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Investigating the replicability of preclinical cancer biology
Replicability is an important feature of scientific research, but aspects of contemporary research culture, such as an emphasis on novelty, can make replicability seem less important than it should be. The Reproducibility Project: Cancer Biology was set up to provide evidence about the replicability of preclinical research in cancer biology by repeating selected experiments from high-impact papers. A total of 50 experiments from 23 papers were repeated, generating data about the replicability of a total of 158 effects. Most of the original effects were positive effects (136), with the rest being null effects (22). A majority of the original effect sizes were reported as numerical values (117), with the rest being reported as representative images (41). We employed seven methods to assess replicability, and some of these methods were not suitable for all the effects in our sample. One method compared effect sizes: for positive effects, the median effect size in the replications was 85% smaller than the median effect size in the original experiments, and 92% of replication effect sizes were smaller than the original. The other methods were binary – the replication was either a success or a failure – and five of these methods could be used to assess both positive and null effects when effect sizes were reported as numerical values. For positive effects, 40% of replications (39/97) succeeded according to three or more of these five methods, and for null effects 80% of replications (12/15) were successful on this basis; combining positive and null effects, the success rate was 46% (51/112). A successful replication does not definitively confirm an original finding or its theoretical interpretation. Equally, a failure to replicate does not disconfirm a finding, but it does suggest that additional investigation is needed to establish its reliability.
Journal Article
Understanding cancer
\"Once upon a time it was fair to say that most people knew little of science. After all, scientists spent years learning their job so it's clearly tough going and, by and large, the rest of the world could get by knowing nothing of superconductivity or the origins of the universe. But increasingly our daily lives have come to be dominated by science and part of that revolution has been the ever-expanding reach of television and the internet as sources of information. It's as though, unwittingly, we've all signed up to the Open University. And, it should be said, when it comes to science this has all been helped by a growing awareness amongst those in the trade that they have an obligation to let the world know how they while away their days\"-- Provided by publisher.
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Challenges for assessing replicability in preclinical cancer biology
We conducted the Reproducibility Project: Cancer Biology to investigate the replicability of preclinical research in cancer biology. The initial aim of the project was to repeat 193 experiments from 53 high-impact papers, using an approach in which the experimental protocols and plans for data analysis had to be peer reviewed and accepted for publication before experimental work could begin. However, the various barriers and challenges we encountered while designing and conducting the experiments meant that we were only able to repeat 50 experiments from 23 papers. Here we report these barriers and challenges. First, many original papers failed to report key descriptive and inferential statistics: the data needed to compute effect sizes and conduct power analyses was publicly accessible for just 4 of 193 experiments. Moreover, despite contacting the authors of the original papers, we were unable to obtain these data for 68% of the experiments. Second, none of the 193 experiments were described in sufficient detail in the original paper to enable us to design protocols to repeat the experiments, so we had to seek clarifications from the original authors. While authors were extremely or very helpful for 41% of experiments, they were minimally helpful for 9% of experiments, and not at all helpful (or did not respond to us) for 32% of experiments. Third, once experimental work started, 67% of the peer-reviewed protocols required modifications to complete the research and just 41% of those modifications could be implemented. Cumulatively, these three factors limited the number of experiments that could be repeated. This experience draws attention to a basic and fundamental concern about replication – it is hard to assess whether reported findings are credible.
Journal Article
Making sense of replications
The first results from the Reproducibility Project: Cancer Biology suggest that there is scope for improving reproducibility in pre-clinical cancer research.DOI:http://dx.doi.org/10.7554/eLife.23383.001
Journal Article
What have we learned?
As the final outputs of the Reproducibility Project: Cancer Biology are published, it is clear that preclinical research in cancer biology is not as reproducible as it should be.As the final outputs of the Reproducibility Project: Cancer Biology are published, it is clear that preclinical research in cancer biology is not as reproducible as it should be.
Journal Article
The fallopian tube as origin of ovarian cancer: Change of diagnostic and preventive strategies
Ovarian cancer is the leading cause of gynecologic cancer death in the world, and its prevention and early diagnosis remain the key to its treatment, especially for high‐grade serous carcinoma (HGSC). Accumulating epidemiological and molecular evidence has shown that HGSC originates from fallopian tube secretory cells through serous tubal intraepithelial carcinoma. Comprehensive molecular analyses and mouse studies have uncovered the key driver events for serous carcinogenesis, providing novel molecular targets. Risk‐reducing bilateral salpingo‐oophorectomy (RRSO) has been proposed to reduce the subsequent occurrence of serous carcinoma in high‐risk patients with BRCA mutations. However, there is no management strategy for isolated precursors detected at RRSO, and the role of subsequent surgery or chemotherapy in preventing serous carcinoma remains unclear. Surgical menopause due to RRSO provides a variety of problems related to patients’ quality of life, and the risks and benefits of hormone replacement are under investigation, especially for women without a previous history of breast cancer. An additional surgical option, salpingectomy with delayed oophorectomy, has been proposed to prevent surgical menopause. The number of opportunistic salpingectomies at the time of surgery for benign disease to prevent the future occurrence of HGSC has increased worldwide. Thus, the changing concept of the origin of serous carcinoma has provided us a great opportunity to develop novel diagnostic and therapeutic approaches. Accumulating epidemiological and molecular evidence has shown that high‐grade serous carcinoma originates from fallopian tube secretory cells through serous tubal intraepithelial carcinoma. The changing concept of the origin of serous carcinoma has provided us a great opportunity to develop novel diagnostic and preventive approaches.
Journal Article
The who, where and how of fusobacteria and colon cancer
The association between the bacterium Fusobacterium nucleatum and human colon cancer is more complicated than it first appeared.The association between the bacterium Fusobacterium nucleatum and human colon cancer is more complicated than it first appeared.
Journal Article
Is preclinical research in cancer biology reproducible enough?
The Reproducibility Project: Cancer Biology (RPCB) was established to provide evidence about reproducibility in basic and preclinical cancer research, and to identify the factors that influence reproducibility more generally. In this commentary we address some of the scientific, ethical and policy implications of the project. We liken the basic and preclinical cancer research enterprise to a vast 'diagnostic machine' that is used to determine which clinical hypotheses should be advanced for further development, including clinical trials. The results of the RPCB suggest that this diagnostic machine currently recommends advancing many findings that are not reproducible. While concerning, we believe that more work needs to be done to evaluate the performance of the diagnostic machine. Specifically, we believe three questions remain unanswered: how often does the diagnostic machine correctly recommend against advancing real effects to clinical testing?; what are the relative costs to society of false positive and false negatives?; and how well do scientists and others interpret the outputs of the machine?
Journal Article