Article
Chemistry, Multidisciplinary
Dan Huang, Hui Deng, Juan Zhou, Guan A. Wang, Qian Lei, Chen Guo, Wanting Peng, Peng Liang, Chenlan Shen, Binwu Ying, Weimin Li, Feng Li
Summary: PANDA technology eliminates the interference caused by high concentrations of wild-type sequences and enables the ultrasensitive detection of cancer mutations with low VAFs. Compared to digital PCR, PANDA has fewer false negatives and lower costs. It also offers multiplex testing and has wide applications in analyzing rare mutations in diverse diseases.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemical Research Methods
Phuc-Loi Luu, Phuc-Thinh Ong, Tran Thai Huu Loc, Dilys Lam, Ruth Pidsley, Clare Stirzaker, Susan J. Clark
Summary: MethPanel is a computational pipeline for rapid analysis of multiplex bisulphite PCR sequencing data, with features such as epipoly-morphism score calculation and PCR bias correction capabilities. It supports processing methylation data from all samples in parallel and automatically forwards outputs to shinyApp for convenient display and sharing.
Article
Biophysics
Samet Kocabey, Guillermo P. Acuna, Curzio Ruegg
Summary: miRNA has the potential to be biomarkers for early disease detection, and the sensitive and accurate detection of miRNA can improve diagnosis and treatment of diseases, especially cancer. This study introduces a DNA origami nanoarray system that uses super-resolution microscopy technique DNA-PAINT to detect miRNAs based on their distance to boundary markers. The sensor can detect up to 4 miRNAs separately or in combination, with high sensitivity and large dynamic range, without the need for amplification. The detection system can also discriminate single base mismatches with low false positive rates. This ultrasensitive and amplification-free miRNA detection method has been successfully applied to detect breast-cancer associated miRNAs in cell extracts and plasma.
BIOSENSORS & BIOELECTRONICS
(2023)
Article
Biochemical Research Methods
Weihan Sun, Wei Guo, Zhiyi Liu, Sennan Qiao, Ziming Wang, Jiayu Wang, Lingxuan Qu, Liang Shan, Fei Sun, Shuping Xu, Ou Bai, Chongyang Liang
Summary: A label-free sensing chip based on porous anodised aluminium (PAA), modified with deactivated Cas9 (dCas9) proteins and synthetic guide RNA (sgRNA), has been developed for the detection of the diffuse large B-cell lymphoma (DLBCL) MYD88(L265P) gene. The sensor utilizes electrochemical ionic current rectification measurement to capture the gene sequence, resulting in a variation in the ion current. The whole sensing process can be completed within 40 minutes without the need for gene amplification.
Article
Genetics & Heredity
Seung-Ho Shin, Woong-Yang Park, Donghyun Park
Summary: Recent studies have shown that next-generation sequencing (NGS) can successfully detect circulating tumor DNA (ctDNA) in various cancers, leading to improved cancer diagnosis and prognosis. However, the low allelic fraction of ctDNA presents a challenge for sensitive and specific detection of tumor variants in cell-free DNA (cfDNA). This study compared error profiles in cfDNA and cellular genomic DNA (gDNA) to identify DNA damage specific to cfDNA, with findings suggesting an increase in cytosine deamination in cfDNA compared to gDNA, potentially due to DNA damage repair attenuation or cytosine deamination accumulation. These results contribute to a better understanding of cfDNA-associated DNA damage for accurate analysis of somatic variants at low frequencies.
BMC MEDICAL GENOMICS
(2021)
Article
Biochemistry & Molecular Biology
Anna S. Zhuk, Anna A. Shiriaeva, Yulia V. Andreychuk, Olga V. Kochenova, Elena R. Tarakhovskaya, Vladimir M. Bure, Youri I. Pavlov, Sergey G. Inge-Vechtomov, Elena I. Stepchenkova
Summary: Spontaneous or induced DNA lesions can cause stable gene mutations and chromosomal aberrations, resulting in phenotype changes. Some DNA lesions can temporarily interfere with transcription and mimic mutations. The direct impact of primary DNA lesions on phenotype is not well understood before they are repaired.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biophysics
Muhit Rana, Tugba Yilmaz, Shirli Cohen, Sinem Beyhan, Avni A. Argun
Summary: Fungal infections pose a significant health concern, especially in immunocompromised population, and a rapid and accurate diagnostic method is needed to improve patient prognosis. In this study, we developed a cost-effective nucleic acid sensor that can detect histoplasmosis-causing fungal genes in whole blood or bronchoalveolar lavage samples earlier than current methods. The sensor uses immobilized nucleic acid probes to directly and label-free detect the presence of specific fungal genes through electrochemical analysis. It provides ultra-sensitive detection of DNA molecules with a limit of detection down to 100 aM, and the turnaround time for sample to result is less than 90 minutes, which is significantly faster than the current clinical procedure.
