A5029808034- Cancer Genomics and Diagnostics
- BRCA gene mutations in cancer
- DNA Repair Mechanisms
- Chromosomal and Genetic Variations
- Genomics and Phylogenetic Studies
- CRISPR and Genetic Engineering
- Cancer-related Molecular Pathways
- Ovarian cancer diagnosis and treatment
- Genomic variations and chromosomal abnormalities
- RNA and protein synthesis mechanisms
- Autism Spectrum Disorder Research
- RNA modifications and cancer
- Pediatric Pain Management Techniques
- Liver Disease Diagnosis and Treatment
- Genomics and Rare Diseases
- MicroRNA in disease regulation
- Genetics and Neurodevelopmental Disorders
- Plant Stress Responses and Tolerance
- Congenital heart defects research
- Pain Mechanisms and Treatments
- Plant responses to water stress
- Genetic factors in colorectal cancer
- PARP inhibition in cancer therapy
- Radiomics and Machine Learning in Medical Imaging
- AI in cancer detection
Gene Tech (China)
2019-2022
Chinese University of Hong Kong
2017-2020
University of Hong Kong
2012-2019
Vision Medicals (China)
2019
Nanjing Agricultural University
2016-2017
BGI Group (China)
2012-2015
Guangzhou HKUST Fok Ying Tung Research Institute
2012-2015
Imaging Center
2012
South China University of Technology
2012
Bioscience (China)
2012
There is a rapidly increasing amount of de novo genome assembly using next-generation sequencing (NGS) short reads; however, several big challenges remain to be overcome in order for this efficient and accurate. SOAPdenovo has been successfully applied assemble many published genomes, but it still needs improvement continuity, accuracy coverage, especially repeat regions. To these challenges, we have developed its successor, SOAPdenovo2, which the advantage new algorithm design that reduces...
The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly such into high-quality, finished sequences remains challenging. Many tools are available, but they differ greatly in terms their performance (speed, scalability, hardware requirements, acceptance newer read technologies) final output (composition assembled sequence). More importantly, it largely unclear how best assess the quality sequences. Assemblathon competitions...
Autism Spectrum Disorder (ASD) demonstrates high heritability and familial clustering, yet the genetic causes remain only partially understood as a result of extensive clinical genomic heterogeneity. Whole-genome sequencing (WGS) shows promise tool for identifying ASD risk genes well unreported mutations in known loci, but an assessment its full utility group has not been performed. We used WGS to examine 32 families with detect de novo or rare inherited variants predicted be deleterious...
Background: With the fast development of next generation sequencing technologies, increasing numbers genomes are being de novo sequenced and assembled. However, most in fragmental incomplete draft status, thus it is often difficult to know accurate genome size repeat content. Furthermore, many highly repetitive or heterozygous, posing problems current assemblers utilizing short reads. Therefore, necessary develop efficient assembly-independent methods for estimation these genomic...
Abstract Motivation: The next-generation high-throughput sequencing technologies, especially from Illumina, have been widely used in re-sequencing and de novo assembly studies. However, there is no existing software that can simulate Illumina reads with real error quality distributions coverage bias yet, which very useful relevant development study designing of projects. Results: We provide a package, pIRS (profile-based pair-end simulator), simulates empirical Base-Calling GC%-depth...
Unlike daily routine images, ultrasound images are usually monochrome and low-resolution. In the cancer regions blurred, vague margin irregular in shape. Moreover, features of region very similar to normal or benign tissues. Therefore, training with original Convolutional Neural Network (CNN) directly is not satisfactory. our study, inspired by state-of-the-art object detection network Faster R-CNN, we develop a detector which more suitable for thyroid papillary carcinoma images. order...
Abstract Motivation: The boost of next-generation sequencing technologies provides us with an unprecedented opportunity for elucidating genetic mysteries, yet the short-read length hinders from better assembling genome scratch. New protocols now exist that can generate overlapping pair-end reads. By joining 3′ ends each read pair, one is able to construct longer reads assembling. However, effectively two overlapped remains a challenging task. Result: In this article, we present efficient...
Sensitivity to pain varies considerably between individuals and is known be heritable. Increased sensitivity experimental a risk factor for developing chronic pain, common debilitating but poorly understood symptom. To understand mechanisms underlying search rare gene variants (MAF<5%) influencing sensitivity, we explored the genetic variation in individuals' responses pain. Quantitative sensory testing heat was performed 2,500 volunteers from TwinsUK (TUK): exome sequencing depth of 70×...
