Exome sequencing in individuals with cardiovascular laterality defects identifies potential candidate genes

The birth prevalence of laterality defects is about 1.1/10,000 comprising different phenotypes ranging from situs inversus totalis to heterotaxy, mostly associated with complex congenital heart defects (CHD) and situs abnormalities such as intestinal malrotation, biliary atresia, asplenia, or polysplenia. A proportion of laterality defects arise in the context of primary ciliary dyskinesia (PCD) accompanied by respiratory symptoms or infertility. In this study, exome sequencing (ES) was performed in 14 case-parent trios/quattros with clinical exclusion of PCD prior to analysis. Moreover, all cases and parents underwent detailed clinical phenotyping including physical examination, echocardiography by a skilled paediatric cardiologist and abdominal ultrasound examinations not to miss mildly affected individuals. Subsequent survey of the exome data comprised filtering for monoallelic de novo, rare biallelic, and X-linked recessive variants. In two families, rare variants of uncertain significance (VUS) in PKD1L1 and ZIC3 were identified. Both genes have been associated with laterality defects. In two of the remaining families, biallelic variants in LMBRD1 and DNAH17, respectively, were prioritized. In another family, an ultra-rare de novo variant in WDR47 was found. Extensive exome survey of 2,109 single exomes of individuals with situs inversus totalis, heterotaxy, or isolated CHD identified two individuals with novel monoallelic variants in WDR47, but no further individuals with biallelic variants in DNAH17 or LMBRD1. Overall, ES of 14 case-parent trios/quattros with cardiovascular laterality defects identified rare VUS in two families in known disease-associated genes PKD1L1 and ZIC3 and suggests DNAH17, LMBRD1, and WDR47 as potential genes involved in laterality defects.Subject terms: Disease genetics, Genetic counselling, Biological sciences     

Systematic Evidence Map for Over One Hundred and Fifty Per- and Polyfluoroalkyl Substances (PFAS)

Background: Per- and polyfluoroalkyl substances (PFAS) are a large class of synthetic (man-made) chemicals widely used in consumer products and industrial processes. Thousands of distinct PFAS exist in commerce. The 2019 U.S. Environmental Protection Agency (U.S. EPA) Per- and Polyfluoroalkyl Substances (PFAS) Action Plan outlines a multiprogram national research plan to address the challenge of PFAS. One component of this strategy involves the use of systematic evidence map (SEM) approaches to characterize the evidence base for hundreds of PFAS.Objective: SEM methods were used to summarize available epidemiological and animal bioassay evidence for a set of ∼150 PFAS that were prioritized in 2019 by the U.S. EPA’s Center for Computational Toxicology and Exposure (CCTE) for in vitro toxicity and toxicokinetic assay testing.Methods: Systematic review methods were used to identify and screen literature using manual review and machine-learning software. The Populations, Exposures, Comparators, and Outcomes (PECO) criteria were kept broad to identify mammalian animal bioassay and epidemiological studies that could inform human hazard identification. A variety of supplemental content was also tracked, including information on in vitro model systems; exposure measurement–only studies in humans; and absorption, distribution, metabolism, and excretion (ADME). Animal bioassay and epidemiology studies meeting PECO criteria were summarized with respect to study design, and health system(s) were assessed. Because animal bioassay studies with ≥21-d exposure duration (or reproductive/developmental study design) were most useful to CCTE analyses, these studies underwent study evaluation and detailed data extraction. All data extraction is publicly available online as interactive visuals with downloadable metadata.Results: More than 40,000 studies were identified from scientific databases. Screening processes identified 44 animal and 148 epidemiology studies from the peer-reviewed literature and 95 animal and 50 epidemiology studies from gray literature that met PECO criteria. Epidemiological evidence (available for 15 PFAS) mostly assessed the reproductive, endocrine, developmental, metabolic, cardiovascular, and immune systems. Animal evidence (available for 40 PFAS) commonly assessed effects in the reproductive, developmental, urinary, immunological, and hepatic systems. Overall, 45 PFAS had evidence across animal and epidemiology data streams.Discussion: Many of the ∼150 PFAS were data poor. Epidemiological and animal evidence were lacking for most of the PFAS included in our search. By disseminating this information, we hope to facilitate additional assessment work by providing the initial scoping literature survey and identifying key research needs. Future research on data-poor PFAS will help support a more complete understanding of the potential health effects from PFAS exposures. https://doi.org/10.1289/EHP10343     

