[C-reactive protein and direct bilirubin as the early diagnostic indicators of primary hepatocellular carcinoma combined with macrovascular invasion]

Objective: To explore the early clinical diagnostic indicators in patients with primary hepatocellular carcinoma (HCC) combined with macrovascular invasion. Methods: The clinical data of 180 cases of HCC diagnosed by histopathology examination in the Second Affiliated Hospital of Chongqing Medical University from 2012 to 2019 were retrospectively analyzed. The factors influencing the development of macrovascular invasion in HCC patients were analyzed. The receiver operating characteristic curve (ROC curve) was used to evaluate the sensitivity and specificity. Results: Serum C-reactive protein (CRP) level was significantly correlated with various clinical characteristics of HCC patients, including the maximum tumor diameter, tumor number, and macrovascular invasion. Further analysis of the risk factors showed that serum direct bilirubin and CRP were independent risk factors for macrovascular invasion in HCC patients, with odds ratios of 1.747 (95% CI 1.119-2.728, P = 0.014) and 2.376 (95% CI 1.495-3.775, P < 0.001). ROC curve analysis showed that serum CRP, direct bilirubin, and the combination of the both had certain diagnostic value for hepatocellular carcinoma combined with macrovascular invasion. The area under the curve, sensitivity and specificity was 0.724, 0.668, 0.743, 79.1%, 70.1%, 79.1%, and 61.9%, 62.8%, 67.3%, respectively. Conclusion: The combination of CRP with direct bilirubin can be used as an important clinical diagnostic indicator for early diagnosis and prevention of hepatocellular carcinoma combined with macrovascular invasion.

[Clinical analysis of 30 cases with asbestos-related occupational tumors]

Asbestos is classified as a Class 1 carcinogen by the International Cancer Organization (IARC) , and almost all types of asbestos are carcinogenic. The clinical data of 30 asbestos-induced occupational tumor patients in Qingdao city from January 2002 to May 2019 were analyzed, including 24 cases of asbestos-induced lung cancer and 6 cases of asbestos-induced malignant mesothelioma. Mesothelioma was significantly worse than lung cancer in terms of malignancy, the survival time of patients is shorter, and the mortality rate was higher. Both its diagnostic methods and treatment methods should be improved. The high incidence of asbestos-caused tumors is coming. It is recommended that workers exposed to asbestos dust should undergo regular chest CT examinations for early detection, early diagnosis and early treatment.

An integrative multi-omics network-based approach identifies key regulators for breast cancer

Although genome-wide association studies (GWASs) have successfully identified thousands of risk variants for human complex diseases, understanding the biological function and molecular mechanisms of the associated SNPs involved in complex diseases is challenging. Here we developed a framework named integrative multi-omics network-based approach (IMNA), aiming to identify potential key genes in regulatory networks by integrating molecular interactions across multiple biological scales, including GWAS signals, gene expression-based signatures, chromatin interactions and protein interactions from the network topology. We applied this approach to breast cancer, and prioritized key genes involved in regulatory networks. We also developed an abnormal gene expression score (AGES) signature based on the gene expression deviation of the top 20 rank-ordered genes in breast cancer. The AGES values are associated with genetic variants, tumor properties and patient survival outcomes. Among the top 20 genes, RNASEH2A was identified as a new candidate gene for breast cancer. Thus, our integrative network-based approach provides a genetic-driven framework to unveil tissue-specific interactions from multiple biological scales and reveal potential key regulatory genes for breast cancer. This approach can also be applied in other complex diseases such as ovarian cancer to unravel underlying mechanisms and help for developing therapeutic targets.

[Establishment and implementation of hepatitis C screening and referral channels in the hospitals]

Discovering and treating potential hepatitis C infections has become an important strategy to eliminate hepatitis C in China. Currently, the rate of screening and misdiagnosis of hepatitis C antibodies in Chinese hospitals is high, but the rate of physician consultation is low. Therefore, with the cooperation of multiple departments of the hospital, the establishment and implementation of hepatitis C screening and referral channels can effectively improve the diagnosis, referral and treatment rate of hepatitis C patients. This article summarizes the recent research progress of hepatitis C screening and referral in the hospitals.

