Sequencing of a Chinese tetralogy of Fallot cohort reveals clustering mutations in myogenic heart progenitors.

Tetralogy of Fallot (TOF) is the most common cyanotic heart defect, yet the underlying genetic mechanisms remain poorly understood. Here, we performed whole-genome sequencing analysis on 146 nonsyndromic TOF parent-offspring trios of Chinese ethnicity. Comparison of de novo variants and recessive genotypes of this data set with data from a European cohort identified both overlapping and potentially novel gene loci and revealed differential functional enrichment between cohorts. To assess the impact of these mutations on early cardiac development, we integrated single-cell and spatial transcriptomics of early human heart development with our genetic findings. We discovered that the candidate gene expression was enriched in the myogenic progenitors of the cardiac outflow tract. Moreover, subsets of the candidate genes were found in specific gene coexpression modules along the cardiomyocyte differentiation trajectory. These integrative functional analyses help dissect the pathogenesis of TOF, revealing cellular hotspots in early heart development resulting in cardiac malformations.

Identification of a wide spectrum of ciliary gene mutations in nonsyndromic biliary atresia patients implicates ciliary dysfunction as a novel disease mechanism.

BACKGROUND: Biliary atresia (BA) is the most common obstructive cholangiopathy in neonates, often progressing to end-stage cirrhosis. BA pathogenesis is believed to be multifactorial, but the genetic contribution, especially for nonsyndromic BA (common form: > 85%) remains poorly defined. METHODS: We conducted whole exome sequencing on 89 nonsyndromic BA trios to identify rare variants contributing to BA etiology. Functional evaluation using patients' liver biopsies, human cell and zebrafish models were performed. Clinical impact on respiratory system was assessed with clinical evaluation, nasal nitric oxide (nNO), high speed video analysis and transmission electron microscopy. FINDINGS: We detected rare, deleterious de novo or biallelic variants in liver-expressed ciliary genes in 31.5% (28/89) of the BA patients. Burden test revealed 2.6-fold (odds ratio (OR) [95% confidence intervals (CI)]= 2.58 [1.15-6.07], adjusted p = 0.034) over-representation of rare, deleterious mutations in liver-expressed ciliary gene set in patients compared to controls. Functional analyses further demonstrated absence of cilia in the BA livers with KIF3B and TTC17 mutations, and knockdown of PCNT, KIF3B and TTC17 in human control fibroblasts and cholangiocytes resulted in reduced number of cilia. Additionally, CRISPR/Cas9-engineered zebrafish knockouts of KIF3B, PCNT and TTC17 displayed reduced biliary flow. Abnormally low level of nNO was detected in 80% (8/10) of BA patients carrying deleterious ciliary mutations, implicating the intrinsic ciliary defects. INTERPRETATION: Our findings support strong genetic susceptibility for nonsyndromic BA. Ciliary gene mutations leading to cholangiocyte cilia malformation and dysfunction could be a key biological mechanism in BA pathogenesis. FUNDING: The study is supported by General Research Fund, HMRF Commissioned Paediatric Research at HKCH and Li Ka Shing Faculty of Medicine Enhanced New Staff Start-up Fund.

Acupuncture for chronic nonspecific low back pain.

