Cell Line Contamination
7.1K views | +N/A today
Follow
Cell Line Contamination
News on cell culture and contaminated cell lines
Your new post is loading...
Your new post is loading...
Scooped by Amanda Capes-Davis
Scoop.it!

ICLAC | The International Cell Line Authentication Committee

ICLAC | The International Cell Line Authentication Committee | Cell Line Contamination | Scoop.it

The International Cell Line Authentication Committee (ICLAC) is a voluntary group formed in March 2012 to make misidentified cell lines more visible to the research community, and promote awareness and authentication testing as effective ways to combat the problem.

 

Scientists have struggled with the problem of cell line cross-contamination for many years.  With many now aware of the issue, the focus is increasingly on positive ways to address the problem.  The key to a positive approach is authentication - testing your own cell line sample, and looking at the existing evidence to see if that cell line is misidentified.

 

For more information on ICLAC, see:

http://iclac.org/about-iclac/

 

To download our list of cross-contaminated or otherwise misidentified cell lines, see:

http://iclac.org/databases/cross-contaminations/

more...
No comment yet.
Scooped by Amanda Capes-Davis
Scoop.it!

US cancer institute to overhaul tumour cell lines

US cancer institute to overhaul tumour cell lines | Cell Line Contamination | Scoop.it

NIH has announced that the NCI-60 panel - a set of 60 cancer cell lines used to test anticancer drugs for more than 25 years - will be retired in favour of patient-derived xenograft (PDX) models, with a closer link to clinical data.


What is a patient-derived xenograft?  Basically, it involves a scientist taking a patient's cancer cells and transferring to a mouse.  The mouse can be treated with anticancer drugs to determine the best treatment choices and also look for side-effects and other problems.


When going back to cell lines established in the 1950s-1980s, it may be impossible to work out whether the donor is male or female, or what treatment the person was given before the cell line was established.  So a closer link to clinical data would certainly be welcome.


Having said that, I hope this does not mean that NIH intends to drop cell lines and move wholesale to PDX models.


Every cell-based model has strengths and weaknesses, whether we are talking cell lines or xenografts.


Cross-contamination and other quality issues can affect PDX models, just as they do cell lines. 


Cell lines also minimise the use of animal models, which is an important consideration when doing any kind of research.


Want to find out more about PDX models?


A good review on PDX models in cancer drug development is here:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3928688/


Three experts in the field give their opinion on PDX models here:

http://www.ncbi.nlm.nih.gov/pubmed/?term=25907221

more...
No comment yet.
Scooped by Amanda Capes-Davis
Scoop.it!

Your Cells. Their Research. Your Permission?

Your Cells. Their Research. Your Permission? | Cell Line Contamination | Scoop.it

2016 will be a year for exciting research - and, hopefully, exciting progress in research ethics.

 

In the US, the "Common Rule" - more formally, the Federal Policy for the Protection of Human Subjects - is open for public consultation until 6 January.  Rebecca Skloot has written an Op-Ed article for the New York Times, encouraging everyone to contribute their views on use of genetic material.

 

Elsewhere, the Australian Code for the Responsible Conduct of Research is under review.  The code sets out requirements for responsible research - including publication, managing data and research materials, and dealing with research misconduct.  Public consultation is again a vital part of the process.

 

Internationally, rapid progress in genetic manipulation is taking everyone by surprise.  Two years after publishing CRISPR/Cas9, Jennifer Doudna is opening a conversation with the science community on its use - and inviting us to join the conversation. 

 

What do these three have in common?  All advocate a broader conversation when it comes to ethical research and handling patient information.

 

Scientists may be afraid that changes in ethics regulations will hinder their research.  But let's look at the bigger picture here. Changes in research over the last decade already affect donor privacy, and will impact patient health, in ways that no-one would have imagined when these documents were first released.

 

Change is already here.  Fear, not change, is what will hinder our research.  Let's not be afraid.  Let's join the conversation.

 

To read Rebecca Skloot's Op-Ed piece, see:

http://www.nytimes.com/2015/12/30/opinion/your-cells-their-research-your-permission.html?_r=1

 

To read about Jennifer Doudna's whirlwind 2015, see:

 http://www.nature.com/news/genome-editing-revolution-my-whirlwind-year-with-crispr-1.19063?WT.mc_id=SFB_NNEWS_1508_RHBox

 

To read about the Australian Code for the Responsible Conduct of Research, see:

https://www.nhmrc.gov.au/guidelines-publications/r39

 

more...
No comment yet.
Scooped by Amanda Capes-Davis
Scoop.it!