Modeling circRNA expression pattern with integrated sequence and epigenetic features demonstrates the potential involvement of H3K79me2 in circRNA expression

MOTIVATION

CircRNAs are an abundant class of non-coding RNAs with widespread, cell-/tissue-specific patterns. Previous work suggested that epigenetic features might be related to circRNA expression. However, the contribution of epigenetic changes to circRNA expression has not been investigated systematically. Here, we built a machine learning framework named CIRCScan, to predict circRNA expression in various cell lines based on the sequence and epigenetic features.

RESULTS

The predicted accuracy of the expression status models was high with area under the curve of receiver operating characteristic (ROC) values of 0.89-0.92 and the false-positive rates of 0.17-0.25. Predicted expressed circRNAs were further validated by RNA-seq data. The performance of expression-level prediction models was also good with normalized root-mean-square errors of 0.28-0.30 and Pearson's correlation coefficient r over 0.4 in all cell lines, along with Spearman's correlation coefficient ρ of 0.33-0.46. Noteworthy, H3K79me2 was highly ranked in modeling both circRNA expression status and levels across different cells. Further analysis in additional nine cell lines demonstrated a significant enrichment of H3K79me2 in circRNA flanking intron regions, supporting the potential involvement of H3K79me2 in circRNA expression regulation.

AVAILABILITY AND IMPLEMENTATION

The CIRCScan assembler is freely available online for academic use at https://github.com/johnlcd/CIRCScan.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Improved Constraints on Sterile Neutrino Mixing from Disappearance Searches in the MINOS, MINOS+, Daya Bay, and Bugey-3 Experiments

Searches for electron antineutrino, muon neutrino, and muon antineutrino disappearance driven by sterile neutrino mixing have been carried out by the Daya Bay and MINOS+ collaborations. This Letter presents the combined results of these searches, along with exclusion results from the Bugey-3 reactor experiment, framed in a minimally extended four-neutrino scenario. Significantly improved constraints on the θ_{μe} mixing angle are derived that constitute the most constraining limits to date over five orders of magnitude in the mass-squared splitting Δm_{41}^{2}, excluding the 90% C.L. sterile-neutrino parameter space allowed by the LSND and MiniBooNE observations at 90% CL_{s} for Δm_{41}^{2}<13  eV^{2}. Furthermore, the LSND and MiniBooNE 99% C.L. allowed regions are excluded at 99% CL_{s} for Δm_{41}^{2}<1.6 eV^{2}.

Research Progress on Forensic Palynology and Its Application in Forensic Science

Abstract

Forensic palynology is to apply palynology to the field of forensic science, using pollen and spores to solve issues in juridical practice, such as civil and criminal issues. Sporopollens have a small size, wide distribution, diverse morphology, can be easily transferred, have durability, and is not easily noticed. It can provide strong investigation and related evidence for case detection as good trace evidence. The application of palynology in forensic science has achieved certain success, but it is underutilized in most countries. This paper analyzes the evidence value provided by sporopollen, collection of the sporopollen samples, the progress in detection technology and challenges ahead, based on the biological characteristics of sporopollen, combined with recent successful cases in forensic science, to comprehensively discuss the research progress in forensic palynology and its application prospects in forensic science.

Application of Eye Tracker in Lie Detection

Objective To investigate the application value of eye tracking in lie detection. Methods The 40 subjects were randomly divided into two groups. The pupil diameter, fixation duration, points of fixation and blink frequency of the subjects in the experimental group in observing target stimulation and non-target stimulation were recorded with eye tracker after they accomplished the mock crime. The eye movement parameters of subjects in the control group were directly collected. The differences in eye movement parameters of the experimental group and the control group in observing target stimulation and non-target stimulation were analyzed by t-test. Pearson coefficient analysis of correlation between eye movement parameters that had differences was conducted. The effectiveness of eye movement parameters to distinguish between the experimental group and the control group was calculated by the receiver operator characteristic （ROC） curve. Results Participants from the experimental group had shorter average pupil diameter, longer average fixation duration and fewer fixation points （P<0.05）, but the differences in blink frequency had no statistical significance. The differences in the above indicators of the control group in observing target stimulation and non-target stimulation had no statistical significance. The average fixation duration showed a negative correlation with fixation points （r=-0.255, P<0.05）; the average fixation duration showed a negative correlation with average pupil diameter （r=-0.218, P<0.05）; the fixation points showed a positive correlation with average pupil diameter （r=0.09, P<0.05）. The area under the curve of average pupil diameter, average fixation duration and fixation points was 0.603, 0.621 and 0.580, respectively. Conclusion The average pupil diameter, average fixation duration and fixation points obtained by the eye tracker under laboratory conditions can be used to detect lies.

