Microphaser

Microphaser performs small-scale phasing of somatic variants in tumor bulk sequencing to improve neoantigen prediction and neopeptidome accuracy in cancer genomics.

Key Features:

• Phasing Approach: Implements a small-scale haplotyping methodology tailored to the aneuploid nature of cancer cells and the presence of multiple clones in tumor bulk sequencing data.
• Improved Accuracy: Determines whether adjacent variants reside on the same chromosomal copy to reduce neoantigen prediction search space relative to traditional diploid-based phasing algorithms.
• Concordance with Existing Pipelines: Shows substantial concordance with phasing-aware neoantigen prediction pipelines such as neoepiscope and incorporates an improved filtering step to refine predictions and handle edge cases.

Scientific Applications:

• Neopeptidome refinement: Produces a more accurate neopeptidome by resolving haplotypes of adjacent somatic variants in tumor samples.
• Neoantigen prediction for immunotherapy: Improves precision of neoantigen prediction used for downstream personalized cancer immunotherapy applications.

Methodology:

Uses a small-scale phasing approach with an improved filtering step to phase adjacent variants in tumor bulk sequencing and is implemented to operate in linear time.