New ovarian tumor cell lines provide a better match to cancer in the clinic

I mostly talk about journal articles with cell line problems.  So it is a refreshing change to talk about a publication that showcases cell lines in a positive way and also teaches us important lessons about ovarian cancer.

 

If you work with cell lines, you probably know that it is difficult to establish cell lines from some cancer types.  Most cell lines are established from aggressive, high grade cancers. Cell line models do not represent the full spectrum of cancer, which makes it difficult to study how tumors develop and work out how to stop them at an early stage.

 

The link in the title above is to a 2015 article published in Nature Communications.  The authors have spent many years establishing cell lines from ovarian cancer.  Through trial and error, they have worked out how to increase success rates for ovarian cancer cell lines.

 

Their techniques result in cell lines that represent a broad range of ovarian cancer subtypes, which is encouraging news for laboratories developing new treatments for ovarian cancer.

 

STR profiling was performed on all cell lines in this paper and results are included as supplementary data for future reference.

 

For another paper looking at ovarian cell lines and how they perform as models for cancer, see:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715866/

more...
No comment yet.
Scooped by Amanda Capes-Davis
Scoop.it!

The culture of cell culture practices and authentication - results from a 2015 survey | BioTechniques

There has been a great deal of attention paid to misidentified cell lines in the last few years.  Cell line repositories and labs that practise good cell culture have been urging authentication testing.  So how much is this work affecting everyday work?

 

Two surveys of cell culture practices say: not enough.

 

The Global Biological Standards Institute (GBSI) has just published the results of a survey conducted in 2015.  A total of 446 respondents replied with information on their cell culture practices.  The survey found that 74% of respondents had never performed STR profiling - the consensus test method to look for cross-contamination of human cell lines.  Only 30% were taught about the importance of authentication testing.

 

These results fit neatly with another recent survey conducted by CellBank Australia, looking at risks that may apply to cell culture practice.  Of the 250 respondents, 54% stated that their laboratory did not typically perform authentication testing, and many were uncertain about how to test their cell lines.

 

These surveys strongly suggest that better training of young scientists is needed.  Cell culture underpins much of basic research and scientists who use it must understand the common problems.

 

For the GBSI survey data in BioTechniques, see:

http://www.biotechniques.com/BiotechniquesJournal/2015/October/The-culture-of-cell-culture-practices-and-authentication-Results-from-a-2015----Survey/biotechniques-360971.html

 

For the abstract from the CellBank Australia survey, see:

http://www.ncbi.nlm.nih.gov/pubmed/26365214

more...
No comment yet.
Scooped by Amanda Capes-Davis
Scoop.it!

What's in a Name? Cell Line Chaos

What's in a Name?  Cell Line Chaos | Cell Line Contamination | Scoop.it

Do you have trouble working out the correct name of your cell line?

 

Yes - me too.  Cell line names may be changed as they are passed from one lab to another, or when they are listed in publications.  The end result is that it can be hard to know if a cell line is misidentified, because you first need to track its usage to see if two different names correspond to the same cell line.

 

This is an area where there is a real need for consistency and harmonisation.  I have already talked about a recent paper from authors at Genentech, published in Nature, that provides resources for cell line nomenclature and description.  Here is another resource that is really helpful: an online thesaurus of cell lines.

 

Cellosaurus (great name!) tries to list all of the cell lines used in biomedical research.  You can use the search on their home page to look up the name of the cell line you are working with.  Cellosaurus also records the species of origin, the sex of the donor, and a great deal more information.

 

Cellosaurus, which is an initiative of the Swiss Insitute of Bioinformatics, can be found here:
http://web.expasy.org/cellosaurus/

 

To look up nomenclature and authentication data in the Genentech dataset, see their abstract here:
http://www.ncbi.nlm.nih.gov/pubmed/25877200

 

ICLAC has a set of guidelines for naming cell lines, for scientists who are establishing new cell lines.  The guidelines can be found here:

http://iclac.org/resources/cell-line-names/

more...
No comment yet.
Scooped by Amanda Capes-Davis
Scoop.it!

Genetic profiling reveals an alarming rate of cross-contamination among human cell lines used in China

The International Cell Line Authentication Committee (ICLAC) is a voluntary group that tries to raise awareness about the problem of cross-contaminated cell lines in research. 

