Article
Microbiology
Hebah S. Mejbel, William Dodsworth, Alexandre Baud, Irene Gregory-Eaves, Frances R. Pick
Summary: Sediment DNA analyses are useful for studying environmental and evolutionary change. This study compared ddPCR and HTS for quantifying cyanobacterial genes in lake sediments, finding that ddPCR results were more consistent with the known lake history.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Parasitology
R. P. Snyder, M. T. Guerin, B. M. Hargis, R. Imai, P. S. Kruth, G. Page, E. Rejman, J. R. Barta
Summary: This study successfully established a quantitative detection method for Eimeria species infection using modern technologies, which can reliably identify and quantify species in samples, providing valuable infection details for commercial chicken production systems.
VETERINARY PARASITOLOGY
(2021)
Article
Multidisciplinary Sciences
Lydia Sagath, Vilma-Lotta Lehtokari, Carina Wallgren-Pettersson, Katarina Pelin, Kirsi Kiiski
Summary: The human genome contains repetitive regions that pose a challenge for most mutation detection methods. The nebulin gene has a large segmental duplication region composed of eight exons repeated three times. Copy number variations in this region are pathogenic when the deviation is two or more copies from the normal number. A custom Droplet Digital PCR method has been established for the detection of these variations.
Article
Microbiology
Bangchuan Hu, Yue Tao, Ziqiang Shao, Yang Zheng, Run Zhang, Xuejing Yang, Jingquan Liu, Xi Li, Renhua Sun
Summary: This study compared the diagnostic utility of ddPCR and mNGS for critically ill patients with suspected BSIs. It found that ddPCR was faster and more sensitive for common isolated pathogens and AMR genes, while mNGS detected a broader range of pathogens, including viruses. Based on their respective strengths and limitations, ddPCR is more suitable for rapid detection of common isolated pathogens and AMR genes, while mNGS is more appropriate for diagnosing BSIs when causative pathogens cannot be identified by traditional methods.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Genetics & Heredity
Lilian Pok Wa Zhong, Rossa W. K. Chiu
Summary: With the increased use of noninvasive screening for fetal chromosomal aneuploidies, researchers are now focusing on noninvasive prenatal assessment for single-gene disorders. Various methods to analyze cell-free DNA in maternal plasma, including relative mutation dosage, relative haplotype dosage, and size-based methods, have expanded the scope of noninvasive prenatal testing to include sex-linked and autosomal recessive disorders. Recently, cell-free fetal DNA analysis for several prevalent single-gene disorders has been implemented in clinical service.
ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS
(2022)
Article
Multidisciplinary Sciences
Mustafa Fatih Abasiyanik, Blake Flood, Jing Lin, Sefika Ozcan, Sherin J. Rouhani, Athalia Pyzer, Jonathan Trujillo, Chaojie Zhen, Ping Wu, Stephen Jumic, Andrew Wang, Thomas F. Gajewski, Peng Wang, Madeline Hartley, Bekim Ameti, Rachael Niemiec, Marian Fernando, Vasudha Mishra, Peter Savage, Bulent Aydogan, Cindy Bethel, Scott Matushek, Kathleen G. Beavis, Nishant Agrawal, Jeremy Segal, Savas Tay, Evgeny Izumchenko
Summary: Saliva has significant advantages as a test medium for detecting SARS-CoV-2 infection, with a developed testing pipeline showing high effectiveness in detecting infected cases in both outpatient and inpatient settings. The saliva-based testing has the potential for higher sensitivity in detecting low-abundance viral loads, making it a reliable alternative to traditional testing methods.
SCIENTIFIC REPORTS
(2021)
Article
Biochemical Research Methods
Carolina Villamil Vallejo, Claudia Patricia Tere, Martha Nancy Calderon, Maria Mercedes Arias, John Emerson Leguizamon
Summary: A candidate genomic DNA reference material for Salmonella enteritidis quantification was developed in this study, with evaluations on its characteristics, homogeneity, and stability through a series of experiments, establishing performance conditions and reference values for normalized RM production.
