Utility of High Throughput Sequence Data in Rare Variant Detection
Viacheslav Y. Fofanov, Tudor Constantin, Heather Koshinsky and Eureka Genomics
from: Next-generation Sequencing: Current Technologies and Applications (Edited by: Jianping Xu). Caister Academic Press, U.K. (2014)
Rare variants (sequence variants present in <1% of the sequence data) detection through the analysis of High Throughput Sequence (HTS) data is an exciting new field. HTS data enables genotype-based, primer and probe-independent detection of variant sequences that are present in low frequency in the population. This exciting technical advance may find clinical, epidemiological, forensic and quality control applications. However, because the field is new, terminology is not yet consistent, sources of potential error are not characterized, controlled or quantitated, and models to test experimental concepts are not common. Herein, we attempt (1) to provide some terminology framework, (2) review variant detection through traditional approaches and through examination of HTS data, (3) propose a minimum coverage model to test how much HTS data is needed for reliable rare variant detection, (4) examine sources of error that contribute to false positive rare variant detection and (5) potential approaches to minimize these errors read more ...