Nature this week brings home next-generation sequencing for cheaper, faster, and more accurate whole genome sequencing. A consortium led by Illumina sequenced the first African genome, that of a male Yoruban from Nigeria. They characterized 4 million SNPs and 400,000 structural variants. Also, Chinese scientists at the Beijing Genomics Institute used Illumina to map the first genome sequence of an Asian individual. They found about 3 million SNPs, of which some 14 percent were not in the dbSNP database. Finally, scientists at Washington University and the University of Washington led the sequencing of an acute myeloid leukemia genome. Of the 10 mutated genes they discovered, only two were previously known to cause cancer. "This is the first of many of these whole cancer genomes to be sequenced," says WashU's Rick Wilson in this New York Times story. "They’ll give us a whole bunch of clues about what's going on in the DNA when cancer starts to bloom." A news and views looks at some of the deficiencies of current methods.
At Genetic Future, Daniel MacArthur argues that this is the beginning of the end of "high-profile 'single human genome' papers," and Nature has a slew of articles on personal genomics. An editorial discusses the challenges to using personal genome sequencing data while a news story checks in on companies working to make the most of personal genomics test data. Three news features cover the limits of finding heritability patterns in single variants, the promise of nanopore sequencing, and a look at the science of integrated genomics. Finally, two commentaries explore issues of consent and regulation.
Japanese researchers have made use of large-scale transcriptome analyses of noncoding RNAs to find that RNA polymerase II transcription of ncRNAs is required for chromatin remodeling at the fbp1 + locus in S. pombe during transcriptional activation.
Two papers published early online focus on alternative RNA splicing. In one, Robert Darnell led work that mapped genome-wide protein-RNA binding sites in vivo using high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation. A paper out of Chris Burge's lab at MIT deep sequenced cDNA fragments of 15 different human tissue and cell line transcriptomes. This "digital inventory" of isoforms showed that 92 to 94 percent of human genes undergo alternative splicing, with 86 percent having a minor isoform frequency of 15 percent or more.