 

"International" is an important part of the title.  The feedback we get shows very clearly that cross-contamination (contamination and overgrowth of one cell culture model by another) is a problem in many countries.  So it is no surprise to see a new paper that shows cell line cross-contamination is a problem in China.

 

The authors come from the China Center for Type Collection.  In this study, they tested 380 cell line samples from 113 sources in China. Testing was done using STR profiling, which allows comparison to international datasets.  They report cross-contamination in 25% (95/380) of samples.  For cell lines established in China, 85% (59/69) of those samples were cross-contaminated, typically with HeLa or HeLa derivatives.

 

The authors suggest that the causes relate to lack of information and language barriers.  I suspect that difficulty finding testing facilities and accessing journal articles may also contribute. This paper will do a great deal to help, along with the work being done by journal editors, funding bodies and others to set reporting standards and improve access to information.

 

The website for the China Center for Type Collection is here:

http://www.cctcc.org/

more...
No comment yet.
Scooped by Amanda Capes-Davis
Scoop.it!

NOT-OD-15-103: Enhancing Reproducibility through Rigor and Transparency

I know some scientists are getting tired of talking about research reproducibility.  Media coverage can cause panic - Lenny Teytelman has a great post on this topic at the link below.  But I also see many publications that use misidentified cell lines, where lack of reproducibility is an important problem.  So I was delighted to see a notice issued by NIH this week on how to improve reproducibility in preclinical research.

 

Amongst other requirements, authentication of cell lines and other key resources will be incorporated as part of grant documentation.  From my reading of the notice, the main aim is to increase transparency - for example, making it clearer if cell lines are tested and what test method is used.

 

The notice follows several high profile publications on reproducibility.  Earlier this week, a paper from Leonard Freedman of GBSI estimated the direct cost of irreproducible research.  The paper estimates that approximately 50% of preclinical research is not reproducible, costing $28 billion dollars per year in the US alone.

 

Several weeks ago, Nature Methods published a commentary (also from Leonard Freedman) looking at reproducibility and how to improve the culture of cell line authentication.  The authors make a number of recommendations - for example, to provide funding for authentication and commit to training and new technologies.

 

Will this notice help to improve the way scientists work with cell lines?  Time will tell.  But getting scientists to think about authentication and making their approach to testing more transparent gets a big tick from me.

 

For Lenny Teytelman's discussion of reproducibility, see:

http://www.thespectroscope.com/read/we-can-and-should-improve-reproducibility-but-its-not-a-by-lenny-teytelman-309

 

For the study looking at the economics of reprodubility, see:

http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002165


To find the commentary on cell line authentication, see:

http://www.ncbi.nlm.nih.gov/pubmed/26020501

more...
No comment yet.
Scooped by Amanda Capes-Davis
Scoop.it!

Do Cancer Cell Lines Really Resemble Tumors? Now Researchers Can Tell

Do Cancer Cell Lines Really Resemble Tumors? Now Researchers Can Tell | Cell Line Contamination | Scoop.it

When I talk about testing cell lines, I try to emphasize that testing is only part of the story. You need to think if your cells have changed over time, and if other factors may influence their behaviour. And - important! - you need to consider if your cells truly represent the tissue or disease you want to look at.

 

I have been looking at this question today and came across a fascinating 2013 article from scientists at Memorial Sloan-Kettering Cancer Center. The authors looked at cell line models of ovarian cancer, comparing data from the Cancer Cell Line Encyclopedia (CCLE) and The Cancer Genome Atlas (TCGA).

 

At first glance they appear quite similar. But closer inspection shows some big differences - for example, five cell lines show "hypermutator" phenotypes with many more mutations compared to tumour samples. These cell lines are not likely to be good models.

 

The authors include a table of which cell lines are likely to be better or poorer models of ovarian cancer - a really helpful resource for those of you working on this tumour type.

 

To view the original paper see:

http://www.nature.com/ncomms/2013/130709/ncomms3126/full/ncomms3126.html

 

To visit the Cancer Cell Line Encyclopedia see:

http://www.broadinstitute.org/ccle/home

more...
No comment yet.
Scooped by Amanda Capes-Davis
Scoop.it!

FACC-29 gathers authenticated canine cancer cell lines for research and drug development

FACC-29 gathers authenticated canine cancer cell lines for research and drug development | Cell Line Contamination | Scoop.it

The recent AACR conference - as usual - has led to some interesting cell culture news.