Sex-specific SNP-SNP interaction analyses within topologically associated domains reveals ANGPT1 as a novel tumor suppressor gene for lung cancer

Genetic interaction has been recognized to be an important cause of the missing heritability. The topologically associating domain (TAD) is a self-interacting genomic region, and the DNA sequences within a TAD physically interact with each other more frequently. Sex differences influence cancer susceptibility at the genetic level. Here, we performed both regular and sex-specific genetic interaction analyses within TAD to identify susceptibility genes for lung cancer in 5204 lung cancer patients and 7389 controls. We found that one SNP pair, rs4262299-rs1654701, was associated with lung cancer in women after multiple testing corrections (combined P = 8.52 × 10^-9 ). Single-SNP analyses did not detect significant association signals for these two SNPs. Both identified SNPs are located in the intron region of ANGPT1. We further found that 5% of nonsmall cell lung cancer patients have an alteration in ANGPT1, indicated the potential role of ANGPT1 in the neoplastic progression in lung cancer. The expression of ANGPT1 was significantly down-regulated in patients in lung squamous cell carcinoma and lung adenocarcinoma. We checked the interaction effect on the ANGPT1 expression and lung cancer and found that the minor allele "G" of rs1654701 increased ANGPT1 gene expression and decreased lung cancer risk with the increased dosage of "A" of rs4262299, which consistent with the tumor suppressor function of ANGPT1. Survival analyses found that the high expression of ANGPT1 was individually associated with a higher survival probability in lung cancer patients. In summary, our results suggest that ANGPT1 may be a novel tumor suppressor gene for lung cancer.

Application of 18S rDNA Clone Library to Detect Diatom Population Diversity in Dianchi

Abstract

Objective To detect the diatom population diversity in Dianchi by constructing a 18S rDNA clone library. Methods DNA from diatoms in 6 water samples of Dianchi was amplified with diatom 18S rDNA specific primer.The 18S rDNA clone library was constructed, and clones were randomly selected for sequence. Sequence alignment was performed by BLAST. The diatom population distribution in Dianchi was analyzed and the phylogenetic tree of diatom 18S rDNA in Dianchi waters was established with the MEGA v7.0.14 software. Results Two hundred and forty clones were sequenced, with 167 diatom sequences obtained, including 11 diatom species such as Stephanodiscus, Diatoma, and Melosira. There were certain differences in diatom population distribution among the 6 samples. Conclusion The population distribution of diatom species in Dianchi shows unique features and the sequence analysis of diatom 18S rDNA has a certain reference value to the inference of forensic drowning sites.

Extraction of the ^{235}U and ^{239}Pu Antineutrino Spectra at Daya Bay

This Letter reports the first extraction of individual antineutrino spectra from ^{235}U and ^{239}Pu fission and an improved measurement of the prompt energy spectrum of reactor antineutrinos at Daya Bay. The analysis uses 3.5×10^{6} inverse beta-decay candidates in four near antineutrino detectors in 1958 days. The individual antineutrino spectra of the two dominant isotopes, ^{235}U and ^{239}Pu, are extracted using the evolution of the prompt spectrum as a function of the isotope fission fractions. In the energy window of 4-6 MeV, a 7% (9%) excess of events is observed for the ^{235}U (^{239}Pu) spectrum compared with the normalized Huber-Mueller model prediction. The significance of discrepancy is 4.0σ for ^{235}U spectral shape compared with the Huber-Mueller model prediction. The shape of the measured inverse beta-decay prompt energy spectrum disagrees with the prediction of the Huber-Mueller model at 5.3σ. In the energy range of 4-6 MeV, a maximal local discrepancy of 6.3σ is observed.

