Engineered Cas12i2 is a versatile high-efficiency platform for therapeutic genome editing.

The CRISPR-Cas type V-I is a family of Cas12i-containing programmable nuclease systems guided by a short crRNA without requirement for a tracrRNA. Here we present an engineered Type V-I CRISPR system (Cas12i), ABR-001, which utilizes a tracr-less guide RNA. The compact Cas12i effector is capable of self-processing pre-crRNA and cleaving dsDNA targets, which facilitates versatile delivery options and multiplexing, respectively. We apply an unbiased mutational scanning approach to enhance initially low editing activity of Cas12i2. The engineered variant, ABR-001, exhibits broad genome editing capability in human cell lines, primary T cells, and CD34+ hematopoietic stem and progenitor cells, with both robust efficiency and high specificity. In addition, ABR-001 achieves a high level of genome editing when delivered via AAV vector to HEK293T cells. This work establishes ABR-001 as a versatile, specific, and high-performance platform for ex vivo and in vivo gene therapy.

A large-scale validation of NOCIt's a posteriori probability of the number of contributors and its integration into forensic interpretation pipelines.

Forensic DNA signal is notoriously challenging to interpret and requires the implementation of computational tools that support its interpretation. While data from high-copy, low-contributor samples result in electropherogram signal that is readily interpreted by probabilistic methods, electropherogram signal from forensic stains is often garnered from low-copy, high-contributor-number samples and is frequently obfuscated by allele sharing, allele drop-out, stutter and noise. Since forensic DNA profiles are too complicated to quantitatively assess by manual methods, continuous, probabilistic frameworks that draw inferences on the Number of Contributors (NOC) and compute the Likelihood Ratio (LR) given the prosecution's and defense's hypotheses have been developed. In the current paper, we validate a new version of the NOCIt inference platform that determines an A Posteriori Probability (APP) distribution of the number of contributors given an electropherogram. NOCIt is a continuous inference system that incorporates models of peak height (including degradation and differential degradation), forward and reverse stutter, noise and allelic drop-out while taking into account allele frequencies in a reference population. We established the algorithm's performance by conducting tests on samples that were representative of types often encountered in practice. In total, we tested NOCIt's performance on 815 degraded, UV-damaged, inhibited, differentially degraded, or uncompromised DNA mixture samples containing up to 5 contributors. We found that the model makes accurate, repeatable and reliable inferences about the NOCs and significantly outperformed methods that rely on signal filtering. By leveraging recent theoretical results of Slooten and Caliebe (FSI:G, 2018) that, under suitable assumptions, establish the NOC can be treated as a nuisance variable, we demonstrated that when NOCIt's APP is used in conjunction with a downstream likelihood ratio (LR) inference system that employs the same probabilistic model, a full evaluation across multiple contributor numbers is rendered. This work, therefore, illustrates the power of modern probabilistic systems to report holistic and interpretable weights-of-evidence to the trier-of-fact without assigning a specified number of contributors or filtering signal.

Statistical modeling of STR capillary electrophoresis signal.

BACKGROUND: In order to isolate an individual's genotype from a sample of biological material, most laboratories use PCR and Capillary Electrophoresis (CE) to construct a genetic profile based on polymorphic loci known as Short Tandem Repeats (STRs). The resulting profile consists of CE signal which contains information about the length and number of STR units amplified. For samples collected from the environment, interpretation of the signal can be challenging given that information regarding the quality and quantity of the DNA is often limited. The signal can be further compounded by the presence of noise and PCR artifacts such as stutter which can mask or mimic biological alleles. Because manual interpretation methods cannot comprehensively account for such nuances, it would be valuable to develop a signal model that can effectively characterize the various components of STR signal independent of a priori knowledge of the quantity or quality of DNA. RESULTS: First, we seek to mathematically characterize the quality of the profile by measuring changes in the signal with respect to amplicon size. Next, we examine the noise, allele, and stutter components of the signal and develop distinct models for each. Using cross-validation and model selection, we identify a model that can be effectively utilized for downstream interpretation. Finally, we show an implementation of the model in NOCIt, a software system that calculates the a posteriori probability distribution on the number of contributors. CONCLUSION: The model was selected using a large, diverse set of DNA samples obtained from 144 different laboratory conditions; with DNA amounts ranging from a single copy of DNA to hundreds of copies, and the quality of the profiles ranging from pristine to highly degraded. Implemented in NOCIt, the model enables a probabilisitc approach to estimating the number of contributors to complex, environmental samples.

