Study protocol: Whole genome sequencing Implementation in standard Diagnostics for Every cancer patient (WIDE)

Abstract Background ‘Precision oncology’ can ensure the best suitable treatment at the right time by tailoring treatment towards individual patient and comprehensive tumour characteristics. In current molecular pathology, diagnostic tests which are part of the standard of care (SOC) only cover a limited part of the spectrum of genomic changes, and often are performed in an iterative way. This occurs at the expense of valuable patient time, available tissue sample, and interferes with ‘first time right’ treatment decisions. Whole Genome Sequencing (WGS) captures a near complete view of genomic characteristics of a tumour in a single test. Moreover, WGS facilitates faster implementation of new treatment relevant biomarkers. At present, WGS mainly has been applied in study settings, but its performance in a routine diagnostic setting remains to be evaluated. The WIDE study aims to investigate the feasibility and validity of WGS-based diagnostics in clinical practice. Methods 1200 consecutive patients in a single comprehensive cancer centre with (suspicion of) a metastasized solid tumour will be enrolled with the intention to analyse tumour tissue with WGS, in parallel to SOC diagnostics. Primary endpoints are (1) feasibility of implementation of WGS-based diagnostics into routine clinical care and (2) clinical validation of WGS by comparing identification of treatment-relevant variants between WGS and SOC molecular diagnostics. Secondary endpoints entail (1) added clinical value in terms of additional treatment options and (2) cost-effectiveness of WGS compared to SOC diagnostics through a Health Technology Assessment (HTA) analysis. Furthermore, the (3) perceived impact of WGS-based diagnostics on clinical decision making will be evaluated through questionnaires. The number of patients included in (experimental) therapies initiated based on SOC or WGS diagnostics will be reported with at least 3 months follow-up. The clinical efficacy is beyond the scope of WIDE. Key performance indicators will be evaluated after every 200 patients enrolled, and procedures optimized accordingly, to continuously improve the diagnostic performance of WGS in a routine clinical setting. Discussion WIDE will yield the optimal conditions under which WGS can be implemented in a routine molecular diagnostics setting and establish the position of WGS compared to SOC diagnostics in routine clinical care.

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Clinical Impact of Prospective Whole Genome Sequencing in Sarcoma Patients

Cancers ◽

10.3390/cancers14020436 ◽

2022 ◽

Vol 14 (2) ◽

pp. 436

Author(s):

Luuk J. Schipper ◽

Kim Monkhorst ◽

Kris G. Samsom ◽

Linda J.W. Bosch ◽

Petur Snaebjornsson ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Large Scale ◽

Clinical Decision Making ◽

Therapeutic Potential ◽

Treatment Plan ◽

Clinical Care ◽

Unmet Need ◽

Whole Genome ◽

Tertiary Referral Center

With more than 70 different histological sarcoma subtypes, accurate classification can be challenging. Although characteristic genetic events can largely facilitate pathological assessment, large-scale molecular profiling generally is not part of regular diagnostic workflows for sarcoma patients. We hypothesized that whole genome sequencing (WGS) optimizes clinical care of sarcoma patients by detection of diagnostic and actionable genomic characteristics, and of underlying hereditary conditions. WGS of tumor and germline DNA was incorporated in the diagnostic work-up of 83 patients with a (presumed) sarcomas in a tertiary referral center. Clinical follow-up data were collected prospectively to assess impact of WGS on clinical decision making. In 12/83 patients (14%), the genomic profile led to revision of cancer diagnosis, with change of treatment plan in eight. All twelve patients had undergone multiple tissue retrieval procedures and immunohistopathological assessments by regional and expert pathologists prior to WGS analysis. Actionable biomarkers with therapeutic potential were identified for 30/83 patients. Pathogenic germline variants were present in seven patients. In conclusion, unbiased genomic characterization with WGS identifies genomic biomarkers with direct clinical implications for sarcoma patients. Given the diagnostic complexity and high unmet need for new treatment opportunities in sarcoma patients, WGS can be an important extension of the diagnostic arsenal of pathologists.

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Whole-genome sequencing

Practical Neurology ◽

10.1136/practneurol-2020-002561 ◽

2021 ◽

pp. practneurol-2020-002561

Author(s):

Huw R Morris ◽

Henry Houlden ◽

James Polke

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genetic Variants ◽

Genetic Disease ◽

Large Scale ◽

Clinical Care ◽

Whole Genome ◽

Routine Clinical Care ◽

Human Genomes ◽

Neurology Clinic

The costs of whole-genome sequencing have rapidly decreased, and it is being increasingly deployed in large-scale clinical research projects and introduced into routine clinical care. This will lead to rapid diagnoses for patients with genetic disease but also introduces uncertainty because of the diversity of human genomes and the potential difficulties in annotating new genetic variants for individual patients and families. Here we outline the steps in organising whole-genome sequencing for patients in the neurology clinic and emphasise that close liaison between the clinician and the laboratory is essential.