BIOSENSORS & BIOELECTRONICS
(2023)
Article
Oncology
Eric Leung, Kathy Han, Jinfeng Zou, Zhen Zhao, Yangqiao Zheng, Ting Ting Wang, Ariana Rostami, Lillian L. Siu, Trevor J. Pugh, Scott V. Bratman
Summary: The HPV-seq method offers accurate quantitative and qualitative assessment of HPV ctDNA, outperforming dPCR, and is associated with disease progression in patients.
CLINICAL CANCER RESEARCH
(2021)
Article
Oncology
Sheng Ju, Zihan Cui, Yuanyuan Hong, Xiaoqing Wang, Weina Mu, Zhuolin Xie, Xuexia Zeng, Lin Su, Xiaojing Lin, Zhuo Zhang, Qi Zhang, Xiaofeng Song, Songxia You, Ruixin Chen, Weizhi Chen, Chun Xu, Jun Zhao
Summary: Researchers developed an RNA-based hybridization panel for detecting actionable driver oncogene mutations in solid tumors. The panel showed high accuracy in detecting fusions and exon-skipping mutations in NSCLC samples. Compared to DNA panel sequencing, the RNA panel had high positive agreement and predictive value for detecting targetable SNVs and indels.
Article
Biochemistry & Molecular Biology
Anshika Narang, Salvatore A. E. Marras, Natalia Kurepina, Varsha Chauhan, Elena Shashkina, Barry Kreiswirth, Mandira Varma-Basil, Christopher Vinnard, Selvakumar Subbian
Summary: The emergence of drug-resistant tuberculosis is a global health issue. This study developed a SuperSelective primer-based real-time PCR assay to efficiently diagnose heteroresistant tuberculosis, which can contribute to managing antimicrobial resistance in tuberculosis and other infectious diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Analytical
Xinrong Yan, Jiangyan Zhang, Qi Jiang, Dan Jiao, Yongqiang Cheng
Summary: This study successfully combines the CRISPR-Cas12a system with the ligase chain reaction (LCR), achieving homogeneous, ultrasensitive, and visual detection of microRNA targets. By designing specific LCR probes and guide RNA, the LCR reaction is initiated and ultrasensitive detection is achieved through the secondary signal amplification mechanism of the Cas12a system. Moreover, microRNA can be visually detected by naked eyes and accurately quantified through image analysis using a cationic conjugated polymer.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Begona Jimenez-Rodriguez, Alfonso Alba-Bernal, Esperanza Lopez-Lopez, Maria Elena Quiros-Ortega, Guillermo Carbajosa, Alicia Garrido-Aranda, Martina Alvarez, Ana Godoy-Ortiz, Maria Isabel Queipo-Ortuno, Luis Vicioso, Gema Diaz-Cordoba, Maria Dunia Roldan-Diaz, Jesus Velasco-Suelto, Cristina Hernando, Begona Bermejo, Ana Julve-Parreno, Ana Lluch, Javier Pascual, Inaki Comino-Mendez, Emilio Alba
Summary: A novel ultrasensitive pipeline for detecting circulating tumor DNA (ctDNA) in localized breast cancer patients was developed. There was a 29.50% mutation concordance between tumor tissue and plasma, and 8 patients had plasma-only mutations. The study also revealed associations between ctDNA characteristics and tumor grade, relapse risk, and hormone receptor-negative tumors.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Dong Xing, Longzhi Tan, Chi-Han Chang, Heng Li, X. Sunney Xie
Summary: A single-cell WGA method called META-CS has been developed to eliminate false positives in single-cell SNV detection, achieving the highest accuracy in measurements so far. Validation studies on kindred cells, human sperm, and other human tissues have confirmed the effectiveness of META-CS, revealing an increase in SNVs in mature single human neurons with age and cell type-dependent SNV frequencies and mutational patterns in single human blood cells.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Analytical
Changjing Yuan, Jie Fang, Weiling Fu
Summary: Recent advances in prokaryotic Argonaute proteins (pAgos) have provided new insights into the development of pAgos-based nucleic acid detection platforms. However, the current challenge lies in achieving isothermal detection using pAgos. This study introduces a true isothermal amplification strategy called Thermus thermophilus Argonaute-based thermostable exponential amplification reaction (TtAgoEAR), which allows for RNA detection with ultra-sensitivity and single-nucleotide resolution at a constant temperature of 66 degrees C. The results demonstrate the potential of TtAgoEAR for reliable and easy RNA detection in point-of-care diagnosis and field analysis.
ANALYTICAL CHEMISTRY
(2023)
Article
Gastroenterology & Hepatology
Jingjing Liang, Xinmiao Liang, Hong Ma, Leng Nie, Ying Tian, Guang Chen, Yu Wang
Summary: A new real-time PCR method was established to quantitatively detect HBV mutations, showing good sensitivity, specificity and efficiency.