Functionally diverse type V CRISPR-Cas systems.

Type V CRISPR-Cas systems are distinguished by a single RNA-guided RuvC domain-containing effector, Cas12. Although effectors of subtypes V-A (Cas12a) and V-B (Cas12b) have been studied in detail, the distinct domain architectures and diverged RuvC sequences of uncharacterized Cas12 proteins suggest unexplored functional diversity. Here, we identify and characterize Cas12c, -g, -h, and -i. Cas12c, -h, and -i demonstrate RNA-guided double-stranded DNA (dsDNA) interference activity. Cas12i exhibits markedly different efficiencies of CRISPR RNA spacer complementary and noncomplementary strand cleavage resulting in predominant dsDNA nicking. Cas12g is an RNA-guided ribonuclease (RNase) with collateral RNase and single-strand DNase activities. Our study reveals the functional diversity emerging along different routes of type V CRISPR-Cas evolution and expands the CRISPR toolbox.

A large-scale dataset of single and mixed-source short tandem repeat profiles to inform human identification strategies: PROVEDIt.

DNA-based human identity testing is conducted by comparison of PCR-amplified polymorphic Short Tandem Repeat (STR) motifs from a known source with the STR profiles obtained from uncertain sources. Samples such as those found at crime scenes often result in signal that is a composite of incomplete STR profiles from an unknown number of unknown contributors, making interpretation an arduous task. To facilitate advancement in STR interpretation challenges we provide over 25,000 multiplex STR profiles produced from one to five known individuals at target levels ranging from one to 160 copies of DNA. The data, generated under 144 laboratory conditions, are classified by total copy number and contributor proportions. For the 70% of samples that were synthetically compromised, we report the level of DNA damage using quantitative and end-point PCR. In addition, we characterize the complexity of the signal by exploring the number of detected alleles in each profile.

Inferring the Number of Contributors to Complex DNA Mixtures Using Three Methods: Exploring the Limits of Low-Template DNA Interpretation.

In forensic DNA casework, the interpretation of an evidentiary profile may be dependent upon the assumption on the number of individuals from whom the evidence arose. Three methods of inferring the number of contributors-NOCIt, maximum likelihood estimator, and maximum allele count, were evaluated using 100 test samples consisting of one to five contributors and 0.5-0.016 ng template DNA amplified with Identifiler® Plus and PowerPlex® 16 HS. Results indicate that NOCIt was the most accurate method of the three, requiring 0.07 ng template DNA from any one contributor to consistently estimate the true number of contributors. Additionally, NOCIt returned repeatable results for 91% of samples analyzed in quintuplicate, while 50 single-source standards proved sufficient to calibrate the software. The data indicate that computational methods that employ a quantitative, probabilistic approach provide improved accuracy and additional pertinent information such as the uncertainty associated with the inferred number of contributors.

Probabilistic characterisation of baseline noise in STR profiles.

There are three dominant contributing factors that distort short tandem repeat profile measurements, two of which, stutter and variations in the allelic peak heights, have been described extensively. Here we characterise the remaining component, baseline noise. A probabilistic characterisation of the non-allelic noise peaks is not only inherently useful for statistical inference but is also significant for establishing a detection threshold. We do this by analysing the data from 643 single person profiles for the Identifiler Plus kit and 303 for the PowerPlex 16 HS kit. This investigation reveals that although the dye colour is a significant factor, it is not sufficient to have a per-dye colour description of the noise. Furthermore, we show that at a per-locus basis, out of the Gaussian, log-normal, and gamma distribution classes, baseline noise is best described by log-normal distributions and provide a methodology for setting an analytical threshold based on that deduction. In the PowerPlex 16 HS kit, we observe evidence of significant stutter at two repeat units shorter than the allelic peak, which has implications for the definition of baseline noise and signal interpretation. In general, the DNA input mass has an influence on the noise distribution. Thus, it is advisable to study noise and, consequently, to infer quantities like the analytical threshold from data with a DNA input mass comparable to the DNA input mass of the samples to be analysed.