https://orcid.org/0000-0002-4393-727X
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Yaxuan Yu, Rhodri Ceredig, Cathal Seoighe, Response to Comment on “A Database of Human Immune Receptor Alleles Recovered from Population Sequencing Data”, The Journal of Immunology, Volume 198, Issue 9, May 2017, Pages 3373–3374, https://doi.org/10.4049/jimmunol.1700349
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We share the view of Dr. Watson and colleagues on the importance of germline databases (GLDB) of immune receptor genes and thank them for their interest in our work (1). Whereas we fully agree with them on many of the caveats that apply to alleles inferred from genome sequence data (discussed further below), we feel that it is important for us first to clarify the objectives of our article, to avoid any misinterpretation. Watson et al. state that we propose a solution to the incompleteness and inaccuracy of existing GLDBs; however, we made no claim that inferring putative germline alleles from genome sequence data represents a complete solution to this problem. We showed evidence in our article that inferred germline alleles can contribute to the solution, particularly concerning incompleteness, and that this can lead to improved alignment performance. But we consider the alleles inferred in this way to be putative, and they are generally referred to as such in our article.