BACKGROUND: Chronic nonspecific low back pain (LBP) is very common; it is defined as pain without a recognizable etiology that lasts for more than three months. Some clinical practice guidelines suggest that acupuncture can offer an effective alternative therapy. This review is a split from an earlier Cochrane review and it focuses on chronic LBP. OBJECTIVES: To assess the effects of acupuncture compared to sham intervention, no treatment, or usual care for chronic nonspecific LBP. SEARCH METHODS: We searched CENTRAL, MEDLINE, Embase, CINAHL, two Chinese databases, and two trial registers to 29 August 2019 without restrictions on language or publication status. We also screened reference lists and LBP guidelines to identify potentially relevant studies. SELECTION CRITERIA: We included only randomized controlled trials (RCTs) of acupuncture for chronic nonspecific LBP in adults. We excluded RCTs that investigated LBP with a specific etiology. We included trials comparing acupuncture with sham intervention, no treatment, and usual care. The primary outcomes were pain, back-specific functional status, and quality of life; the secondary outcomes were pain-related disability, global assessment, or adverse events. DATA COLLECTION AND ANALYSIS: Two review authors independently screened the studies, assessed the risk of bias and extracted the data. We meta-analyzed data that were clinically homogeneous using a random-effects model in Review Manager 5.3. Otherwise, we reported the data qualitatively. We used the GRADE approach to assess the certainty of the evidence. MAIN RESULTS: We included 33 studies (37 articles) with 8270 participants. The majority of studies were carried out in Europe, Asia, North and South America. Seven studies (5572 participants) conducted in Germany accounted for 67% of the participants. Sixteen trials compared acupuncture with sham intervention, usual care, or no treatment. Most studies had high risk of performance bias due to lack of blinding of the acupuncturist. A few studies were found to have high risk of detection, attrition, reporting or selection bias. We found low-certainty evidence (seven trials, 1403 participants) that acupuncture may relieve pain in the immediate term (up to seven days) compared to sham intervention (mean difference (MD) -9.22, 95% confidence interval (CI) -13.82 to -4.61, visual analogue scale (VAS) 0-100). The difference did not meet the clinically important threshold of 15 points or 30% relative change. Very low-certainty evidence from five trials (1481 participants) showed that acupuncture was not more effective than sham in improving back-specific function in the immediate term (standardized mean difference (SMD) -0.16, 95% CI -0.38 to 0.06; corresponding to the Hannover Function Ability Questionnaire (HFAQ, 0 to 100, higher values better) change (MD 3.33 points; 95% CI -1.25 to 7.90)). Three trials (1068 participants) yielded low-certainty evidence that acupuncture seemed not to be more effective clinically in the short term for quality of life (SMD 0.24, 95% CI 0.03 to 0.45; corresponding to the physical 12-item Short Form Health Survey (SF-12, 0-100, higher values better) change (MD 2.33 points; 95% CI 0.29 to 4.37)). The reasons for downgrading the certainty of the evidence to either low to very low were risk of bias, inconsistency, and imprecision. We found moderate-certainty evidence that acupuncture produced greater and clinically important pain relief (MD -20.32, 95% CI -24.50 to -16.14; four trials, 366 participants; (VAS, 0 to 100), and improved back function (SMD -0.53, 95% CI -0.73 to -0.34; five trials, 2960 participants; corresponding to the HFAQ change (MD 11.50 points; 95% CI 7.38 to 15.84)) in the immediate term compared to no treatment. The evidence was downgraded to moderate certainty due to risk of bias. No studies reported on quality of life in the short term or adverse events. Low-certainty evidence (five trials, 1054 participants) suggested that acupuncture may reduce pain (MD -10.26, 95% CI -17.11 to -3.40; not clinically important on 0 to 100 VAS), and improve back-specific function immediately after treatment (SMD: -0.47; 95% CI: -0.77 to -0.17; five trials, 1381 participants; corresponding to the HFAQ change (MD 9.78 points, 95% CI 3.54 to 16.02)) compared to usual care. Moderate-certainty evidence from one trial (731 participants) found that acupuncture was more effective in improving physical quality of life (MD 4.20, 95% CI 2.82 to 5.58) but not mental quality of life in the short term (MD 1.90, 95% CI 0.25 to 3.55). The certainty of evidence was downgraded to moderate to low because of risk of bias, inconsistency, and imprecision. Low-certainty evidence suggested a similar incidence of adverse events immediately after treatment in the acupuncture and sham intervention groups (four trials, 465 participants) (RR 0.68 95% CI 0.46 to 1.01), and the acupuncture and usual care groups (one trial, 74 participants) (RR 3.34, 95% CI 0.36 to 30.68). The certainty of the evidence was downgraded due to risk of bias and imprecision. No trial reported adverse events for acupuncture when compared to no treatment. The most commonly reported adverse events in the acupuncture groups were insertion point pain, bruising, hematoma, bleeding, worsening of LBP, and pain other than LBP (pain in leg and shoulder). AUTHORS' CONCLUSIONS: We found that acupuncture may not play a more clinically meaningful role than sham in relieving pain immediately after treatment or in improving quality of life in the short term, and acupuncture possibly did not improve back function compared to sham in the immediate term. However, acupuncture was more effective than no treatment in improving pain and function in the immediate term. Trials with usual care as the control showed acupuncture may not reduce pain clinically, but the therapy may improve function immediately after sessions as well as physical but not mental quality of life in the short term. The evidence was downgraded to moderate to very low-certainty considering most of studies had high risk of bias, inconsistency, and small sample size introducing imprecision. The decision to use acupuncture to treat chronic low back pain might depend on the availability, cost and patient's preferences.

A random forest-based framework for genotyping and accuracy assessment of copy number variations.

Detection of copy number variations (CNVs) is essential for uncovering genetic factors underlying human diseases. However, CNV detection by current methods is prone to error, and precisely identifying CNVs from paired-end whole genome sequencing (WGS) data is still challenging. Here, we present a framework, CNV-JACG, for Judging the Accuracy of CNVs and Genotyping using paired-end WGS data. CNV-JACG is based on a random forest model trained on 21 distinctive features characterizing the CNV region and its breakpoints. Using the data from the 1000 Genomes Project, Genome in a Bottle Consortium, the Human Genome Structural Variation Consortium and in-house technical replicates, we show that CNV-JACG has superior sensitivity over the latest genotyping method, SV2, particularly for the small CNVs (≤1 kb). We also demonstrate that CNV-JACG outperforms SV2 in terms of Mendelian inconsistency in trios and concordance between technical replicates. Our study suggests that CNV-JACG would be a useful tool in assessing the accuracy of CNVs to meet the ever-growing needs for uncovering the missing heritability linked to CNVs.

