A5086550383- Cancer Genomics and Diagnostics
- Prenatal Screening and Diagnostics
- Renal cell carcinoma treatment
- Parvovirus B19 Infection Studies
- Renal and related cancers
- Fetal and Pediatric Neurological Disorders
- Molecular Biology Techniques and Applications
- Single-cell and spatial transcriptomics
- Immunotherapy and Immune Responses
- Glioma Diagnosis and Treatment
- CAR-T cell therapy research
- Cancer Immunotherapy and Biomarkers
- Blood groups and transfusion
- Birth, Development, and Health
- Helicobacter pylori-related gastroenterology studies
- Cancer Risks and Factors
- Lung Cancer Treatments and Mutations
- Oral Health Pathology and Treatment
- Hemoglobinopathies and Related Disorders
- Genomics and Phylogenetic Studies
- Pregnancy and preeclampsia studies
- CRISPR and Genetic Engineering
- Cervical Cancer and HPV Research
- Genetic factors in colorectal cancer
- Hemophilia Treatment and Research
Cancer Research UK
2018-2021
University of Cambridge
2018-2021
Cancer Research UK Cambridge Center
2018-2021
Prince of Wales Hospital
2014-2017
Chinese University of Hong Kong
2014-2017
Comenius University Bratislava
2011
Selective sequencing or in silico analysis for differences DNA fragment size can improve the detection of circulating tumor DNA.
Significance Patients with microsatellite stable (MSS) pancreatic (PDA) or colorectal cancer (CRC) do not respond to immunotherapy inhibitors of T cell checkpoints. A possible explanation is suggested by finding that cells in these tumors are coated the chemokine, CXCL12, and stimulation CXCR4, CXCL12 receptor on immune cells, suppresses directed migration mediated other chemokine receptors cells. We assessed relevance findings treating patients for seven days continuous infusion...
Significance We explored the limit of noninvasive prenatal testing by performing genome-wide sequencing maternal plasma DNA at 195× and 270× haploid genome coverages. Combined with use a series bioinformatics filters, fetal de novo mutations could be detected positive predictive value that was two orders magnitude higher than previously reported. A BRAF mutation noninvasively in case cardiofaciocutaneous syndrome. The inheritance fetus ascertained on level without haplotypes, hence greatly...
Integration of variant reads across patient-specific mutation loci enables sensitive ctDNA quantification in plasma cell-free DNA sequencing data.
Recently published international guidelines recommend the clinical use of noninvasive prenatal test (NIPT) for aneuploidy screening only among pregnant women whose fetuses are deemed at high risk. The applicability NIPT to average risk pregnancies requires additional supportive evidence. A key determinant reliability is fetal DNA fraction in maternal plasma. In this report, we investigated if differences fractions existed between different pregnancy groups. One hundred and ninety-five...
Abstract Background Cell-free tumor-derived DNA (ctDNA) allows non-invasive monitoring of cancers, but its utility in renal cell cancer (RCC) has not been established. Methods Here, a combination untargeted and targeted sequencing methods, applied to two independent cohorts patients ( n = 91) with various tumor subtypes, were used determine ctDNA content plasma urine. Results Our data revealed lower levels RCC relative other cancers similar size stage, detection 27.5% from both cohorts. A...
Current evidence suggests that plasma cell-free DNA (cfDNA) is fragmented around a mode of 166 bp. Data supporting this view has been mainly acquired through the analysis double-stranded cfDNA. The characteristics and diagnostic potential single-stranded damaged cfDNA in healthy individuals cancer patients remain unclear. Here, combination high-affinity magnetic bead-based extraction sequencing library preparation (MB-ssDNA), we report discovery large proportion fragments centered at ∼50 We...
Abstract Background Recent advances in the study and clinical applications of circulating tumor DNA (ctDNA) are limited by practical considerations sample collection. Whole-genome sequencing (WGS) is increasingly used for analysis ctDNA, identifying copy-number alterations fragmentation patterns. We hypothesized that low-depth/shallow WGS (sWGS) data may be generated from minute amounts cell-free DNA, fragment-size selection remove contaminating genomic small blood volumes. Dried spots have...
Abstract Objective The aim of this study is to develop an approach for analyzing plasma DNA sequencing data noninvasive fetal chromosomal aneuploidy testing that does not require the comparison with control samples or a series selected genomic regions. Results We developed control‐free examination (COFFEE) algorithm by utilizing size differences between fetally derived and maternally molecules in maternal plasma. applied COFFEE on three datasets generated different experimental settings....
Abstract Circulating tumor-derived DNA (ctDNA) can be used to monitor cancer dynamics noninvasively. Patients with small tumors have few copies of ctDNA in plasma, resulting limited sensitivity detect low-volume or residual disease. We show that sampling limitations overcome and for detection improved by massively parallel sequencing when hundreds thousands mutations are identified tumor genotyping. describe the INtegration VAriant Reads (INVAR) analysis pipeline, which combines...
Abstract Recent advances in the research and clinical applications of circulating tumour DNA (ctDNA) is limited by practical considerations sample collection. Whole genome sequencing (WGS) increasingly used for analysis ctDNA, identifying copy-number alterations, fragment size patterns, other genomic features. We hypothesised that low-depth WGS data may be generated from minute amounts cell-free DNA, fragment-size selection effective to remove contaminating (gDNA) small volumes blood. There...
Abstract Glioma-derived cell-free tumor DNA is challenging to detect using standard liquid biopsy techniques as its levels in body fluids are very low, similar those patients with early stage carcinomas. By sequencing across thousands of clonal and private mutations identified individually each patient’s we detected tumor-derived plasma (10/12, 83%) urine samples (8/11, 72%) from the majority (7/8, 87.5%) glioma tested. One Sentence Summary Circulating can be primary brain guided by...
Abstract Inhibition of the chemokine receptor CXCR4 in combination with blockade PD-1/PD-L1 T cell checkpoint induces infiltration and anti-cancer responses murine human pancreatic cancer. Here we elucidate mechanism by which inhibition effects tumor immune microenvironment. In cell-based chemotaxis assays, find that CXCL12-stimulated inhibits directed migration mediated CXCR1, CXCR3, CXCR5, CXCR6, CCR2, respectively, receptors expressed all types participate an integrated responses....
Presence of fetal cells and circulating free DNA RNA in maternal circulation represents the basic concept developement non-invasive prenatal diagnostic methods based on molecular biology genetics.We introduced new for isolation detection via from plasma using real-time PCR SYBRGreen targeting newly designed primers focused SRY sequence.We determined gender 46 singleton pregnancies, 22 boys 24 girls assessed analytical clinical validity.We reached 95.45% sensitivity 95.83% specificity.We...
Abstract Cell-free tumour-derived DNA (ctDNA) allows non-invasive monitoring of cancers but its utility in renal cell cancer (RCC) has not been established. Here, untargeted and targeted sequencing methods, applied to two independent cohorts tumour patients (n=90), were used determine ctDNA content plasma urine. Our data revealed lower levels RCC relative other cancers, with detection ∼33%. A sensitive personalised approach, urine from select improved ∼50%, including early-stage even benign...