A5023632317- Cancer Genomics and Diagnostics
- Lung Cancer Treatments and Mutations
- Genetic factors in colorectal cancer
- Colorectal Cancer Treatments and Studies
- Cholangiocarcinoma and Gallbladder Cancer Studies
- Ferroptosis and cancer prognosis
- RNA modifications and cancer
- Genomics and Rare Diseases
- Genomics and Phylogenetic Studies
- Cancer Immunotherapy and Biomarkers
- Sarcoma Diagnosis and Treatment
- Lung Cancer Research Studies
- Hepatocellular Carcinoma Treatment and Prognosis
- MicroRNA in disease regulation
- Cancer Mechanisms and Therapy
- Molecular Biology Techniques and Applications
- BRCA gene mutations in cancer
- Cancer Cells and Metastasis
- Radiomics and Machine Learning in Medical Imaging
- Cancer-related molecular mechanisms research
- Gastric Cancer Management and Outcomes
- Amino Acid Enzymes and Metabolism
- Synthesis of Organic Compounds
- Genetics, Bioinformatics, and Biomedical Research
- Drug Transport and Resistance Mechanisms
Shenzhen Bioeasy Biotechnology (China)
2017-2024
Mellanox Technologies (Israel)
2018-2023
Sixth Affiliated Hospital of Sun Yat-sen University
2021
Sun Yat-sen University
2021
Wenzhou Medical University
2010
Some applications, especially those clinical applications requiring high accuracy of sequencing data, usually have to face the troubles caused by unavoidable errors. Several tools been proposed profile quality, but few them can quantify or correct This unmet requirement motivated us develop AfterQC, a tool with functions errors and most them, plus highly automated quality control data filtering features. Different from tools, AfterQC analyses overlapping paired sequences for pair-end data....
The genetic basis of colorectal cancer (CRC) and its clinical associations remain poorly understood due to limited samples or targeted genes in current studies. Here, we perform ultradeep whole-exome sequencing on 1015 patients with CRC as part the ChangKang Project. We identify 46 high-confident significantly mutated genes, 8 which mutate 14.9% patients: LYST, DAPK1, CR2, KIF16B, NPIPB15, SYTL2, ZNF91, KIAA0586. With an unsupervised clustering algorithm, propose a subtyping strategy that...
Late-stage or recurrent intrahepatic cholangiocarcinoma (ICC) patients exhibit poor prognosis due to limited sensitivity chemotherapy radiotherapy and coexistence of multiple lesions. Programmed cell death protein 1 (PD-1) blockade provides a therapeutic opportunity for with high tumor mutation burden (TMB), microsatellite instability (MSI-H), deficient mismatch repair (dMMR) and/or positive programmed ligand (PD-L1) expression. However, it is currently believed that low TMB, stable (MSS),...
Removing duplicates might be considered as a well-resolved problem in next-generation sequencing (NGS) data processing domain. However, NGS technology gains more recognition clinical application, researchers start to pay attention its errors, and prefer remove these errors while performing deduplication operations. Recently, new called unique molecular identifier (UMI) has been developed better identify reads derived from different DNA fragments. Most existing duplicate removing tools cannot...
Germline variations may contribute to lung cancer susceptibility besides environmental factors. The influence of germline mutations on and their correlation with somatic has not been systematically investigated.In this study, from 1,026 non-small cell (NSCLC) patients were analyzed a 58-gene next-generation sequencing (NGS) panel containing known hereditary cancer-related genes, categorized based American College Medical Genetics Genomics (ACMG) guidelines in pathogenicity, the corresponding...
POLE/POLD1 gene variants have been suggested as potential markers for immunotherapy due to their significant association with the tumor mutational burden (TMB), an effective indicator response prediction in immunotherapy. However, correlation of MSI, MMR, TMB, MMR-related and key driver mutations needs be defined support patient recruitment therapeutic effect assessment 1,392 Chinese cancer patients were recruited, existing immunotherapeutic pathways was investigated. A next-generation...
