ADAM Genomics Schema - Extension for Precision Medicine Research*

Abstract

High-throughput sequencing technologies have made research on precision medicine possible. Precision medicine treatments will be effective for individual patients based on their genomic, environmental, and lifestyle factors. This requires integrating this data to find one, or a combination of, single nucleotide polymorphisms (SNPs) linked to a disease or treatment [1]. In 2013, the University of California Berkeley's AmpLab created the ADAM genomic format that allows the transformation, analysis and querying of large amounts of genomics data by using a columnar file format. However, while ADAM addresses the issue of processing large genomics data; it lacks the ability to link the patients' clinical and demographical data, which is crucial in precision medicine research. This paper presents an ADAM genomic schema extension to support clinical and demographical data by automating the addition of data items to the currently available ADAM schema. This extension allows for clinical, demographical and epidemiological analysis at large scale as initially intended by the AmpLab.