Epidemiological characteristics of Hirschsprung's disease (HSCR): Results of a case series of fifty patients from Bangladesh.

BACKGROUND: The epidemiology of Hirschsprung's disease (HSCR) in Bangladesh has never been studied. The aim of this study was to determine the epidemiological characteristics of HSCR in Bangladesh. METHODS: Data from fifty patients were collected prospectively from two hospitals in Chittagong, Bangladesh. RESULTS: The rate of consanguinity (16%) among parents of HSCR patients was higher than that of the general population (10%). Maternal age at the time of birth of the affected child was ≤30years in all cases except one. No association was found between parents' occupation and HSCR. No patient was born preterm and only three patients (6%) had low birth weight. Nine patients (18%) had associated anomalies. We found coexistence of bilateral accessory tragi and ankyloglossia in one patient, and coexistence of rectal duplication cyst in another. Neither anomaly had been previously reported in HSCR patients. CONCLUSIONS: Our study suggests that consanguinity might increase the risk of HSCR whereas advanced maternal age does not. HSCR patients were found more likely to born at term and with normal birth weight. The coexistence of HSCR with previously unreported anomalies highlights the diversity of conditions that can co-occur with HSCR. LEVELS OF EVIDENCE: IV.

Uncovering the genetic lesions underlying the most severe form of Hirschsprung disease by whole-genome sequencing.

Hirschsprung disease (HSCR) is a complex birth defect characterized by the lack of ganglion cells along a variable length of the distal intestine. A large proportion of HSCR patients remain genetically unexplained. We applied whole-genome sequencing (WGS) on 9 trios where the probands are sporadically affected with the most severe form of the disorder and harbor no coding sequence variants affecting the function of known HSCR genes. We found de novo protein-altering variants in three intolerant to change genes-CCT2, VASH1, and CYP26A1-for which a plausible link with the enteric nervous system (ENS) exists. De novo single-nucleotide and indel variants were present in introns and non-coding neighboring regions of ENS-related genes, including NRG1 and ERBB4. Joint analysis with those inherited rare variants found under recessive and/or digenic models revealed both patient-unique and shared genetic features where rare variants were found to be enriched in the extracellular matrix-receptor (ECM-receptor) pathway (p = 3.4 × 10-11). Delineation of the genetic profile of each patient might help finding common grounds that could lead to the discovery of shared molecules that could be used as drug targets for the currently ongoing cell therapy effort which aims at providing an alternative to the surgical treatment.

Types of Control in Acupuncture Clinical Trials Might Affect the Conclusion of the Trials: A Review of Acupuncture on Pain Management.

Analgesic effects of acupuncture have been extensively studied in various clinical trials. However, the conclusion remains controversial, even among large scale randomized controlled trials. This study aimed to evaluate the association between the conclusion of the trials and the types of control used in those trials via systematic review. Published randomized controlled trials of acupuncture for pain were retrieved from electronic databases (Medline, AMED, Cochrane libraries, EMBASE, PsycINFO, Clinicaltrials.gov, and CAB Abstracts) using a prespecified search strategy. One hundred and thirty-nine studies leading to 166 pairs of acupuncture-control treatment effect comparisons (26 studies comprised of 53 intervention-control pairs) were analyzed based on the proportion of positive conclusions in different control designs. We found that treatment effects of acupuncture compared with nontreatment controls had the highest tendency to yield a positive conclusion (84.3%), compared with nonneedle-insertion controls (53.3%). Whereas with needle-insertion controls, the lowest tendency of positive conclusions was observed (37.8%). Consistently, in studies reporting successful blinding, a higher tendency of positive findings on the treatment effect of acupuncture was found in the noninsertion sham controls compared with that in the insertion sham controls. We conclude that the type of control is likely to affect the conclusion in acupuncture analgesic trials. Appropriate control should be chosen according to the aims of studies.

Using models to identify routes of nosocomial infection: a large hospital outbreak of SARS in Hong Kong.

Two factors dominated the epidemiology of severe acute respiratory syndrome (SARS) during the 2002-2003 global outbreak, namely super-spreading events (SSE) and hospital infections. Although both factors were important during the first and the largest hospital outbreak in Hong Kong, the relative importance of different routes of infection has not yet been quantified. We estimated the parameters of a novel mathematical model of hospital infection using SARS episode data. These estimates described levels of transmission between the index super-spreader, staff and patients, and were used to compare three plausible hypotheses. The broadest of the supported hypotheses ascribes the initial surge in cases to a single super-spreading individual and suggests that the per capita risk of infection to patients increased approximately one month after the start of the outbreak. Our estimate for the number of cases caused by the SSE is substantially lower than the previously reported values, which were mostly based on self-reported exposure information. This discrepancy suggests that the early identification of the index case as a super-spreader might have led to biased contact tracing, resulting in too few cases being attributed to staff-to-staff transmission. We propose that in future outbreaks of SARS or other directly transmissible respiratory pathogens, simple mathematical models could be used to validate preliminary conclusions concerning the relative importance of different routes of transmission with important implications for infection control.