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Whose sample is it anyway? Widespread misannotation of samples in transcriptomics studies.

ABSTRACT: Concern about the reproducibility and reliability of biomedical research has been rising. An understudied issue is the prevalence of sample mislabeling, one impact of which would be invalid comparisons. We studied this issue in a corpus of human transcriptomics studies by comparing the provided annotations of sex to the expression levels of sex-specific genes. We identified apparent mislabeled samples in 46% of the datasets studied, yielding a 99% confidence lower-bound estimate for all studies of 33%. In a separate analysis of a set of datasets concerning a single cohort of subjects, 2/4 had mislabeled samples, indicating laboratory mix-ups rather than data recording errors. While the number of mixed-up samples per study was generally small, because our method can only identify a subset of potential mix-ups, our estimate is conservative for the breadth of the problem. Our findings emphasize the need for more stringent sample tracking, and that re-users of published data must be alert to the possibility of annotation and labelling errors.

SUBMITTER: Toker L

PROVIDER: S-EPMC5034794 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Whose sample is it anyway? Widespread misannotation of samples in transcriptomics studies.

Toker Lilah L Feng Min M Pavlidis Paul P

F1000Research 20160830

Concern about the reproducibility and reliability of biomedical research has been rising. An understudied issue is the prevalence of sample mislabeling, one impact of which would be invalid comparisons. We studied this issue in a corpus of human transcriptomics studies by comparing the provided annotations of sex to the expression levels of sex-specific genes. We identified apparent mislabeled samples in 46% of the datasets studied, yielding a 99% confidence lower-bound estimate for all studies ...[more]

PMID: 27746907

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Project description:AIM:The aims of this literature review were to better understand the current literature about person-centred care (PCC) and identify a clear definition of the term PCC relevant to nursing practice. METHOD/DATA SOURCES:An integrative literature review was undertaken using The Cumulative Index to Nursing and Allied Health Literature (CINAHL), Medline, Scopus and Pubmed databases. The limitations were English language, full text articles published between 1998 and 2018 within Australian, New Zealand, Canada, USA, Europe, Ireland and UK were included. The international context off PCC is then specifically related to the Australian context. REVIEW METHODS:The review adopted a thematic analysis to categorise and summarise themes with reference to the concept of PCC. The review process also adhered to the Preferred Reporting System for Meta-Analysis (PRISMA) and applied the Critical Appraisal Skills Programme (CASP) tools to ensure the quality of the papers included for deeper analysis. RESULTS:While definitions of PCC do exist, there is no universally used definition within the nursing profession. This review has found three core themes which contribute to how PCC is understood and practiced, these are People, Practice and Power. This review uncovered a malalignment between the concept of PCC and the operationalisation of the term; this misalignment was discovered at both the practice level, and at the micro, meso and micro levels of the healthcare service. CONCLUSION:The concept of PCC is well known to nurses, yet ill-defined and operationalised into practice. PCC is potentially hindered by its apparent rhetorical nature, and further investigation of how PCC is valued and operationalised through its measurement and reported outcomes is needed. Investigation of the literature found many definitions of PCC, but no one universally accepted and used definition. Subsequently, PCC remains conceptional in nature, leading to disparity between how it is interpreted and operationalised within the healthcare system and within nursing services.

Project description:Social psychologists have not fully investigated the role of leadership in mobilizing widespread support for social change, particularly gender equality. The burden of achieving gender equality is typically placed on women (particularly female leaders) - the main targets of such inequality. Traditional approaches frame workplace gender equality as either a women's issue, which limits men's (non-target's) involvement in the movement, or a meritocratic non-issue that exists due to women's (target's) tendency to pursue less intensive careers. In contrast to such work focusing on women's experiences as targets of discrimination or men's role in preserving inequality, we propose a solidarity-based approach that positions men and women as agents of change. This approach relies on two processes: leadership processes - particularly leadership as a form of influence based on shared identities among leaders and followers (e.g., their gender group); and political solidarity as a way to mobilize the silent majority (men) to work as allies beside a minority (women) and embrace equality as a common cause for both groups. In two experiments (Ns = 338, 336) we studied how leader gender and message framing affect men's and women's support for equality by contrasting a solidarity-based framing of gender equality as a common cause for men and women, with a women's issue frame (Experiment 1) or a meritocratic frame (Experiment 2). The statement was attributed to a male or female leader (Experiments 1-2) or, additionally, to a government agency (Experiment 1). Women reported higher sense of common cause (Experiment 2) and collective action intentions than men (Experiments 1-2), and higher intentions under common cause compared to meritocracy frames (Experiment 2). Interestingly, male leaders invoked higher sense of common cause and collective action intentions for both men and women regardless of framing (Experiment 2). Irrespective of leader gender however, as predicted common cause framing boosted perceived leader prototypicality, legitimacy, and influence across the board (Experiments 1-2). Yet this was qualified by women (compared to men) rating leaders as more legitimate and influential under common cause compared to meritocracy framing (Experiment 2). Women's reactions to equality messages, and the intersection of leadership and solidarity toward equality are discussed.

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Whose sample is it anyway? Widespread misannotation of samples in transcriptomics studies.

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Whose sample is it anyway? Widespread misannotation of samples in transcriptomics studies.

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