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Article ; Online: What is the Importance of Analyzing Tumor Tissues and Blood Cells in the Study of Circulating Tumor-Derived DNA?

Yu, Stephanie C Y / Chan, K C Allen

2022 Volume 68, Issue 12, Page(s) 1481–1483

Language	English
Publishing date	2022-10-17
Publishing country	England
Document type	Editorial ; Comment
ZDB-ID	80102-1
ISSN	1530-8561 ; 0009-9147
ISSN (online)	1530-8561
ISSN	0009-9147
DOI	10.1093/clinchem/hvac168
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Article: Clinical applications of the latest molecular diagnostics in noninvasive prenatal diagnosis.

Chan, K C Allen

Topics in current chemistry

2014 Volume 336, Page(s) 47–65

Abstract: The presence of cell-free fetal DNA in the plasma of pregnant women has opened up the possibility of noninvasive prenatal diagnosis. With the advances in molecular techniques of microfluidics and massive parallel sequencing, an increasing number of fetal ...

Abstract	The presence of cell-free fetal DNA in the plasma of pregnant women has opened up the possibility of noninvasive prenatal diagnosis. With the advances in molecular techniques of microfluidics and massive parallel sequencing, an increasing number of fetal genetic diseases/conditions can be noninvasively detected using maternal plasma DNA analysis. Remarkably, it has recently been shown that the genome-wide genetic map of an unborn fetus can be constructed through extensive sequencing of maternal plasma DNA. In this chapter the different qualitative and quantitative approaches and related methodology for the analysis of fetal DNA in maternal plasma are discussed.
MeSH term(s)	Alleles ; DNA/blood ; Female ; Fetus ; Humans ; Pregnancy ; Prenatal Diagnosis/methods ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2014
Publishing country	Germany
Document type	Journal Article ; Review
ISSN	0340-1022
ISSN	0340-1022
DOI	10.1007/128_2012_352
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Article ; Online: Liver-derived cell-free nucleic acids in plasma: Biology and applications in liquid biopsies.

Jiang, Peiyong / Chan, K C Allen / Lo, Y M Dennis

Journal of hepatology

2019 Volume 71, Issue 2, Page(s) 409–421

Abstract: There is much global research interest surrounding the use of cell-free DNA (cfDNA) for liquid biopsies. cfDNA-based non-invasive prenatal testing for foetal chromosomal aneuploidies was the first successful application of cfDNA technology that ... ...

Abstract	There is much global research interest surrounding the use of cell-free DNA (cfDNA) for liquid biopsies. cfDNA-based non-invasive prenatal testing for foetal chromosomal aneuploidies was the first successful application of cfDNA technology that transformed clinical practice - it has since been rapidly adopted in dozens of countries and is used by millions of pregnant women every year. Prompted by such developments, efforts to use cfDNA in other fields, especially for cancer detection and monitoring have been actively pursued in recent years. Cancer-associated aberrations including single nucleotide mutations, copy number aberrations, aberrations in methylation and alterations in DNA fragmentation patterns have been detected in the cfDNA of patients suffering from a wide variety of cancers. In addition, the analysis of methylation and fragmentomic patterns has enabled the tissue origin of cfDNA to be determined. In this review, different approaches for detecting circulating liver-derived nucleic acids and cancer-associated aberrations, as well as their potential clinical applications for the detection, monitoring and management of hepatocellular carcinoma, will be discussed.
MeSH term(s)	Biomarkers, Tumor/genetics ; Carcinoma, Hepatocellular/diagnosis ; Carcinoma, Hepatocellular/genetics ; Cell-Free Nucleic Acids/blood ; Cell-Free Nucleic Acids/genetics ; Chromosome Aberrations ; DNA Methylation ; Female ; Humans ; Liquid Biopsy ; Liver/pathology ; Liver Neoplasms/diagnosis ; Liver Neoplasms/genetics ; Neoplastic Cells, Circulating ; Pregnancy
Chemical Substances	Biomarkers, Tumor ; Cell-Free Nucleic Acids
Language	English
Publishing date	2019-04-18
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	605953-3
ISSN	1600-0641 ; 0168-8278
ISSN (online)	1600-0641
ISSN	0168-8278
DOI	10.1016/j.jhep.2019.04.003
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Article: Plasma Epstein-Barr virus DNA as a biomarker for nasopharyngeal carcinoma.

