GeneToCN

GeneToCN estimates gene copy number variations directly from NGS reads using alignment-free analysis of gene-specific k-mer frequencies in FASTQ files to infer copy number across genomes.

Key Features:

• Alignment-Free Methodology: Eliminates sequence alignment by operating directly on sequencing reads to derive copy number estimates.
• K-mer Frequency Analysis: Counts gene-specific k-mers in FASTQ files and uses their frequencies to infer gene copy number.
• Cross-Technology Compatibility: Has been tested on Illumina, PacBio, and Oxford Nanopore sequencing data to support diverse sequencing platforms.
• Validation with Experimental Data: Copy number predictions were validated against digital droplet PCR (ddPCR), including a reported correlation of R = 0.99 for AMY1, AMY2A, and AMY2B across 39 individuals.
• Comparative Performance: Demonstrated higher concordance for FCGR3A compared to two other methods while showing reduced accuracy for FCGR3B.
• Broad Applicability: Applied to genomic regions including SMN, NPY4R, and the LPA Kringle IV-2 domain, with predicted copy number distributions from 500 individuals in the Estonian Biobank aligning with prior studies.

Scientific Applications:

• Segmental and multiallelic CNV analysis: Analysis of copy number variation encompassing entire genes and multiallelic regions such as SMN, NPY4R, and LPA Kringle IV-2.
• Population-scale CNV studies: Large-cohort copy number distribution analyses, exemplified by application to 500 individuals from the Estonian Biobank.
• Benchmarking and validation: Comparison and validation of CNV estimates against ddPCR and other methods for loci including AMY genes and FCGR3 genes.

Methodology:

Alignment-free computation by counting gene-specific k-mers in FASTQ NGS reads and using k-mer frequency profiles to infer gene copy number.