Posts in Core Rigor and Reproducibility (CoRRe)

Rigor and Reproducibility funding opportunities
Funding
Opportunities<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.nih.gov_research-2Dtraining_rigor-2Dreproducibility_funding-2Dopportunities&d=DQMFaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=qT7fPVDkMOYTVUp8gyBQd_AI8ia1-pr3jfWi81PL--8&m=0El9ppwgmic-GASl4LBhhCtQas0XP-rhrEpP0EKJJ9w&s=xboiKpKU6eMcJRIIb7sS7nyhTXJW1jKlsecQESnlhWY&e=>
Title: Administrative Supplements for Validation Studies of Analytical Methods
for Dietary Supplements and Natural Products (Admin
Supp)<https://urldefense.proofpoint.com/v2/url?u=https-3A__grants.nih.gov_grants_guide_pa-2Dfiles_PA-2D17-2D447.html&d=DQMFaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=qT7fPVDkMOYTVUp8gyBQd_AI8ia1-pr3jfWi81PL--8&m=0El9ppwgmic-GASl4LBhhCtQas0XP-rhrEpP0EKJJ9w&s=z4BqCHdnAbpDDbXglpRlGOeCSiYhqm9VmBj3dg-fRz8&e=>
ID Number: PA-17-447
Earliest Submission Date: September 15, 2017
Application Due Date: October 13, 2016; June 13, 2017; October 13, 2017; June
13, 2018; October 15, 2018; June 13, 2019
Title: Program to Assess the Rigor and Reproducibility of Exosome-Derived
Analytes for Cancer Detection
(R21)<https://urldefense.proofpoint.com/v2/url?u=https-3A__grants.nih.gov_grants_guide_pa-2Dfiles_PAR-2D16-2D277.html&d=DQMFaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=qT7fPVDkMOYTVUp8gyBQd_AI8ia1-pr3jfWi81PL--8&m=0El9ppwgmic-GASl4LBhhCtQas0XP-rhrEpP0EKJJ9w&s=1accdIuP7zU_ooMFMC5Rbj-IKsWTk_yaoVh29BAvVak&e=>
ID Number: PAR-16-277
Earliest Submission Date: September 13, 2016
Application Due Date: October 13, 2016; June 13, 2017; October 13, 2017; June
13, 2018; October 15, 2018; June 13, 2019
Title: Program to Assess the Rigor and Reproducibility of Exosome-Derived
Analytes for Cancer Detection
(R01)<https://urldefense.proofpoint.com/v2/url?u=https-3A__grants.nih.gov_grants_guide_pa-2Dfiles_PAR-2D16-2D276.html&d=DQMFaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=qT7fPVDkMOYTVUp8gyBQd_AI8ia1-pr3jfWi81PL--8&m=0El9ppwgmic-GASl4LBhhCtQas0XP-rhrEpP0EKJJ9w&s=pcc1jhdBcBTKuQByHFbgvKYvOBseOwYX5ciauQ_hjSw&e=>
ID Number: PAR-16-276
Earliest Submission Date: September 13, 2016
Application Due Date: October 13, 2016; June 13, 2017; October 13, 2017; June
13, 2018; October 15, 2018; June 13, 2019
Title: Tools for Cell Line Identification (SBIR
[R43/R44])<https://urldefense.proofpoint.com/v2/url?u=http-3A__grants.nih.gov_grants_guide_pa-2Dfiles_PA-2D16-2D186.html&d=DQMFaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=qT7fPVDkMOYTVUp8gyBQd_AI8ia1-pr3jfWi81PL--8&m=0El9ppwgmic-GASl4LBhhCtQas0XP-rhrEpP0EKJJ9w&s=SnTbEqvBQX8W0OLogxgKBm7dos1nP1b05KYuxfk05nQ&e=>
ID Number: PA-16-186
Earliest Submission Date: August 5, 2016
Application Due Date: Standard dates
apply<https://urldefense.proofpoint.com/v2/url?u=http-3A__grants.nih.gov_grants_how-2Dto-2Dapply-2Dapplication-2Dguide_due-2Ddates-2Dand-2Dsubmission-2Dpolicies_standard-2Ddue-2Ddates.htm&d=DQMFaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=qT7fPVDkMOYTVUp8gyBQd_AI8ia1-pr3jfWi81PL--8&m=0El9ppwgmic-GASl4LBhhCtQas0XP-rhrEpP0EKJJ9w&s=0B4kxj6jTYdyY-g4VrwC7dCgT-Dis0O3bDgqh0dpXnE&e=>


Sheenah M. Mische, Ph.D.
Sr. Director, Division of Advanced Research Technologies
Associate Professor (Research)
Department of Pathology
NYU Medical Center
550 First Avenue
MSB 346
New York, NY 10016
O: 212 263 0859
M: 347 407 2768
http://ocs.med.nyu.edu/


------------------------------------------------------------
This email message, including any attachments, is for the sole use of the
intended recipient(s) and may contain information that is proprietary,
confidential, and exempt from disclosure under applicable law. Any unauthorized
review, use, disclosure, or distribution is prohibited. If you have received
this email in error please notify the sender by return email and delete the
original message. Please note, the recipient should check this email and any
attachments for the presence of viruses. The organization accepts no liability
for any damage caused by any virus transmitted by this email.
=================================

Hi,

I was recently working with an investigator on trouble shooting their ChIP-Seq
experiment that apparently had “stopped working”.  They insisted nothing had
changed.  During the discussion they indicated that they had “even purchased a
brand new Ab” against the target they were pulling down.  After hearing this,
some of the horror stories about Ab specificity that were shared at the ABRF
2017 annual meeting suddenly came to mind.  I suggested to the investigator
that he may want to confirm the specificity and working titer of this “new”
antibody. He did a titration experiment and found that the experiment was now
“working again” if he used a higher titer of the Ab for the pull down.