[Clinical study on traditional Chinese medicine syndrome differentiation and treatment of pneumoconiosis]

Objective: To explore the clinical effect of traditional Chinese medicine (TCM) syndrome differentiation in the treatment of pneumoconiosis. Methods: We selected 160 pneumoconiosis patients who were hospitalized in our hospital from July 2015 to July 2016. 102 patients were divided into experimental groups, and the other 58 patients were assigned to the control group. These patients were randomly assigned. The control group was given routine treatment, while the experimental group received conventional treatment combined with TCM syndrome differentiation. We rated patients' quality of life using the SF-36 Quality of Life Scale. C-reactive protein levels in both groups before and after treatment were detected by ELISA. Furthermore, we detected the expression levels of IL-6 mRNA and TGF-β mRNA in serum before and after treatment by RT-PCR.The analysis was performed with SPSS19.0 software. The normal distribution measurement data was expressed by Mean±SD, and the t-test was used for statistical analysis. Non-normal distribution measurement data were expressed as median(M) and interquartile range (P(25), P(75)), and non-parametric test was used for statistical analysis. Results: Compared with the control group, the readmission rate in the experimental group decreased within 3 months; The SF-36 quality of life score results of the two groups showed a statistically significant difference in BP, VT and RE (P<0.05);The levelofCRPdecreasedsignificantlyafter treatment in bothgroups,and thedifferencewasstatistically significant (P<0.05).Comparedwith thecontrolgroup, the levelsofIL-6mRNAandTGF-β1mRNA alsodecreased (P<0.05). Conclusion: TCM syndromedifferentiation and treatmentofpneumoconiosis can effectively improve the patient's condition and life quality. We predict that it may inhibit the progression of pulmonary fibrosis in pneumoconiosis.

[Clinical analysis of 24 cases of occupational chromium rhinopathy]

Occupational chromium rhinopathy is chronic nasal damage caused by chromic anhydride, chromate and dichromate 6-valent chromium compounds. In 2016, 700 people who were exposed to chromium slag in steel plant were checked out. 24 people were found to have nasal injuries. The expert group confirmed 1 case of occupational severe chromium rhinosis and 23 cases of occupational mild chromium rhinosis.There was no significant difference in the incidence, type of work and duration of injury among 24 patients (P>0.05) . Active measures should be taken to prevent chromium rhinopathy and the technological process should be reformed. Occupational health education and occupational health monitoring should be strengthened to avoid exposure of chromium and its compounds through nose and respiratory tract, and to reduce or eliminate the occurrence of chromium rhinosis.

[Emotional and behavioral problems associated with sleep problems in preschool aged children]

Objective: To examine whether sleep problems are related to both emotional and behavioral problems in children aged 3-6 years. Methods: A large cross-sectional study was conducted in Anqing, Wuhu, Tongling and Yangzhou from March to June 2015. A total of 8 900 preschool aged children were included. Sleep problems were obtained by using adapted BISQ completed by the parents or the people who took care of children. Emotional and behavioral problems of the children were accessed by using Strengths and Difficulties Questionnaire (SDQ), and multivariate logistic regression model was used for statistical analyses. Results: The detected rates of emotional symptoms, conduct problems, hyperactivity problems, peer problems, total difficulties and prosocial behavior in preschool aged children were 9.0%, 13.9%, 18.9%, 25.5%, 13.6% and 16.2% respectively. All the detected rates were higher in boys than in girls except the higher rate of emotional symptoms. The proportions of children with high sleep quality, moderate sleep quality and poor or worse sleep quality were 3.9%, 52.9% and 43.2% respectively. After controlling the confounding factors of demographic variables, including gender, age, delivery mode, birth weight, birth height and patent's educational level, multinomial logistic regression analysis showed that the risk of emotional symptoms, conduct problems, hyperactivity problems, peer problems, total difficulties and prosocial behavior in children with longer sleep duration was lower than that in children with shorter sleep duration, the ORs were 0.86 (95%CI: 0.77-0.95), 0.85 (95%CI: 0.78-0.93), 0.85 (95%CI: 0.79-0.92), 0.87(95%CI: 0.81-0.93), 0.83 (95%CI: 0.76-0.91) and 0.82 (95%CI: 0.76-0.89) respectively. Compared with the children with good sleep quality, the risk of emotional symptoms, conduct problems, hyperactivity problems, peer problems, total difficulties and prosocial behavior were higher in children with poor or worse sleep quality, the ORs were 3.26 (95%CI: 2.40-4.42), 2.86 (95%CI: 2.16-3.78), 2.60 (95%CI: 2.00-3.38), 1.96 (95%CI: 1.52-2.54), 4.02 (95%CI: 3.06-5.27) and 2.56 (95%CI: 1.96-3.35) respectively. Conclusion: There was a negative impact of shorter sleep and poor or worse sleep on emotional and behavioral problems of preschool aged children.

