Detecting Disease Association With Rare Variants Using Weighted Entropy

BackgroundThe rapid development of sequencing technology and simultaneously the availability of large quantities of sequence data provides an unprecedented opportunity for researchers to conduct studies to detect rare variants associated with the disease. However, none of current existing statistical methods has uniform power in all scenarios because they more or less are affected by nonfunctional variants and variants with opposite effect. The present study focuses on identifying rare variant associated with the disease.Resultswe present a robust approach to identify rare variant using weighted entropy theory.This approach here takes the proportion of the minor allele among all k variants as its probability distribution, which reduces the noise incurred by non-causal variants, and uses a weight to strike a balance between deleterious rare variants and protective rare variants, which makes our method impacted less by variants with opposite effect. Through simulation studies, we investigate the performance of our method for rare variant association analyses as well as for common variant association analyses and compared it with Burden test and the SKAT-O test. Simulation study show that the proposed method is valid and outperform two existing methods. Meanwhile, the proposed method is affected slightly by non-causal variants and opposite effect variants with high and stable power for various paraments set.ConclusionsWe conclude that the proposed method here can be used effectively to detect rare variant associated with the disease.

Targeted whole exome sequencing and Drosophila modelling to unveil the molecular basis of primary ovarian insufficiency

STUDY QUESTION Can a targeted whole exome sequencing (WES) on a cohort of women showing a primary ovarian insufficiency (POI) phenotype at a young age, combined with a study of copy number variations, identify variants in candidate genes confirming their deleterious effect on ovarian function? SUMMARY ANSWER This integrated approach has proved effective in identifying novel candidate genes unveiling mechanisms involved in POI pathogenesis. WHAT IS KNOWN ALREADY POI, a condition occurring in 1% of women under 40 years of age, affects women’s fertility leading to a premature loss of ovarian reserve. The genetic causes of POI are highly heterogeneous and several determinants contributing to its prominent oligogenic inheritance pattern still need to be elucidated. STUDY DESIGN, SIZE, DURATION WES screening for pathogenic variants of 41 Italian women with non-syndromic primary and early secondary amenorrhoea occurring before age 25 was replicated on another 60 POI patients, including 35 French and 25 American women, to reveal statistically significant shared variants. PARTICIPANTS/MATERIALS, SETTING, METHODS The Italian POI patients’ DNA were processed by targeted WES including 542 RefSeq genes expressed or functioning during distinct reproductive or ovarian processes (e.g. DNA repair, meiosis, oocyte maturation, folliculogenesis and menopause). Extremely rare variants were filtered and selected by means of a Fisher Exact test using several publicly available datasets. A case-control Burden test was applied to highlight the most significant genes using two ad-hoc control female cohorts. To support the obtained data, the identified genes were screened on a novel cohort of 60 Caucasian POI patients and the same case-control analysis was carried out. Comparative analysis of the human identified genes was performed on mouse and Drosophila melanogaster by analysing the orthologous genes in their ovarian phenotype, and two of the selected genes were fruit fly modelled to explore their role in fertility. MAIN RESULTS AND THE ROLE OF CHANCE The filtering steps applied to search for extremely rare pathogenic variants in the Italian cohort revealed 64 validated single-nucleotide variants/Indels in 59 genes in 30 out of 41 screened women. Burden test analysis highlighted 13 ovarian genes as being the most enriched and significant. To validate these findings, filtering steps and Burden analysis on the second cohort of Caucasian patients yielded 11 significantly enriched genes. Among them, AFP, DMRT3, MOV10, FYN and MYC were significant in both patient cohorts and hence were considered strong candidates for POI. Mouse and Drosophila comparative analysis evaluated a conserved role through the evolution of several candidates, and functional studies using a Drosophila model, when applicable, supported the conserved role of the MOV10 armitage and DMRT3 dmrt93B orthologues in female fertility. LARGE SCALE DATA The datasets for the Italian cohort generated during the current study are publicly available at ClinVar database (http://www.ncbi.nlm.nih.gov/clinvar/): accession numbers SCV001364312 to SCV001364375. LIMITATIONS, REASONS FOR CAUTION This is a targeted WES analysis hunting variants in candidate genes previously identified by different genomic approaches. For most of the investigated sporadic cases, we could not track the parental inheritance, due to unavailability of the parents’ DNA samples; in addition, we might have overlooked additional rare variants in novel candidate POI genes extracted from the exome data. On the contrary, we might have considered some inherited variants whose clinical significance is uncertain and might not be causative for the patients’ phenotype. Additionally, as regards the Drosophila model, it will be extremely important in the future to have more mutants or RNAi strains available for each candidate gene in order to validate their role in POI pathogenesis. WIDER IMPLICATIONS OF THE FINDINGS The genomic, statistical, comparative and functional approaches integrated in our study convincingly support the extremely heterogeneous oligogenic nature of POI, and confirm the maintenance across the evolution of some key genes safeguarding fertility and successful reproduction. Two principal classes of genes were identified: (i) genes primarily involved in meiosis, namely in synaptonemal complex formation, asymmetric division and oocyte maturation and (ii) genes safeguarding cell maintenance (piRNA and DNA repair pathways). STUDY FUNDING/COMPETING INTEREST(S) This work was supported by Italian Ministry of Health grants ‘Ricerca Corrente’ (08C621_2016 and 08C924_2019) provided to IRCCS Istituto Auxologico Italiano, and by ‘Piano Sostegno alla Ricerca’ (PSR2020_FINELLI_LINEA_B) provided by the University of Milan; M.P.B. was supported by Telethon-Italy (grant number GG14181). There are no conflicts of interest.