 

The link in the title above is to an announcement by the University of Colorado that they have assembled a new panel of validated canine cell lines.  The new FACC-29 is analogous to the NCI-60, a well known panel of validated human cell lines.

 

The FACC-29 has been authenticated using STR profiling developed for canine cell lines by University of Colorado scientist Dawn Duval.  Their method of authenticating canine cell lines was published here:

 

http://vdi.sagepub.com/content/23/4/780.long

 

AACR also included a methods workshop focused on cell line authentication.  Leonard Freedman and Vivien Siegel discussed policy and training, while Stephen Ethier and Richard Neve discussed methodology.  Full text content can be found here:

 

http://educationbook.aacrjournals.org/cgi/content/full/2015/1/95

http://educationbook.aacrjournals.org/cgi/content/full/2015/1/99

more...
No comment yet.
Scooped by Amanda Capes-Davis
Scoop.it!

Cell Culture Shock

Cell Culture Shock | Cell Line Contamination | Scoop.it

Earlier this week, scientists at Genentech published a new set of resources for cell line naming and authentication.  The link in the title above goes to an entertaining summary of what that work is all about.

 

To look at the publication, see:

http://www.nature.com/nature/journal/v520/n7547/full/nature14397.html

more...
No comment yet.
Scooped by Amanda Capes-Davis
Scoop.it!

Announcement: Time to tackle cells’ mistaken identity

Announcement: Time to tackle cells’ mistaken identity | Cell Line Contamination | Scoop.it

Nature has written an editorial that sets out new ways to tackle the problem of misidentified cell lines.  Changes will apply to all Nature journals from 1st May 2015.

 

Authors will be asked to check their cell lines against the ICLAC list of known misidentified cell lines.  If the authors use a known problematic cell line, they will be asked to provide a scientific justification for its use, and clearly state its identity in the Methods section.

 

Authors must report on a cell line's source, authentication testing, and Mycoplasma testing status.  For authentication testing, authors are asked to state the test method, test result, and when testing was last performed.

 

This type of reporting is only possible if resources exist for authentication testing.  The ICLAC list of known misidentified cell lines is a voluntary initiative.  Many other individuals and organizations have also worked to develop resources over many years.  The new requirements by Nature represent a tribute to everyone's hard work and dedication.

 

For Nature's full cell line reporting requirements and resources, see:

http://www.nature.com/authors/policies/availability.html#further

 

For ICLAC's list of known misidentified cell lines, see:

http://iclac.org/databases/cross-contaminations/

more...
No comment yet.
Scooped by Amanda Capes-Davis
Scoop.it!

Which Journals Ask for Cell Line Authentication?

Lots of people ask me this question.  So I like to keep a list online to share with everyone.  If you spot any mistakes or can think of any journals I have missed, please leave a comment to let me know.

 

The journals or publishers that I have found with some kind of authentication requirement are listed below.  Requirements vary with each journal - for example, Nature has a checklist that sets out reporting requirements for cell lines, including authentication testing status.  The International Journal of Cancer has a mandatory requirement for authentication, and authors are asked about this specifically during manuscript submission.

 

Including a requirement for cell line authentication means more effort from everyone involved - editors, reviewers and authors.  But the end result is more reliable research.  Kudos to all involved here.

 

Eight AACR journals, including Cancer Research
http://www.aacrjournals.org/site/InstrAuthors/ifora.xhtml#celllineuse

 

200+ BioMed Central journals, including BMC Cancer

http://www.biomedcentral.com/about/editorialpolicies#StandardsofReporting

 

Five Endocrine Society journals, including the Journal of Clinical Endocrinology and Metabolism
http://press.endocrine.org/page/authors#mozTocId949960

 

All Nature journals, including Nature and Nature Methods
http://www.nature.com/authors/policies/availability.html#further

 

Three Society for Endocrinology journals, including Journal of Endocrinology
http://joe.endocrinology-journals.org/site/misc/For-Authors.xhtml

 

Biotechniques

http://www.biotechniques.com/authors/

 

Carcinogenesis
http://www.oxfordjournals.org/our_journals/carcin/for_authors/general.html

 

Cell Biochemistry and Biophysics
http://www.springer.com/life+sciences/biochemistry+%26+biophysics/journal/12013

 

Cell Biology International
http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1095-8355/homepage/ForAuthors.html

 

International Journal of Cancer
http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1097-0215/homepage/ForAuthors.html

 

