Reconstruction of evolving gene variants and fitness from short sequencing reads.
Max W ShenKevin Tianmeng ZhaoDavid R LiuPublished in: Nature chemical biology (2021)
Directed evolution can generate proteins with tailor-made activities. However, full-length genotypes, their frequencies and fitnesses are difficult to measure for evolving gene-length biomolecules using most high-throughput DNA sequencing methods, as short read lengths can lose mutation linkages in haplotypes. Here we present Evoracle, a machine learning method that accurately reconstructs full-length genotypes (R2 = 0.94) and fitness using short-read data from directed evolution experiments, with substantial improvements over related methods. We validate Evoracle on phage-assisted continuous evolution (PACE) and phage-assisted non-continuous evolution (PANCE) of adenine base editors and OrthoRep evolution of drug-resistant enzymes. Evoracle retains strong performance (R2 = 0.86) on data with complete linkage loss between neighboring nucleotides and large measurement noise, such as pooled Sanger sequencing data (~US$10 per timepoint), and broadens the accessibility of training machine learning models on gene variant fitnesses. Evoracle can also identify high-fitness variants, including low-frequency 'rising stars', well before they are identifiable from consensus mutations.
Keyphrases
- copy number
- drug resistant
- machine learning
- single cell
- big data
- genome wide
- high throughput
- physical activity
- body composition
- electronic health record
- multidrug resistant
- pseudomonas aeruginosa
- single molecule
- artificial intelligence
- randomized controlled trial
- gene expression
- dna methylation
- clinical trial
- deep learning
- cystic fibrosis
- hepatitis c virus