Published: 2021-09-06 12:51 | Updated: 2021-09-07 09:34

The Centre for Bioinformatics and Biostatistics at Campus Flemingsberg is now open

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The Centre for Bioinformatics and Biostatistics (CBB) has now formally opened, offering expertise and networking opportunities for the preclinical and clinical research in the area.

The Centre for Bioinformatics and Biostatistics (CBB) aims to be a natural partner for research groups located at Campus Flemingsberg with a need for assistance on bioinformatics or biostatistics. CBB has now formally opened and can offer the following services:

  • Mentoring of PhD-students and postdocs, where there is additional need for support on issues of bioinformatics or biostatistics. Interested supervisors are welcome to contact CBB at cbb@ki.se for discussions or more information.
  • Basic (roughly 1-hour consultations) support on issues like power calculations, which statistical test to use, or input on grant writing related to CBB’s competence.

Further, a seminar series in biostatistics for clinicians is in the planning and will be launched during the autumn 2021.

We also intend to regularly offer a physical room in Neo, where interactions between people working in bioinformatics or biostatistics can network or share competences on specific projects. More information about this will be posted on our website (www.ki.se/cbb) during the coming time. We are happy to present more specifics of how CBB can help your research group in for instance departmental meetings.

If you think CBB should offer any other specific support, feel free to reach out to us at: cbb@ki.se.

Contact

Event type
Lectures and seminars
Sfo Epi Seminar in Biostatistics: Distributed Privacy-Preserving Estimation of Time-to-Event Models

17-09-2021 3:00 pm Add to iCal
Campus Solna
Location
https://ki-se.zoom.us/j/68906707686
Lead

Welcome to attend the SfoEpi Seminar Series in Biostatistics!
Title: Distributed Privacy-Preserving Estimation of Time-to-Event Models

Content

Speaker:

Dr. C Jason Liang PhD, Biostatistics Research Branch, NIAID, NIH, USA

Abstract:

There has been a proliferation of EHR data in recent years. However, the data tends to be splintered across institutional silos. Integration of the data across silos at the patient level has many challenges, including patient privacy and the practical necessities of minimizing the rounds of communication between sites.

Informally, there is a trade-off between efficiency and privacy. Freely sharing patient-level information across silos is efficient but impractical. Restricting information sharing to coarse aggregate summaries (e.g. meta-analytic approaches that essentially average treatment effects across different studies) preserves privacy but is inefficient and may lead to bias. There is a need to identify approaches that lie between these two extremes of privacy and efficiency.

Building on the communication-efficient surrogate likelihood work of Jordan et al. (2018 JASA), we outline approaches for fitting Cox models and its extensions when data is distributed among multiple sites. We show that our approaches are more accurate than naive meta-analytic approaches while preserving privacy and minimizing the frequency of communication required between separate data sites.

Zoom Link: https://ki-se.zoom.us/j/68906707686

*Webinar format: unless you are on the panel you will be muted and with no video. Participants can raise their hands during the Q&A to be recognized to ask questions.

If you have any questions, please contact Erin Gabriel.

Contact

Event type
Conferences and symposiums
NorPEN 2021

10-11-2021 to
12-11-2021 Add to iCal
Campus Solna
Location
to be posted
NorPen 2021
Photo: N/A
Lead

The 13th Annual Nordic Pharmacoepidemiological Network (NorPEN) meeting. Hosted by the Centre for Pharmacoepidemiology at Karolinska Institutet.

Content

Theme: Sustainability of Nordic Collaboration

November 11-12th 2021

Hosted by the Centre for Pharmacoepidemiology at Karolinska Institutet

Questions? Contact us at norpen@meds.ki.se

 

Registration is now open!

