How many percentage of cdr3 are exactly the same between two people?


#1

or same people between two time point? in bcr heavy chain.

If you know, thanks for telling me. If not, take a guess?


#2

Between two people - depends on assembly probability (see my other reply) and sampling depth. The deeper we sample the higher is the chance of finding matching CDR3. For TCRb CDR3 amino acid sequence we’ve identified that upon exhaustive sampling one can get up to ~40% overlap (http://journal.frontiersin.org/article/10.3389/fimmu.2013.00466/full), for B-cells this should be smaller due to hypermutations and CDR3 length.

Between the same person - depending on sample composition. Naive cells will mostly not overlap, as for other subsets this depends on sampling probability and method biases.


#3

As well as sampling depth, it also depends on what B cell isotype/subset you are looking at, and whether there is a common immune stimulus. You also need to be wary that cross-sample contamination will contribute to this. As a very rough guide, I would say ~0.1%.

It is a topic that we have looked at quite a lot, and you can get a bit more information from these. Happy to answer any questions on them:



http://www.ebiomedicine.com/article/S2352-3964(15)30217-6/abstract


#4

I finally sit down and spend some time to check the data I have. we use similar method to process tcr and bcr data. for each patient, there are several time point.

tcr

bcr

as said by @mikhail.shugay, there are many factors affect the result and I did not provide a detailed method we obtain and process the data.

the result I provide probably are not very useful, but someone may be interested.


#5

That is very interesting. Thanks for sharing!


#6

another paper related.

Table 1.

PS: Thanks to the author for publishing the data. (although not the raw sequence data, it is still good to have the cdr3 data)