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Article ; Online: Monitoring immunotherapy outcomes with circulating tumor DNA.

Goldberg, Sarah B / Patel, Abhijit A

Immunotherapy

2018 Volume 10, Issue 12, Page(s) 1023–1025

MeSH term(s)	Animals ; Antibodies, Monoclonal/therapeutic use ; B7-H1 Antigen/immunology ; Biomarkers, Pharmacological/analysis ; Carcinoma, Non-Small-Cell Lung/immunology ; Carcinoma, Non-Small-Cell Lung/therapy ; Circulating Tumor DNA/analysis ; Humans ; Immunotherapy/methods ; Lung Neoplasms/immunology ; Lung Neoplasms/therapy ; Monitoring, Immunologic ; Patient Selection ; Prognosis ; Programmed Cell Death 1 Receptor/immunology
Chemical Substances	Antibodies, Monoclonal ; B7-H1 Antigen ; Biomarkers, Pharmacological ; Circulating Tumor DNA ; PDCD1 protein, human ; Programmed Cell Death 1 Receptor
Language	English
Publishing date	2018-09-05
Publishing country	England
Document type	Editorial ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1750-7448
ISSN (online)	1750-7448
DOI	10.2217/imt-2018-0084
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Article ; Online: Direct capture and sequencing reveal ultra-short single-stranded DNA in biofluids.

Cheng, Lauren Y / Dai, Peng / Wu, Lucia R / Patel, Abhijit A / Zhang, David Yu

iScience

2022 Volume 25, Issue 10, Page(s) 105046

Abstract: Cell-free DNA (cfDNA) has become the predominant analyte of liquid biopsy; however, recent studies suggest the presence of subnucleosomal-sized DNA fragments in circulation that are likely single-stranded. Here, we report a method called direct capture ... ...

Abstract	Cell-free DNA (cfDNA) has become the predominant analyte of liquid biopsy; however, recent studies suggest the presence of subnucleosomal-sized DNA fragments in circulation that are likely single-stranded. Here, we report a method called direct capture and sequencing (DCS) tailored to recover such fragments from biofluids by directly capturing them using short degenerate probes followed by single strand-based library preparation and next-generation sequencing. DCS revealed a new DNA population in biofluids, named ultrashort single-stranded DNA (ussDNA). Evaluation of the size distribution and abundance of ussDNA manifested generality of its presence in humans, animal species, and plants. In humans, red blood cells were found to contain abundant ussDNA; plasma-derived ussDNA exhibited modal size at 50 nt. This work reports the presence of an understudied DNA population in circulation, and yet more work is awaiting to study its generation mechanism, tissue of origin, disease implications, etc.
Language	English
Publishing date	2022-09-01
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2022.105046
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Article ; Online: Circulating Tumor DNA Dynamics Fail to Predict Efficacy of Poly(ADP-ribose) Polymerase/VEGFR Inhibition in Patients With Heavily Pretreated Advanced Solid Tumors.

Hu, Yiduo / Narayan, Azeet / Xu, Yunshan / Wolfe, Julia / Vu, Dennis / Trinh, Thi / Kantak, Chaitanya / Ivy, S Percy / Eder, Joseph Paul / Deng, Yanhong / LoRusso, Patricia / Kim, Joseph W / Patel, Abhijit A

JCO precision oncology

2024 Volume 8, Page(s) e2300289

Abstract: Purpose: Cell-free circulating tumor DNA (ctDNA) has shown its potential as a quantitative biomarker for longitudinal monitoring of response to anticancer therapies. However, ctDNA dynamics have not been studied in patients with heavily pretreated, ... ...