In recent years, gene fusion detection for cancer treatment has become increasingly important since more therapeutic agents have been developed to suppress kinases. Although a number of tools detect fusions from DNA sequencing data, most them are not sensitive enough processing the data samples with low tumor composition, like cell-free DNA. this paper, we will introduce GeneFuse, tool and visualize high sensitivity specificity. GeneFuse focuses on curated fusions, which available in COSMIC...
Abstract The increasing incidence of bladder cancer and its high rate recurrence over a 5-year period necessitate the need for diagnosis surveillance amelioration. Cystoscopy urinary cytology are current tools, molecular techniques such as BTA stat, NMP22, survivin mRNA, urovysion FISH have attracted attention; however, they suffer from insufficient sensitivity or specificity. We developed novel microfluidic approach harvesting intact urinary-exfoliated tumor cells (UETC), either...
Colorectal cancer (CRC) is a highly lethal disease worldwide. The majority of patients receiving targeted therapy or chemotherapy develop drug resistance, while its molecular mechanism remains to be elucidated. plasma circulating tumor DNA (ctDNA) exhibited the potential in identifying gene variations and monitoring resistance CRC treatment. In this study, we monitored ctDNA mutational changes advanced underwent first-line with bevacizumab cetuximab combined chemotherapy. mutation spectrum...
Anaplastic lymphoma kinase (ALK) fusion events account for approximately 3-7% genetic alterations in non-small cell lung cancer (NSCLC) patients. In this study, we revealed the comprehensive genomic landscape of 44 ALK positive NSCLC patients using a 605-gene panel, and identified partners. The most common partner is EML4, forming variant 1 (v1, E13:A20, 18/44), 2 (v2, E20:A20, 5/44), 3 (v3, E6:A20, 13/44). Except novel gene detected new HMBOX1. At mutation level, TP53 frequently mutated...
Postoperative monitoring for patients with colorectal cancer (CRC) requires sensitive biomarkers that are associated medical response and adjuvant therapy following surgery. Conventional tumor [including carcinoembryonic antigen (CEA), CA19‑9 CA125] widely used, but none of the markers provide high sensitivity or specificity. Previous studies indicated circulating DNA (ctDNA) is useful postoperative cancer. However, majority previous involved lung cancer, therefore further required which...
Some types of clinical genetic tests, such as cancer testing using circulating tumor DNA (ctDNA), require sensitive detection known target mutations. However, conventional next-generation sequencing (NGS) data analysis pipelines typically involve different steps filtering, which may cause miss-detection key mutations with low frequencies. Variant validation is also indicated for detected by bioinformatics pipelines. Typically, this process can be executed alignment visualization tools IGV or...
Abstract Subclonal reconstruction algorithms use bulk DNA sequencing data to quantify parameters of tumor evolution, allowing an assessment how cancers initiate, progress and respond selective pressures. We launched the ICGC–TCGA (International Cancer Genome Consortium–The Atlas) DREAM Somatic Mutation Calling Tumor Heterogeneity Evolution Challenge benchmark existing subclonal algorithms. This 7-year community effort used cloud computing 31 on 51 simulated tumors. Algorithms were scored...
Radical or palliative surgery with subsequent adjuvant therapy is the routine treatment for stage II/III colorectal cancer(CRC) and some IV CRC patients. This study aimed to clarify prognostic clinicopathological genetic factors these patients.Fifty-five II-IV patients undergoing were recruited, including without liver metastasis(5 at II, 21 III) metastasis(29 IV). Genetic alterations of primary cancer tissues investigated by whole exome sequencing(WES). Patients followed up 1652 days(median...
Abstract Background Removing duplicates might be considered as a well-resolved problem in next-generation sequencing (NGS) data processing domain. However, NGS technology gains more recognition clinical applications (i.e. cancer testing), researchers start to pay attention its errors, and prefer remove these errors while performing deduplication operations. Recently, new called unique molecular identifier (UMI) has been developed better identify reads derived from different DNA fragments....