Investigative Ophthalmology & Visual Science

http://iovs.arvojournals.org/ss/forauthors.aspx

 

In Vitro Cellular & Developmental Biology - Animal
http://www.sivb.org/info_IVA.pdf

 

Journal of Molecular Biology
http://www.elsevier.com/wps/find/journaldescription.cws_home/622890/authorinstructions#N10E75

 

Journal of the National Cancer Institute
http://www.oxfordjournals.org/our_journals/jnci/for_authors/ms_prep.html

 

Molecular Vision
http://www.molvis.org/molvis/instructions.html

 

Neuro-Oncology
http://www.oxfordjournals.org/our_journals/neuonc/for_authors/

 

PLOS One

http://www.plosone.org/static/guidelines#cell

more...
No comment yet.
Scooped by Amanda Capes-Davis
Scoop.it!

ICLAC Nature correspondence urges authentication of xenograft models

Today's issue of Nature includes correspondence from the International Cell Line Authentication Committee (ICLAC), urging that new cancer models need authentication testing.

We desperately need good models to explore why cancer happens and how we can treat it. Cell lines have been used for many years and have enabled many cancer breakthroughs. But, as noted by NIH previously, older models do not always have good clinical data. We need new models, particularly for cancer types that are difficult to study - for example, from cancer types that do not grow well outside the body and so where cell lines are difficult to establish.

But there is always a risk when we develop new models that we start back at the beginning, without learning from previous work.  For cancer models, we have learned from the last five decades of cell culture. We know that contamination and misidentification are common. We know that authentication testing and other quality control is essential for research to be reliable and reproducible. We must not lose those hard-earned lessons.

We urge researchers who are developing new models to think about how to make their models last for the next five decades. There are very simple steps that you can take to "future proof" your work.

Storing original material for quality control comparison is easy.

Recording basic information - even the date that you started work on that model - is easy and will help other scientists in future.

Considering the risks to your research - including the possibility of contamination and misidentification - is harder, but there are guidelines and resources out there to help you work out what to do.

Owning the possible flaws in your model system or your research is perhaps the hardest thing to do. But as scientists, we must all think critically about the strengths and weaknesses of our research. And that includes the cell-based models that we rely on for biomedical research.

ICLAC's Nature correspondence can be found here:

The corresponding author is yours truly (Amanda Capes-Davis @CellDetective). If you would like to discuss further, please contact me on Twitter or send me an email using the contact details on the correspondence page.
more...
No comment yet.
Scooped by Amanda Capes-Davis
Scoop.it!

Zika virus shows importance of cell culture for viral research

Zika virus shows importance of cell culture for viral research | Cell Line Contamination | Scoop.it

Zika virus is a hot topic in the news right now.  But the news articles also show that cell culture remains a hot topic for viral research.

 

The link in the title above is to an article in The Scientist magazine by Kerry Grens, talking about the need for better diagnostics.  When reading Kerry's article, I noticed that scientists at the CDC continue to use cell culture to see if a person has been exposed to Zika virus.

 

A similar technique was used in the 1950s for polio virus.  HeLa cells were grown on a massive scale at the Tuskegee Institute, producing approximately 600,000 cultures that were then used to evaluate the success of the Salk polio vaccine.

 

Cell culture is not typically used as a diagnostic test; the number of labs that work with live Zika virus are limited.  However, Zika virus grows well in certain cell lines and can be grown for sequencing and study of the virus.

 

The nature of a cell line is important, even for virus research.  A recent study showed that different strains of HeLa have varying effects on growth of coxsackievirus.  The study included STR profiling to confirm that cultures were not misidentified.

 

For more information on Zika virus, see:

http://www.cdc.gov/zika/

https://www.phe-culturecollections.org.uk/news/ncpv-news/growing-concerns-over-zika-virus-epidemic.aspx

 

For a historical perspective on HeLa at the Tuskegee Institute, see:

http://www.ncbi.nlm.nih.gov/pubmed/?term=6358339

 

For the study looking at heterogeneity of HeLa strains, see:

http://www.ncbi.nlma.nih.gov/pubmed/?term=23408555

more...
No comment yet.
Scooped by Amanda Capes-Davis
Scoop.it!

Hundreds of researchers are using the wrong cells. That's a major problem. - Retraction Watch

Hundreds of researchers are using the wrong cells. That's a major problem. - Retraction Watch | Cell Line Contamination | Scoop.it

Many of you are familiar with the website Retraction Watch, established by Ivan Oransky and Adam Marcus to keep an eye on retractions in the scientific literature.  Retraction Watch ran a two-part feature on misidentified cell lines this week.

