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Liquid biopsy-derived DNA sources as tools for comprehensive mutation profiling in multiple myeloma: a comparative study

ABSTRACT: Mutation profiling in multiple myeloma using liquid biopsies

PROVIDER: PRJEB56136 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR10360500_1.fastq.gz	Fastqsanger.gz
	ERR10360500_2.fastq.gz	Fastqsanger.gz
	ERR10360600_1.fastq.gz	Fastqsanger.gz
	ERR10360600_2.fastq.gz	Fastqsanger.gz
	ERR10360501_1.fastq.gz	Fastqsanger.gz

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Liquid Biopsy-Derived DNA Sources as Tools for Comprehensive Mutation Profiling in Multiple Myeloma: A Comparative Study.

Project description:The analysis of bone marrow (BM) samples in multiple myeloma (MM) patients can lead to the underestimation of the genetic heterogeneity within the tumor. Blood-derived liquid biopsies may provide a more comprehensive approach to genetic characterization. However, no thorough comparison between the currently available circulating biomarkers as tools for mutation profiling in MM has been published yet and the use of extracellular vesicle-derived DNA for this purpose in MM has not yet been investigated. Therefore, we collected BM aspirates and blood samples in 30 patients with active MM to isolate five different DNA types, i.e., cfDNA, EV-DNA, BM-DNA and DNA isolated from peripheral blood mononucleated cells (PBMNCs-DNA) and circulating tumor cells (CTC-DNA). DNA was analyzed for genetic variants with targeted gene sequencing using a 165-gene panel. After data filtering, 87 somatic and 39 germline variants were detected among the 149 DNA samples used for sequencing. cfDNA showed the highest concordance with the mutation profile observed in BM-DNA and outperformed EV-DNA, CTC-DNA and PBMNCs-DNA. Of note, 16% of all the somatic variants were only detectable in circulating biomarkers. Based on our analysis, cfDNA is the preferable circulating biomarker for genetic characterization in MM and its combined use with BM-DNA allows for comprehensive mutation profiling in MM.

| S-EPMC9563447 | biostudies-literature

Diagnostic accuracy of liquid biopsy in endometrial cancer

Project description:INTRODUCTION. Liquid biopsies are a minimally invasive collection of a patient body fluid sample. In oncology, they offer several advantages compared to traditional tissue biopsies. However, potential of this method in endometrial cancer (EC) remains poorly explored. We studied the utility of tumor educated platelets (TEPs) and circulating tumor DNA (ctDNA) for preoperative EC diagnosis, including histology determination. MATERIALS AND METHODS. TEPs from 297 subjects (53 EC patients, 40 patients with benign gynecologic conditions and 204 healthy women) were RNA-sequenced. DNA sequencing was performed in 519 primary tumor tissue samples and in16 plasma samples. Artificial intelligence was applied to sample classification. RESULTS. Platelet-dedicated classifier yielded AUC of 93.1% in test set when discriminating between healthy subjects and cancer patients. However, the discrimination between endometrial cancer and benign gynecologic conditions was relatively low, with AUC of 60.7%. ctDNA-dedicated classifier discriminated primary tumor tissue samples with AUC of 91.4% and ctDNA blood samples with AUC of 87.5%. CONCLUSIONS Liquid biopsies show potential in EC diagnosis. Both TEPs and ctDNA profiles coupled with artificial intelligence constitute a source of useful information. Further work, involving more cases, is warranted.

2021-12-01 | GSE184904 | GEO

Multi-parametric liquid biopsy approach

Project description:Multi-parametric liquid biopsy approach

| PRJEB39331 | ENA

Project description:Monitoring Multiple Myeloma in liquid biopsies

| PRJNA881246 | ENA

Retinoblastoma Aqueous Humor Liquid Biopsy Repository

Project description:Retinoblastoma Aqueous Humor Liquid Biopsy Repository

| PRJNA887892 | ENA

Retinoblastoma Aqueous Humor Liquid Biopsy Repository

Project description:Retinoblastoma Aqueous Humor Liquid Biopsy Repository

| PRJNA887893 | ENA

Deacetylation of HP1g enhances multiple myeloma drug resistance through DNA damage repair and liquid-liquid phase separation

Project description:Deacetylation of HP1g enhances multiple myeloma drug resistance through DNA damage repair and liquid-liquid phase separation

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Determination of RAS Mutation Status in Liquid Biopsies in Subjects With RAS Wild-type.PERSEIDA Study

Project description:Analysis of freely circulating DNA in liquid biopsies using the BEAMing method

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Tumor cell-based liquid biopsy using high-throughput microfluidic enrichment of entire leukapheresis product

Project description:Circulating Tumor Cells (CTCs) encompass multiple analytes, interrogated by sampling blood from patients with cancer. However, the clinical utility of tumor cell-based liquid biopsy has proven to be limited since CTCs are rare, and current technologies cannot process larger blood volumes required to isolate a sufficient number of tumor cells. We have described a high-throughput microfluidic prototype utilizing high-flow channels and amplification of cell sorting forces through magnetic lenses. Here, we apply this technology to analyze patient-derived leukapheresis products, interrogating a mean blood volume of 5.83 liters from patients with metastatic cancer and achieving a median of 2,799 CTCs per patient. Isolation of many CTCs from individual patients enables characterization of their morphological and molecular heterogeneity, including cell and nuclear size and RNA expression. It also allows robust detection of gene copy number variation (CNV), a definitive cancer marker with potential diagnostic applications. High-volume microfluidic enrichment of CTCs constitutes a new dimension in liquid biopsies.

2024-08-27 | GSE255889 | GEO

lead-in FOLICOLOR Trial: Following Therapy Response Through Liquid Biopsy in Metastatic Colorectal Cancer Patients

Project description:Detection of progressive disease by neuropeptide Y (NPY) methylation in liquid biopsies in patients with RAS and BRAF wild-type, unresectable, metastatic colorectal cancer receiving first-line treatment FOLFOX/FOLFIRI and panitumumab.

| 2365936 | ecrin-mdr-crc

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