Chan, K C Allen

Chinese journal of cancer

2014 Volume 33, Issue 12, Page(s) 598–603

Abstract: Nasopharyngeal carcinoma (NPC) is common in southern China and Southeast Asia. Epstein-Barr virus (EBV) infection is an important etiology for NPC, and EBV genome can be detected in almost all tumor tissues of NPC in this region. Plasma EBV DNA, when ... ...

Abstract	Nasopharyngeal carcinoma (NPC) is common in southern China and Southeast Asia. Epstein-Barr virus (EBV) infection is an important etiology for NPC, and EBV genome can be detected in almost all tumor tissues of NPC in this region. Plasma EBV DNA, when quantitatively analyzed using real-time polymerase chain reaction (PCR), has been developed as a biomarker for NPC. In this review, the different clinical applications of plasma EBV DNA in the management of NPC, including screening, monitoring, and prognostication, are discussed. In addition, the biological issues of circulating EBV DNA, including the molecular nature and clearance kinetics, are also explored.
MeSH term(s)	Biomarkers ; Carcinoma ; China ; DNA, Viral ; Epstein-Barr Virus Infections ; Herpesvirus 4, Human ; Humans ; Nasopharyngeal Carcinoma ; Nasopharyngeal Neoplasms/virology ; Real-Time Polymerase Chain Reaction
Chemical Substances	Biomarkers ; DNA, Viral
Language	English
Publishing date	2014-11-21
Publishing country	England
Document type	Journal Article
ZDB-ID	1045160-2
ISSN	1944-446X ; 1000-467X
ISSN (online)	1944-446X
ISSN	1000-467X
DOI	10.5732/cjc.014.10192
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Zs.A 6213: Show issues

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Article ; Online: Scanning for cancer genomic changes in plasma: toward an era of personalized blood-based tumor markers.

Chan, K C Allen

Clinical chemistry

2013 Volume 59, Issue 11, Page(s) 1553–1555

MeSH term(s)	Biomarkers, Tumor/blood ; Breast Neoplasms/secondary ; DNA, Neoplasm/blood ; Female ; Humans ; Mucin-1/blood ; Neoplasm Metastasis/diagnosis
Chemical Substances	Biomarkers, Tumor ; DNA, Neoplasm ; Mucin-1
Language	English
Publishing date	2013-07-10
Publishing country	England
Document type	Journal Article ; Comment
ZDB-ID	80102-1
ISSN	1530-8561 ; 0009-9147
ISSN (online)	1530-8561
ISSN	0009-9147
DOI	10.1373/clinchem.2013.207381
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Article ; Online: Droplet digital PCR is a cost-effective method for analyzing long cell-free DNA in maternal plasma: Application in preeclampsia.

Gai, Wanxia / Yu, Stephanie C Y / Chan, W T Charlotte / Peng, Wenlei / Lau, So Ling / Leung, Tak Y / Jiang, Peiyong / Chan, K C Allen / Lo, Y M Dennis

Prenatal diagnosis

2023 Volume 43, Issue 11, Page(s) 1385–1393

Abstract: Objective: Long cell-free DNA (cfDNA) can be found in the plasma of pregnant women and cancer patients. We investigated if droplet digital PCR (ddPCR) can analyze such molecules for diagnostic purposes using preeclampsia as a model.: Method: Plasma ... ...