[From evidence to clinical practice: myopia control among children in refraction clinics]

Over the past decade, breakthrough has been made on myopia progression control with a lot of evidence from clinical trials, but the effective clinical application of many of them remained immature. Though refraction clinics have been set up in many specialized hospitals offering spectacles to correct refractive error, there was few protocol or standard of treatment for reducing myopia progression. This commentary reviews the latest and essential publications and presents critical advice on applying the research findings to clinical practice. (Chin J Ophthalmol, 2019, 55: 89-92).

Comprehensive functional annotation of susceptibility SNPs prioritized 10 genes for schizophrenia

Nearly 95% of susceptibility SNPs identified by genome-wide association studies (GWASs) are located in non-coding regions, which causes a lot of difficulty in deciphering their biological functions on disease pathogenesis. Here, we aimed to conduct a comprehensive functional annotation for all the schizophrenia susceptibility loci obtained from GWASs. Considering varieties of epigenomic regulatory elements, we annotated all 22,688 acquired susceptibility SNPs according to their genomic positions to obtain functional SNPs. The comprehensive annotation indicated that these functional SNPs are broadly involved in diverse biological processes. Histone modification enrichment showed that H3K27ac, H3K36me3, H3K4me1, and H3K4me3 were related to the development of schizophrenia. Transcription factors (TFs) prediction, methylation quantitative trait loci (meQTL) analyses, expression quantitative trait loci (eQTL) analyses, and proteomic quantitative trait loci analyses (pQTL) identified 447 target protein-coding genes. Subsequently, differential expression analyses between schizophrenia cases and controls, nervous system phenotypes from mouse models, and protein-protein interaction with known schizophrenia-related pathways and genes were carried out with our target genes. We finaly prioritized 10 target genes for schizophrenia (CACNA1C, CLU, CSNK2B, GABBR1, GRIN2A, MAPK3, NOTCH4, SRR, TNF, and SYNGAP1). Our results may serve as an encyclopedia of schizophrenia susceptibility SNPs and offer holistic guides for post-GWAS functional experiments.

[Clinical characteristics and risk factors in pregnancy with severe community-acquired pneumonia]

Objective: To analyze clinical characteristics of severe community-acquired pneumonia during pregnancy and its outcomes, and to explore the relevant risk factors. Methods: From September 2012 to September 2017, 324 398 pregnancies admitted in 7 tertiary hospitals were included. Clinical data of 33 cases of pregnancies with severe community-acquired pneumonia (severe pneumonia group) and 214 cases of pregnancies with common community-acquired pneumonia (control group) were reviewed retrospectively, including the clinical information, manifestations, laboratory examinations and pregnancy outcomes. Relevant risk factors were analyzed by multivariate logistic regression analysis. Results: (1) General data: pregnancies with severe community-acquired pneumonia accounted for 0.010% (33/324 398) of hospitalized pregnancies, the gestational age of two groups were (28±8) and (23±8) weeks, body mass index were (21.7±2.1) and (25.5±3.4) kg/m(2), rate of low income were 54.5% (18/33) and 31.8% (68/214) , respectively. The differences between two groups were all statistically significant (all P<0.05). No significant differences were found in age, pregnancy and parity times, rate of main pregnant complications such as diabetes and hypertension, educational level, asthma and onset seasons between two groups (all P>0.05). (2) Clinical data: the severe pneumonia group had significantly higher incidence of fever [100.0% (33/33) vs 75.2% (161/214) ], shortness of breath (90.9% vs 16.8%) compared with the control group (all P<0.05) .The median peripheral leukocytes counts were 12.3×10(9)/L and 10.2×10(9)/L, the hemoglobin level were (84±18) and (107±14) g/L,the albumin level were (26±4) and (37±3) g/L, the median serum urea nitrogen level were 3.7 and 2.4 mmol/L, the serum creatinine level were (72±25) and (45±11) μmol/L, respectively in two groups. The differences were all statistically significant (all P<0.05). No significantly statistical differences were found in coagulation indicator and cardiac function between two groups (all P>0.05). (3) Treatments: in severe pneumonia group, 12 patients (36.4%,12/33) needed invasive mechanical ventilation, 9 patients (27.3%,9/33) needed non-invasive mechanical ventilation, average time of mechanical ventilation was (7±4) days;8 patients (24.2%,8/33) with septic shock needed vasoactive drugs. However, there was no patient in control group needing mechanical ventilation and vasoactive drugs. (4) Pregnant outcomes: one patient (3.0%,1/33) died in the severe pneumonia group, while no death occurred in the control group. The hospital stay between two groups were (15.1±4.1) and (7.0±1.9) days, the rates of abortion and stillbirth between two groups were 42.4% (14/33) and 3.3% (7/214) , the rates of premature were 10/19 and 6.3% (13/207) , the rates of cesarean were 15/19 and 43.0% (89/207) , the rates of low birth weight newborn were 17/19 and 14.0% (29/207) , the rates of infected newborn were 15/19 and 10.1% (21/207) , the birth weights were (2 165±681) and (3 102±400) g, respectively. The differences between two groups were all statistically significant (all P<0.05). (5) Multivariate logistic regression analysis demonstrated that anemia, low body mass index, hypoproteinemia were risk factors for severe pneumonia in pregnancy (all P<0.05) . Conclusions: Pregnancy with severe community-acquired pneumonia may be complicated by multiple organ dysfunctions, lead to adverse outcomes. Anemia, malnutrition are risk factors for pregnancy with severe pneumonia. Active and effective treatment may improve its prognosis.

