Background CRISPR-Cas9 gene-editing technology has facilitated the generation of knockout mice, providing an alternative to cumbersome and time-consuming traditional embryonic stem cell-based methods. An earlier study reported up to 16% efficiency in generating conditional knockout (cKO or floxed) alleles by microinjection of 2 single guide RNAs (sgRNA) and 2 single-stranded oligonucleotides as donors (referred herein as “two-donor floxing” method). Results We re-evaluate the two-donor method from a consortium of 20 laboratories across the world. The dataset constitutes 56 genetic loci, 17,887 zygotes, and 1718 live-born mice, of which only 15 (0.87%) mice contain cKO alleles. We subject the dataset to statistical analyses and a machine learning algorithm, which reveals that none of the factors analyzed was predictive for the success of this method. We test some of the newer methods that use one-donor DNA on 18 loci for which the two-donor approach failed to produce cKO alleles. We find that the one-donor methods are 10- to 20-fold more efficient than the two-donor approach. Conclusion We propose that the two-donor method lacks efficiency because it relies on two simultaneous recombination events in cis , an outcome that is dwarfed by pervasive accompanying undesired editing events. The methods that use one-donor DNA are fairly efficient as they rely on only one recombination event, and the probability of correct insertion of the donor cassette without unanticipated mutational events is much higher. Therefore, one-donor methods offer higher efficiencies for the routine generation of cKO animal models. Electronic supplementary material The online version of this article (10.1186/s13059-019-1776-2) contains supplementary material, which is available to authorized users.

Fundic gland polyp (FGP) is the most common gastric polyp. It occurs sporadically or in association with familial adenomatous polyposis (FAP). FAP patients carry germline mutations of the adenomatous polyposis coli (APC) gene, and previous studies have revealed frequent somatic mutations of the APC gene in FGPs associated with FAP. Although inactivation of the APC gene contributes to histogenesis of FGPs associated with FAP, this rarely happens in sporadic cases. Loss of the APC gene promotes abnormal accumulation of beta-catenin, and mutation of GSK-3 beta phosphorylation sites in the beta-catenin gene can have a similar effect. To elucidate the contribution of beta-catenin gene mutation to the histogenesis of sporadic FGP, we analyzed beta-catenin gene mutation in exon 3 in 45 FGP lesions obtained from 35 patients. Somatic mutations were found in 29 lesions: 28 were missense mutations and one was an in-frame deletion. All of the missense mutations were confined to the former two serine residues of the GSK-3 beta phosphorylation sites and their flanking residues (codons 32, 33, 34, 37). Analysis in cases with multiple FGPs revealed a different mutation in each lesion, indicating their multicentric origin. Therefore, a significant proportion of sporadic FGPs have genetic alterations involving beta-catenin stabilization, as did FAP-associated FGPs.

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Novel coronavirus SARS-CoV-2 outbreaks have rapidly spread to multiple countries, highlighting the urgent necessity for fast, sensitive, and specific diagnostic tools for virus surveillance. Here, the previously unknown collateral single-stranded DNA cleavage we observed with type I CRISPR-Cas3 highlights its potential for development as a Cas3-mediated rapid (within 40 min), low-cost, instrument-free detection method for SARS-CoV-2. This Cas3-based assay is comparable with Cas12- and real-time reverse-transcriptase PCR-based assays in its speed and sensitivity, but offers greater specificity for single-base-pair discrimination while negating the need for highly trained operators. These findings support the use of CRISPR diagnostics for point-of-care testing in patients with suspected SARS-CoV-2 infections.