GenotypeTissue

GenotypeTissue is a framework and database concept that links individuals' genomic variation to tissue-specific molecular phenotypes. It aims to map how genetic differences influence gene expression, epigenetic marks, and other molecular traits across multiple human tissues, enabling tissue-resolved interpretation of genetic variation and its role in health and disease.

Data sources include genotype data from sequencing or arrays and tissue-derived measurements such as RNA-seq, DNA methylation, proteomics, and chromatin accessibility. Donor metadata (age, sex, ancestry) and detailed tissue annotation are stored alongside samples. Standardized processing and harmonization are applied to enable cross-sample analyses, with privacy-preserving access controls to protect donor identities.

Analyses typically cover tissue-specific QTL mapping (expression, methylation, protein), cross-tissue networks, and causal inference linking variants to phenotypes. Use cases include annotating GWAS signals, prioritizing tissue-relevant drug targets, and elucidating mechanisms of complex diseases. Limitations include uneven tissue representation, batch effects, technical variability, and the challenge of integrating diverse data types across platforms.

Future directions may include single-cell resolution, longitudinal data, and integration with multi-omics at the single-cell level, as well as expanding data standards and open-access policies to improve reproducibility and collaborative discovery.