Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Profane earth,

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Generation of minimal protein identifiers of proteins from two-dimensional gels and recombinant proteins

We describe the technical feasibility and methodology to characterize a protein by a minimal set of structural information generated by matrix assisted laser desorption/ionization (MALDI)-mass spectrometry, termed a minimal protein Identifier (MPI). MPIs can be determined for proteins from two-dimensional gels and recombinant proteins and can be used to compare and identify proteins from these sources

Lessons from photo analyses of Autonomous Reef Monitoring Structures as tools to detect (bio-)geographical, spatial, and environmental effects

International audienceWe investigated the validity of Autonomous Reef Monitoring Structures (ARMS) as monitoring tools for hard bottoms across a wide geographic and environmental range. We deployed 36 ARMS in the northeast Atlantic, northwest Mediterranean, Adriatic and Red Sea at 7–17 m depth. After 12–16 months, community composition was inferred from photographs, in six plate-faces for each ARMS. Overall, we found a highly significant effect of sea region, site (within seas), and plate-face on community composition. Plate-faces thus represent distinct micro-habitats and provide pseudo-replicates, increasing statistical power. Within each sea region taken individually, there was also a highly significant effect of site and plate-face. Because strong effects were obtained despite the fusion of taxonomic categories at high taxonomic ranks (to ensure comparability among biogeographic provinces), ARMS photo-analysis appears a promising monitoring tool for each sea region. We recommend keeping three ARMS per site and analyzing more numerous sites within a sea region to investigate environmental effects