Design and application of methods for curating genetic variation databases

Abstract

for providing additional feedback and work to support my own work. Thanks to Bryce Diestelmeier and Sang Kyun Kang for aiding me in the process of writing this work. A very special thanks to my parents, Janice and Stephen Ephraim, for their endless support throughout the duration of my time in graduate school and, well, life. Additional thanks goes to all of my wonderful family and friends whose continuous encouragement has kept me motivated.

Variant-curation and database instantiation (Variant-CADI)

“…Kafeen was developed by the authors of Cordova [2] [3]. It is a collection of Ruby [30] applications harnessing community tools and public data repositories to collect and format genetic variation data.…”

“…Variant Effect Predictor (VEP) [24] is executed to collect coding regions and, when available, protein HGVS nomenclature, in addition to the variant and mutation functional effect. All collected data up to this point is used to make a final pathogenicity prediction [3]. This final prediction takes into account ClinVar [20] pathogenicity annotation, HGMD [22] pathogenicity annotation, MAF, expert curated pathogenicity, and the collected pathogenicity predictions from dbNSFP [21].…”

“…The Cordova system and complementary data pipeline, Kafeen, acquires and integrates genomic data (genes), variant data (variants, allele frequencies, and pathogenicity predictions), and phenotypes (benign, pathogenic) and generates displays for this data [3].…”