Abstract	Objective: Long cell-free DNA (cfDNA) can be found in the plasma of pregnant women and cancer patients. We investigated if droplet digital PCR (ddPCR) can analyze such molecules for diagnostic purposes using preeclampsia as a model. Method: Plasma samples from ten preeclamptic and sixteen normal pregnancies were analyzed. Two ddPCR assays targeting a single-copy gene, VCP, and one ddPCR assay targeting LINE-1 repetitive regions were used to measure the percentages of long cfDNA >533, 1001, and 170 bp, respectively. The LINE-1 assay was developed as guided by in silico PCR analyses to better differentiate preeclamptic and normal pregnancies. Results: Preeclamptic patients had a significantly lower median percentage of long cfDNA than healthy pregnant controls, as determined by the LINE-1 170 bp assay (28.9% vs. 35.1%, p < 0.0001) and the VCP 533 bp assay (6.6% vs. 8.7%, p = 0.014). The LINE-1 assay provided a better differentiation than the VCP 533 bp assay (area under ROC curves, 0.94 vs. 0.79). Conclusion: ddPCR is a cost-effective approach for unlocking diagnostic information carried by long cfDNA in plasma and may have applications for the detection of preeclampsia. Further longitudinal studies with larger cohorts are required to assess the clinical utility of this test.
Language	English
Publishing date	2023-09-01
Publishing country	England
Document type	Journal Article
ZDB-ID	82031-3
ISSN	1097-0223 ; 0197-3851
ISSN (online)	1097-0223
ISSN	0197-3851
DOI	10.1002/pd.6432
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Zs.A 1625: Show issues

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Article ; Online: Quality Materials for Quality Assurance in the Analysis of Liquid Biopsy Samples.

Tsang, Jason C H / Chan, K C Allen

Clinical chemistry

2017 Volume 63, Issue 9, Page(s) 1431–1432

MeSH term(s)	Cell-Free Nucleic Acids ; Humans ; Liquid Biopsy ; Mutation ; Neoplasms ; Quality Control
Chemical Substances	Cell-Free Nucleic Acids
Language	English
Publishing date	2017-07-18
Publishing country	England
Document type	Editorial ; Research Support, Non-U.S. Gov't ; Comment
ZDB-ID	80102-1
ISSN	1530-8561 ; 0009-9147
ISSN (online)	1530-8561
ISSN	0009-9147
DOI	10.1373/clinchem.2017.276014
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Article ; Online: Ambient Temperature and Screening for Nasopharyngeal Cancer.

Chan, K C Allen / Chu, Sam W I / Lo, Y M Dennis

The New England journal of medicine

2018 Volume 378, Issue 10, Page(s) 962–963

MeSH term(s)	Adult ; Age Factors ; Carcinoma/diagnosis ; DNA, Viral/blood ; Early Detection of Cancer ; False Positive Reactions ; Herpesvirus 4, Human/genetics ; Herpesvirus 4, Human/isolation & purification ; Humans ; Logistic Models ; Male ; Middle Aged ; Nasopharyngeal Carcinoma ; Nasopharyngeal Neoplasms/diagnosis ; Smoking/adverse effects ; Temperature
Chemical Substances	DNA, Viral
Language	English
Publishing date	2018-03-30
Publishing country	United States
Document type	Letter
ZDB-ID	207154-x
ISSN	1533-4406 ; 0028-4793
ISSN (online)	1533-4406
ISSN	0028-4793
DOI	10.1056/NEJMc1800433
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Article ; Online: Genomic origin, fragmentomics, and transcriptional properties of long cell-free DNA molecules in human plasma.

Che, Huiwen / Jiang, Peiyong / Choy, L Y Lois / Cheng, Suk Hang / Peng, Wenlei / Chan, Rebecca W Y / Liu, Jing / Zhou, Qing / Lam, W K Jacky / Yu, Stephanie C Y / Lau, So Ling / Leung, Tak Y / Wong, John / Wong, Vincent Wai-Sun / Wong, Grace L H / Chan, Stephen L / Chan, K C Allen / Lo, Y M Dennis

Genome research

2024 Volume 34, Issue 2, Page(s) 189–200

Abstract: Recent studies have revealed an unexplored population of long cell-free DNA (cfDNA) molecules in human plasma using long-read sequencing technologies. However, the biological properties of long cfDNA molecules (>500 bp) remain largely unknown. To this ... ...

