Article
Oncology
Meijia Gu, Meimei Yang, Jing He, Sixuan Xia, Zhe Zhang, Yudong Wang, Congyi Zheng, Chao Shen
Summary: Continuous cell lines are widely used practical models in the study of disease mechanisms, particularly cancers. However, the issue of cell line cross-contamination has persisted since the 1960s, despite calls for cell line authentication by experts. Cell line abuse is also underestimated and underreported. The China Center for Type Culture Collection (CCTCC) has seen an improvement in the quality of cell lines from 2010 to 2019, which bodes well for the future.
INTERNATIONAL JOURNAL OF CANCER
(2022)
Article
Cell Biology
Indrajit Nanda, Sarah K. Schroeder, Claus Steinlein, Thomas Haaf, Eva M. Buhl, Domink G. Grimm, Ralf Weiskirchen
Summary: Hepatic stellate cells (HSCs) are liver-specific mesenchymal cells that play a key role in maintaining the liver sinusoid microenvironment. Cultured HSCs are valuable tools for studying liver diseases, but their isolation requires special equipment and trained personnel. To overcome these limitations, immortalized HSC lines, such as CFSC, have been established.
Article
Multidisciplinary Sciences
Steffen K. Meurer, David A. Brenner, Ralf Weiskirchen
Summary: Misidentification, cross-contamination, and genetic drift of continuous animal cell lines are common problems in biomedical research, which can lead to erroneous results and inconsistent or invalidated studies. This study established a multi-loci short tandem repeat signature for the immortalized hepatic stellate cell line Col-GFP HSC, allowing for unique cell line authentication.
Article
Biochemistry & Molecular Biology
Jidong Lang, Zhihua Xu, Yue Wang, Jiguo Sun, Zhi Yang
Summary: Short tandem repeats (STRs) are widely present in the human genome and have associations with various diseases. NanoSTR, a method based on nanopore sequencing, improves the accuracy and efficiency of STR detection and genotyping compared to existing methods. NanoSTR shows high performance in detecting target STR markers and expands the applications of nanopore sequencing in research and clinical scenarios.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Oncology
Julien De Wolf, Edouard Robin, Alexandre Vallee, Justine Cohen, Abdul Hamid, Antoine Roux, Morgan Leguen, Romane Beaurepere, Ivan Bieche, Julien Masliah-Planchon, Matthieu Glorion, Yves Allory, Edouard Sage, Foch lung Transplant Grp
Summary: This study examines the origin of graft cancer in lung transplant recipients and finds that the prevalence of lung cancer in these recipients is very low, but there are cases where the cancer originates from the recipient. These results highlight the importance of donor selection and medical supervision after lung transplantation.
FRONTIERS IN ONCOLOGY
(2023)
Article
Medicine, Legal
Bowei Jiang, Weifeng Qu, Feng Wang, Liming Zhang, Haibo Rong, Jienan Li, Dan Wen, Moutanou Modeste Judes Zeye, Wei He, Chudong Wang, Hao Xing, Tao Zhang, Chuan Jin, Li Chen, Ying Liu, Jifeng Cai, Lagabaiyila Zha
Summary: The novel 8-dye STR multiplex system containing 18 autosomal loci and the sex-determining locus Amelogenin shows promising results in genotyping even with low input DNA. Complete profiles were obtained with input DNA as low as 0.0625 ng, and the system also performed well in the presence of inhibitors and with degraded DNA samples. This multiplex system is suitable for human DNA genotyping, including difficult forensic materials.
INTERNATIONAL JOURNAL OF LEGAL MEDICINE
(2021)
Article
Medicine, Legal
Hailun Nan, Weiwei Wu, Honglei Hao, Wenran Ren, Dejian Lu
Summary: The study analyzed genotypes of 42 Y chromosome STR loci in a Chinese Han population, observing deletions and duplications at various loci. Duplications were more common than deletions, especially at palindrome loci. These variations may be specific to the Chinese Han population and could impact the interpretation of Y-STR genetic profiles in forensic casework.