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Whole-genome sequencing to improve sarcoma diagnosis and patient care.

Journal of Clinical Oncology ◽

10.1200/jco.2021.39.15_suppl.11540 ◽

2021 ◽

Vol 39 (15_suppl) ◽

pp. 11540-11540

Author(s):

Luuk J. Schipper ◽

Kim Monkhorst ◽

Kris Samsom ◽

Petur Snaebjornsson ◽

Hester Van Boven ◽

...

Keyword(s):

Decision Making ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Large Scale ◽

Clinical Decision Making ◽

Therapeutic Potential ◽

Clinical Care ◽

Unmet Need ◽

Clinical Decision ◽

Whole Genome

11540 Background: With more than 70 different histological subtypes, accurate classification sarcomas is challenging. Although pathognomonic genetic events aid accurate classification, large-scale molecular profiling is generally not incorporated in regular diagnostic workflows for sarcoma patients. We hypothesized that whole genome sequencing (WGS) optimizes clinical care of sarcoma patients by detection of pathognomonic and actionable variants, and of underlying hereditary conditions. Methods: WGS of tumor and germline DNA was incorporated in the diagnostic work-up of 83 patients with a (presumed) sarcoma as part of the WIDE (Whole genome sequencing Implementation in standard Diagnostics for Every cancer patient) study in a tertiary referral center. WGS results were reported back to the pathologist and treating clinician. Clinical follow-up data were collected prospectively to assess impact of WGS on clinical decision making. Results: WGS analysis had impact on multiple levels. First, in 14% of cases (12/83 patients), the genomic profile led to a revision of the diagnosis (table). All patients had undergone multiple diagnostic procedures (mean number: 4) and pathologist assessments (mean: 6) before WGS analysis was performed. Secondly, actionable biomarkers with therapeutic potential were detected for 36/83 patients and finally, 8 pathogenic germline variants were present. Taken together, WGS had implications for clinical decision making in 52% of patients with (presumed) sarcomas. Conclusions: WGS is an important extension of the diagnostic arsenal of pathologists and has contributed to change of care in 52% of patients with sarcomas. Given the diagnostic complexity and high unmet need for new treatment opportunities in sarcomas we advocate the use of WGS for sarcoma patients early in the disease course. Clinical trial information: NL68609.031.18. [Table: see text]

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Clinical utility of whole-genome sequencing in precision oncology

Seminars in Cancer Biology ◽

10.1016/j.semcancer.2021.06.018 ◽

2021 ◽

Author(s):

Richard Rosenquist ◽

Edwin Cuppen ◽

Reinhard Buettner ◽

Carlos Caldas ◽

Helene Dreau ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Clinical Utility ◽

Precision Oncology ◽

Whole Genome

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A combined RNA-seq and whole genome sequencing approach for identification of non-coding pathogenic variants in single families

Human Molecular Genetics ◽

10.1093/hmg/ddaa016 ◽

2020 ◽

Vol 29 (6) ◽

pp. 967-979 ◽

Cited By ~ 6

Author(s):

Revital Bronstein ◽

Elizabeth E Capowski ◽

Sudeep Mehrotra ◽

Alex D Jansen ◽

Daniel Navarro-Gomez ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genetic Diagnosis ◽

Genetic Diagnostics ◽

Whole Genome ◽

Unique Challenge ◽

Coding Regions ◽

Pathogenic Variants ◽

Number Of Patients ◽

Coding Variants

Abstract Inherited retinal degenerations (IRDs) are at the focus of current genetic therapeutic advancements. For a genetic treatment such as gene therapy to be successful, an accurate genetic diagnostic is required. Genetic diagnostics relies on the assessment of the probability that a given DNA variant is pathogenic. Non-coding variants present a unique challenge for such assessments as compared to coding variants. For one, non-coding variants are present at much higher number in the genome than coding variants. In addition, our understanding of the rules that govern the non-coding regions of the genome is less complete than our understanding of the coding regions. Methods that allow for both the identification of candidate non-coding pathogenic variants and their functional validation may help overcome these caveats allowing for a greater number of patients to benefit from advancements in genetic therapeutics. We present here an unbiased approach combining whole genome sequencing (WGS) with patient-induced pluripotent stem cell (iPSC)-derived retinal organoids (ROs) transcriptome analysis. With this approach, we identified and functionally validated a novel pathogenic non-coding variant in a small family with a previously unresolved genetic diagnosis.

