molecularly characterized = with molecular features?

This is difficult English, jargon for the most part imho.

"characterised by" means, having (the following) recognisable features in common

Thanks.
With your explanation, we've moved a step forward.
Still waiting though.

Please yourself.

Let's break it down into parts.

primary immunodeficiency diseases = autoimmune diseases that are congenital = inherited as a chromosomal deficiency and present since birth. This contrasts with acquired autoimmune diseases that arise as a result of infection, other diseases, or possible environmental exposures.

molecularly charactarized = the molecular characterization (=gene expression) of a particular primary immunodeficiency disease.

autoimmune phenotype = all of the observable traits of a particular autoimmune disease.

So, a large number of molecular characterizations of primary immunodeficiency diseases have been completed. These immunodeficiencies are present in one or more autoimmune phenotypes.

I think the focus of this statement are the words "surprisingly large" and "already". This is a fairly new research field and they were somewhat amazed at how much they'd accomplished in such a short time.

Thank you JPB.

Since there is a conjunction "in which," so, the word "which" refers to the sentence ("the surprisingly large number of primary immunodeficiency diseases already molecularly characterized")?

That is: the primary immunodeficiency diseases present before us the traits of autoimmune (autoimmune phenotype)?

I'm sorry, ori, I don't understand your question.

In short, which = ?

I read the sentence as:
These immunodeficiency diseases are characterized with one or more autoimmune phenotypes.

Am I on the right track?