TIGER

TIGER infers DNA replication timing from whole-genome sequence data derived from proliferating cell samples to map the spatiotemporal program of genomic DNA replication.

Key Features:

• Whole-Genome Sequence Data Utilization: TIGER leverages whole-genome sequence data to extract replication timing information from proliferating cell samples.
• Non-Uniform DNA Representation Analysis: TIGER assesses DNA copy number along chromosomes and accounts for other sources of sequence coverage variation arising from the presence of replicating cells.
• Applicability Across Species: The method requires only a contiguous genome assembly and can be applied to any species with such an assembly.
• High-Quality Replication Timing Measurements: TIGER produces replication timing estimates that are comparable in quality to experimental methods.
• Scalability: The approach is implemented to allow application at scale across large genomic datasets.

Scientific Applications:

• Cancer Genomics: Characterizing aberrant replication timing patterns associated with oncogenesis.
• Developmental Biology: Investigating the role of replication timing in developmental processes.
• Genomic Stability Studies: Exploring relationships between replication timing and genomic stability.

Methodology:

TIGER analyzes DNA copy number along chromosomes from whole-genome sequence data while controlling for other sequence coverage variation to infer replication dynamics and requires input from proliferating cell samples and a contiguous genome assembly.