the genetic overlap in polyclonal samples (21,37).…”

Section: Discussionmentioning

confidence: 99%

Spatiotemporal Heterogeneity Characterizes the Genetic Landscape of Pheochromocytoma and Defines Early Events in Tumorigenesis

Crona

Backman

Maharjan

et al. 2015

Clinical Cancer Research

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Purpose: Pheochromocytoma and paraganglioma (PPGL) patients display heterogeneity in the clinical presentation and underlying genetic cause. The degree of inter-and intratumor genetic heterogeneity has not yet been defined.Experimental Design: In PPGLs from 94 patients, we analyzed LOH, copy-number variations, and mutation status of SDHA, SDHB, SDHC, SDHD, SDHAF2, VHL, EPAS1, NF1, RET, TMEM127, MAX, and HRAS using high-density SNP array and targeted deep sequencing, respectively. Genetic heterogeneity was determined through (i) bioinformatics analysis of individual samples that estimated absolute purity and ploidy from SNP array data and (ii) comparison of paired tumor samples that allowed reconstruction of phylogenetic trees.Results: Mutations were found in 61% of the tumors and correlated with specific patterns of somatic copy-number aberrations (SCNA) and degree of nontumoral cell admixture. Intratumor genetic heterogeneity was observed in 74 of 136 samples using absolute bioinformatics estimations and in 22 of 24 patients by comparison of paired samples. In addition, a low genetic concordance was observed between paired primary tumors and distant metastases. This allowed for reconstructing the life history of individual tumors, identifying somatic mutations as well as copy-number loss of 3p and 11p (VHL subgroup), 1p (Cluster 2), and 17q (NF1 subgroup) as early events in PPGL tumorigenesis.Conclusions: Genomic landscapes of PPGL are specific to mutation subtype and characterized by genetic heterogeneity both within and between tumor lesions of the same patient.

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Section: Discussionmentioning

confidence: 99%

Spatiotemporal Heterogeneity Characterizes the Genetic Landscape of Pheochromocytoma and Defines Early Events in Tumorigenesis

Crona

Backman

Maharjan

et al. 2015

Clinical Cancer Research

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“…Discordant read pairs were extracted by alignments against the reference assembly using GSNAP (version 2012-07-20) (Wu and Nacu 2010). To detect copy number alterations, CNAnorm (Gusnanto et al 2012) was used to evaluate read depths of WGS data in 50-kb windows for each sample. Combined read depth data from 20 normal individuals of both genders were used as a control.…”

Section: Whole-genome Sequencing and Analysismentioning

confidence: 99%

“…The relationship between HPV breakpoints and predicted DNA copy number change was evaluated using CNAnorm (Gusnanto et al 2012). For this analysis, the human genome was divided into 50-kb bins.…”

Section: Analysis Of the Relationship Between Hpv Breakpoints Human mentioning

confidence: 99%

Genome-wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instability

et al. 2013

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Genomic instability is a hallmark of human cancers, including the 5% caused by human papillomavirus (HPV). Here we report a striking association between HPV integration and adjacent host genomic structural variation in human cancer cell lines and primary tumors. Whole-genome sequencing revealed HPV integrants flanking and bridging extensive host genomic amplifications and rearrangements, including deletions, inversions, and chromosomal translocations. We present a model of ''looping'' by which HPV integrant-mediated DNA replication and recombination may result in viral-host DNA concatemers, frequently disrupting genes involved in oncogenesis and amplifying HPV oncogenes E6 and E7. Our high-resolution results shed new light on a catastrophic process, distinct from chromothripsis and other mutational processes, by which HPV directly promotes genomic instability.

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“…Copy number is then inferred from the observed read counts across the genome. To compensate for technological bias, many DOC algorithms, such as CNV-seq (Xie and Tammi 2009), SegSeq (Chiang et al 2009), BIC-seq (Xi et al 2011), and CNAnorm (Gusnanto et al 2012), compare tumor signal to a normal reference signal, similar to array CGH. Commonly, a pool of different individuals is used as a normal reference DNA.…”

mentioning

confidence: 99%

DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly

et al. 2014

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Detection of DNA copy number aberrations by shallow whole-genome sequencing (WGS) faces many challenges, including lack of completion and errors in the human reference genome, repetitive sequences, polymorphisms, variable sample quality, and biases in the sequencing procedures. Formalin-fixed paraffin-embedded (FFPE) archival material, the analysis of which is important for studies of cancer, presents particular analytical difficulties due to degradation of the DNA and frequent lack of matched reference samples. We present a robust, cost-effective WGS method for DNA copy number analysis that addresses these challenges more successfully than currently available procedures. In practice, very useful profiles can be obtained with~0.13 genome coverage. We improve on previous methods by first implementing a combined correction for sequence mappability and GC content, and second, by applying this procedure to sequence data from the 1000 Genomes Project in order to develop a blacklist of problematic genome regions. A small subset of these blacklisted regions was previously identified by ENCODE, but the vast majority are novel unappreciated problematic regions. Our procedures are implemented in a pipeline called QDNAseq. We have analyzed over 1000 samples, most of which were obtained from the fixed tissue archives of more than 25 institutions. We demonstrate that for most samples our sequencing and analysis procedures yield genome profiles with noise levels near the statistical limit imposed by read counting. The described procedures also provide better correction of artifacts introduced by low DNA quality than prior approaches and better copy number data than high-resolution microarrays at a substantially lower cost.

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Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 157 publications

References 22 publications

Spatiotemporal Heterogeneity Characterizes the Genetic Landscape of Pheochromocytoma and Defines Early Events in Tumorigenesis

Spatiotemporal Heterogeneity Characterizes the Genetic Landscape of Pheochromocytoma and Defines Early Events in Tumorigenesis

Genome-wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instability

DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly

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