Precision medicine in cancer: challenges and recommendations from an EU-funded cervical cancer biobanking study

Samuels, Sanne; Bálint, Balázs; Leyen, Heiko von der; Hupé, Philippe; Koning, Leanne de; Kamoun, Choumouss; Rondof, Windy; Wittkop, Ulrike; Bagrintseva, Ksenia; Popović, Marina; Kereszt, A.; Berns, Els M.J.J.; Kenter, Gemma G.; Jordanova, Ekaterina S.; Kamal, Maud; Scholl, Susy

doi:10.1038/bjc.2016.340

Cited by 17 publications

(22 citation statements)

References 45 publications

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“…The need is driven by immense challenges, such as mechanistically understanding and curing cancer (NIH et al . 2016; S amuels et al . 2016), mapping genotypes to phenotypes in personalized medicine and elsewhere (R oden 2011; M ackay et al .…”

Section: Discussionmentioning

confidence: 99%

“…Efficiently constructing many VBIRs like FlyClockbase is necessary for integrating biological information at the scale needed for current research. The need is driven by immense challenges, such as mechanistically understanding and curing cancer (NIH et al 2016; S amuels et al 2016), mapping genotypes to phenotypes in personalized medicine and elsewhere (R oden 2011; M ackay et al 2012; K irk et al 2015; A shley 2016), or the evolutionary systems biology goal of mechanistically predicting realistic fitness landscapes (L oewe 2016). Irrespective of whether it is possible to realize these broader visions, any serious attempt will require the diligent construction of many interoperable VBIRs that connect well to state of the art expertise, and advance biological research in the relevant areas.…”

Section: Discussionmentioning

confidence: 99%

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FlyClockbase: Importance of Biological Model Curation for Analyzing Variability in the Circadian Clock of Drosophila melanogaster by Integrating Time Series from 25 Years of Research

Scheuer

Hanlon

Dresel

et al. 2017

Preprint

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General Article SummarySubstantial biological model curation was essential for identifying differences in peak 23 time variance of the clock-proteins 'PERIOD' and 'TIMELESS', which probably stem 24 from differences in phosphorylation-network complexity. 25 We repeatedly encountered systemic limitations of contemporary data analysis 26 strategies in our work on circadian clocks. Thus, we used it as an opportunity for 27 composing a panoramic view of the broader challenges in biological model curation, 28 which are likely to increase as biologists aim to integrate all existing expertise in order to 29 address diverse grand challenges. We developed and tested a trans-disciplinary 30 research workflow, which enables biologists and compiler-architects to define biology-31 friendly compilers for efficiently constructing and maintaining Versioned Biological 32 Information Resources (VBIRs). We report insights gleaned from our practical clock 33 research that are essential for defining a VBIRs infrastructure, which improves the 34 efficiency of biological model curation to the point where it can be democratized. . CC-BY 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/099192 doi: bioRxiv preprint first posted online Jan. 9, 2017;. CC-BY 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/099192 doi: bioRxiv preprint first posted online Jan. 9, 2017;. CC-BY 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/099192 doi: bioRxiv preprint first posted online Jan. 9, 2017;. CC-BY 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/099192 doi: bioRxiv preprint first posted online Jan. 9, 2017;. CC-BY 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/099192 doi: bioRxiv preprint first posted online Jan. 9, 2017;. CC-BY 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/099192 doi: bioRxiv preprint first posted online Jan. 9, 2017;. CC-BY 4.0 International license It ...

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

FlyClockbase: Importance of Biological Model Curation for Analyzing Variability in the Circadian Clock of Drosophila melanogaster by Integrating Time Series from 25 Years of Research

Scheuer

Hanlon

Dresel

et al. 2017

Preprint

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“…The mouse papillomavirus MmuPV has also been used recently to study the influence of immunological factors on HPV infection and associated lesions, and transgenic models of disease have provided insights into the influence of external factors such as hormones and UV irradiation transformation and disease. Continued research in this area is thus welcome [61]. …”

Section: Basic Science and Biobankingmentioning

confidence: 99%

“…Certainly, given the increase in self-sampling in the current screening programmes, biobanks that contain a heterogeneity of both clinician and self-taken samples would be valuable including those from studies where matched samples (clinician vs. self) have been collected. International efforts to support both hard protocols (specimen manipulation) and soft protocols (linkage and governance considerations) for prospective biobanking could be game changing with respect to the speed of how new developments are assessed and implemented [61]. …”

Section: Basic Science and Biobankingmentioning

confidence: 99%

Human Papillomavirus Research: Where Should We Place Our Bets?