Circulating tumor DNA (ctDNA) has been recognized as a promising biomarker for colorectal cancer (CRC) early diagnosis and postoperative monitoring. However, we hypothesize that the clinical value of ctDNA sequencing may differ colon (CC) rectal (RC).Forty-three patients with primary CRC were prospectively enrolled. Tumor tissue samples, paired preoperative plasma samples series obtained. Mutations in each sample identified compared.For 73.0% patients, at least one concordant mutation was...
Lung cancer is the most commonly occurring type of worldwide and also has highest mortality rate. Although targeted therapy non-small cell lung carcinoma (NSCLC) become common, majority patients receiving first-line epithelial growth factor receptor (EGFR)-TKI treatment develop drug resistance. The EGFR T790M (NM_005228.4(EGFR):c.2369C>T (p.Thr790Met)) mutation accounts for half all reported resistance cases; however, molecular mechanism resulting in remains to be characterized. Circulating...
Abstract This article reports a case of advanced metastatic low-grade sarcoma. The patient was diagnosed with an inoperable large (14 × 12 cm) lesion on his neck in September 2015 and underwent two ineffective chemotherapies the following 4 months. Interestingly, although several pathologists could not agree histopathological diagnosis, precise molecular pathological diagnosis obtained using next-generation sequencing (NGS) finally brought excellent therapeutic effects. detected to have...
The title compound, C(17)H(14)F(2)O(3), is approximately planar, the dihedral angle between rings being 5.46 (2)°. H atoms of central propenone group are trans. crystal structure stabilized by inter-molecular C-H⋯F hydrogen bonds.
Objective: Hereditary colorectal cancer (CRC) accounts for approximately 5%–10% of all CRC cases. The full profile CRC-related germline mutations and the corresponding somatic mutational have not been fully determined in Chinese population. Methods: We performed first population study investigating mutation status more than 1,000 (n = 1,923) patients with examined their relationship landscape. Germline alterations were a 58-gene next-generation sequencing panel, 605-gene panel. Results: A...
Approximately 1-2% of non-small cell lung cancer (NSCLC) patients harbor RET (rearranged during transfection) fusions. The oncogenic fusions could lead to constitutive kinase activation and oncogenesis.1746 Chinese NSCLC were analyzed in this study. Tumor tissues collected, formalin fixed, paraffin-embedded (FFPE) archived. Peripheral blood (PB) samples also collected from each patient as control. In addition, we selected 17 them for cfDNA NGS testing 14 tumor immunohistochemistry using...
e13052 Background: Although multiplex PCR is still the golden standard technology for detecting microsatellite instability (MSI), it has some disadvantages. Firstly, its results are not quantized, and interpretation of can be varying different operators. Secondly, requires extra sample amount may affect next-generation sequencing (NGS). So we developed a method to detect MSI status from NGS data. Methods: We tool called VisualMSI, which simulates behaviors level loci. For each locus, pair...
e13546 Background: Liver cancer is the sixth most common in world and fourth cause of mortality. Genomic alterations including homologous recombination deficiency (HRD) mutations often lead to aberrant regulations signaling pathways, which play an important role tumorigenesis. The prognostic value HRD mutation its correlation with overall survival liver unclear. Methods: We used cBioPortal platform analyze a cohort 978 samples. Mutations 13 genes (BRCA1, BRCA2, ATM, BARD1, BRIP1, CHEK1,...
Hepatic metastases were reported in up to 70% of colorectal cancer patients, among which multifocal hepatic metastasis represents one the complications that lead poor prognosis. The majority patients carrying required pharmaceutical treatments reduce tumor size prior surgical resection. However, clinical responses agents difficult predict due heterogeneous nature tumors. Here, we report a case with from was resistant primary chemotherapy and Bevacizumab plus chemotherapy, but responded...