Abstract	Recent studies have revealed an unexplored population of long cell-free DNA (cfDNA) molecules in human plasma using long-read sequencing technologies. However, the biological properties of long cfDNA molecules (>500 bp) remain largely unknown. To this end, we have investigated the origins of long cfDNA molecules from different genomic elements. Analysis of plasma cfDNA using long-read sequencing reveals an uneven distribution of long molecules from across the genome. Long cfDNA molecules show overrepresentation in euchromatic regions of the genome, in sharp contrast to short DNA molecules. We observe a stronger relationship between the abundance of long molecules and mRNA gene expression levels, compared with short molecules (Pearson's
MeSH term(s)	Humans ; Animals ; Mice ; Cell-Free Nucleic Acids/genetics ; Carcinoma, Hepatocellular/genetics ; Liver Neoplasms/genetics ; DNA/genetics ; Genomics ; Mice, Knockout ; Endodeoxyribonucleases/genetics
Chemical Substances	Cell-Free Nucleic Acids ; DNA (9007-49-2) ; Dnase1l3 protein, mouse (EC 3.1.-) ; Endodeoxyribonucleases (EC 3.1.-)
Language	English
Publishing date	2024-03-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	1284872-4
ISSN	1549-5469 ; 1088-9051 ; 1054-9803
ISSN (online)	1549-5469
ISSN	1088-9051 ; 1054-9803
DOI	10.1101/gr.278556.123
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Article ; Online: Early detection of nasopharyngeal carcinoma: performance of a short contrast-free screening MRI.

King, Ann D / Ai, Qi Yong H / Lam, W K Jacky / Tse, Irene O L / So, Tiffany Y / Wong, Lun M / Tsang, Jayden Yip Man / Leung, Ho Sang / Zee, Benny C Y / Hui, Edwin P / Ma, Brigette B Y / Vlantis, Alexander C / van Hasselt, Andrew C / Chan, Anthony T C / Woo, John K S / Chan, K C Allen

Journal of the National Cancer Institute

2024

Abstract: Background: While contrast-enhanced MRI detects early-stage nasopharyngeal carcinoma (NPC) not detected by endoscopic-guided biopsy (EGB), a short contrast-free screening MRI would be desirable for NPC screening programs. This study evaluated a ... ...

Abstract	Background: While contrast-enhanced MRI detects early-stage nasopharyngeal carcinoma (NPC) not detected by endoscopic-guided biopsy (EGB), a short contrast-free screening MRI would be desirable for NPC screening programs. This study evaluated a screening MRI in a plasma Epstein-Barr virus (EBV)-DNA NPC screening program. Methods: EBV-DNA screen positive patients underwent endoscopy and endoscopy-positive patients underwent EGB. EGB was negative if biopsy was negative or was not performed. Patients also underwent a screening MRI. Diagnostic performance was based on histologic confirmation of NPC in the initial study or during a follow-up period of at least 2 years. Results: The study prospectively recruited 354 patients for MRI and endoscopy, 40/354 (11.3%) endoscopy-positive patients underwent EGB. Eighteen had NPC (5.1%) and 336 without NPC (94.9%) were followed-up for a median of 44.8 months. MRI detected additional NPCs in 3/18 (16.7%) endoscopy-negative and 2/18 (11.1%) EGB-negative patients (stage I/II, n = 4; stage III, n = 1). None of the 24 EGB-negative patients who were MRI-negative had NPC. MRI missed NPC in 2/18 (11.1%), one of which was also endoscopy-negative. The sensitivity, specificity, positive predictive value, negative predictive value and accuracy of MRI, endoscopy and EGB were 88.9%, 91.1%, 34.8%, 99.4% and 91.0%; 77.8%, 92.3%, 35.0%, 98.7% and 91.5%; 66.7%, 92.3%, 31.6%, 98.1% and 91.0%, respectively. Conclusion: A quick contrast-free screening MRI complements endoscopy in NPC screening programs. In EBV-screen-positive patients, MRI enables early detection of NPC that is endoscopically occult or negative on EGB and increases confidence that NPC has not been missed.
Language	English
Publishing date	2024-01-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	2992-0
ISSN	1460-2105 ; 0027-8874 ; 0198-0157
ISSN (online)	1460-2105
ISSN	0027-8874 ; 0198-0157
DOI	10.1093/jnci/djad260
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