For more information visit:https://ki.se/en/meds/norpen-2021

Format

The NorPEN 2021 meeting will be held online with live participation capability by attendees

Abstracts

  • Abstract submissions for the 10-minute oral presentations and 3-minute PharmacoepiSLAMs are now welcome
  • The submission form is available here https://ki.se/en/meds/norpen-2021
  • Deadline Friday September 10th

Pre-conference course: A general overview of G methods in relation to pharmacoepidemiology

Wednesday November 10th 2021, afternoon, time: TBA

Funded by SFO Epi (The Strategic Research Area in Epidemiology and Biostatistics, KI)

*Note that registration for the course is separate from the conference

Contact

Event type
Lectures and seminars
Sfo Epi Seminar in Biostatistics: Reconsideration of the Kaplan-Meier Estimator: Censoring and Time-varying Covariates

11-06-2021 3:00 pm Add to iCal
Campus Solna
Location
https://ki-se.zoom.us/j/65377392771
Lead

Welcome to attend the SfoEpi Seminar Series in Biostatistics!
Title: Reconsideration of the Kaplan-Meier Estimator: Censoring and Time-varying Covariates

Content

Speaker:

Professor Rebecca Betensky, Chair of the Department of Biostatistics, School of Global Public Health at New York University

Abstract:

In this talk I will present two extensions of the Kaplan-Meier estimator that address a nuance of censoring and incorporation of time-varying covariates. Clinical studies with time to event endpoints typically report the median follow-up (i.e., censoring) time for the subjects in the trial, alongside the median time to event.  The reason for this is to provide information about the opportunity for subjects in the study to experience the event of interest.  In most clinical studies, the censoring time is a composite measure, defined as the minimum of the time to drop-out from the study and time to the administrative end of study.  The time to drop-out component may or may not be observed, while the time to the end of study is observed for each subject. I consider whether this decomposition of the censoring time into a time that is itself potentially censored and a time that is fully observed offers any improvement of the estimation of the censoring distribution.

Extensions of the Kaplan-Meier estimator have been developed to illustrate the relationship between a time-varying covariate of interest and survival, however they are limited to displaying survival for patients who always have a certain value of a time-varying covariate.  I present extensions of these estimators that provide crude and covariate-adjusted estimates of the survival function for patients defined by covariate paths. 

Zoom Link: https://ki-se.zoom.us/j/65377392771

*Webinar format: unless you are on the panel you will be muted and with no video. Participants can raise their hands during the Q&A to be recognized to ask questions.

If you have any questions, please contact Erin Gabriel.

Contact

Event type
Lectures and seminars
Sfo Epi Seminar in Biostatistics: Using EHR to Extend Understanding of Treatment Effectiveness Beyond Clinical Trials

10-05-2021 3:30 pm Add to iCal
Campus Solna
Location
https://ki-se.zoom.us/j/65923678214
Lead

Welcome to attend the SfoEpi Seminar Series in Biostatistics!
Title: Using EHR to Extend Understanding of Treatment Effectiveness Beyond Clinical Trials

Content

Speakers:

Professor Rebecca Hubbard PhD, Division of Biostatistics, Perelman School of Medicine, University of Pennsylvania and

Dr. Ronac Mamtani MD, Assistant Professor, Division of Hematology/Oncology, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania 

Abstract:

Randomized clinical trials (RCTs) are considered the gold standard for evaluating efficacy of novel treatments but suffer from limitations. Some treatments cannot be ethically or feasibly allocated via random assignment. Moreover, vulnerable populations are under-represented in RCTs, raising concerns about equity and the external validity of results. Clinical trial treatment settings may not reflect care and outcomes as they are experienced in routine practice. Real-world data (RWD) sources, including electronic health records (EHR), have the potential to address many of these concerns. However, limitations of RWD necessitate careful attention to study design and application of appropriate statistical methods. In this talk, we will discuss sources of RWD, their strengths and limitations, and their potential to supplement RCT evidence on treatment efficacy. We present two novel statistical developments aimed at extending evidence on treatment efficacy beyond clinical trials: (1) a method for addressing data quality issues in EHR data to obtain valid treatment effectiveness estimates in the presence of differential outcome misclassification without requiring specification of the measurement error models and (2) an approach to combining clinical trial and EHR-derived effectiveness estimates. The overarching objective of this presentation is to introduce data sources, study design considerations, and statistical challenges arising in the analysis of RWD. Through judicious application of these methods RWD have the potential to aid clinical decision making through the creation of evidence on treatment effectiveness that would not be possible using RCTs alone.