Measurement of the Electron Antineutrino Oscillation with 1958 Days of Operation at Daya Bay

We report a measurement of electron antineutrino oscillation from the Daya Bay Reactor Neutrino Experiment with nearly 4 million reactor ν[over ¯]_{e} inverse β decay candidates observed over 1958 days of data collection. The installation of a flash analog-to-digital converter readout system and a special calibration campaign using different source enclosures reduce uncertainties in the absolute energy calibration to less than 0.5% for visible energies larger than 2 MeV. The uncertainty in the cosmogenic ^{9}Li and ^{8}He background is reduced from 45% to 30% in the near detectors. A detailed investigation of the spent nuclear fuel history improves its uncertainty from 100% to 30%. Analysis of the relative ν[over ¯]_{e} rates and energy spectra among detectors yields sin^{2}2θ_{13}=0.0856±0.0029 and Δm_{32}^{2}=(2.471_{-0.070}^{+0.068})×10^{-3}  eV^{2} assuming the normal hierarchy, and Δm_{32}^{2}=-(2.575_{-0.070}^{+0.068})×10^{-3}  eV^{2} assuming the inverted hierarchy.

Formula Derivation for the Probability Distribution of IBS Score in Unrelated Individual Pairs

OBJECTIVES

To derive the probability equation given by STR allele frequencies of identity by state （IBS） score shared by unrelated individual pairs.

METHODS

By comparing the STR genotypes of two unrelated individuals, three mutually exclusive combinations could be obtained： （1） sharing 2 identical alleles, a₂=1, otherwise a₂=0; （2） sharing 1 identical allele, a₁=1, otherwise a₁=0; （3） sharing 0 identical allele, a₀=1, otherwise a₀=0. And the IBS score of the one STR locus in this unrelated individual pair could be given by the formula： ibs=2a₂+a₁. The probability of a₂=1 （p₂）, a₁=1 （p₁） and a₀=1 （p₀） were derived and expressed in powers of the allele frequencies. Subsequently, for a genotyping system including n independent STR loci, the characteristics of binomial distribution of IBS score shared by a pair of unrelated individuals could be given by p₂_l and p₁_l （l=1, 2, …, n）.

RESULTS

All the general equations of p₂, p₁ and p₀ were derived from the basic conceptions of a₂, a₁ and a₀, respectively. Given f_i （i=1, 2, …, m） as the ith allele frequency of a STR locus, the general equations of p₂, p₁ and p₀ could be respectively expressed in powers of f_i： [Formula: see text],[Formula: see text] and [Formula: see text]. The sum of p₂, p₁ and p₀ must be equal to 1. Then, the binomial distribution of IBS score shared by unrelated individual pairs genotyped with n independently STR loci could be written by： IBS~B（2n, π）, and the general probability, π, could be given by the formula： [Formula: see text].

CONCLUSIONS

In the biological full sibling identification, the probability of null hypothesis corresponding to any specific IBS score can be directly calculated by the general equations presented in this study, which is the basement of the evidence explanation.