Abstract	Purpose: Cell-free circulating tumor DNA (ctDNA) has shown its potential as a quantitative biomarker for longitudinal monitoring of response to anticancer therapies. However, ctDNA dynamics have not been studied in patients with heavily pretreated, advanced solid tumors, for whom therapeutic responses can be weak. We investigated whether changes in ctDNA could predict clinical outcomes in such a cohort treated with combined poly(ADP-ribose) polymerase/vascular endothelial growth factor receptor inhibitor therapy. Materials and methods: Patients with metastatic pancreatic ductal adenocarcinoma (PDAC), triple-negative breast cancer (TNBC), small-cell lung cancer (SCLC), or non-small-cell lung cancer (NSCLC) received up to 7 days of cediranib 30 mg orally once daily monotherapy lead-in followed by addition of olaparib 200 mg orally twice daily. Patients had progressed on a median of three previous lines of therapy. Plasma samples were collected before and after cediranib monotherapy lead-in and on combination therapy at 7 days, 28 days, and every 28 days thereafter. ctDNA was quantified from plasma samples using a multigene mutation-based assay. Radiographic assessment was performed every 8 weeks. Results: ctDNA measurements were evaluable in 63 patients. The median baseline ctDNA variant allele fractions (VAFs) were 20%, 28%, 27%, and 34% for PDAC, TNBC, SCLC, and NSCLC, respectively. No association was observed between baseline VAF and radiographic response, progression-free survival, or overall survival (OS). Similarly, no association was found between ctDNA decline and radiographic response or survival. However, an increase in ctDNA at 56 days of combination therapy was associated with disease progression and inferior OS in a landmark analysis. Conclusion: ctDNA levels or dynamics did not correlate with radiographic response or survival outcomes in patients with advanced metastatic malignancies treated with olaparib and cediranib.
MeSH term(s)	Humans ; Circulating Tumor DNA/genetics ; Carcinoma, Non-Small-Cell Lung/drug therapy ; Carcinoma, Non-Small-Cell Lung/genetics ; Poly(ADP-ribose) Polymerases/therapeutic use ; Triple Negative Breast Neoplasms ; Vascular Endothelial Growth Factor A/therapeutic use ; Lung Neoplasms/drug therapy ; Lung Neoplasms/genetics ; Biomarkers, Tumor/genetics ; Pancreatic Neoplasms/drug therapy ; Pancreatic Neoplasms/genetics
Chemical Substances	Circulating Tumor DNA ; Poly(ADP-ribose) Polymerases (EC 2.4.2.30) ; Vascular Endothelial Growth Factor A ; Biomarkers, Tumor
Language	English
Publishing date	2024-02-23
Publishing country	United States
Document type	Journal Article
ISSN	2473-4284
ISSN (online)	2473-4284
DOI	10.1200/PO.23.00289
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Article ; Online: Limitations and opportunities of technologies for the analysis of cell-free DNA in cancer diagnostics.

Song, Ping / Wu, Lucia Ruojia / Yan, Yan Helen / Zhang, Jinny X / Chu, Tianqing / Kwong, Lawrence N / Patel, Abhijit A / Zhang, David Yu

Nature biomedical engineering

2022 Volume 6, Issue 3, Page(s) 232–245

Abstract: Cell-free DNA (cfDNA) in the circulating blood plasma of patients with cancer contains tumour-derived DNA sequences that can serve as biomarkers for guiding therapy, for the monitoring of drug resistance, and for the early detection of cancers. However, ... ...

Abstract	Cell-free DNA (cfDNA) in the circulating blood plasma of patients with cancer contains tumour-derived DNA sequences that can serve as biomarkers for guiding therapy, for the monitoring of drug resistance, and for the early detection of cancers. However, the analysis of cfDNA for clinical diagnostic applications remains challenging because of the low concentrations of cfDNA, and because cfDNA is fragmented into short lengths and is susceptible to chemical damage. Barcodes of unique molecular identifiers have been implemented to overcome the intrinsic errors of next-generation sequencing, which is the prevailing method for highly multiplexed cfDNA analysis. However, a number of methodological and pre-analytical factors limit the clinical sensitivity of the cfDNA-based detection of cancers from liquid biopsies. In this Review, we describe the state-of-the-art technologies for cfDNA analysis, with emphasis on multiplexing strategies, and discuss outstanding biological and technical challenges that, if addressed, would substantially improve cancer diagnostics and patient care.
MeSH term(s)	Biomarkers/analysis ; Cell-Free Nucleic Acids/analysis ; Cell-Free Nucleic Acids/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Liquid Biopsy/methods ; Neoplasms/diagnosis ; Neoplasms/genetics
Chemical Substances	Biomarkers ; Cell-Free Nucleic Acids
Language	English
Publishing date	2022-01-31
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ISSN	2157-846X
ISSN (online)	2157-846X
DOI	10.1038/s41551-021-00837-3
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Article: META RNA profiling: Multiplexed quantitation of targeted RNAs across large numbers of samples

Narayan, Azeet / Johnkennedy, Rofina / Zakaria, Maheen / Lee, Victor / Patel, Abhijit A

Methods. 2019 Jan. 01, v. 152

2019

Abstract: META RNA profiling is a simple and inexpensive method to measure the expression of multiple targeted RNAs across many samples. By assigning sample-specific tags up-front during reverse-transcription, cDNAs from multiple samples can be pooled prior to ... ...