2019

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Background: Massive strides have been made with respect to primary and secondary prevention of human papillomavirus (HPV)-associated disease as a result of prophylactic vaccination and cervical screening based on molecular HPV testing. However, cervical cancer continues to be an important clinical and societal burden. Additionally, other HPV-associated cancers, for which there are no screening programmes, are rising. Finally, the optimal combination of vaccination and screening strategies will require careful thinking. Considering this unprecedented and important time, we were keen to solicit the views of the expert community to determine what they perceived were the key priorities for HPV research. Our objective was to identify consensus and key priorities for HPV-based research through provision of a questionnaire disseminated to a multidisciplinary group of key opinion leaders (KOLs). Summary: A structured survey composed of 46 HPV research “categories” was sent to 73 KOLs who were invited to “rank” the categories according to priority. The invitees represented clinical and public health disciplines as well as basic scientists. Scores were weighted according to the number of responses. Invitees also had the opportunity to comment on barriers to the research and suggest other research areas that required attention not reflected in the survey. We received 29 responses in total; overall, the 3 highest-ranked categories were “optimal cervical screening in low and middle-income countries (LMICs),” “primary disease prevention in LMICs” and “impact of vaccine on HPV infection and associated disease.” “HPV and the microbiome” and “mechanisms of transformation” were the highest-ranked categories with respect to basic research. Consistent barriers to research were around governance on the use of samples and data and funding, particularly in an era of vaccination. Key Messages: Research to support the management of disease in LMICs is clearly perceived as a priority in the international community in addition to other diverse areas which necessitate an improved basic understanding of viral mechanisms and interactions. International, multidisciplinary efforts which articulate the broader HPV research agenda will be important when seeking funding in addition to international endeavours to support the efficient use of existing samples and cohorts to facilitate such research.

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“…Guidelines or publications focused on the responsible application of large-scale genetic sequencing are mostly 406 S Vos et al genome sequencing (WES, WGS) and not on targeted (cancer) gene panels as used generally in MP practice [7,22,23]. As a result, large differences have been shown in the process of tumor sequencing analysis between laboratories [4,[24][25][26].…”

Section: Introductionmentioning

confidence: 99%

Ethical considerations for modern molecular pathology

Vos

Diest

Ausems

et al. 2018

The Journal of Pathology

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Molecular pathology is becoming an increasingly important discipline in oncology as molecular tumor characteristics will increasingly determine targeted clinical cancer care. In recent years, many technological advances have taken place that contributed to the development of molecular pathology. However, attention to ethical aspects has been lagging behind as illustrated by the lack of publications or professional guidelines. Existing guidelines or publications on ethical aspects of DNA sequencing are mostly aimed at germline or tumor sequencing in clinical genetics or biomedical research settings. As a result, large differences have been demonstrated in the process of tumor sequencing analysis between laboratories. In this perspective we discuss the ethical issues to consider in molecular pathology by following the process of tumor DNA sequencing analysis from the preanalytical to postanalytical phase. For the successful and responsible use of DNA sequencing in clinical cancer care, several moral requirements must be met, for example, those related to the interpretation and returning of genetic results, informed consent, and the retrospective as well as future use of genetic data for biomedical research. Many ethical issues are new to pathology or more stringent than in current practice because DNA sequencing could yield sensitive and potentially relevant data, such as clinically significant unsolicited findings. The context of molecular pathology is unique and complex, but many issues are similar to those applicable to clinical genetics. As such, existing scholarship in this discipline may be translated to molecular pathology with some adaptations and could serve as a basis for guideline development. For responsible use and further development of clinical cancer care, we recommend that pathologists take responsibility for the adequate use of molecular analyses and be fully aware and capable of dealing with the diverse, complex, and challenging aspects of tumor DNA sequencing, including its ethical issues. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

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Precision medicine in cancer: challenges and recommendations from an EU-funded cervical cancer biobanking study

Cited by 17 publications

References 45 publications

FlyClockbase: Importance of Biological Model Curation for Analyzing Variability in the Circadian Clock of Drosophila melanogaster by Integrating Time Series from 25 Years of Research

FlyClockbase: Importance of Biological Model Curation for Analyzing Variability in the Circadian Clock of Drosophila melanogaster by Integrating Time Series from 25 Years of Research

Human Papillomavirus Research: Where Should We Place Our Bets?

Ethical considerations for modern molecular pathology

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