As noted above, we also discussed Ab validation.  I pointed out an article by
Natan Blow on page 51 of the August Issue of BioTechniques. He noted that “many
articles have been written about the problem of antibody validation, but far
fewer have focused on the solutions.  In the article, there is reference to a
scoring system that was develop by the GBSI that could be used to evaluate Abs.
There was also a reference to David Rimm (2010)  that illustrated a proposed
validation flowchart.

I shared these validation workflows with the investigator and he indicated that
he would not likely follow through the validation workflows suggested by this
article.   He expects the provider of the Ab to have already done the
validation.

I am curious to know if other cores have had similar experiences when working
with investigators who are using Abs to prepare samples for use in your
facility.  Minimally, what are you advising your users to do when working with
Abs?

Thanks,

Kevin
--
Kevin L. Knudtson, Ph.D.
University of Iowa
Director, IIHG Genomics Division
323 EMRB
Iowa City, IA  52242

TEL: 319-335-7251
FAX: 319-335-6737
E-mail: <email obscured><email obscured>>

Please disregard.

This is just to test the system.

Nancy,

Under Kevin's leadership CoRRe is pulling a manuscript together to publish in
JBT.  I am sure we will post it here, as well as the ABRF Newsletter once it is
online.

Was there something in particular you were interested in knowing from what was
presented on the poster at ABRF2017?

Frances

Dear All,
This is a test of the response function

Henriette
CCoRRe member
University of Michigan

Dear CoRRe Discussion Forum Participants,

Paula Turpen shared a new term that she and I were unfamiliar with until
she heard it on NPR ... the “R” Index or Replicability Index.  Have any of
you heard about it?

Click this link for a podcast of the interview with interview with Ulrich
Schimmack on the NPR radio show “on the media”
<http://www.npr.org/podcasts/452538775/on-the-media> where Paula first
heard about it.  Uli’s session comes in at the 10:45 minute mark, and lasts
for 10 minutes.

You can also check out their blog on this topic
<https://replicationindex.wordpress.com/>.

Thought on the "new" R Index?

Frances

Hi Brian,
As far as I know, NCI asks investigators to add to their grant applications a
section named "Rigor and reproducibility". This is mandatory for any grant,
disregarding if you are a Core Facility or research or clinical laboratory. For
that reason, I created one for my Core, based on the assays that we perform to
validate internally our antibodies. In my organization also exists a CLIA
laboratory that further validates antibodies that are intending to be used in
diagnostic or potential therapy. That lab is not a Core.
I found an interesting Commentary, signed by authors from academic laboratories
that are also consultants for Biopharma companies. But may be you already have
it.
"A proposal for validation of antibodies", published in
Nature Methods 13, 823–827 (2016) doi:10.1038/nmeth.3995
http://www.nature.com/nmeth/journal/v13/n10/full/nmeth.3995.html

Taking into account that recently another failure of a therapeutic antibody was
reported,
please see bellow from a blog in Antibody Network, rules should be specific,
clear and international. Not comparable to this failure but bad enough, once I
was using a commercial antibody anti BST-2, sold by a recognize vendor, and
happened to be an anti BEST-2, wrongly reported in the company website.

Another antibody failure story in clinical application
"After having seen two out of three HER2 antibodies used as FDA-approved
diagnostics cross-reactive to HER4 (Schrohl et al, Histopathology 2011 Nov;
59(5):975-983), here we have another example of failed antibody
characterization with clinical consequences: The most popular ERbeta
antibodies, used in breast cancer research, turn out non-specific. Worse, ER
beta is not even a validated marker for breast cancer at all. See
http://www.nature.com/articles/ncomms15840"

Microscopy labs may be interested in this latest report by Deagle, Wee and
Brown from McGill titled:  'Reproducibility in light microscopy: Maintenance,
standards and SOPs'

The International Journal of Biochemistry & Cell Biology
Volume 89, August 2017, Pages 120–124

http://www.sciencedirect.com/science/article/pii/S1357272517301449

Great idea for a discussion forum!

Is there a link to the results from the R&R survey from this spring?

We are setting up some R&R recommendations for our cores at our University. I'd
love to hear what other institutions are doing to make R&R more visible and
accessible.

Thanks to Kevin Knudtson and the CCoRRE Committee for addressing this important
topic through ABRF.

Nancy Fisher
University of North Carolina at Chapel Hill

Hello all,

Are there any resources that describe validation protocols for antibodies used
in research labs?  Is NIH adopting any antibody validation standards that
investigators must comply with to obtain grant funding or to publish work
funded by NIH?

Thanks in advance,

Brian