AluScan: a method for genome-wide scanning of sequence and structure variations in the human genome

<p>Abstract</p> <p>Background</p> <p>To complement next-generation sequencing technologies, there is a pressing need for efficient pre-sequencing capture methods with reduced costs and DNA requirement. The Alu family of short interspersed nucleotide elements is the most abundant type of transposable elements in the human genome and a recognized source of genome instability. With over one million Alu elements distributed throughout the genome, they are well positioned to facilitate genome-wide sequence amplification and capture of regions likely to harbor genetic variation hotspots of biological relevance.</p> <p>Results</p> <p>Here we report on the use of inter-Alu PCR with an enhanced range of amplicons in conjunction with next-generation sequencing to generate an Alu-anchored scan, or 'AluScan', of DNA sequences between Alu transposons, where Alu consensus sequence-based 'H-type' PCR primers that elongate outward from the head of an Alu element are combined with 'T-type' primers elongating from the poly-A containing tail to achieve huge amplicon range. To illustrate the method, glioma DNA was compared with white blood cell control DNA of the same patient by means of AluScan. The over 10 Mb sequences obtained, derived from more than 8,000 genes spread over all the chromosomes, revealed a highly reproducible capture of genomic sequences enriched in genic sequences and cancer candidate gene regions. Requiring only sub-micrograms of sample DNA, the power of AluScan as a discovery tool for genetic variations was demonstrated by the identification of 357 instances of loss of heterozygosity, 341 somatic indels, 274 somatic SNVs, and seven potential somatic SNV hotspots between control and glioma DNA.</p> <p>Conclusions</p> <p>AluScan, implemented with just a small number of H-type and T-type inter-Alu PCR primers, provides an effective capture of a diversity of genome-wide sequences for analysis. The method, by enabling an examination of gene-enriched regions containing exons, introns, and intergenic sequences with modest capture and sequencing costs, computation workload and DNA sample requirement is particularly well suited for accelerating the discovery of somatic mutations, as well as analysis of disease-predisposing germline polymorphisms, by making possible the comparative genome-wide scanning of DNA sequences from large human cohorts.</p

Efficacy, safety and immunogenicity of a human rotavirus vaccine (RIX4414) in Hong Kong children up to three years of age: A randomized, controlled trial

AbstractBackgroundA phase III, double-blind, randomized, controlled trial was conducted in Hong Kong to evaluate the efficacy, safety and immunogenicity of a human rotavirus vaccine, RIX4414 (Rotarix™) against severe rotavirus gastroenteritis in children up to three years of age.MethodsHealthy infants aged 6–12 weeks were enrolled between 08-December-2003 and 31-August-2005 and received two oral doses of either RIX4414 vaccine (N=1513) or placebo (N=1512) given 2 months apart. Vaccine efficacy was assessed from two weeks post-Dose 2 until the children were two and three years of age. Anti-rotavirus IgA seroconversion rate was calculated pre-vaccination and 1–2 months post-Dose 2 using ELISA (cut-off=20U/mL) for 100 infants. Safety was assessed until the children were two years of age; serious adverse events (SAEs) were recorded throughout the study period.ResultsIn children aged two and three years of life, vaccine efficacy against severe rotavirus gastroenteritis was 95.6% (95% CI: 73.1%–99.9%) and 96.1% (95% CI: 76.5%–99.9%), respectively. The seroconversion rate 1–2 months after the second dose of RIX4414 was 97.5% (95% CI: 86.8%–99.9%). At least one SAE was recorded in 439 and 477 infants who were administered RIX4414 and placebo, respectively (p-value=0.130). Six intussusception cases were reported (RIX4414=4; placebo=2) and none was assessed to be vaccine-related.ConclusionRIX4414 was efficacious, immunogenic and safe in the prevention of rotavirus gastroenteritis for at least two years post-vaccination in Hong Kong children

Chronic ulcerative gastroduodenitis as a first gastrointestinal manifestation of Hermansky-Pudlak syndrome in a 10-year-old child

A 10-year-old Chinese boy who had a history of congenital thrombocytopathy presented with severe iron deficiency anemia secondary to chronic gastric inflammation and duodenal ulcerations. Subtle oculocutaneous albinism led to the finding of diminished dense bodies in the platelets under electron microscopy, hence the diagnosis of Hermansky-Pudlak syndrome (HPS). Biopsies from the stomach and duodenum revealed a lymphocytic infiltration in the submucosa, but H pylori infection was absent. The gastroduodenitis responded to the treatment with omeprazole while iron deficiency anemia was corrected by oral iron therapy. HPS is a rare cause of congenital bleeding disorder with multisystemic manifestations. Upper gastrointestinal involvement is rare and should be distinguished from a mere manifestation of the bleeding diathesis

Living donor hepatectomy in female donors with ongoing menstruation: Safety and ethical issues

Purpose: The purpose of this study was to study the safety of the major hepatectomy in female donors with ongoing menstruation in situations where the recipient needs urgent liver transplantation and its impact on menstrual bleeding and subsequent menstrual cycles. Materials and Methods: Fifty-eight female donors that underwent adult-to-adult living donor liver transplantation were enrolled in this study and were categorized into two groups. Group A comprised 49 female donors with normal physiological state and Group B comprised nine female donors with ongoing menstruation during the surgery. All the donors in the cohort underwent right hepatectomy including the middle hepatic vein without any blood transfusion in perioperative period. Results: Preoperative international normalized ratio (INR) in Group A and B was 1.05 ± 0.08 and 1.07 ± 0.08, respectively, while INR at postoperative day 7 in Group A donors was 1.72 ± 0.22 while in Group B donors, it was 1.75 ± 0.26. Perioperative hemoglobin drop in Group A and B was statistically insignificant (1.59 ± 0.83 g% vs 1.68 ± 1.51 g%, P = 0.78). The menstrual blood loss in both the groups was statistically comparable. Conclusions: Our study shows safety of right lobe living donation in female donors with ongoing menstruation with no increased risk of intraoperative excessive bleeding and postoperative physiological impact on their general health