Accuracy and reliability of forensic handwriting comparisons

Forensic handwriting examination involves the comparison of writing samples by forensic document examiners (FDEs) to determine whether or not they were written by the same person. Here we report the results of a large-scale study conducted to assess the accuracy and reliability of handwriting comparison conclusions. Eighty-six practicing FDEs each conducted up to 100 handwriting comparisons, resulting in 7,196 conclusions on 180 distinct comparison sets, using a five-level conclusion scale. Erroneous “written by” conclusions (false positives) were reached in 3.1% of the nonmated comparisons, while 1.1% of the mated comparisons yielded erroneous “not written by” conclusions (false negatives). False positive rates were markedly higher for nonmated samples written by twins (8.7%) compared to nontwins (2.5%). Notable associations between training and performance were observed: FDEs with less than 2 y of formal training generally had higher error rates, but they also had higher true positive and true negative rates because they tended to provide more definitive conclusions; FDEs with at least 2 y of formal training were less likely to make definitive conclusions, but those definitive conclusions they made were more likely to be correct (higher positive predictive and negative predictive values). We did not observe any association between writing style (cursive vs. printing) and rates of errors or incorrect conclusions. This report also provides details on the repeatability and reproducibility of conclusions, and reports how conclusions are affected by the quantity of writing and the similarity of content.

Forensic science is under scrutiny, particularly for pattern-based disciplines in which source conclusions are reported. The National Research Council report Strengthening Forensic Science in the United States: A Path Forward (1) stated that “The scientific basis for handwriting comparisons needs to be strengthened” and noted that “there has been only limited research to quantify the reliability and replicability of the practices used by trained document examiners.” The President’s Council of Advisors on Science and Technology (PCAST) report Forensic Science in Criminal Courts: Ensuring Scientific Validity of Feature-Comparison Methods (2) expressed concerns regarding the validity and reliability of conclusions made by forensic examiners, and called for empirical testing: “The only way to establish the scientific validity and degree of reliability of a subjective forensic feature-comparison method—that is, one involving significant human judgment—is to test it empirically by seeing how often examiners actually get the right answer. Such an empirical test of a subjective forensic feature-comparison method is referred to as a ‘black-box test.’” The National Commission on Forensic Science also called for such testing (3). Although the accuracy and reliability of conclusions made by forensic document examiners (FDEs) have been the focus of multiple studies over the years (4–10), the designs of those studies are notably different from this study (and from PCAST’s recommendations), and therefore the resulting rates are not directly comparable (in particular, when comparing open-set to closed-set studies, comparing studies based on one-to-one vs. one-to-many examinations, and comparing studies that use notably different conclusion scales; see SI Appendix, Appendix B for a summary).This study was conducted to provide data that can be used to assess the scientific validity of handwriting comparisons, for use by policy makers, laboratory managers, the legal community, and FDEs. This study follows the approach used in the previous FBI Laboratory–Noblis latent print black box study (11) and later recommended by the PCAST report. The design utilizes open-set, one-to-one document comparisons to evaluate the conclusions reached by practicing FDEs when comparing writing samples selected to be broadly comparable to casework. The primary purposes of the study are to measure the accuracy of conclusions by FDEs when comparing handwriting samples and to assess reliability by measuring the reproducibility (interexaminer variability) and repeatability (intraexaminer variability) of those conclusions. Secondary purposes include reporting any associations between the accuracy of the decisions in this study, factors related to the participants (such as training or experience), and factors related to the samples (such as quantity of writing, comparability of content, limitations, or style of writing).     

Aftershocks: Home Loss and Long-Term Health after the 2011 Great East Japan Earthquake