Abstract Background To gain biological insights into lung metastases from hepatocellular carcinoma (HCC), we compared the whole-genome sequencing profiles of primary HCC and paired metastases. Methods We used at 33X-43X coverage to profile somatic mutations in (HBV+) metachronous (> 2 years interval). Results In total, 5,027-13,961 5,275-12,624 single-nucleotide variants (SNVs) were detected metastases, respectively. Generally, 38.88-78.49% SNVs present tumors. identified 65–221...
To investigate the BRCA status in Chinese patients with ovarian cancer (OC). Though there were two large prevalence studies OC patients, this was first time to observe it healthy controls.We performed mutation screening using next-generation sequencing determine of germline deleterious mutations an unselected cohort (n = 1331) versus controls 1763) and describe types spectrum variants.Among 1331 OC, 227 (17.1%) carried variants BRCA1 70 (5.3%) BRCA2. Of 1763 control subjects, 6 (0.3%) 2...
Copy-number variations (CNV), loss of heterozygosity (LOH), and uniparental disomy (UPD) are large genomic aberrations leading to many common inherited diseases, cancers, other complex diseases. An integrated tool identify these is essential in understanding diseases designing clinical interventions. Previous discovery methods based on whole-genome sequencing (WGS) require very high depth coverage the whole genome scale, cost-wise inefficient. Another approach, exome (WEGS), limited...
Abstract Background The purpose of this study was to evaluate the association between single-nucleotide polymorphisms and chronic postsurgical pain. Methods Using GoldenGate genotyping assays, we genotyped 638 within 54 pain-related genes in 1,152 surgical patients who were enrolled our Persistent Pain after Surgery Study. Patients contacted by phone determine whether they had pain at 12 months. Polymorphisms identified validated a matched cohort 103 with free. functions targeted tested an...
Abstract Genetic testing for germline mutations in BRCA1/2 of patients with breast cancer (BC) is part routine patient care. However, account only a fraction familial BC. A custom panel 22 gene sequencing was performed on each patient. Among the 481 female patients, 135 were detected to carry pathogenic (P)/likely (LP) (28.1%), which corresponded 12 different predisposition genes [14.6% (70/481) BRCA1 gene, 5.0% (24/481) BRCA2 8.5% (41/481) non‐ genes]. Moreover, 24.7% (119/481) had mutation...
Abstract Susceptible genetic polymorphisms and altered expression levels of protein kinase C (PKC)-encoding genes suggest overactivation PKC in autism spectrum disorder (ASD) development. To delineate the pathological role PKC, we pharmacologically stimulated its activity during early development zebrafish. Results demonstrated that hyper-activation perturbs zebrafish induces a long-lasting head size deficit. The anatomical cellular analysis revealed reduced neural precursor proliferation...
MiR-430 is considered an important regulator during embryonic development, but genetic loss-of-function study still lacking. Here we demonstrated that deletion of the miR-430 cluster resulted in developmental defects cell movement, germ layer specification, axis patterning and organ progenitor formation zebrafish. Transcriptome analysis indicated maternally provided transcripts were not properly degraded whereas zygotic genome expressed genes fully activated mutants. We further found a...
Germline BRCA1/2 prevalence is relatively low in sporadic triple-negative breast cancer (TNBC). We hypothesized that non-BRCA genes may also have significant germline contribution to Chinese TNBC, and the somatic mutational landscape of TNBC vary between ethnic groups. therefore conducted this study investigate mutations 43 susceptibility TNBC.Sixty-six patients were enrolled study. tumor DNA each patient subjected capture-based next-generation sequencing using a 43-gene panel. Standard...
Gynecologic cancers have become a major threat to women's health. The molecular biology of gynecologic is not as well understood that breast cancer, and precision targeting still new. Although viewed collectively group within the female reproductive system, they are more often studied separately. A comprehensive within-group comparison on profiles lacking.We conducted whole-exome sequencing study cervical/endometrial/ovarian cancer samples from 209 Chinese patients. We combined our data with...
Although previous results showed that β-cyclodextrin-hemin complex (β-CDH) could induce tomato lateral root (LR) formation, the corresponding downstream messengers are still not fully understood. In this report, similar to inducing effects of exogenously applied hydrogen peroxide (H2O2), we discovered β-CDH elicited RBOH1 transcript upregulation, endogenous H2O2 accumulation, and thereafter LR development. Above responses were sensitive dimethylthiourea (DMTU) ascorbic acid (AsA), two...