Protective Effects of Testosterone on Presynaptic Terminals against Oligomeric β-Amyloid Peptide in Primary Culture of Hippocampal Neurons

Increasing lines of evidence support that testosterone may have neuroprotective effects. While observational studies reported an association between higher bioavailable testosterone or brain testosterone levels and reduced risk of Alzheimer’s disease (AD), there is limited understanding of the underlying neuroprotective mechanisms. Previous studies demonstrated that testosterone could alleviate neurotoxicity induced by β-amyloid (Aβ), but these findings mainly focused on neuronal apoptosis. Since synaptic dysfunction and degeneration are early events during the pathogenesis of AD, we aim to investigate the effects of testosterone on oligomeric Aβ-induced synaptic changes. Our data suggested that exposure of primary cultured hippocampal neurons to oligomeric Aβ could reduce the length of neurites and decrease the expression of presynaptic proteins including synaptophysin, synaptotagmin, and synapsin-1. Aβ also disrupted synaptic vesicle recycling and protein folding machinery. Testosterone preserved the integrity of neurites and the expression of presynaptic proteins. It also attenuated Aβ-induced impairment of synaptic exocytosis. By using letrozole as an aromatase antagonist, we further demonstrated that the effects of testosterone on exocytosis were unlikely to be mediated through the estrogen receptor pathway. Furthermore, we showed that testosterone could attenuate Aβ-induced reduction of HSP70, which suggests a novel mechanism that links testosterone and its protective function on Aβ-induced synaptic damage. Taken together, our data provide further evidence on the beneficial effects of testosterone, which may be useful for future drug development for AD

Initial viral load and the outcomes of SARS

BACKGROUND: Severe acute respiratory syndrome (SARS) is caused by a novel coronavirus. It may progress to respiratory failure, and a significant proportion of patients die. Preliminary data suggest that a high viral load of the SARS coronavirus is associated with adverse outcomes in the intensive care unit, but the relation of viral load to survival is unclear. METHODS: We prospectively studied an inception cohort of 133 patients with virologically confirmed SARS who were admitted to 2 general acute care hospitals in Hong Kong from Mar. 24 to May 4, 2003. The patients were followed until death or for a minimum of 90 days. We used Cox proportional hazard modelling to analyze potential predictors of survival recorded at the time of presentation, including viral load from nasopharyngeal specimens (measured by quantitative reverse transcriptase polymerase chain reaction [PCR] of the SARS-associated coronavirus). RESULTS: Thirty-two patients (24.1%) met the criteria for acute respiratory distress syndrome, and 24 patients (18.0%) died. The following baseline factors were independently associated with worse survival: older age (61–80 years) (adjusted hazard ratio [HR] 5.24, 95% confidence interval [CI] 2.03–13.53), presence of an active comorbid condition (adjusted HR 3.36, 95% CI 1.44–7.82) and higher initial viral load of SARS coronavirus, according to quantitative PCR of nasopharyngeal specimens (adjusted HR 1.21 per log(10) increase in number of RNA copies per millilitre, 95% CI 1.06–1.39). INTERPRETATION: We found preliminary evidence that higher initial viral load is independently associated with worse prognosis in SARS. Mortality data for patients with SARS should be interpreted in light of age, comorbidity and viral load. These considerations will be important in future studies of SARS

Vaccine Resistance and Hesitancy among Older Adults Who Live Alone or Only with an Older Partner in Community in the Early Stage of the Fifth Wave of COVID-19 in Hong Kong

Vaccination is an effective way in providing protection against COVID-19 infection and severe outcomes. However, vaccine resistance and hesitancy are a great concern among vulnerable populations including older adults who live alone or only with an older partner. This study examined their vaccination status and reasons and associated factors of vaccine resistance and hesitancy. A cross-sectional study was conducted among older adults living alone or only with an older partner in communities in Hong Kong. Participants were interviewed between October 2021 and February 2022. Logistic regression analyses were employed to examine factors associated with vaccine resistance and hesitancy. Of the 2109 included participants, the mean age was 79.3 years (SD 7.6), 1460 (69.2%) were female, 1334 (63.3%) lived alone, and 1621 (76.9%) were receiving social security support. The vaccine uptake, non-uptake (i.e., resistance), and hesitancy rates were 50.1%, 34.4%, and 15.5%, respectively. The top four reasons for vaccine resistance and hesitancy were &ldquo;Not feeling in good health&rdquo; (27%), &ldquo;Worry about vaccine side effects&rdquo; (18%), &ldquo;Feeling no need&rdquo; (10%), and &ldquo;Lack of recommendation from doctors&rdquo; (9%). Vaccine resistance and hesitancy was significantly associated with older age, living alone, more chronic conditions, fewer types of social media use, and lower self-rated health status. Similar associations can be observed in their separate analysis for vaccine resistance and vaccine hesitancy, and ever hospital admission over the past 6 months was additionally related to vaccine hesitancy. Older people who live alone or only with an older partner had a low vaccination rate. Poor health or worry about vaccine side effects were the most common reasons for their vaccine resistance and hesitancy. Actions are greatly needed to improve the uptake rate among this vulnerable population, especially those who were older, have poorer health, and use less social media