Zoom Link: https://ki-se.zoom.us/j/65923678214

*Webinar format: unless you are on the panel you will be muted and with no video. Participants can raise their hands during the Q&A to be recognized to ask questions.

If you have any questions, please contact Erin Gabriel.

Contact

Event type
Internal meeting
Information meeting April 29, Centre for Bioinformatics and Biostatistics (CBB) at Campus Flemingsberg

29-04-2021 12:15 pm - 12:55 pm Add to iCal
Online
Location
Zoom
Lead

Welcome to an information meeting regarding the new Centre for Bioinformatics and Biostatistics (CBB) at KI, Campus Flemingsberg. We will present why CBB has been formed, what it is and intends to do, our initial activities and infrastructure.

Content

We welcome submission of questions prior to the meeting, these can be made to cbb@ki.se.

Join the meeting on Zoom:
https://ki-se.zoom.us/j/67124032304?pwd=cEVaZnJBTUFNTC9mdVhMbVNMZ3pnUT09  

Agenda: 

  1. Welcome and introduction 
  2. Background to why CBB is needed  
  3. Present plans for services at CBB 
  4. Addressing submitted questions (please put these to cbb@ki.se) prior to the meeting

Contact

Event type
Lectures and seminars
SFOepi Seminar in Biostatistics: New Approaches for Inference on Optimal Treatment Regimes

16-04-2021 3:00 pm Add to iCal
Campus Solna
Location
https://ki-se.zoom.us/j/65431068521
Lead

Welcome to attend the SFOepi Seminar Series in Biostatistics!
Title: New Approaches for Inference on Optimal Treatment Regimes

Content

Speaker: Professor Lan Wang, Department of Management Science, University of Miami

Abstract: 

Finding the optimal treatment regime (or a series of sequential treatment regimes)based on individual characteristics has important applications in precision medicine. We propose two new approaches to quantify uncertainty in optimal treatment regime estimation. First, we consider inference in the model-free setting, which does not require to specify an outcome regression model. Existing model-free estimators for optimal treatment regimes are usually not suitable for the purpose of inference, because they either have nonstandard asymptotic distributions or do not necessarily guarantee consistent estimation of the parameter indexing the Bayes rule due to the use of surrogate loss. We study a smoothed robust estimator that directly targets the parameter corresponding to the Bayes decision rule for optimal treatment regimes estimation. We verify that a resampling procedure provides asymptotically accurate inference for both the parameter indexing the optimal treatment regime and the optimal value function. Next, we consider the high-dimensional setting and propose a semiparametric model-assisted approach for simultaneous inference. Simulations results and real data examples are used for illustration.

Zoom Link: https://ki-se.zoom.us/j/65431068521

*Webinar format: unless you are on the panel you will be muted and with no video. Participants can raise their hands during the Q&A to be recognized to ask questions.

If you have any questions, please contact Erin Gabriel.

Contact

Published: 2021-03-25 13:16 | Updated: 2021-03-25 13:17

Enoch Yi-Tung Chen awarded prize for best student paper in medical statistics from the Swedish Society for Medical Statistics

Portrait of the PhD student Enoch Yi-Tung Chen
Enoch Yi-Tung Chen. Photo: Gunilla Sonnebring

Enoch Yi-Tung Chen has been awarded the Swedish Society for Medical Statistics (Föreningen för Medicinsk Statistik, FMS) prize for best student project in the area of medical statistics during 2020. The prize, which includes an award of 5000 SEK, was announced at the FMS annual general meeting on 25 March 2021.

The competition is open to undergraduate and master’s students in all programs at all Swedish higher education institutions and was introduced to draw attention to the importance of medical statistics, and to promote interest among students and doctoral students.

Enoch was awarded the prize for his degree project “Extrapolating cancer patient survival: a comparison of the flexible parametric model and the rolling-over algorithm” that he completed under the supervision of Professor Paul Dickman at the Department of Medical Epidemiology and Biostatistics (MEB), Karolinska Institutet, and Professor Jung-Der Wang at National Cheng Kung University as part of his studies in the KI Master’s Programme in Public Health Sciences.

