De novo variants in the RNU4-2 snRNA cause a frequent neurodevelopmental syndrome

Around 60% of individuals with neurodevelopmental disorders (NDD) remain undiagnosed after comprehensive genetic testing, primarily of protein-coding genes1. Large genome-sequenced cohorts are improving our ability to discover new diagnoses in the non-coding genome. Here we identify the non-coding RNA RNU4-2 as a syndromic NDD gene. RNU4-2 encodes the U4 small nuclear RNA (snRNA), which is a critical component of the U4/U6.U5 tri-snRNP complex of the major spliceosome2. We identify an 18 base pair region of RNU4-2 mapping to two structural elements in the U4/U6 snRNA duplex (the T-loop and stem III) that is severely depleted of variation in the general population, but in which we identify heterozygous variants in 115 individuals with NDD. Most individuals (77.4%) have the same highly recurrent single base insertion (n.64_65insT). In 54 individuals in whom it could be determined, the de novo variants were all on the maternal allele. We demonstrate that RNU4-2 is highly expressed in the developing human brain, in contrast to RNU4-1 and other U4 homologues. Using RNA sequencing, we show how 5′ splice-site use is systematically disrupted in individuals with RNU4-2 variants, consistent with the known role of this region during spliceosome activation. Finally, we estimate that variants in this 18 base pair region explain 0.4% of individuals with NDD. This work underscores the importance of non-coding genes in rare disorders and will provide a diagnosis to thousands of individuals with NDD worldwide

Mitochondrial Changes in Ageing Caenorhabditis elegans – What Do We Learn from Superoxide Dismutase Knockouts?

One of the most popular damage accumulation theories of ageing is the mitochondrial free radical theory of ageing (mFRTA). The mFRTA proposes that ageing is due to the accumulation of unrepaired oxidative damage, in particular damage to mitochondrial DNA (mtDNA). Within the mFRTA, the “vicious cycle” theory further proposes that reactive oxygen species (ROS) promote mtDNA mutations, which then lead to a further increase in ROS production. Recently, data have been published on Caenorhabditis elegans mutants deficient in one or both forms of mitochondrial superoxide dismutase (SOD). Surprisingly, even double mutants, lacking both mitochondrial forms of SOD, show no reduction in lifespan. This has been interpreted as evidence against the mFRTA because it is assumed that these mutants suffer from significantly elevated oxidative damage to their mitochondria. Here, using a novel mtDNA damage assay in conjunction with related, well established damage and metabolic markers, we first investigate the age-dependent mitochondrial decline in a cohort of ageing wild-type nematodes, in particular testing the plausibility of the “vicious cycle” theory. We then apply the methods and insights gained from this investigation to a mutant strain for C. elegans that lacks both forms of mitochondrial SOD. While we show a clear age-dependent, linear increase in oxidative damage in WT nematodes, we find no evidence for autocatalytic damage amplification as proposed by the “vicious cycle” theory. Comparing the SOD mutants with wild-type animals, we further show that oxidative damage levels in the mtDNA of SOD mutants are not significantly different from those in wild-type animals, i.e. even the total loss of mitochondrial SOD did not significantly increase oxidative damage to mtDNA. Possible reasons for this unexpected result and some implications for the mFRTA are discussed