Abstract	META RNA profiling is a simple and inexpensive method to measure the expression of multiple targeted RNAs across many samples. By assigning sample-specific tags up-front during reverse-transcription, cDNAs from multiple samples can be pooled prior to amplification and deep sequencing. Such early parallelization of samples simplifies the workflow, minimizes cross-sample experimental variability, and reduces reagent and sequencing costs. Herein we describe the theoretical framework of the method and provide a detailed protocol to facilitate its implementation.
Keywords	RNA ; complementary DNA ; high-throughput nucleotide sequencing ; reverse transcription
Language	English
Dates of publication	2019-0101
Size	p. 41-47.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	1066584-5
ISSN	1095-9130 ; 1046-2023
ISSN (online)	1095-9130
ISSN	1046-2023
DOI	10.1016/j.ymeth.2018.09.012
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Article ; Online: Selective multiplexed enrichment for the detection and quantitation of low-fraction DNA variants via low-depth sequencing.

Song, Ping / Chen, Sherry X / Yan, Yan Helen / Pinto, Alessandro / Cheng, Lauren Y / Dai, Peng / Patel, Abhijit A / Zhang, David Yu

Nature biomedical engineering

2021 Volume 5, Issue 7, Page(s) 690–701

Abstract: DNA sequence variants with allele fractions below 1% are difficult to detect and quantify by sequencing owing to intrinsic errors in sequencing-by-synthesis methods. Although molecular-identifier barcodes can detect mutations with a variant-allele ... ...

Abstract	DNA sequence variants with allele fractions below 1% are difficult to detect and quantify by sequencing owing to intrinsic errors in sequencing-by-synthesis methods. Although molecular-identifier barcodes can detect mutations with a variant-allele frequency (VAF) as low as 0.1% using next-generation sequencing (NGS), sequencing depths of over 25,000× are required, thus hampering the detection of mutations at high sensitivity in patient samples and in most samples used in research. Here we show that low-frequency DNA variants can be detected via low-depth multiplexed NGS after their amplification, by a median of 300-fold, using polymerase chain reaction and rationally designed 'blocker' oligonucleotides that bind to the variants. Using an 80-plex NGS panel and a sequencing depth of 250×, we detected single nucleotide polymorphisms with a VAF of 0.019% and contamination in human cell lines at a VAF as low as 0.07%. With a 16-plex NGS panel covering 145 mutations across 9 genes involved in melanoma, we detected low-VAF mutations (0.2-5%) in 7 out of the 19 samples of freshly frozen tumour biopsies, suggesting that tumour heterogeneity could be notably higher than previously recognized.
MeSH term(s)	Carcinoma, Non-Small-Cell Lung/genetics ; Carcinoma, Non-Small-Cell Lung/pathology ; Cell Line ; DNA/analysis ; DNA/genetics ; DNA/metabolism ; Databases, Genetic ; Gene Frequency ; Gene Library ; Genetic Heterogeneity ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Lung Neoplasms/genetics ; Lung Neoplasms/pathology ; Melanoma/genetics ; Melanoma/pathology ; Multiplex Polymerase Chain Reaction/methods ; Mutation ; Polymorphism, Single Nucleotide
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2021-05-03
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	2157-846X
ISSN (online)	2157-846X
DOI	10.1038/s41551-021-00713-0
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Platelet-derived TLT-1 promotes tumor progression by suppressing CD8+ T cells.

Tyagi, Tarun / Jain, Kanika / Yarovinsky, Timur O / Chiorazzi, Michael / Du, Jing / Castro, Cecilia / Griffin, Jules / Korde, Asawari / Martin, Kathleen A / Takyar, Shervin S / Flavell, Richard A / Patel, Abhijit A / Hwa, John

The Journal of experimental medicine

2022 Volume 220, Issue 1

Abstract: Current understanding of tumor immunosuppressive mechanisms forms the basis for modern day immunotherapies. Immunoregulatory role of platelets in cancer remains largely elusive. Platelets from non-small cell lung cancer (NSCLC) patients revealed a ... ...

