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

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 2103 ◽  
Author(s):  
Lilah Toker ◽  
Min Feng ◽  
Paul Pavlidis

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.

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 2103
Author(s):  
Lilah Toker ◽  
Min Feng ◽  
Paul Pavlidis

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.


2016 ◽  
Author(s):  
Lilah Toker ◽  
Min Feng ◽  
Paul Pavlidis

AbstractConcern 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 genomics 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 mislabelled 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.


Author(s):  
Marc Lipsitch ◽  
Rebecca Kahn

ABSTRACTRandomized controlled trials (RCTs) have shown high efficacy of multiple vaccines against SARS-CoV-2 disease (COVID-19), but evidence remains scarce about vaccines’ efficacy against infection with, and ability to transmit, the virus. We describe an approach to estimate these vaccines’ effects on viral positivity, a prevalence measure which under reasonable assumptions forms a lower bound on efficacy against transmission. Specifically, we recommend separate analysis of positive tests triggered by symptoms (usually the primary outcome) and cross-sectional prevalence of positive tests obtained regardless of symptoms. The odds ratio of carriage for vaccine vs. placebo provides an unbiased estimate of vaccine effectiveness against viral positivity, under certain assumptions, and we show through simulations that likely departures from these assumptions will only modestly bias this estimate. Applying this approach to published data from the RCT of the Moderna vaccine, we estimate that one dose of vaccine reduces the potential for transmission by at least 61%, possibly considerably more. We describe how these approaches can be translated into observational studies of vaccine effectiveness.HighlightsSARS-CoV-2 vaccine trials did not directly estimate vaccine efficacy against transmission.We describe an approach to estimate a lower bound of vaccine efficacy against transmission.We estimate one dose of the Moderna vaccine reduces the potential for transmission by at least 61%.We recommend approaches for analyzing data from trials and observational studies.


2014 ◽  
Vol 20 (1) ◽  
pp. 53-79 ◽  
Author(s):  
Roger Fosdick ◽  
Pilade Foti ◽  
Aguinaldo Fraddosio ◽  
Salvatore Marzano ◽  
Mario Daniele Piccioni

2007 ◽  
Vol 76 (1) ◽  
pp. 155-160 ◽  
Author(s):  
A. Carbonaro ◽  
G. Mauceri

In a recent paper Miranda Jr., Pallara, Paronetto and Preunkert have shown that the classical De Giorgi's heat kernel characterisation of functions of bounded variation on Euclidean space extends to Riemannian manifolds with Ricci curvature bounded from below and which satisfy a uniform lower bound estimate on the volume of geodesic balls of fixed radius. We give a shorter proof of the same result assuming only the lower bound on the Ricci curvature.


Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 2037-2037
Author(s):  
Daniele Laszlo ◽  
Giancarlo Pruneri ◽  
Giovanna Andreola ◽  
Davide Radice ◽  
Liliana Calabrese ◽  
...  

Abstract DLBCL can be divided into two prognostically different subgroups, germinal center B-cell-like (GCB) and activated B-cell-like (ABC), according to twodifferent gene patterns identified with cDNA microarray technology. Though valuable, this technology is expensive and not generally available. However, the identification of individual antigens related to different stages of B-cell differentiation using immunohistochemistry, can be used to assess the two profiles yielding comparable results with respect to cDNA microarray technique. We have retrospectively investigated 105 patients (pts) diagnosed with de novo DLBCL and treated at our centre between November 2001 and June 2004; the only inclusion criteria was the availability of a tissue biopsy at diagnosis. Median age was 62 (19–85); stage at diagnosis was I–II in 49 pts (47%), III in 14 pts (13%) and IV in 42 pts (40%); according to IPI, 74 (70%) pts were defined as low (0–2) and 31 (30%) as high risk (3–5). Interestingly, the majority (53%) of our pts, had a primary extranodal lymphoma at diagnosis. TMA analysis was performed with antibodies to CD10, bcl-6 and MUM1 allowing the following classification: 50 pts (48%) were considered having CGB lymphoma and 55 pts (52%) having ABC disease. According to IPI risk score, 38 pts with CGB and 36 with ABC lymphoma were at low risk (0–2) whereas 10 with CGB and 16 with ABC lymphoma were at high risk (3–5). All pts received a median of 6 cycles of a CHOP-like, antracycline-based polychemotherapy. Observed ORR was 89% (94/105); 62 (59%) pts achieved a CR, 32 (30.5%) a PR while 11 (10.5%) failed to respond to treatment. Median follow-up of the surviving pts was 45 months ( 5–110). The 3-year OS for the entire group was 71% and the 3-year EFS was 54%. In terms of CR, PD and resistance to therapy, no difference was observed between the two TMA types of DLBCL. Pts obtaining a CR after 1st line treatment were equally distributed in both groups (28.6% in CGB vs 30.5% in ABC) as were those not responding to therapy (3.8% in CGB versus 6.7% in ABC). A separate analysis in pts with stage IV disease at diagnosis was also performed and showed similar results (40.5% of CR, 23.8% of NR; no difference was observed between the two TMA defined subgroups). Pts who experienced a PD at any time, were equally distributed between the 2 subgroups, either if they relapsed after first line therapy (6 pts in CGB group , 10 in the ABC one) or after any other subsequent treatment (12 in the CGB group, 18 in the ABC one). Furthermore, 39 of 56 (69%) patients with extranodal presentation at diagnosis showed a CR independently of their subgroup distribution (37.5% in the CGL group vs 32.1% in the ABC one), and pts experiencing a PR were equally distributed between the two groups. Our data do not support the use of TMA to predict outcome in DLBCL. However, previously published data supporting the prognostic impact of TMA, have not enrolled pts with lymphomas of primary extranodal origin which, instead, were the majority in our study. Indeed, the study by Colomo et al, which enrolled 39% of pts affected by extranodal lymphomas, also failed to demonstrate a role of TMA in predicting outcome in DLBCL pts. Furthermore, the use of a limited number of antigens to define different subtypes of DLBCL may not be sufficient to identify the same patterns as defined by cDNA microarray technology.


1973 ◽  
Vol 40 (2) ◽  
pp. 433-438
Author(s):  
L. M. Butzel ◽  
H. C. Merchant

An important use of shock spectra is to make estimates of the maximum responses of linearly modeled multidegree-of-freedom structures to shock excitations. In this paper a lower-bound estimate to complement a well known upper bound on such a maximum response is proposed and examined. The conditions under which the estimate is a lower bound are delineated. The set of bounds is applied to an examination of the performance of two maximum response estimators in current use, the root-mean-square, and one which is a function of the root-mean-square and dominant mode. The results of an empirical study show that the estimators do not perform well except when the bounds are close together.


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