Novel Common Genetic Susceptibility Loci for Colorectal Cancer

BACKGROUND: Previous genome-wide association studies (GWAS) have identified 42 loci (P < 5 × 10-8) associated with risk of colorectal cancer (CRC). Expanded consortium efforts facilitating the discovery of additional susceptibility loci may capture unexplained familial risk. METHODS: We conducted a GWAS in European descent CRC cases and control subjects using a discovery-replication design, followed by examination of novel findings in a multiethnic sample (cumulative n = 163 315). In the discovery stage (36 948 case subjects/30 864 control subjects), we identified genetic variants with a minor allele frequency of 1% or greater associated with risk of CRC using logistic regression followed by a fixed-effects inverse variance weighted meta-analysis. All novel independent variants reaching genome-wide statistical significance (two-sided P < 5 × 10-8) were tested for replication in separate European ancestry samples (12 952 case subjects/48 383 control subjects). Next, we examined the generalizability of discovered variants in East Asians, African Americans, and Hispanics (12 085 case subjects/22 083 control subjects). Finally, we examined the contributions of novel risk variants to familial relative risk and examined the prediction capabilities of a polygenic risk score. All statistical tests were two-sided. RESULTS: The discovery GWAS identified 11 variants associated with CRC at P < 5 × 10-8, of which nine (at 4q22.2/5p15.33/5p13.1/6p21.31/6p12.1/10q11.23/12q24.21/16q24.1/20q13.13) independently replicated at a P value of less than .05. Multiethnic follow-up supported the generalizability of discovery findings. These results demonstrated a 14.7% increase in familial relative risk explained by common risk alleles from 10.3% (95% confidence interval [CI] = 7.9% to 13.7%; known variants) to 11.9% (95% CI = 9.2% to 15.5%; known and novel variants). A polygenic risk score identified 4.3% of the population at an odds ratio for developing CRC of at least 2.0. CONCLUSIONS: This study provides insight into the architecture of common genetic variation contributing to CRC etiology and improves risk prediction for individualized screenin

Meta-modeling social programs: Methodological reflections on a practical application

Research syntheses have become an increasingly popular approach for summarizing primary research. The broad range of publications, conference presentations, journals, and books dedicated to research syntheses speaks to this point. Over the past twenty years, interest in mixed methods syntheses has steadily grown. Yet, despite the growing array of approaches for mixing methods, published applications of mixed methods syntheses are to this date few and far between. The proposed dissertation steps into this gap by illustrating the practical application of meta-modeling—a mixed methods synthesis approach. The proposed methodology structures the synthesis around the development of a meta-model and integrates findings from both effectiveness and implementation studies to determine and explain program effects. This meta-modeling does double-duty: It allows for a more nuanced appreciation of program effectiveness and allows for a better understanding of program components generating the effects

sj-docx-3-evi-10.1177_13563890231200291 – Supplemental material for The curious case of the realist trial: Methodological oxymoron or unicorn?

Supplemental material, sj-docx-3-evi-10.1177_13563890231200291 for The curious case of the realist trial: Methodological oxymoron or unicorn? by Steffen Bohni Nielsen, Sofie Østergaard Jaspers and Sebastian Lemire in Evaluation</p

We Can’t Hear You – You’re on Mute: Findings From a Review of Evaluation Capacity Building (ECB) Practice Online

Background: In her presidential address to the American Evaluation Association (AEA) in 2007, Hallie Preskill (2008) highlighted the potential role of technology to promote learning from evaluation, noting the increased use of computers, the internet, and social media as untapped ways to facilitate evaluation. More than ten years later in the context of the COVID-19 pandemic, evaluators and evaluation capacity building (ECB) practitioners found themselves needing to shift to online modalities to conduct evaluation and build capacity. The COVID-19 pandemic, technological advancements, and the rapid shift to remote work have changed our way of working (Gratton, 2021; Kane et al., 2021). Building evaluation capacity is no exception to this trend. Purpose: This study aimed to examine ways that practitioners have built evaluation capacity online or have used technology to do so, to capture lessons learned that can be applied in a COVID and post-normal context. Setting: Findings from this study can be applied in online contexts for developing evaluation capacity. Intervention: Not applicable. Research Design: The study design consisted of a rapid review of the ECB literature published from 2000 to 2019 in eight academic journals focused on evaluation research and practice. Data Collection and Analysis: Twenty-nine case applications of ECB practice that: 1) mentioned use of technology as a strategy for building evaluation capacity or 2) noted that at least one component of the ECB intervention was carried out online or virtually were reviewed for this study. Quantitative data were analyzed via descriptive statistics. Qualitative data were coded in MAXQDA using conventional content analysis (Hsieh &amp; Shannon, 2005). Findings: More diverse online interventions have increased over time. Less than half (45%) of ECB interventions made use of both asynchronous and synchronous strategies for building capacity while more than one-third (38%) made use of asynchronous only strategies. Key barriers to implementing ECB strategies online included lack of social connections to other participants during the capacity building activity, technical malfunctions, lack of access to or familiarity with the technology in use, and limited resources for carrying out evaluation activities. Key facilitators for enhancing implementation included facilitating participant interaction and relationship-building both on and off-line, tailoring ECB activities to participant work contexts, and providing tutorials for accessing and using the technology in play