LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets.
The study of cell-population heterogeneity in a range of biological systems, from viruses to bacterial isolates to tumor samples, has been transformed by recent advances in sequencing throughput. While the high-coverage afforded can be used, in principle, to identify very rare variants in a population, existing ad hoc approaches frequently fail to distinguish true variants from sequencing errors. We report a method (LoFreq) that models sequencing run-specific error rates to accurately call variants occurring in <0.05% of a population. Using simulated and real datasets (viral, bacterial and human), we show that LoFreq has near-perfect specificity, with significantly improved sensitivity compared with existing methods and can efficiently analyze deep Illumina sequencing datasets without resorting to approximations or heuristics. We also present experimental validation for LoFreq on two different platforms (Fluidigm and Sequenom) and its application to call rare somatic variants from exome sequencing datasets for gastric cancer. Source code and executables for LoFreq are freely available at http://sourceforge.net/projects/lofreq/.
Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore 138672, Singapore.
Andreas
A
Wilm
Pauline Poh Kim
PP
Aw
Denis
D
Bertrand
Grace Hui Ting
GH
Yeo
Swee Hoe
SH
Ong
Chang Hua
CH
Wong
Chiea Chuen
CC
Khor
Rosemary
R
Petric
Martin Lloyd
ML
Hibberd
Niranjan
N
Nagarajan
D003198:Computer Simulation; D003716:Dengue Virus / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics; D014644:Genetic Variation; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods* / Q000592:standards; D006801:Humans; D009154:Mutation; D012680:Sensitivity and Specificity; D013274:Stomach Neoplasms / Q000235:genetics; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics
D014764:Viral Proteins