In Nature this week, a group of European researchers describe the creation of a reversible haploid mouse embryonic stem cell biobank for functional genomics. Using genome-saturated mutagenesis, the team constructed Haplobank — a biobank of more than 100,000 individual haploid mouse embryonic stem (mES) cell lines targeting 16,970 genes with genetically barcoded conditional and reversible mutations. They used Haplobank in reverse genetic screens to investigate the temporal resolution of essential genes in mES cells, as well as to identify novel genes that control sprouting angiogenesis and lineage specification of blood vessels. The resource was also used in a genome-wide forward screen, which identified a host factor required for cytotoxicity by rhinoviruses.
And in Nature Genetics, scientists from Decode Genetics report a new computational tool for population-scale genotyping. Called Graphtyper, the publicly available novel algorithm and software enables the discovery and genotyping of sequence variants by realigning short-read sequence data to a pangenome, a variation-aware graph structure that encodes sequence variation within a population by representing possible haplotypes as graph paths. Graphtyper is fast, highly scalable, and provides sensitive and accurate genotype calls, the researchers say.