Category Ranking
98%
Total Visits
921
Avg Visit Duration
2 minutes
Citations
20
Article Abstract
The increasing applicability and sensitivity of next generation sequencing methods exacerbate one of the main issues in the molecular biology laboratory, namely cross-sample contamination. This type of contamination, which could massively increase the rate of false-positive calls in sequencing experiments, can originate at each step during the processing of multiple myeloma samples, such as CD138-selection of tumor cells, RNA and DNA isolation or the processing of sequencing libraries. Here we describe a Droplet Digital PCR (ddPCR) method and a simple bioinformatic solution for the detection of contamination in patient's samples and derived sequencing data, which are based on the same principle: detection of alternative alleles for single-nucleotide polymorphisms (SNPs) that are homozygous according to the control (germ line) sample.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9481068 | PMC |
| http://dx.doi.org/10.1007/978-1-4939-7865-6_10 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Device for automated aseptic sampling: Automated sampling solution for future cell and gene manufacturing.
Front Bioeng Biotechnol
November 2024
Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
Cell sampling is a key step performed regularly throughout the cell manufacturing process to gather cell samples for cell growth, progress, and characteristics analysis. While the current method of sampling by pipetting in a biosafety cabinet is commonly used, it is labour-intensive and susceptible to contamination risks. We have developed Device for Automated Aseptic Sampling (DAAS), to enable automated, small volume (0.
View Article and Find Full Text PDFCleaning protocols in forensic genetic laboratories.
Int J Legal Med
September 2024
Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
It is pivotal to avoid cross-sample contamination in forensic genetic laboratories and optimal cleaning protocols for the removal of DNA are essential. A survey was performed, and ten forensic genetic laboratories shared their cleaning protocols in pre-PCR and post-PCR laboratories. The cleaning frequencies on different surface areas were somewhat similar, whereas none of the laboratories used the same cleaning reagents.
View Article and Find Full Text PDFA comprehensive performance evaluation, comparison, and integration of computational methods for detecting and estimating cross-contamination of human samples in cancer next-generation sequencing analysis.
J Biomed Inform
April 2024
Beijing ChosenMed Clinical Laboratory Co. Ltd., Beijing 100176, China; ChosenMed Technology (Zhejiang) Co. Ltd., Zhejiang 311103, China. Electronic address:
Cross-sample contamination is one of the major issues in next-generation sequencing (NGS)-based molecular assays. This type of contamination, even at very low levels, can significantly impact the results of an analysis, especially in the detection of somatic alterations in tumor samples. Several contamination identification tools have been developed and implemented as a crucial quality-control step in the routine NGS bioinformatic pipeline.
View Article and Find Full Text PDFAchieving pan-microbiome biological insights via the dbBact knowledge base.
Nucleic Acids Res
July 2023
Dept. of Computer Science, The Open University of Israel, Israel.
16S rRNA amplicon sequencing provides a relatively inexpensive culture-independent method for studying microbial communities. Although thousands of such studies have examined diverse habitats, it is difficult for researchers to use this vast trove of experiments when interpreting their own findings in a broader context. To bridge this gap, we introduce dbBact - a novel pan-microbiome resource.
View Article and Find Full Text PDFThe Intra-Tumoral T Cell Receptor Repertoire: Steps Towards a Useful Clinical Biomarker.
Methods Mol Biol
September 2022
Division of Infection and Immunity, UCL, London, UK.
Adaptive immunity recognizes and responds to tumors, although they are part of the immunological "self." T cells, both CD4+ and CD8+, play a key role in the process, and the specific set of receptors which recognize tumor antigens therefore has the potential to provide prognostic biomarkers for tracking tumor growth after cancer therapy, including immunotherapy. Most published data on the T cell repertoire continue to rely on commercial proprietary methods, which often do not allow access to the raw data, and are difficult to validate.
View Article and Find Full Text PDF