Gene Expression Analysis in Patients with Cocaine-Induced Midline Destructive Lesions

Background and Objectives: Cocaine users may present with positive antineutrophil cytoplasmic antibodies (ANCA) and severe midline destructive lesions (CIMDL) which are histologically characterized by massive apoptosis. However, histopathological and laboratory studies suggest that autoimmunity may not be the main pathogenic driver. We analyzed gene expression both in cell lines of nasal mucosa exposed to cocaine and in CIMDL patients to determine whether genetic predisposition might cause such lesions, which are observed in a minority of cocaine abusers. Materials and Methods: The genetic expression profile of nasal mucosa exposed to cocaine was analyzed. Rare variants of expressed genes were searched in patients with CIMDL using exome sequencing and bio-informatics. Results: We identified 462 genes that were induced by cocaine, mainly related to apoptosis and autophagy in response to oxidative stress. Under the hypothesis that genes linked to the phenotype are also induced by cocaine itself, a rare variants burden test was performed to select genes that were significantly enriched in rare mutations. Next, 11 cocaine abusers with CIMDL and no other relevant medical comorbidities underwent exome sequencing, and 12 genes that were significantly enriched in the burden test and present in at least 10 patients were identified. An in-depth analysis of these genes revealed their involvement in apoptosis, tissue homeostasis, autophagy, and response to oxidative stress. Conclusions: Oxidative stress and rare genetic alterations in the response to reactive oxygen species, apoptosis, autophagy, and tissue regeneration are plausible drivers of damage affecting nasal mucosa exposed to cocaine crystals and, consequently, the pathogenic mechanism behind CIMDL.

Revisiting an Expression Dataset of Discordant Inflammatory Bowel Disease Twin Pairs Using a Mutation Burden Test Reveals CYP2C18 as a Novel Marker

The aim of this study was to investigate the expression features of discordant inflammatory bowel disease (IBD) twin pairs to identify novel molecular features and markers. We collected an expression dataset of discordant twin pairs with ulcerative colitis and performed integrative analysis to identify the genetic-independent expression features. Through deconvolution of the immune cell populations and tissue expression specificity, we refined the candidate genes for susceptibility to ulcerative colitis. We found that dysregulated immune systems and NOD-related pathways were enriched in the expression network of the discordant IBD twin pairs. Among the identified factors were significantly increased proportions of immune cells, including megakaryocytes, neutrophils, natural killer T cells, and lymphatic endothelial cells. The differentially expressed genes were significantly enriched in a gene set associated with cortical and medullary thymocytes. Finally, by combining these expression features with genetic resources, we identified some candidate genes with potential to serve as novel markers of ulcerative colitis, such as CYP2C18. Ulcerative colitis is a subtype of inflammatory bowel disease and a polygenic disorder. Through integrative analysis, we identified some genes, such as CYP2C18, that are involved in the pathogenesis of IBD as well as some candidate therapeutic targets, such as LOXL2.

