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Tumors often contain multiple subpopulations of cancerous cells defined by distinct somatic mutations. We describe a new method, PhyloWGS, that can be applied to WGS data from one or more tumor samples to reconstruct complete genotypes of these subpopulations based on variant allele frequencies (VAFs) of point mutations and population frequencies of structural variations. We introduce a principled phylogenic correction for VAFs in loci affected by copy number alterations and we show that this correction greatly improves subclonal reconstruction compared to existing methods.
The Roma people, living throughout Europe, are a diverse population linked by the Romani language and culture. Previous linguistic and genetic studies have suggested that the Roma migrated into Europe from South Asia about 1000-1500 years ago. Geneti
In recent years, Whole Genome Sequencing (WGS) evolved from a futuristic-sounding research project to an increasingly affordable technology for determining complete genome sequences of complex organisms, including humans. This prompts a wide range of
Understanding the relationship between genomic variation and variation in phenotypes for quantitative traits such as physiology, yield, fitness or behavior, will provide important insights for both predicting adaptive evolution and for breeding schem
Recent genetic studies and whole-genome sequencing projects have greatly improved our understanding of human variation and clinically actionable genetic information. Smaller ethnic populations, however, remain underrepresented in both individual and
Reconstructing multiple molecularly defined neurons from individual brains and across multiple brain regions can reveal organizational principles of the nervous system. However, high resolution imaging of the whole brain is a technically challenging