We thank the Human Gene Mutation Database (HGMD) team for critically analysing our results and highlighting some potential problems with our analysis.1

Many of the criticisms raised by Stenson et al2 relate to mutations that were outside the terms of reference of the study. For instance, a major criticism raised by Stenson et al was that the review was not comprehensive in that we neglected to compare all categories of mutations. We limited our comparison to single-base mutations, as it was found to be too difficult to reliably text-mine other mutation types from Online Mendelian Inheritance in Man (OMIM). This could be viewed as indirect discrimination against HGMD, but these mutations do represent the majority of characterised mutations in the database and thus represent a reasonable variable to quantify.

We concluded that both OMIM and HGMD were the most comprehensive resources, but differences between them, including missing genes, highlighted the importance of using both resources when searching for information on a gene.

Another criticism was our failure to distinguish between somatic and heritable mutations; however, we did not claim to do so. Both are associated with disease. It is not clear why HGMD does not include mitochondrial mutations, as these are inherited.

Several claims made by us, which are disputed by Stenson et al, are addressed in detail below.

Claim 1: 143 genes are present in OMIM but have no corresponding HGMD entry

Of the 143 genes identified as not having single-base mutations in HGMD, even though they are present in OMIM, 30% of these genes were missing from HGMD because the database was not up to date, and another 45% were excluded from …