Re: Reproducibility: Standardize antibodies used in research

Posted by George McNamara on
URL: http://confocal-microscopy-list.275.s1.nabble.com/Reproducibility-Standardize-antibodies-used-in-research-tp7583440p7583444.html

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Hi Tim, Martin and listserv,

the second graphic "Money down the drain" in the article

http://www.nature.com/news/reproducibility-standardize-antibodies-used-in-research-1.16827

estimates that $350 million out of $700 million spent in the US annually
on protein binding reagents is wasted on 'bad' antibodies. There are
several (perhaps many) companies that can generate and deliver
substantial protein AND DNA sequences for recombinant antibodies or
alternatives for $3,500 or less. So, if all $350M in bad spending were
moved to 'g&d', this would enable 100,000 new antibodies or antibody
like molecules to be made and delivered every year (and that scale would
drive costs down even more and increase options). Depending on
need/value of each new antibody, this could be exclusively distributed
by a company, available through many companies, or available as a $65
expression plasmid from addgene.org (and addgene sells some multiwell
plates of plasmids for less than $65/plasmid).

If US researchers continue to waste money on bad reagents, they should
not be surprised if NIH stops funding them. Similar changes may happen
in other countries.

It is now straightforward to sequence paired immunoglobulin VH and VL
(first abstract) or TCR Valpha/Vbeta (from single cells - not the only
papers):

http://www.ncbi.nlm.nih.gov/pubmed/23334449

DeKosky BJ, Ippolito GC, Deschner RP, Lavinder JJ, Wine Y, Rawlings BM,
Varadarajan N, Giesecke C, Dörner T, Andrews SF, Wilson PC, Hunicke-Smith SP,
Willson CG, Ellington AD, Georgiou G. High-throughput sequencing of the paired
human immunoglobulin heavy and light chain repertoire. Nat Biotechnol. 2013
Feb;31(2):166-9. doi: 10.1038/nbt.2492. Epub 2013 Jan 20. PubMed PMID: 23334449;
PubMed Central PMCID: PMC3910347.

http://www.ncbi.nlm.nih.gov/pubmed/24952902

Han A, Glanville J, Hansmann L, Davis MM. Linking T-cell receptor sequence to
functional phenotype at the single-cell level. Nat Biotechnol. 2014
Jul;32(7):684-92. doi: 10.1038/nbt.2938. Epub 2014 Jun 22. PubMed PMID: 24952902.


As for antibodies or TCR's that will be used therapeutically -- for
Ebola virus victims, for example -- it makes sense to use recombinant
human proteins instead of "humanizing" mouse antibodies.

See also my and others comments at

http://www.nature.com/news/reproducibility-standardize-antibodies-used-in-research-1.16827

and the Baskin editorial and Hewitt article (both open access) at

http://jhc.sagepub.com/content/62/10.toc

Sincerely,

George


On 2/23/2015 12:06 PM, Feinstein, Timothy wrote:

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>
> I could imagine a Œsoft¹ introduction working fine.  These will be far
> more expensive than standard antibodies, at least at first, but large
> vendors could easily introduce high demand products like anti-smooth
> muscle actin as an alternative reagent for people who want to spend more
> for extra validation and reproducibility.  The value for diagnostic
> medicine would be quite high.   Eventually the economy of scale would make
> these accessible to research labs.  As just another new and useful
> technology I think it has a lot of use, but I cannot imagine journals
> would ever demand that researchers use nothing but.  It will never be
> practical to submit every possible type of antibody to cloning and in
> vitro synthesis.
>
> Best,
>
>
> Tim
>
> Timothy Feinstein, Ph.D. | Manager, Core for
> Confocal Microscopy and Quantitative Imaging
> 333 Bostwick Ave., N.E., Grand Rapids, Michigan 49503
> Phone: [phone] | Email: [hidden email]
>
>
>
>
>
>
>
> On 2/23/15, 10:13 AM, "Martin Wessendorf"<[hidden email]>  wrote:
>
>    
>> *****
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>>
>> George et al.--
>>
>> On 2/22/2015 11:31 PM, George McNamara wrote:
>>      
>>> I encourage everyone on the listserv to read Bradbury et al's comment
>>> in Nature, and to pass it on to your colleagues who use antibodies and
>>> similar reagents.
>>>
>>> full text is freely available at
>>>
>>>
>>> http://www.nature.com/news/reproducibility-standardize-antibodies-used-in
>>> -research-1.16827
>>>
>>>
>>> Summary:
>>>
>>> *To save millions of dollars and dramatically improve reproducibility,
>>> protein-binding reagents must be defined by their sequences and
>>> produced as recombinant proteins, say Andrew Bradbury, Andreas
>>> Plückthun and 110 co-signatories.*
>>>
>>>        
>> Interesting idea, as long as you aren't doing research in an area for
>> which the soon-to-be required recombinant antibodies aren't available.
>>
>> To quote from the article, "If these steps are taken, scientists will not
>> want to use unsequenced binding reagents, and the absence of sequencing
>> information will lead to market disadvantages for vendors. The
>> uncharacterized, unsequenced research antibody will become obsolete."
>> --Not all antibodies are generated by companies--many of the most
>> important are generated by researchers themselves.  This proposal could
>> have the effect of forcing most all
>> biomedical research down a set of predetermined, prescribed channels,
>> with only limited room for development of new reagents.  Their goal is
>> worthy, but this policy strikes me as likely to have some unintended bad
>> consequences.
>>
>> Martin Wessendorf
>>
>>
>> --
>> Martin Wessendorf, Ph.D.                   office: [phone]
>> Assoc Prof, Dept Neuroscience                 lab: [phone]
>> University of Minnesota             Preferred FAX: [phone]
>> 6-145 Jackson Hall, 321 Church St. SE    Dept Fax: [phone]
>> Minneapolis, MN  55455                    e-mail: [hidden email]
>>      
>    

--



George McNamara, Ph.D.
Single Cells Analyst
L.J.N. Cooper Lab
University of Texas M.D. Anderson Cancer Center
Houston, TX 77054
Tattletales http://works.bepress.com/gmcnamara/42