MOTIVATION: Across-chromosome phasing identifies which haplotypes of different chromosomes come from the same parent. This differs from within-chromosome phasing, which uses linkage disequilibrium patterns to determine which alleles were co-inherited within each chromosome but does not match haplotypes across different chromosomes. While across-chromosome phasing can be conducted using genotypes from parents or close relatives, current methods perform poorly for samples of unrelated individuals. Here, we introduce a novel approach for across-chromosome phasing that employs a window-based SNP-similarity metric, eliminating the need for data from close relatives or detection of identical-by-descent haplotypes. RESULTS: Using UK Biobank offspring with both parents genotyped as a gold standard, we evaluated the performance of our method by phasing the offspring without using parental data. In genomic data with no within-chromosome phase errors, our algorithm achieved a mean across-chromosome phasing accuracy of 95%, with 53% of individuals phased perfectly. When data was pre-phased computationally using a standard within-chromosome phasing algorithm, mean accuracy for across-chromosome phasing dropped to 83.1%. Thus, our method is limited primarily by the accuracy of within-chromosome phasing accuracy and can approach near-perfect across-chromosome phasing accuracy as within-chromosome phasing accuracy improves. AVAILABILITY AND IMPLEMENTATION: The implementation was executed within a multi-node computational environment of University of Colorado Boulder Research Computing (Blanca Cluster: https://www.colorado.edu/rc/resources/blanca), employing parallelization techniques in the C programming language. The source code has been made publicly accessible online at https://github.com/emmanuelsapin/AcrossChromosomesPhasing, thereby facilitating reproducibility of the results for researchers with authorized access to the UK Biobank dataset.

Optical coherence tomography (OCT) is a non-invasive diagnostic method that offers real-time visualization of the layered architecture of the skin in vivo. The 1.7-micron OCT system has been applied in cardiology, gynecology and dermatology, demonstrating an improved penetration depth in contrast to conventional 1.3-micron OCT. To further extend the capability, we developed a 1.7-micron OCT/OCT angiography (OCTA) system that allows for visualization of both morphology and microvasculature in the deeper layers of the skin. Using this imaging system, we imaged human skin with different benign lesions and described the corresponding features of both structure and vasculature. The significantly improved imaging depth and additional functional information suggest that the 1.7-micron OCTA system has great potential to advance both dermatological clinical and research settings for characterization of benign and cancerous skin lesions.