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Cell-free tumour DNA analysis detects copy number alterations in gastro-oesophageal cancer patients

PLoS ONE ◽

10.1371/journal.pone.0245488 ◽

2021 ◽

Vol 16 (2) ◽

pp. e0245488

Author(s):

Karin Wallander ◽

Jesper Eisfeldt ◽

Mats Lindblad ◽

Daniel Nilsson ◽

Kenny Billiau ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Oesophageal Cancer ◽

Copy Number ◽

Dna Analysis ◽

Tissue Sample ◽

Whole Genome ◽

Copy Number Alterations ◽

Plasma Dna ◽

Low Coverage

Background Analysis of cell-free tumour DNA, a liquid biopsy, is a promising biomarker for cancer. We have performed a proof-of principle study to test the applicability in the clinical setting, analysing copy number alterations (CNAs) in plasma and tumour tissue from 44 patients with gastro-oesophageal cancer. Methods DNA was isolated from blood plasma and a tissue sample from each patient. Array-CGH was applied to the tissue DNA. The cell-free plasma DNA was sequenced by low-coverage whole-genome sequencing using a clinical pipeline for non-invasive prenatal testing. WISECONDOR and ichorCNA, two bioinformatic tools, were used to process the output data and were compared to each other. Results Cancer-associated CNAs could be seen in 59% (26/44) of the tissue biopsies. In the plasma samples, a targeted approach analysing 61 regions of special interest in gastro-oesophageal cancer detected cancer-associated CNAs with a z-score >5 in 11 patients. Broadening the analysis to a whole-genome view, 17/44 patients (39%) had cancer-associated CNAs using WISECONDOR and 13 (30%) using ichorCNA. Of the 26 patients with tissue-verified cancer-associated CNAs, 14 (54%) had corresponding CNAs in plasma. Potentially clinically actionable amplifications overlapping the genes VEGFA, EGFR and FGFR2 were detected in the plasma from three patients. Conclusions We conclude that low-coverage whole-genome sequencing without prior knowledge of the tumour alterations could become a useful tool for cell-free tumour DNA analysis of total CNAs in plasma from patients with gastro-oesophageal cancer.

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OXA-900, a Novel OXA Sub-Family Carbapenemase Identified in Citrobacter freundii, Evades Detection by Commercial Molecular Diagnostics Tests

Microorganisms ◽

10.3390/microorganisms9091898 ◽

2021 ◽

Vol 9 (9) ◽

pp. 1898

Author(s):

Sammy Frenk ◽

Nadya Rakovitsky ◽

Hadas Kon ◽

Reut Rov ◽

Shirin Abramov ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Molecular Diagnostics ◽

Target Gene ◽

Whole Genome ◽

Citrobacter Freundii ◽

The Novel ◽

Class D ◽

Marine Environmental ◽

Wide Dissemination

Using whole-genome sequencing and cloning of the target gene, we identified blaOXA-900 carbapenemase, a novel blaOXA belonging to a distant and distinct sub-family of blaOXA-48-like. The plasmid-mediated gene was identified in a C. freundii isolate with elevated carbapenem MICs that evaded detection by commercial DNA-based methods. The novel gene, an OXA-48 family carbapenem-hydrolyzing class D β-lactamase, OXA-900, likely originates from marine environmental Shewanella. Since this plasmid-mediated gene has entered a member of the Enterobacterales and evades detection by commonly used tests, it may gain wide dissemination among Enterobacterales.

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Review of 200 consecutive patients with mutation profiling in a lung cancer individualized medicine clinic.

Journal of Clinical Oncology ◽

10.1200/jco.2013.31.15_suppl.e19013 ◽

2013 ◽

Vol 31 (15_suppl) ◽

pp. e19013-e19013

Author(s):

Michael Asiedu ◽

Julian R. Molina ◽

Jin Jen ◽

Jin Sung Jang ◽

Anja Roden ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Individualized Medicine ◽

Treatment Decisions ◽

Mutation Testing ◽

Egfr Mutations ◽

Driver Gene ◽

Whole Genome ◽

Number Of Patients ◽

Mutation Profiling

e19013 Background: Mutation profiling to assess for potentially druggable mutations in NSCLC is being offered at an increasing number of cancer centers throughout North America and internationally. Although data continue to accumulate for the potential value of mutation testing in designing chemotherapeutic regimens, the treatment impact of obtaining information beyond assessment of EGFR and ALK status remains unclear. How best to obtain and clinically utilize these data, including information from exome and whole genome sequencing, also remains unclear. Methods: Patients were reviewed electronically in a multidisciplinary conference regarding indications for testing and results of mutation profiling from various methods, including the mass-spec based LungCarta test, targeted NexGen sequencing, exome, and whole genome sequencing. Outcomes of the multidisciplinary review were communicated back to treating physicians. Results: Mutation testing was performed on 200 patients using a variety of approaches. The majority (>150) were surgically resected stage I and II tumors. Mutations in at least 1 major cancer driver gene, including EGFR, KRAS, MET, BRAF and PIK3CA, were found in 47% of all patients tested. EGFR mutations were present in 14.8% of patients tested, KRAS 21.3%, BRAF 2.6%, PIK3CA 3.2%, and MET 4.5%. A total of 8 patients underwent either exome or whole genome sequencing. A limited number of patients (<10) had mutation results that impacted treatment decisions from this cohort. Conclusions: Mutation profiling can influence treatment decisions in NSCLC, but at a low frequency. The role of exome and or whole genome sequencing for patients with NSCLC is evolving and remains undefined.

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