The committee states that they are very happy to give the 2021 award to Enoch Yi-Tung Chen.The motivation continues; “The author presents two methods, the flexible parametric model (FPM) and the rolling-over algorithm (ROA), for estimating survival functions. Both methods have previously been used to extrapolate patients’ survival over the observed time but also applied for estimation of the loss of life expectancy due to cancer. In Chen’s master thesis the two approaches are also applied and compared to the Kaplan Meier estimates for studies of patients with colon cancer and breast cancer.

Chen gives a simple but precise presentation of the statistical theoretical concepts and definitions related to the problem under study within survival analysis. He presents motivating data sets, two cohorts of colon cancer patients and two cohorts of breast cancer patients, together with a comparative investigation of the FPM and ROA. Chen has carried out his task in a commendable way and his thesis can serve as an excellent example of a comparative study of statistical estimation approaches with a motivating empirical example for statistics in medicine. “

Enoch was recently admitted to doctoral studies at MEB to further study “Extrapolating survival with applications in health technology assessment” under the supervision of Paul Dickman, Mark Clements, and Magnus Björkholm.

Contact

Published: 2021-03-15 09:00 | Updated: 2021-03-15 09:51

Karolinska Institutet and Karolinska University Hospital establish new centre for bioinformatics and biostatistics at Campus Flemingsberg

street and buildings
Alfred Nobels allé, Campus Flemingsberg. Photo: Erik Cronberg

Today's research is generating more and more big data, which means that the demand for bioinformatics and biostatistics is growing. Karolinska Institutet and Karolinska University Hospital are therefore establishing a new centre at Campus Flemingsberg that will offer expertise and networking opportunities for the preclinical and clinical research environment in the area.

The dean of KI South has appointed Carsten Daub, associate professor at the Department of Biosciences and Nutrition, Karolinska Institutet, as acting director of the Centre for Bioinformatics and Biostatistics (CBB). Together with Hannes Hagström, docent at the Department of Medicine and assistant chief physician at Karolinska University Hospital, Huddinge, he will establish a long-term plan for both the centre and the regional collaboration.

Initially, the purpose of the centre is to coordinate existing competence and infrastructure and to function as a knowledge hub for bioinformatics and biostatistics for research groups in the area.

"By organising expertise under one roof, we can utilize all available knowledge among the researchers and ensure it is used the best way possible. The centre will also increase the contact areas between the research groups and create better conditions for networking", Carsten Daub explains.

Some of the future services of the centre include mentoring for researchers at the beginning of their careers (doctoral students and postdoctoral researchers), support in project planning and grant writing, as well as seminars and discussion groups around bioinformatics and biostatistics methods and their application to biomedical data.

Looking for experienced bioinformaticians and biostatisticians

During 2021, a steering board will be established, where the members come from various KI departments at Campus Flemingsberg and Karolinska University Hospital, Huddinge. But at this time, the centre in mainly focused on finding new coworkers.

"We are now looking for experienced bioinformaticians and biostatisticians who would like to work with us on a part time-basis, to establish the CBB at Campus Flemingsberg. The application is open, and we look forward to answering questions and discussing the centre's future planning", says co-director Hannes Hagström.

Contact

Event type
Dissertations
Dissertation: Cecilia Lundholm

26-03-2021 9:00 am Add to iCal
Campus Solna
Location
https://ki-se.zoom.us/j/7883937720
Portrait of Cecilia Lundholm
Cecilia Lundholm Photo: Gunilla Sonnebring
Lead

Title: Causes and consequences of stress and tobacco exposure in utero on birth size asthma and academic achievement

Content

Opponent: Associate Professor Liesbeth Duijts, Department of Pediatrics, University Medical Center Rotterdam

Supervisors: Catarina Almqvist Malmros, Henrik Larsson, Göran Pershagen, Brian D’Onofrio

Follow the event on Zoom: https://ki-se.zoom.us/j/7883937720

Read the full thesis in KI's open archive: https://openarchive.ki.se/xmlui/handle/10616/47536

Contact

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