MOLECULAR AND CELLULAR PROBES
(2021)
Article
Biochemistry & Molecular Biology
Ruihua Ding, Liying Liu, Jiali Zhang, Pengxiao Lv, Lin Zhou, Tinglu Zhang, Shenwei Li, Ran Zhao, Zhuo Yang, Peng Xiong, Hu Chen, Wei Wang, Hualiang Wang, Zhengan Tian, Bo Liu, Chang Chen
Summary: Despite the challenges in accurate nucleic acid quantification, we have developed a method that combines the strengths of qPCR and dPCR using silicon-based microfluidic chips. This method demonstrates high quantification accuracy across a wide concentration range and enables the identification of individual template molecules. With this approach, we can remove nonspecific amplification and greatly improve quantification accuracy, as shown in our improved detection of COVID in patient samples using a sectioning algorithm.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biology
Annarita Oranger, Caterina Manzari, Matteo Chiara, Elisabetta Notario, Bruno Fosso, Antonio Parisi, Angelica Bianco, Michela Iacobellis, Morena D'Avenia, Anna Maria D'Erchia, Graziano Pesole
Summary: Oranger et al. utilized digital droplet PCR to develop an assay that offers a real-time snapshot of SARS-CoV-2 sub-genomic messenger RNA levels in infected individuals, potentially enhancing diagnostic precision for COVID-19.
COMMUNICATIONS BIOLOGY
(2021)
Article
Virology
Xiuyu Lou, Hao Yan, Lingxuan Su, Yi Sun, Xinyin Wang, Liming Gong, Yin Chen, Zhen Li, Zhongbiao Fang, Haiyan Mao, Keda Chen, Yanjun Zhang
Summary: A RT-dd PCR method was developed to detect the R294K mutation in H7N9 and successfully detected 2 R294K mutations in clinical samples. The sensitivity and specificity of RT-dd PCR were similar to RT-qPCR, and the accuracy was comparable to NGS.
Article
Gastroenterology & Hepatology
Man Hung Choi, Erling Tjora, Rakel Brendsdal Forthun, Trond Engjom, Helge Raeder, Randi Hovland, Anders Molven
Summary: KRAS mutations were detectable in duodenal juice from MODY8 patients, but with low abundance similar to patients with chronic pancreatitis. The discriminative value of the analysis with regard to other pancreatic diseases was limited.
Article
Medical Laboratory Technology
Fei Huang, Yihui Yang, Xinning Chen, Huiqin Jiang, Hao Wang, Minna Shen, Yiyi Yu, Tianshu Liu, Baishen Pan, Beili Wang, Wei Guo
Summary: CH-derived mutations of KRAS gene were identified in metastatic CRC patients, predominantly in those with mutation frequencies < 5% and prior chemotherapy history. It is recommended to perform genotyping analysis of PBCs following plasma cfDNA genotyping in patients with a history of chemotherapy and mutation frequencies < 5%.
CLINICAL BIOCHEMISTRY
(2021)
Article
Microbiology
Changwoo Park, Seung Bum Kim, Sang Ho Choi, Seil Kim
Summary: Microbial community analysis based on the 16S rRNA-gene is important for studying microorganisms, and next-generation sequencing technology has improved the accuracy and speed of analysis. However, biases can still occur in the results due to factors like sample handling and sequencing platforms. Different primer pairs and sequencing platforms can lead to varying levels of bias in microbial community analysis.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biophysics
Juhwan Park, Kyoung G. Lee, Dong Hyun Han, Ji-Soo Lee, Seok Jae Lee, Je-Kyun Park
Summary: The study introduces a portable microfluidic device, PAMD, for generating and dispensing droplets for ddPCR with a simple pushbutton operation. PAMD can control multiple droplet generation units simultaneously with a single pushbutton, and the size of droplets can be adjusted by changing the geometry of the droplet generation channel.
BIOSENSORS & BIOELECTRONICS
(2021)
Article
Biochemical Research Methods
Sang-Soo Lee, Seil Kim, Hee Min Yoo, Da-Hye Lee, Young-Kyung Bae
Summary: This study reported the production of a lentiviral SARS-CoV-2 reference material, which can be used to evaluate the quality and performance of SARS-CoV-2 molecular testing, providing accurate copy number values to improve the reliability of SARS-CoV-2 molecular testing.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)