 

The first blog post on misidentified cell lines was from yours truly:

http://retractionwatch.com/2015/12/08/hela-is-the-tip-of-the-contamination-iceberg-guest-post-from-cell-culture-scientist/

 

The second blog post on the economic cost of misidentified cell lines, and changes that could have a real impact on the problem, was from Leonard Freedman of GBSI:

http://retractionwatch.com/2015/12/09/its-time-to-set-standards-in-the-lab-guest-post-from-leonard-freedman/

 

Journal articles get retracted when results are found to be unreliable - for all sorts of reasons, from honest error to deliberate fraud.  However, it is worth noting that very few articles get retracted because of cell line problems. 

 

In 2014, a study was published looking at the sources of error in the retracted scientific literature.  Authors Arturo Casadevall, Ferric Fang and Grant Steen could only find six retractions due to problems with cell lines.

 

To read their article in FASEB Journal, see:

http://www.fasebj.org/content/28/9/3847.long

more...
No comment yet.
Scooped by Amanda Capes-Davis
Scoop.it!

Cell Line Authentication: Finding the Core Solution

Cell Line Authentication: Finding the Core Solution | Cell Line Contamination | Scoop.it

A previous post talked about a recent survey and editorial on cell authentication, published by BioTechniques.

 

BioTechniques has now announced a five-part series focused on reproducibility.  The first article looks at cell line authentication and the importance of core facilities in making testing more accessible.

 

Authentication testing services are becoming more widely available and core facilities are an important part of that progression.  However, as this article emphasizes, services from core facilities are underutilized.  For whatever reason, despite easy access, the core facilities here report only a handful of cell lines are being tested.

 

Cost is commonly quoted as a barrier.  However, the average price quoted in this article ($100-150) is less than the cost of a restriction enzyme.

 

Duke University has recently announced free authentication testing for a short period of time from its core facility.  I would challenge any scientist working at the Duke University Faculty of Medicine to take up this offer and make sure your cell lines are fit for purpose.

 

MD Anderson has a policy for cell line authentication that requires researchers to test their cell lines on an annual basis, and provide authentication data when transporting to an external laboratory.  This sets a fantastic benchmark for other institutions to consider.

 

For more on Duke University's offer, see:

https://www.dtmi.duke.edu/news/free-human-cell-line-authentication-assays-short-time

 

For more information on MD Anderson's Cell Line Authentication Policy from its Characterized Cell Line Core Facility, see:

http://www.mdanderson.org/education-and-research/resources-for-professionals/scientific-resources/core-facilities-and-services/characterized-cell-line-core-facility/index.html

more...
No comment yet.
Scooped by Amanda Capes-Davis
Scoop.it!

NIH Workshop on Reproducibility in Cell Culture Studies

NIH Workshop on Reproducibility in Cell Culture Studies | Cell Line Contamination | Scoop.it

One of the challenges we face doing good cell culture is that it is hard to define what "good" cell culture actually is.  Many of us are trained by the lab where we first use cell culture techniques.  There can be a great deal of variability in that training - from very good to limited to none at all.  So how we do pass "good" cell culture on to others?

 

NIH has recently held a workshop focused on reproducibility in cell culture studies.  As part of looking at reproducibility, the workshop is also thinking about "good" cell culture and how to report that for others to reproduce.  NIH has videocasted the two-day workshop.

 

Day 1 of the workshop can be found at:

http://videocast.nih.gov/summary.asp?Live=16876&bhcp=1

 

Day 2 of the workshop can be found at:

http://videocast.nih.gov/summary.asp?Live=16884&bhcp=1

 

I see this as a great step forward and hope to learn a great deal myself from the workshop discussion.

more...
No comment yet.
Scooped by Amanda Capes-Davis
Scoop.it!

Cell Culture Resources

Sometimes it can be difficult to find information on how to do good cell culture.  If you do not have access to journals and cannot afford to buy a good textbook, where do you go for information?

 

There are some excellent free resources out there if you know where to look.

