ECNano: A cost-effective workflow for target enrichment sequencing and accurate variant calling on 4800 clinically significant genes using a single MinION flowcell.

Background: The application of long-read sequencing using the Oxford Nanopore Technologies (ONT) MinION sequencer is getting more diverse in the medical field. Having a high sequencing error of ONT and limited throughput from a single MinION flowcell, however, limits its applicability for accurate variant detection. Medical exome sequencing (MES) targets clinically significant exon regions, allowing rapid and comprehensive screening of pathogenic variants.

HKG: an open genetic variant database of 205 Hong Kong cantonese exomes.

HKG is the first fully accessible variant database for Hong Kong Cantonese, constructed from 205 novel whole-exome sequencing data. There has long been a research gap in the understanding of the genetic architecture of southern Chinese subgroups, including Hong Kong Cantonese. HKG detected 196 325 high-quality variants with 5.

Rapid and economical drug resistance profiling with Nanopore MinION for clinical specimens with low bacillary burden of Mycobacterium tuberculosis.

Objective: We designed and tested a Nanopore sequencing panel for direct tuberculosis drug resistance profiling. The panel targeted 10 resistance-associated loci. We assessed the feasibility of amplifying and sequencing these loci from 23 clinical specimens with low bacillary burden.

Predictive QSAR model confirms flavonoids in Chinese medicine can activate voltage-gated calcium (CaV) channel in osteogenesis.

Background: Flavonoids in Chinese Medicine have been proven in animal studies that could aid in osteogenesis and bone formation. However, there is no consented mechanism for how these phytochemicals action on the bone-forming osteoblasts, and henceforth the prediction model of chemical screening for this specific biochemical function has not been established. The purpose of this study was to develop a novel selection and effective approach of flavonoids on the prediction of bone-forming ability via osteoblastic voltage-gated calcium (CaV) activation and inhibition using molecular modelling technique.

Potential utility of metagenomic sequencing for improving etiologic diagnosis of infective endocarditis.

To explore potential utility of metagenomic sequencing for improving etiologic diagnosis of infective endocarditis (IE) caused by fastidious bacteria. Plasma and heart valves of two patients, who were diagnosed with IE caused by and species, were sequenced by using Illumina MiSeq and Nanopore MinION. For patient 1, was detected in the plasma pool collected 4 days before valvular replacement surgery.

Draft Genome Sequence of Helicobacter cinaedi, Compiled by Direct Whole-Genome Sequencing of a Blood Culture-Positive Isolate in Hong Kong.

Isolation of Helicobacter cinaedi from a positive blood culture requires prolonged and stringent subculture conditions. Direct whole-genome sequencing (WGS) of a positive blood culture may provide timely treatment-associated genetic information. Here, we report a draft genome sequence of H.

A powerful conditional gene-based association approach implicated functionally important genes for schizophrenia.

Motivation: It remains challenging to unravel new susceptibility genes of complex diseases and the mechanisms in genome-wide association studies. There are at least two difficulties, isolation of the genuine susceptibility genes from many indirectly associated genes and functional validation of these genes.

Results: We first proposed a novel conditional gene-based association test which can use only summary statistics to isolate independently associated genes of a disease.

AC-DIAMOND v1: accelerating large-scale DNA-protein alignment.

Summary: AC-DIAMOND (v1) is a DNA-protein alignment tool designed to tackle the efficiency challenge of aligning large amount of reads or contigs to protein databases. When compared with the previously most efficient method DIAMOND, AC-DIAMOND gains a 6- to 7-fold speed-up, while retaining a similar degree of sensitivity. The improvement is rooted at two aspects: first, using a compressed index of seeds with adaptive-length to speed-up the matching between query and reference sequences; second, adopting a compact form of dynamic programing to fully utilize the parallelism of the SIMD capability.

Prevalence of Mental Illness among Homeless People in Hong Kong.

Metholodogy: This study examined the prevalence and correlates of mental illness in homeless people in Hong Kong and explored the barriers preventing their access to health care. Ninety-seven Cantonese-speaking Chinese who were homeless during the study period were selected at random from the records of the three organisations serving the homeless population. The response rate was 69%.

Prevalence of borderline personality disorder and its clinical correlates in Chinese patients with recent deliberate self-harm.

This study examined the point prevalence of Borderline Personality Disorder (BPD) and its clinical correlates in patients with recent deliberate self-harm (DSH) in Hong Kong. A representative consecutive sample (n = 160) of patients with DSH referred to Prince of Wales Hospital from April 1, 2007 to March 31, 2008 was recruited. Their BPD status was determined according to the BPD subscale of the Chinese version of Structured Clinical Interview for DSM-IV Axis II Personality Disorders (SCID-II).

Unsupervised binning of environmental genomic fragments based on an error robust selection of l-mers.

Background: With the rapid development of genome sequencing techniques, traditional research methods based on the isolation and cultivation of microorganisms are being gradually replaced by metagenomics, which is also known as environmental genomics. The first step, which is still a major bottleneck, of metagenomics is the taxonomic characterization of DNA fragments (reads) resulting from sequencing a sample of mixed species. This step is usually referred as "binning".

Clustering-based approach for predicting motif pairs from protein interaction data.

Unlabelled: Predicting motif pairs from a set of protein sequences based on the protein-protein interaction data is an important, but difficult computational problem. Tan et al. proposed a solution to this problem.

Effect of piracetam on ECT-induced cognitive disturbances: a randomized, placebo-controlled, double-blind study.

Electroconvulsive therapy (ECT) is still the fastest, most effective, and frequently life-saving therapeutic intervention in several forms of depression and some other psychiatric disorders. Transient memory disturbances are frequent after ECT. A randomized, double-blind, placebo-controlled study was conducted to investigate the effects of piracetam on ECT-induced confusion and memory disturbances.