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From hurricanes to earthquakes, natural disasters affect survivors in innumerable ways, including adverse effects on mental¹ and physical² health. Only a few studies have been able to assess a consistent set of health indicators both before and after a disaster due to the unpredictability of such events. However, in a study recently published in Environmental Health Perspectives,³ a team of researchers was able to use preexisting data from the Japan Gerontological Evaluation Study to assess a wide array of health and well-being outcomes before and up to 9 years after the 2011 Great East Japan Earthquake.The authors used data from a cohort of older individuals who came from the city of Iwanuma. The tsunami that followed the earthquake killed more than 180 people in Iwanuma, inundated nearly half the city, and destroyed 5,542 houses. Most of the 2,167 individuals in the current study sustained some degree of damage to their homes during the 2011 disaster; 4% suffered a complete home loss.Open in a separate windowThe Great East Japan Earthquake and related tsunami completely destroyed 122,000 dwellings in all and damaged another 1 million, according to estimates from 2021.⁵ Image: © Gallo Images/Contributor via Getty Images.The study examined the longitudinal associations between complete home loss specifically and 34 health indicators categorized as physical health, mental health (e.g., symptoms of depression or posttraumatic stress), health behaviors/sleep (e.g., dozing off during the day), social well-being (participation in society), cognitive social capital (perceptions about social relations in the community), subjective well-being (happiness and life satisfaction), and prosocial or altruistic behaviors (e.g., sharing). This “outcome-wide” framework—namely, assessing the relationship between a single exposure and multiple outcomes—is a relatively new approach.⁴“Epidemiologic research on disaster survivors has focused on mental health problems as an outcome,” says lead author Koichiro Shiba, a postdoctoral research fellow at the Harvard T.H. Chan School of Public Health. “We know little about how a disaster influences key aspects of human well-being that cannot be captured by looking at mental health alone. This knowledge gap motivated us to employ the outcome-wide framework to examine the relationship between the disaster experience and well-being.”After 9 years, complete home loss was associated with increased symptoms of posttraumatic stress, depression, and hopelessness. People who lost their homes were also more likely to experience daytime sleepiness along with lower levels of trust in the community, community attachment, perceptions of mutual help in the community, and prosociality. The researchers saw more modest associations between complete home loss and having more chronic conditions, higher body mass index, and decreased happiness. Home loss was not associated with the remaining indicators.“The most surprising result to me was the strong association between home loss and decreased social capital; it is notable that the association persisted even nine years after the disaster,” Shiba says. “By that time, buildings in the flooded area had been rebuilt and people had already moved out of the temporary shelters and lived in permanent housing. It is difficult and takes time to reconstruct social capital once it is destroyed, highlighting the importance of efforts to preserve preexisting social capital.”“This is an excellent piece of scholarship. The longevity of the disruptive effect is astonishing: 9 years post-event, participants are still experiencing distress related to the earthquake event,” says Katie E. Cherry, the Emogene Pliner Distinguished Professor of Aging Studies at Louisiana State University and author The Other Side of Suffering, which covers her research on survivor recovery after Hurricanes Katrina and Rita. “Most important from a methodological point of view is the authors’ use of a prospective design,” she says, explaining that the availability of pre-event data allowed for a cleaner assessment of earthquake exposure effects.“It’s nice to see the authors’ inclusion of social capital and mental health consequences as outcome variables,” Cherry adds. Yet she found the notion of cognitive social capital to be conceptually ambiguous. The authors included in that term trust and mutual help in the community, as well as community attachment. “There is a large [body of] literature on social capital, which is a well-established social science construct,” Cherry says. “To my knowledge, there may be a dimension of social capital that is cognitive, but I am not aware of a ‘cognitive social capital.’”“Although we intuitively understand that losing a home during a natural hazard or disaster is incredibly harmful, this study has used extensive quantitative data from more than 2,000 survivors over a decade to show how broadly damaging it can be,” says Daniel Aldrich, a professor of political science and public policy at Northeastern University. “It is not just the loss of one’s physical property that changes one’s life. It is also the forced relocation that follows which pulls people away from their pre-disaster family, neighbors, and friends. In short, they lose their social networks, and these networks are powerful determinants of social and mental health.”     

Altered Regulation of mRNA and miRNA Expression in Epithelial and Stromal Tissue of Keratoconus Corneas

PurposeEvaluation of mRNA and microRNA (miRNA) expression in epithelium and stroma of patients with keratoconus.MethodsThe epithelium and stroma of eight corneas of eight patients with keratoconus and eight corneas of eight non-keratoconus healthy controls were studied separately. RNA was extracted, and mRNA and miRNA analyses were performed using microarrays. Differentially expressed mRNAs and miRNAs in epithelial and stromal keratoconus samples compared to healthy controls were identified. Selected genes and miRNAs were further validated using RT-qPCR.ResultsWe discovered 170 epithelial and 1498 stromal deregulated protein-coding mRNAs in KC samples. In addition, in epithelial samples 180 miRNAs and in stromal samples 379 miRNAs were significantly deregulated more than twofold compared to controls. Pathway analysis revealed enrichment of metabolic and axon guidance pathways for epithelial cells and enrichment of metabolic, mitogen-activated protein kinase (MAPK), and focal adhesion pathways for stromal cells.ConclusionsThis study demonstrates significant differences in the expression and regulation of mRNAs and miRNAs in the epithelium and stroma of Patients with KC. Also, in addition to the well-known target candidates, we were able to identify further genes and miRNAs that may be associated with keratoconus. Signaling pathways influencing metabolic changes and cell contacts are affected in epithelial and stromal cells of patients with keratoconus.