HPDB: a comprehensive human pigmentation gene database

Abstract

The pigmentation of human skin, eyes, and hair is a polygenic, heritable and multifactorial trait. The present day global variation in pigmentation across the globe is shaped by a fine tuning of natural selection and UV exposure. Sequencing technologies have fast paced the discovery of associated variants. However, with the increasing lists of associated variants in pigmentation biology, there is an imperative need to catalog them. Although many databases based on gene function, genetic phenotype, mouse coat color, and pigmentation disorders exist currently, there are hardly any databases that explicitly focus on the human pigmentation genes. Furthermore, it is imperative that clinicians have access to information on genetic variants associated with pigmentation disorders. To address this need, we developed the Human Pigmentation Database (HPDB) v1.0, an open-access, web-based, manually curated resource integrating data from 663 peer-reviewed publications on pigmentation variants and disorders. HPDB currently catalogs 4,771 genetic variants across 866 human pigmentation-associated genes, enabling efficient retrieval of gene-and variant-specific information through multiple search interfaces. HPDB is an open-access, user-friendly resource with intuitive basic and advanced search functions, enabling efficient retrieval of information by rsID, gene, author, keyword, and other attributes. Furthermore, it provides a dedicated search interface for 111 pigmentation disorders, encompassing 326 genetic variants across 145 associated genes. With regard to the interoperability of biological data, information, knowledge, and computational resources, the database adheres to standards of the minimal information about bioinformatics investigation (MIABiI) guidelines. We anticipate that HPDB will serve as a valuable resource for researchers and clinicians by providing a comprehensive catalog of the genetic architecture underlying normal pigmentation variation and pigmentation disorders. Beyond advancing pigmentation biology, HPDB has the potential to facilitate genetic diagnosis, translational research, precision medicine, and public health initiatives.