CRISPR RNA-guided nucleases (RGNs) are widely used genome-editing reagents, but methods to delineate their genome-wide off-target cleavage activities have been lacking. Here we describe an approach for global detection of DNA double-stranded breaks (DSBs) introduced by RGNs and potentially other nucleases. This method, called Genome-wide Unbiased Identification of DSBs Enabled by Sequencing (GUIDE-Seq), relies on capture of double-stranded oligodeoxynucleotides into breaks Application of GUIDE-Seq to thirteen RGNs in two human cell lines revealed wide variability in RGN off-target activities and unappreciated characteristics of off-target sequences. The majority of identified sites were not detected by existing computational methods or ChIP-Seq. GUIDE-Seq also identified RGN-independent genomic breakpoint ‘hotspots’. Finally, GUIDE-Seq revealed that truncated guide RNAs exhibit substantially reduced RGN-induced off-target DSBs. Our experiments define the most rigorous framework for genome-wide identification of RGN off-target effects to date and provide a method for evaluating the safety of these nucleases prior to clinical use.

We describe a rapid target enrichment method for next-generation sequencing, termed anchored multiplex PCR (AMP), that is compatible with low nucleic acid input from formalin-fixed paraffin-embedded (FFPE) specimens. AMP is effective in detecting gene rearrangements (without prior knowledge of the fusion partners), single nucleotide variants, insertions, deletions and copy number changes. Validation of a gene rearrangement panel using 319 FFPE samples showed 100% sensitivity (95% confidence limit: 96.5-100%) and 100% specificity (95% confidence limit: 99.3-100%) compared with reference assays. On the basis of our experience with performing AMP on 986 clinical FFPE samples, we show its potential as both a robust clinical assay and a powerful discovery tool, which we used to identify new therapeutically important gene fusions: ARHGEF2-NTRK1 and CHTOP-NTRK1 in glioblastoma, MSN-ROS1, TRIM4-BRAF, VAMP2-NRG1, TPM3-NTRK1 and RUFY2-RET in lung cancer, FGFR2-CREB5 in cholangiocarcinoma and PPL-NTRK1 in thyroid carcinoma. AMP is a scalable and efficient next-generation sequencing target enrichment method for research and clinical applications.

Our data suggest that mucinous adenocarcinoma is typified by (1) frequent KRAS mutations and a growing list of gene fusions, but rare TP53 mutations, (2) a low mutation burden overall, and (3) a recurrence-free survival similar to stage-matched nonmucinous tumors, with recurrences limited to the lungs.

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The seasonal decline in clutch size in birds can be a response to the environmentally conditioned decrease in prospects for offspring or a consequence of a lower physical ability of late‐breeding females. To find out which of the explanations apply in Tree Swallows Tachycineta bicolor, we assessed whether replacement clutch size in this species is affected by an individual female's ability to lay a certain number of eggs. To do this, we measured the decline in clutch size as a function of laying date between first and replacement clutches in individuals that re‐nested following natural failure, and compared this with the rate of decline in clutch size with laying date for Tree Swallows that laid only a single clutch in that season. Additionally, we assessed whether the clutch size and the rate of its seasonal decline varied across years. We accounted for the truncated and under‐dispersed nature of clutch size data by using a Bayesian approach in the analysis. We found little variation in the rate of clutch size decline across years at our breeding site. Accounting for this seasonal decline in clutch size, mean clutch size was similar between single‐time breeding females and those that laid replacement clutches, implying that the number of eggs laid on the second attempt by female Tree Swallows is determined by laying date, rather than by the female's physical ability to produce a clutch of a certain size.

Precision medicine broadly refers to both the science and practice of medicine that can be personalized to an individual patient level. The clinical applications of precision medicine have gradually and meaningfully followed related scientific and technological advances. While genetics, genomics and molecular diagnostics comprise some of the most important aspects of precision medicine, many other tools, such as imaging and analytics, are also employed. The intent of these high-resolution diagnostics is to improve the selection of optimal therapies for patients, which is a thesis that has already seen promise, most notably in oncology. The rapid pace of biological discovery alongside advances in analytics and technology suggest a future with increasing clinical applications of precision medicine across many disease areas, especially as important diagnostics continue to see reductions in cost.