 

The ICLAC website has some freely available resources on misidentified cell lines and how to do authentication testing:

http://iclac.org/resources/

 

The British Journal of Cancer has published Guidelines for the Use of Cell Lines in Biomedical Research, with a wealth of information on how to do good cell culture.  The article is freely available on their website:

http://www.nature.com/bjc/journal/v111/n6/full/bjc2014166a.html

 

ATCC has released some very helpful guides for a number of cell culture applications, from animal cell culture to stem cell culture to microbiology.  The guides can be found on their website:

http://www.atcc.org/en/Guides/Guides.aspx

 

The Culture Collections of Public Health England have an excellent manual on Fundamental Techniques in Cell Culture, and a DVD Guide to Successful Cell Culture.  These can be found at:

https://www.phe-culturecollections.org.uk/promotions/labhandbook.aspx

https://www.phe-culturecollections.org.uk/promotions/cellculturedvd.aspx

 

Finally, thinking of individual scientists, a big thank you goes to John Ryan of Corning, who wrote a number of technical bulletins on cell culture and whose work has helped many scientists become more aware of the issues.  John Ryan's articles are harder to find these days, but still very well worth reading.

more...
No comment yet.
Scooped by Amanda Capes-Davis
Scoop.it!

12 Top Tips for Working in Your Cell Culture Hood

12 Top Tips for Working in Your Cell Culture Hood | Cell Line Contamination | Scoop.it

Question: Why do we use a biosafety cabinet to work with cell lines?

 

Answer: any live culture carries some degree of biohazard risk.  Cells can carry infectious agents from a number of sources.  The donor may carry an infectious disease - this risk applies to both human and animal tissue, and is an important reason why modern animal facilities perform health monitoring of animals on a regular basis.  Other cell lines can also act as biohazard risks.  Transmission of infectious agents across cell cultures is well documented and has led to disease in research workers.

 

Fortunately, good cell culture practice minimizes those risks.  Wearing personal protective equipment (PPE), working in a biohazard cabinet, reducing your contact with aerosols - these are all important and will help to keep you safe when working with live cells.

 

Bitesize Bio is a handy resource when it comes to biosafety.  The link in the title above goes to a blog on the site with great tips on how to work in a biosafety cabinet.  For more tips on lab safety, see:

 

http://bitesizebio.com/category/survive-thrive/lab-safety/

 

The scientists amongst us might also be interested in these recent publications on biosafety and the risk of viral contamination:

 

http://www.ncbi.nlm.nih.gov/pubmed/25973418

http://www.ncbi.nlm.nih.gov/pubmed/25927683

more...
No comment yet.
Scooped by Amanda Capes-Davis
Scoop.it!

BioSample Takes Big Step Forward with 2992 human cell line STR profiles

I am a strong supporter of community databases where scientists can share their data for everyone's benefit.  I have used NCBI's reference database PubMed for more than 15 years.  Now I am excited to see another NCBI database take a big step forward.

 

NCBI's BioSample database stores information about biological samples, including cell lines.  The BioSample database is designed to record STR profiles - essential testing to show that cell lines are authentic and help ensure they are fit for purpose.  The database framework follows recommendations set out in a written Standard for human cell line authentication.

 

To be successful, BioSample needs to hold results from lots of different cell lines.  So the research community needs to submit STR profiles - which admittedly takes time to do.  I was delighted to see a paper come out in Nature recently with new cell line resources, including both STR and SNP profiles.  The authors from Genentech have taken that time and submitted their STR profiles to BioSample as a community resource.

 

BioSample now holds 2992 STR profiles from a wide variety of human cell lines.  Each STR profile entry has additional information on the cell line and may include the raw data.  You can search the database for a specific cell line name, tissue type etc.  You cannot search for a specific STR profile yet, but hopefully that will come, now that staff have a good size dataset to work with.

 

You can find more information about BioSample here:

http://www.ncbi.nlm.nih.gov/books/NBK169436/

 

More information on the human cell line authentication Standard is here:

http://www.ncbi.nlm.nih.gov/pubmed/20448633

 

You can view the abstract of the recent Nature resources paper here:

http://www.ncbi.nlm.nih.gov/pubmed/25877200

 

For other important STR profile databases, see the ICLAC website:

http://iclac.org/databases/

more...
No comment yet.
Scooped by Amanda Capes-Davis
Scoop.it!

Personalised cancer treatment a step closer with world's first 'living biobank'

Personalised cancer treatment a step closer with world's first 'living biobank' | Cell Line Contamination | Scoop.it

Hans Clevers has done it again.

 

I have posted several times on the 3D organoid cultures grown by Hans Clevers and his team at the Hubrecht Institute.  The link in the title above goes to a news item in the Guardian, talking about applying these organoid cultures to patient treatment.

