Phylovar: toward scalable phylogeny-aware inference of single-nucleotide variations from single-cell DNA sequencing data.

MOTIVATION: Single-nucleotide variants (SNVs) are the most common variations in the human genome. Recently developed methods for SNV detection from single-cell DNA sequencing data, such as SCIΦ and scVILP, leverage the evolutionary history of the cells to overcome the technical errors associated with single-cell sequencing protocols. Despite being accurate, these methods are not scalable to the extensive genomic breadth of single-cell whole-genome (scWGS) and whole-exome sequencing (scWES) data. RESULTS: Here, we report on a new scalable method, Phylovar, which extends the phylogeny-guided variant calling approach to sequencing datasets containing millions of loci. Through benchmarking on simulated datasets under different settings, we show that, Phylovar outperforms SCIΦ in terms of running time while being more accurate than Monovar (which is not phylogeny-aware) in terms of SNV detection. Furthermore, we applied Phylovar to two real biological datasets: an scWES triple-negative breast cancer data consisting of 32 cells and 3375 loci as well as an scWGS data of neuron cells from a normal human brain containing 16 cells and approximately 2.5 million loci. For the cancer data, Phylovar detected somatic SNVs with high or moderate functional impact that were also supported by bulk sequencing dataset and for the neuron dataset, Phylovar identified 5745 SNVs with non-synonymous effects some of which were associated with neurodegenerative diseases. AVAILABILITY AND IMPLEMENTATION: Phylovar is implemented in Python and is publicly available at https://github.com/NakhlehLab/Phylovar.

National registry of haemophilia and other coagulopathies: A multisector initiative in the Colombian Health System.

INTRODUCTION: Haemophilia is an orphan and high-cost disease worldwide and, especially in middle-income countries as Colombia. Given its burden of disease, in 2014, a national administrative registry was created to centralize demographic, clinical and economic information regarding to haemophilia and other coagulopathies. OBJECTIVE: To describe the building and implementation processes of the Colombian registry of haemophilia and other coagulopathies. METHODS: The 'consensus conference' methodology was used to design the registry. It was a multisector process, which included different actors of the health system (healthcare payers and providers, government institutions, academic and scientific organizations and patients). RESULTS: Colombia's national registry includes 95 variables, grouped in four sections: (1) sociodemographic data, (2) clinical condition, (3) economic costs, and (4) administrative updates. According to a resolution, stated by the Ministry of Health, payers and providers of healthcare must report annually to the registry the information of new and existing patients with coagulopathies. CONCLUSIONS: A national registry serves as an organized and interactive system for monitoring morbidity and mortality, assessing healthcare access and its impact on disease complications, as well as associated costs to medical assistance. Furthermore, registry information can guide a rational making decision process to use economic resources efficiently. On the other hand, data about orphan diseases can encourage health research and evidence-based care to improve quality of life and reduce associated disability.