Region-based analysis of rare genomic variants in whole-genome sequencing datasets reveal two novel Alzheimer's disease-associated genes: DTNB and DLG2

Alzheimer's disease (AD) is a genetically complex disease for which roughly 30 genes have been identified via genome-wide association studies. We attempted to identify rare variants (minor allele frequency <0.01) associated with AD in a region-based, whole genome sequencing (WGS) association study (GSAS) of two independent AD family datasets (NIMH/NIA; 2247 individuals; 605 families). Employing a sliding window approach across the genome, we identified several regions that achieved p-values < 10-6, using the burden test or the SKAT statistic. The genomic region around the dystobrevin beta (DTNB) gene was identified with the burden test and replicated in case/control samples from the ADSP study (pmeta= 4.74*10-8). SKAT analysis revealed region-based association around the discs large homolog 2 (DLG2) gene and replicated in case/control samples from the ADSP study (pmeta=1*10-6). Here, in a region-based GSAS of AD we identified two novel AD genes, DLG2 and DTNB, based on association with rare variants.

Implementation of flipped classroom combined with case- and team-based learning in residency training

The core problem of Chinese resident doctor training is that medical educators present content in an attractive teaching mode to make students more motivated to learn and improve their clinical thinking ability, humanistic care, and practical ability. The traditional classroom mode of teaching cannot meet the needs of modern medical education. The purpose of this study is to explore the benefits and challenges of the flipped classroom (FC) combined with case- and team-based learning (FC-CTBL) for residency training. In this study, 60 junior surgical residents of Xiangya Medical College were enrolled. “Diabetic foot” was selected as the content of this study. Residents were divided into an FC-CTBL group and an FC group. FC-CTBL and FC were compared on the basis of residents’ feedback questionnaires, residents’ learning burden, test scores from a pre-quiz, and objective structured clinical examinations (OSCE). Residents were more satisfied with the FC-CTBL model compared with FC. In the FC-CTBL group, more participants said that the course improved their teamwork skills, analytical skills and their confidence in tackling unfamiliar problems. Residents in the FC-CTBL group also spent significantly less time preparing for class and performed better in the OSCE than those in the FC group. FC-CTBL stimulates residents’ learning motivation, decreases their workload, improves their performance in the OSCE and may help to enhance clinical thinking and teamwork skills. The FC-CTBL approach is a good option for residency training.

What Constitutes a “Due” Burden on Women’s Access to Abortion: A Cultural Discourse Analysis of Whole Woman’s Health v. Hellerstedt

We can find numerous international treaties and legal documents that support women’s choice for safe and legal abortion. However, there are constant different, incompatible and even opposing discourses around abortion globally. This paper examines a 2016 legal case (Whole Women’s Health v. Hellerstedt) to explore how anti-abortion discourse in the U.S. has found its way into the legal text. I begin by addressing women’s right to abortion as a human rights issue and then I investigate how U.S. abortion law entangles with social and cultural reality in the country; I then offer a close reading of the Supreme Court’s judgement and discuss the implications of such a legal text. Public opinions on reproductive rights in the U.S. are closely related to the dynamics between religious culture and feminist activism, and political manipulation leads to divided opinions over the issue. A close reading of the case shows that the court’s constant emphasis on “right to privacy” sets the stage for the current fragility of the reproductive rights in the U.S. cultural and political context. First, it opens a gate for anti-abortion groups to burden women with moral responsibility; second, under TRAP laws it becomes difficult for the abortion providers to justify their stand. I further argue that the undue burden test, which was central to winning this case, is not a strong test for future lawsuits over abortion rights.