 

In a new publication in Cell, Clevers and a host of distinguished colleagues established organoids from patients with colorectal cancer.  Organoids were also established from the patients' normal tissue.  The normal and tumor cells were sequenced and used for high-throughput drug screening.  Bottom line: this information is used for therapy that is targeted specifically to the complex genetic signature displayed by each tumor.

 

Clevers points out that although cell lines remain the workhorse of cancer research, short term culture is a better approach for the individual patient.  The technique also gives good representation of clonal populations, allowing better modeling of cancer behaviour.

 

The original article is well worth reading and can be found at:

 

http://www.cell.com/cell/abstract/S0092-8674(15)00373-6

more...
No comment yet.
Scooped by Amanda Capes-Davis
Scoop.it!

Know Thy Cells | The Scientist

Know Thy Cells | The Scientist | Cell Line Contamination | Scoop.it

Recent changes to policies on cell line authentication are being noticed.

 

This quick "nutshell" summary comes from The Scientist magazine.  Helpful links in the article go to:

 

Nature editorial, "Time to tackle cells' mistaken identity"

http://www.nature.com/news/announcement-time-to-tackle-cells-mistaken-identity-1.17316

 

Nature article with new resources for cell line authentication, annotation and quality control

http://www.nature.com/nature/journal/v520/n7547/full/nature14397.html

 

ICLAC list of misidentified cell lines

http://iclac.org/databases/cross-contaminations/

more...
No comment yet.
Scooped by Amanda Capes-Davis
Scoop.it!

#authenticate - Global Biological Standards Institute

#authenticate - Global Biological Standards Institute | Cell Line Contamination | Scoop.it

How many scientists know about common cell culture problems?  Answer: not many.  Scientists who work with cell lines every day often do not know that common cell culture problems can make their work less reliable and reproducible.

 

Well, it's time to change that answer.

 

The Global Biological Standards Institute (GBSI) has just launched a campaign to raise awareness about cell line authentication.  The #authenticate campaign has a pledge that individuals or organizations can sign; a survey; a video competition; and more.  To find out more visit their website:

http://www.gbsi.org/work/authenticate/

 

Six organizations have signed up as early pledge signatories and champions, including the International Cell Line Authentication Committee (ICLAC).  ICLAC shows its support for the #authenticate campaign here:

http://iclac.org/can-help/authenticate/

more...
No comment yet.
Scooped by Amanda Capes-Davis
Scoop.it!

Biotech firm announces fast test to unmask imposter cell lines

Biotech firm announces fast test to unmask imposter cell lines | Cell Line Contamination | Scoop.it

A new Nature publication provides a great set of resources for cell line authentication, annotation and overall quality control.

 

The authors at Genentech look at a large dataset of human cell lines, obtained from cell line repositories and other sources.  Cell lines are compared using STR and SNP analysis.

 

SNP is a fast and relatively new test for cell line authentication, although other laboratories have already shown it can work well.  Here STR profiling is used when a cell line arrives in the lab, to check against other stocks held worldwide.  The authors then use SNP profiling for internal quality control.

 

But this work is not just about authentication.  The team at Genentech has also developed a standardised framework for naming and describing cell lines, which has the potential to greatly improve cell line searches.

 

The full article - including extensive supplementary information - can be found at:

http://www.nature.com/nature/journal/v520/n7547/full/nature14397.html

more...
No comment yet.
Scooped by Amanda Capes-Davis
Scoop.it!

Male or Female? Why a Cell's Sex Matters | RealClearScience

Male or Female? Why a Cell's Sex Matters | RealClearScience | Cell Line Contamination | Scoop.it

Do you know the sex of the cells that you use for research?

 

An interesting review was published in 2014 on this question.  The authors, from the Rosalind Franklin University of Medicine and Science, conclude that there are differences between male and female cells that may influence experimental results.

 

The review can be found here:

http://ajpcell.physiology.org/content/ajpcell/306/1/C3.full.pdf

 

The review includes a table of cell lines that are commonly used in that journal (AJP-Cell Physiol), which looks like a really helpful resource.

 

The NIH has recently announced a policy to balance sex in cell and animal studies, although some feel that this may cause more problems than solutions:

http://www.nature.com/news/policy-nih-to-balance-sex-in-cell-and-animal-studies-1.15195

http://www.nature.com/nature/journal/v510/n7505/full/510340b.html

more...
No comment yet.