ALICE provides an integrated analysis of genotypehybridization intensity based on our core technologies in coefficient of preferential amplification/hybridization, estimation of individual-level allele frequency (AF), intensity-based allelic imbalance (AI) detection, loss of heterozygosity (LOH) detection, copy number variationalteration (CNV/CNA) detection,genomic segmentation.

The proposed AF adjustment method considerably increased the accuracy of AF estimation. The proposed quick segmentation algorithm significantly reduced computation time. The proposed CNV/CNA detection had a promising true positivewell-controlled false positive rates. The results were validated by statistical, biological,genomic data. ALICE outperformed the international benchmark method.

ALICE has great potentials in clinical applications such as (1) genetic screeningtesting, (2) copy number alteration detection in large-scale biobank such as Taiwan BiobankUK Biobank,(3) cancer risk assessmentprecision medicine. ALICE can be applied to new-generation population-optimized SNP arrays. We are collaborating with international teams from Taiwan, Japan,USA.