Abstract	Current understanding of tumor immunosuppressive mechanisms forms the basis for modern day immunotherapies. Immunoregulatory role of platelets in cancer remains largely elusive. Platelets from non-small cell lung cancer (NSCLC) patients revealed a distinct activation phenotype. TREM-like transcript 1 (TLT-1), a platelet protein, was increased along with enhanced extracellular release from NSCLC platelets. The increased platelet TLT-1 was also evident in humanized mice with patient-derived tumors. In immunocompetent mice with syngeneic tumors, TLT-1 binding to T cells, in vivo, led to suppression of CD8 T cells, promoting tumor growth. We identified direct interaction between TLT-1 and CD3ε on T cells, implicating the NF-κB pathway in CD8 T cell suppression. Anti-TLT-1 antibody rescued patients' T cells from platelet-induced suppression ex vivo and reduced tumors in mice in vivo. Clinically, higher TLT-1 correlated with reduced survival of NSCLC patients. Our findings thus identify TLT-1 as a platelet-derived immunosuppressor that suppresses CD8 T cells and demonstrate its therapeutic and prognostic significance in cancer.
MeSH term(s)	Mice ; Animals ; Receptors, Immunologic/metabolism ; Carcinoma, Non-Small-Cell Lung/metabolism ; Lung Neoplasms/metabolism ; Blood Platelets/metabolism ; CD8-Positive T-Lymphocytes
Chemical Substances	Receptors, Immunologic
Language	English
Publishing date	2022-10-28
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	218343-2
ISSN	1540-9538 ; 0022-1007
ISSN (online)	1540-9538
ISSN	0022-1007
DOI	10.1084/jem.20212218
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Article ; Online: High-throughput RNA profiling via up-front sample parallelization.

Narayan, Azeet / Bommakanti, Ananth / Patel, Abhijit A

Nature methods

2015 Volume 12, Issue 4, Page(s) 343–346

Abstract: We describe a method called modular, early-tagged amplification (META) RNA profiling that can quantify a broad panel of microRNAs or mRNAs simultaneously across many samples and requires far less sequence depth than existing digital profiling ... ...

Abstract	We describe a method called modular, early-tagged amplification (META) RNA profiling that can quantify a broad panel of microRNAs or mRNAs simultaneously across many samples and requires far less sequence depth than existing digital profiling technologies. The method assigns quantitative tags during reverse transcription to permit up-front sample pooling before competitive amplification and deep sequencing. This simple, scalable and inexpensive approach improves the practicality of large-scale gene expression studies.
MeSH term(s)	Cell Line ; Gene Expression Profiling/methods ; High-Throughput Nucleotide Sequencing ; Humans ; RNA/blood ; RNA/genetics ; RNA/radiation effects
Chemical Substances	RNA (63231-63-0)
Language	English
Publishing date	2015-04
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2169522-2
ISSN	1548-7105 ; 1548-7091
ISSN (online)	1548-7105
ISSN	1548-7091
DOI	10.1038/nmeth.3311
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Article ; Online: Publisher Correction: Multiplexed enrichment of rare DNA variants via sequence-selective and temperature-robust amplification.

Wu, Lucia R / Chen, Sherry X / Wu, Yalei / Patel, Abhijit A / Zhang, David Yu

Nature biomedical engineering

2018 Volume 1, Issue 12, Page(s) 1005

Abstract: In the version of this Article originally published, owing to a technical error, the Life Sciences Reporting Summary was not included; this summary is now available. ...

Abstract	In the version of this Article originally published, owing to a technical error, the Life Sciences Reporting Summary was not included; this summary is now available.
Language	English
Publishing date	2018-01-10
Publishing country	England
Document type	Journal Article ; Published Erratum
ISSN	2157-846X
ISSN (online)	2157-846X
DOI	10.1038/s41551-017-0156-z
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: META RNA profiling: Multiplexed quantitation of targeted RNAs across large numbers of samples.

Narayan, Azeet / Johnkennedy, Rofina / Zakaria, Maheen / Lee, Victor / Patel, Abhijit A

Methods (San Diego, Calif.)

2018 Volume 152, Page(s) 41–47

Abstract	META RNA profiling is a simple and inexpensive method to measure the expression of multiple targeted RNAs across many samples. By assigning sample-specific tags up-front during reverse-transcription, cDNAs from multiple samples can be pooled prior to amplification and deep sequencing. Such early parallelization of samples simplifies the workflow, minimizes cross-sample experimental variability, and reduces reagent and sequencing costs. Herein we describe the theoretical framework of the method and provide a detailed protocol to facilitate its implementation.
MeSH term(s)	Gene Expression Profiling ; Gene Expression Regulation ; MicroRNAs/metabolism ; RNA/metabolism ; Sequence Analysis, RNA
Chemical Substances	MicroRNAs ; RNA (63231-63-0)
Language	English
Publishing date	2018-10-09
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1066584-5
ISSN	1095-9130 ; 1046-2023
ISSN (online)	1095-9130
ISSN	1046-2023
DOI	10.1016/j.ymeth.2018.09.012
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