Autozygosity mapping and time-to-spontaneous delivery in Norwegian parent-offspring trios

Parental genetic relatedness may lead to adverse health and fitness outcomes in the offspring. However, the degree to which it affects human delivery timing is unknown. We use genotype data from ≃25 000 parent-offspring trios from the Norwegian Mother, Father and Child Cohort Study to optimize runs of homozygosity (ROH) calling by maximising the correlation between parental genetic relatedness and offspring ROHs. We then estimate the effect of maternal, paternal, and fetal autozygosity and that of autozygosity mapping (common segments and gene burden test) on the timing of spontaneous onset of delivery. The correlation between offspring ROH using a variety of parameters and parental genetic relatedness ranged between −0.2 and 0.6, revealing the importance of the minimum number of genetic variants included in a ROH and the use of genetic distance. The optimized compared to predefined parameters showed a ≃45% higher correlation between parental genetic relatedness and offspring ROH. We found no evidence of an effect of maternal, paternal nor fetal overall autozygosity on spontaneous delivery timing. Yet, through autozygosity mapping, we identified three maternal loci TBC1D1, SIGLECs and EDN1 gene regions reducing median time-to-spontaneous onset of delivery by ≃2–5% (P-value&lt; 2.3 × 10−6). We also found suggestive evidence of a fetal locus at 3q22.2, near the RYK gene region (P-value= 2.0 × 10−6). Autozygosity mapping may provide new insights on the genetic determinants of delivery timing beyond traditional genome-wide association studies, but particular and rigorous attention should be given to ROH calling parameter selection.

Retracted: Identification of de novo mutations in prenatal neurodevelopment-associated genes in schizophrenia in two Han Chinese patient-sibling family-based cohorts

Schizophrenia (SCZ) is a severe psychiatric disorder with a strong genetic component. High heritability of SCZ suggests a major role for transmitted genetic variants. Furthermore, SCZ is also associated with a marked reduction in fecundity, leading to the hypothesis that alleles with large effects on risk might often occur de novo. In this study, we conducted whole-genome sequencing for 23 families from two cohorts with unaffected siblings and parents. Two nonsense de novo mutations (DNMs) in GJC1 and HIST1H2AD were identified in SCZ patients. Ten genes (DPYSL2, NBPF1, SDK1, ZNF595, ZNF718, GCNT2, SNX9, AACS, KCNQ1, and MSI2) were found to carry more DNMs in SCZ patients than their unaffected siblings by burden test. Expression analyses indicated that these DNM implicated genes showed significantly higher expression in prefrontal cortex in prenatal stage. The DNM in the GJC1 gene is highly likely a loss function mutation (pLI = 0.94), leading to the dysregulation of ion channel in the glutamatergic excitatory neurons. Analysis of rare variants in independent exome sequencing dataset indicates that GJC1 has significantly more rare variants in SCZ patients than in unaffected controls. Data from genome-wide association studies suggested that common variants in the GJC1 gene may be associated with SCZ and SCZ-related traits. Genes co-expressed with GJC1 are involved in SCZ, SCZ-associated pathways, and drug targets. These evidences suggest that GJC1 may be a risk gene for SCZ and its function may be involved in prenatal and early neurodevelopment, a vulnerable period for developmental disorders such as SCZ.

Studying The Settlement of Backfill Sandy Soil Behind Retaining Wall Under Dynamic Loads

For a long time, the seismic examination of retaining walls has been contemplated by a few strategies dependent on the basic augmentation of Coulomb's limit equilibrium investigation. These techniques cannot gauge the removal of the refill soil upheld by the wall. A trial examination is completed to contemplate the vertical settlement on sandy soil under dynamic loads with other burden amplitudes, vibration frequencies, relative density, and various separations between the establishment and holding divider. The model balance utilized in this investigation is square. Dynamic burden test is done on cohesion less soil with three burden amplitudes (0.25 ton, 0.5 ton and 1 ton), three vibration recurrence (0.5 Hz, 1 Hz and 2 Hz), two density of sandy soil (30% loose sand and 70% dense sand) and three unique separations between the establishment and retaining wall. It has been seen that the change is increment with the burden of abundance and decreased by increasing the separation between the establishment and retaining wall. There is an unimportant result of recurrence on the aggregate settlement. The settlement decrement by incrementing the relative density