Runs of homozygosity associate with decreased risks of lung cancer in never-smoking East Asian females

Although genome-wide association studies (GWASs) have identified some risk single-nucleotide polymorphisms in East Asian never-smoking females, the unexplained missing heritability is still required to be investigated. Runs of homozygosity (ROHs) are thought to be a type of genetic variation acting on human complex traits and diseases. We detected ROHs in 8,881 East Asian never-smoking women. The summed ROHs were used to fit a logistic regression model which noteworthily revealed a significant association between ROHs and the decreased risk of lung cancer (P < 0.05). We identified 4 common ROHs regions located at 2p22.1, which were significantly associated with decreased risk of lung cancer (P = 2.00 × 10^-4 - 1.35 × 10^-4). Functional annotation was conducted to investigate the regulatory function of ROHs. The common ROHs were overlapped with potential regulatory elements, such as active epigenome elements and chromatin states in lung-derived cell lines. SOS1 and ARHGEF33 were significantly up-regulated as the putative target genes of the identified ROHs in lung cancer samples according to the analysis of differently expressed genes. Our results suggest that ROHs could act as recessive contributing factors and regulatory elements to influence the risk of lung cancer in never-smoking East Asian females.

Multiple Functional Variants at 13q14 Risk Locus for Osteoporosis Regulate RANKL Expression Through Long-Range Super-Enhancer

RANKL is a key regulator involved in bone metabolism, and a drug target for osteoporosis. The clinical diagnosis and assessment of osteoporosis are mainly based on bone mineral density (BMD). Previous powerful genomewide association studies (GWASs) have identified multiple intergenic single-nucleotide polymorphisms (SNPs) located over 100 kb upstream of RANKL and 65 kb downstream of AKAP11 at 13q14.11 for osteoporosis. Whether these SNPs exert their roles on osteoporosis through RANKL is unknown. In this study, we conducted integrative analyses combining expression quantitative trait locus (eQTL), genomic chromatin interaction (high-throughput chromosome conformation capture [Hi-C]), epigenetic annotation, and a series of functional assays. The eQTL analysis identified six potential functional SNPs (rs9533090, rs9594738, r8001611, rs9533094, rs9533095, and rs9594759) exclusively correlated with RANKL gene expression (p < 0.001) at 13q14.11. Co-localization analyses suggested that eQTL signal for RANKL and BMD-GWAS signal shared the same causal variants. Hi-C analysis and functional annotation further validated that the first five osteoporosis SNPs are located in a super-enhancer region to regulate the expression of RANKL via long-range chromosomal interaction. Particularly, dual-luciferase assay showed that the region harboring rs9533090 in the super-enhancer has the strongest enhancer activity, and rs9533090 is an allele-specific regulatory SNP. Furthermore, deletion of the region harboring rs9533090 using CRISPR/Cas9 genome editing significantly reduced RANKL expression in both mRNA level and protein level. Finally, we found that the rs9533090-C robustly recruits transcription factor NFIC, which efficiently elevates the enhancer activity and increases the RANKL expression. In summary, we provided a feasible method to identify regulatory noncoding SNPs to distally regulate their target gene underlying the pathogenesis of osteoporosis by using bioinformatics data analyses and experimental validation. Our findings would be a potential and promising therapeutic target for precision medicine in osteoporosis. © 2018 American Society for Bone and Mineral Research.

An Osteoporosis Risk SNP at 1p36.12 Acts as an Allele-Specific Enhancer to Modulate LINC00339 Expression via Long-Range Loop Formation

Genome-wide association studies (GWASs) have reproducibly associated variants within intergenic regions of 1p36.12 locus with osteoporosis, but the functional roles underlying these noncoding variants are unknown. Through an integrative functional genomic and epigenomic analyses, we prioritized rs6426749 as a potential causal SNP for osteoporosis at 1p36.12. Dual-luciferase assay and CRISPR/Cas9 experiments demonstrate that rs6426749 acts as a distal allele-specific enhancer regulating expression of a lncRNA (LINC00339) (∼360 kb) via long-range chromatin loop formation and that this loop is mediated by CTCF occupied near rs6426749 and LINC00339 promoter region. Specifically, rs6426749-G allele can bind transcription factor TFAP2A, which efficiently elevates the enhancer activity and increases LINC00339 expression. Downregulation of LINC00339 significantly increases the expression of CDC42 in osteoblast cells, which is a pivotal regulator involved in bone metabolism. Our study provides mechanistic insight into how a noncoding SNP affects osteoporosis by long-range interaction, a finding that could indicate promising therapeutic targets for osteoporosis.