JOURNAL OF CLINICAL AND TRANSLATIONAL HEPATOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Philipp Hermann, Angelika Heissl, Irene Tiemann-Boege, Andreas Futschik
MOLECULAR ECOLOGY RESOURCES
(2019)
Article
Biochemistry & Molecular Biology
Monika Cechova, Robert S. Harris, Marta Tomaszkiewicz, Barbara Arbeithuber, Francesca Chiaromonte, Kateryna D. Makova
MOLECULAR BIOLOGY AND EVOLUTION
(2019)
Article
Evolutionary Biology
Han Mei, Barbara Arbeithuber, Marzia A. Cremona, Michael DeGiorgio, Anton Nekrutenko
GENOME BIOLOGY AND EVOLUTION
(2019)
Article
Multidisciplinary Sciences
Arslan A. Zaidi, Peter R. Wilton, Marcia Shu-Wei Su, Ian M. Paul, Barbara Arbeithuber, Kate Anthony, Anton Nekrutenko, Rasmus Nielsen, Kateryna D. Makova
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Biochemical Research Methods
Nicholas Stoler, Barbara Arbeithuber, Gundula Povysil, Monika Heinzl, Renato Salazar, Kateryna D. Makova, Irene Tiemann-Boege, Anton Nekrutenko
BMC BIOINFORMATICS
(2020)
Article
Biology
Alison Barrett, Barbara Arbeithuber, Arslan Zaidi, Peter Wilton, Ian M. Paul, Rasmus Nielsen, Kateryna D. Makova
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2020)
Article
Biochemistry & Molecular Biology
Barbara Arbeithuber, James Hester, Marzia A. Cremona, Nicholas Stoler, Arslan Zaidi, Bonnie Higgins, Kate Anthony, Francesca Chiaromonte, Francisco J. Diaz, Kateryna D. Makova
Review
Biochemistry & Molecular Biology
Irene Tiemann-Boege, Theresa Mair, Atena Yasari, Michal Zurovec
Summary: Postzygotic mosaicism (PZM) is a common biological phenomenon often overlooked as a source of disease. Lethal mutations in a mosaic state can lead to new clinical manifestations. Key questions remain unanswered, including the level of mosaicism resulting in a pathogenic phenotype and how clinical outcomes change with development and age.
Article
Biochemistry & Molecular Biology
Renato Salazar, Barbara Arbeithuber, Maja Ivankovic, Monika Heinzl, Sofia Moura, Ingrid Hartl, Theresa Mair, Angelika Lahnsteiner, Thomas Ebner, Omar Shebl, Johannes Proell, Irene Tiemann-Boege
Summary: Researchers have discovered highly recurrent selfish mutations associated with congenital disorders in male germline. Using duplex sequencing, they examined the FGFR3 coding region and found that older donors harbor more mutations associated with congenital disorders.
Article
Multidisciplinary Sciences
Barbara Arbeithuber, Marzia A. Cremona, James Hester, Alison Barrett, Bonnie Higgins, Kate Anthony, Francesca Chiaromonte, Francisco J. Diaz, Kateryna D. Makova
Summary: Duplex sequencing technology reveals the accumulation of mtDNA mutations in somatic tissues and germline cells of primates as they age. The frequency of these mutations significantly increases in liver and muscle tissues with age, while it stabilizes in oocytes of older animals after 9 years of age.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Ingrid Hartl, Veronika Brumovska, Yasmin Striedner, Atena Yasari, Gerhard J. Schuetz, Eva Sevcsik, Irene Tiemann-Boege
Summary: This study utilized micropatterning to enrich FGFR3 in specific areas of the cell membrane, and quantified receptor activation by observing the recruitment of downstream signaling molecule GRB2 to FGFR3 micropatterns. The results showed that mutations in FGFR3 altered receptor activity, with increased activity in G380R and K650Q mutants upon ligand addition, while decreased activity in K650E mutant. These findings provide further insight into the functional effects of mutations to FGFR3.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Genetics & Heredity
Gundula Povysil, Monika Heinzl, Renato Salazar, Nicholas Stoler, Anton Nekrutenko, Irene Tiemann-Boege
Summary: Duplex sequencing is the most reliable method for identifying ultra-low frequency DNA variants, but only a small proportion of reads are assembled into duplex consensus sequences. A bioinformatics toolset was developed to analyze tag and family composition, identifying errors that contribute to data loss and proposing modifications to maximize data output. This tool also re-examines variant calls from raw reads, categorizing the confidence level of a variant call and increasing sequencing depth for variant calling.
NAR GENOMICS AND BIOINFORMATICS
(2021)
Article
Biology
Theresa Schwarz, Yasmin Striedner, Andreas Horner, Karin Haase, Jasmin Kemptner, Nicole Zeppezauer, Philipp Hermann, Irene Tiemann-Boege
LIFE SCIENCE ALLIANCE
(2019)
Article
Biology
Angelika Heissl, Andrea J. Betancourt, Philipp Hermann, Gundula Povysil, Barbara Arbeithuber, Andreas Futschik, Thomas Ebner, Irene Tiemann-Boege
LIFE SCIENCE ALLIANCE
(2019)