Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue

Kader, Tanjina; Goode, David; Wong, Stephen Q.; Connaughton, Jacquie; Rowley, Simone M.; Devereux, Lisa; Byrne, David; Fox, Stephen B.; Arnau, Gisela Mir; Tothill, Richard W.; Campbell, Ian; Gorringe, Kylie L.

doi:10.1186/s13073-016-0375-z

Cited by 43 publications

(52 citation statements)

References 25 publications

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“…In order to reduce cost lower coverage sequencing with high accuracy is desirable. Several reports have addressed low coverage sequencing strategies and have yielded high detection rates of translocations and CNA, although this was not yet done in MM [32,41,42] . The inherent problem with low coverage strategies is that small clones are missed.…”

Section: Discussionmentioning

confidence: 99%

The combination of WGS and RNA-Seq is superior to conventional diagnostic tests in multiple myeloma: Ready for prime time?

et al. 2020

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The diagnosis and risk stratification of multiple myeloma (MM) is based on clinical and cytogenetic tests. Magnetic CD138 enrichment followed by interphase FISH (fluorescence in situ hybridisation) is the gold standard to identify prognostic translocations and copy number alterations (CNA). Although clinical implications of gene expression profiling (GEP) or panel based sequencing results are evident, those tests have not yet reached routine clinical application. We set up a single workflow to analyse MM of 211 patients at first diagnosis by whole genome sequencing (WGS) and RNA-Seq and validate the results by FISH analysis. We observed a 96% concordance of FISH and WGS results when assessing translocations involving the IGH locus and an overall concordance of FISH and WGS of 92% when assessing CNA. WGS analysis resulted in the identification of 17 additional MYC-translocations that were missed by FISH analysis. RNA-Seq followed by supervised clustering grouped patients in their expected genetically defined subgroup and prompted the assessment of WGS data in cases that were not congruent with FISH. This allowed the identification of additional IGH-translocations and hyperdiploid cases. We show the reliability of WGS an RNA-Seq in a clinical setting, which is a prerequisite for a novel routine diagnostic test.

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Section: Discussionmentioning

confidence: 99%

The combination of WGS and RNA-Seq is superior to conventional diagnostic tests in multiple myeloma: Ready for prime time?

et al. 2020

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“…In the pilot study of 'Novaria', we recovered deletions with approximately threefold coverage per sample. Such low-coverage whole-genome sequencing was previously shown to be an effective means of recovering CNV in poplar, rice and Arabidopsis and has been applied for evaluation of human clinical samples Kader et al, 2016;Tan et al, 2016). In our pilot, we chose to evaluate four leaves from the 'Novaria' cultivar and four nontreated 'Grande Naine' samples.…”

Section: Discussionmentioning

confidence: 99%

Induction and recovery of copy number variation in banana through gamma irradiation and low‐coverage whole‐genome sequencing

Datta

Jankowicz-Cieślak

Nielen

et al. 2018

Plant Biotechnology Journal

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SummaryTraditional breeding methods are hindered in bananas due to the fact that major cultivars are sterile, parthenocarpic, triploid and thus clonally propagated. This has resulted in a narrow genetic base and limited resilience to biotic and abiotic stresses. Mutagenesis of in vitro propagated bananas is one method to introduce novel alleles and broaden genetic diversity. We previously established a method for the induction and recovery of single nucleotide mutations generated with the chemical mutagen EMS. However, officially released mutant banana varieties have been created using gamma rays, a mutagen that can produce large genomic insertions and deletions (indels). Such dosage mutations may be important for generating observable phenotypes in polyploids. In this study, we establish a low‐coverage whole‐genome sequencing approach in triploid bananas to recover large genomic indels caused by treatment with gamma irradiation. We first evaluated the commercially released mutant cultivar ‘Novaria’ and found that it harbours multiple predicted deletions, ranging from 0.3 to 3.8 million base pairs (Mbp). In total, predicted deletions span 189 coding regions. To evaluate the feasibility of generating and maintaining new mutations, we developed a pipeline for mutagenesis and screening for copy number variation in Cavendish bananas using the cultivar ‘Williams’. Putative mutations were recovered in 70% of lines treated with 20 Gy and 60% of the lines treated with 40 Gy. While deletion events predominate, insertions were identified in 20 Gy‐treated material. Based on these results, we believe this approach can be scaled up to support large breeding projects.

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“…CNAs were called if the log 2 ratio was ± 0.15. Blacklisted regions identified by Scheinin et al were filtered out as described previously . The fraction of the genome altered (FGA) was calculated as described in the supplementary material, Supplementary materials and methods.…”

Section: Methodsmentioning

confidence: 99%

“…CNAs were called if the log 2 ratio was ± 0.15. Blacklisted regions identified by Scheinin et al [24] were filtered out as described previously [22]. The Multipotent nature of atypical ductal hyperplasia 331 Figure 2.…”

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confidence: 99%

Atypical ductal hyperplasia is a multipotent precursor of breast carcinoma

Kader

Hill

Zethoven

et al. 2019

The Journal of Pathology

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The current model for breast cancer progression proposes independent ‘low grade (LG)‐like’ and ‘high grade (HG)‐like’ pathways but lacks a known precursor to HG cancer. We applied low‐coverage whole‐genome sequencing to atypical ductal hyperplasia (ADH) with and without carcinoma to shed light on breast cancer progression. Fourteen out of twenty isolated ADH cases harboured at least one copy number alteration (CNA), but had fewer aberrations than LG or HG ductal carcinoma in situ (DCIS). ADH carried more HG‐like CNA than LG DCIS (e.g. 8q gain). Correspondingly, 64% (7/11) of ADH cases with synchronous HG carcinoma were clonally related, similar to LG carcinoma (67%, 6/9). This study represents a significant shift in our understanding of breast cancer progression, with ADH as a common precursor lesion to the independent ‘low grade‐like’ and ‘high grade‐like’ pathways. These data suggest that ADH can be a precursor of HG breast cancer and that LG and HG carcinomas can evolve from a similar ancestor lesion. We propose that although LG DCIS may be committed to a LG molecular pathway, ADH may remain multipotent, progressing to either LG or HG carcinoma. This multipotent nature suggests that some ADH cases could be more clinically significant than LG DCIS, requiring biomarkers for personalising management. Copyright © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

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Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue

Cited by 43 publications

References 25 publications

The combination of WGS and RNA-Seq is superior to conventional diagnostic tests in multiple myeloma: Ready for prime time?

The combination of WGS and RNA-Seq is superior to conventional diagnostic tests in multiple myeloma: Ready for prime time?

Induction and recovery of copy number variation in banana through gamma irradiation and low‐coverage whole‐genome sequencing

Atypical ductal hyperplasia is a multipotent precursor of breast carcinoma

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