Pitfalls in Single Clone CRISPR-Cas9 Mutagenesis to Fine-Map Regulatory Intervals

The majority of genetic variants affecting complex traits map to regulatory regions of genes, and typically lie in credible intervals of 100 or more SNPs. Fine mapping of the causal variant(s) at a locus depends on assays that are able to discriminate the effects of polymorphisms or mutations on gene expression. Here, we evaluated a moderate-throughput CRISPR-Cas9 mutagenesis approach, based on replicated measurement of transcript abundance in single-cell clones, by deleting candidate regulatory SNPs, affecting four genes known to be affected by large-effect expression Quantitative Trait Loci (eQTL) in leukocytes, and using Fluidigm qRT-PCR to monitor gene expression in HL60 pro-myeloid human cells. We concluded that there were multiple constraints that rendered the approach generally infeasible for fine mapping. These included the non-targetability of many regulatory SNPs, clonal variability of single-cell derivatives, and expense. Power calculations based on the measured variance attributable to major sources of experimental error indicated that typical eQTL explaining 10% of the variation in expression of a gene would usually require at least eight biological replicates of each clone. Scanning across credible intervals with this approach is not recommended.

Effective aggregation of gappy replicated time series using INLA

<p>Soil CO2 efflux data from automated chambers provide an important constraint for ecosystem and soil respiration. Usually, half-hourly time series of several replicated chambers have to be aggregated to plot-level while gaps in the time series have to be accommodated. Gaps cause jumps and other problems in aggregation of replicated measurement in each half-hour, therefore, lookup tables and machine learning approaches are used to fill gaps beforehand.</p><p>Here, we present an alternative fully Bayesian approach for the combined gap-filling and aggregation based on Integrated Nested Laplace Approximation (INLA). This method integrates all information from every measurement across replicates and across time and therefore efficiently estimates the correlation structure among all observations. It provides the full marginal posterior distribution of the aggregated time series at the plot level across the time span of the time series. We compare several aggregation approaches using four years of data from 16 automatic chambers at the eddy-covariance site in Majadas de Tietar in Spain (ES-LM1, ES-LMa).</p><p>This approach is applicable for other replicated time series as well. We further explore its usage for analysing time-varying effects across treatments and habitats and its usage for gap-filling net ecosystem exchange (NEE) data based on the full correlation structure in a data-cube of time and environmental conditions.</p>

Replication of Associations With Psychotic-Like Experiences in Middle Childhood From the Adolescent Brain Cognitive Development (ABCD) Study

The fields of psychology and psychiatry are increasingly recognizing the importance of replication efforts. The current study aimed to replicate previous findings examining the construct validity and psychometric properties of a psychotic-like experiences (PLEs) measure in middle childhood using an independent subset of the baseline Adolescent Brain Cognitive Development (ABCD) sample. Using a remainder baseline sample of 7013 nine- to eleven-year-old children with complete data, we examined measurement invariance across race/ethnicity and sex, and examined the associations between the Prodromal Questionnaire Brief-Child Version (PQ-BC) and other measures of PLEs, internalizing symptoms, neuropsychological test performance, and developmental milestones, to determine whether previously obtained results replicated in this nonoverlapping baseline sample subset. The results replicated measurement invariance across ethnicity and sex, and analyses again found higher PQ-BC scores for African American (β = .364, 95% CI = 0.292, 0.435) and Hispanic (β = .255, 95% CI = 0.185, 0.324) groups. We also replicated that higher PQ-BC scores were associated with psychosis risk measures, higher rates of child-reported internalizing symptoms (Distress: β = .378, 95% CI = 0.357,0.398), neuropsychological test performance deficits (eg, working memory; Distress: β = −.069, 95% CI = −0.096, −0.042), and motor (Distress: β = .026, 95% CI = 0.003, 0.049) and speech (Distress: β = .042, 95% CI = 0.018, 0.065) developmental milestone delays. The current results replicated many findings from the original study examining the PQ-BC. We replicated evidence for mean differences in race/ethnicity, and associations with other PLE measures, greater internalizing symptoms, cognitive impairments, and developmental milestone delays. These findings indicate robust and reliable associations between PLEs and hypothesized correlates can be found in middle childhood nonclinical samples.