neomerDB

neomerDB catalogs neomers, which are short k-mers absent from the human reference genome but recurrently present in cancer tissues due to somatic mutations, across cancer types and organs.

Key Features:

• Cancer-type and organ-specific neomer catalogues: The database encompasses neomers associated with each cancer type and organ derived from tumour-matched samples.
• Population germline filtering: Nullomers and neomers that can arise due to germline variants were removed using data from 76,215 whole genomes and 730,947 whole exomes of individuals from diverse ancestries.
• Liquid biopsy detection support: The database includes neomers demonstrated to detect glioblastoma from cell-free DNA and cell-free RNA samples.
• Interactive data access: Advanced search capabilities, interactive visualizations, and download options for neomer biomarkers are provided.

Scientific Applications:

• Cancer biomarker discovery: neomerDB supports identification of neomer biomarkers for population screening, early cancer detection, monitoring, and recurrence surveillance.
• Liquid biopsy cancer detection: Neomers from the database can be utilized to detect glioblastoma from liquid biopsy samples, achieving a Receiver Operating Characteristic - Area Under the Curve score of 0.98 and a precision-recall score of 0.99.
• Cross-cancer comparative analysis: The database enables examination of neomer patterns across different cancer types and organs.

Methodology:

neomerDB was constructed by examining 10,000 whole exome sequencing and 2,658 whole genome sequencing tumour-matched samples to identify neomers associated with each cancer type and organ, followed by removal of nullomers and neomers arising from germline variants using 76,215 whole genomes and 730,947 whole exomes from diverse ancestries.