INTERNATIONAL JOURNAL OF LEGAL MEDICINE
(2021)
Article
Biophysics
Olivier Tytgat, Maarten Fauvart, Tim Stakenborg, Dieter Deforce, Filip Van Nieuwerburgh
Summary: The demand for forensic DNA profiling is increasing, leading to challenges in decentralized workflow due to the need for bulky equipment. Researchers developed a novel hybridization-based STR genotyping method using STRide probes, showing high sensitivity and potential for on-site forensic DNA fingerprinting.
BIOSENSORS & BIOELECTRONICS
(2021)
Article
Multidisciplinary Sciences
Readman Chiu, Indhu-Shree Rajan-Babu, Inanc Birol, Jan M. Friedman
Summary: This study explores how the long-range sequence information of barcode linked-read sequencing (BLRS) can improve the detection of STR expansions. A novel algorithm using BLRS barcodes for distance estimation is devised and evaluated for STR genotyping. The utility of barcode and phasing information is validated through simulated and experimental data, showing improved STR genotypes compared to standard short-read sequencing.
SCIENTIFIC REPORTS
(2022)
Article
Biochemical Research Methods
Xuewen Wang, Bruce Budowle, Jianye Ge
Summary: USAT is a user-friendly bioinformatics software that allows for interpretation, visualization, and comparisons of TRs. It offers various functions such as allele size conversion, sequence comparison of haplotypes, figure plotting, comparison for allele distribution, and interactive visualization. An exemplary application of USAT for analyzing the CODIS core STR loci for DNA forensics showcased its capabilities in benchmarking human individuals.
BMC BIOINFORMATICS
(2022)
Article
Genetics & Heredity
Shuanglin Li, Jinfeng Lin, Honglei Hao, Haiying Jin, Danlu Song, Bofeng Zhu
Summary: The study demonstrates that the SureID (R) S6 system performs stably in multiplex amplification, effectively amplifying DNA within a certain range, and showing good stability and species specificity. Population and concordance studies show that the system's CPD and CPE values exhibit high identification and exclusion probabilities.
FRONTIERS IN GENETICS
(2021)
Article
Plant Sciences
Huan Mei, Ting Zhao, Zeyu Dong, Jin Han, Biyu Xu, Rui Chen, Jun Zhang, Juncheng Zhang, Yan Hu, Tianzhen Zhang, Lei Fang
Summary: This study conducted a population-scale analysis of short tandem repeats (STRs) in the cotton genome, revealing a large number of polymorphic STRs, some of which were found in coding regions of genes and significantly associated with transcription, ribosome biogenesis, and signal transduction. The study also introduced an alternative strategy using STR-GWAS to identify STRs associated with agronomic traits, leading to the discovery of novel alleles undetectable by previous SNP-GWAS methods. Additionally, a CottonSTRDB database was developed to serve as a valuable resource for the cotton breeding community.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Ja Hyun Lee, Jeongyong Kim, Hyojeong Kim, Hyo Sook Kim, Eungsoo Kim
Summary: A new smaller-sized STR panel containing the SE33 locus was designed using MPS technology to improve STR analysis and paternity index; SE33 marker was found to effectively determine match probability and typical paternity index; Multiple new alleles and SNP variations were detected through MPS analysis, and full profiles could be obtained with concentrations as low as 80 pg.
Article
Chemistry, Analytical
Olivier Tytgat, Sonja Skevin, Maarten Fauvart, Tim Stakenborg, Dieter Deforce, Filip Van Nieuwerburgh
Summary: A hybridization-based genotyping assay called QueSTR probes was developed for miniaturized lab-on-a-chip STR profiling. The QueSTR probes rely on the recognition and cleavage of an RNA:DNA duplex to achieve genotyping. The study demonstrated that the QueSTR probes have high accuracy in genotyping three core loci.
SENSORS AND ACTUATORS B-CHEMICAL
(2022)
Article
Biotechnology & Applied Microbiology
Li Fang, Qian Liu, Alex Mas Monteys, Pedro Gonzalez-Alegre, Beverly L. Davidson, Kai Wang
Summary: DeepRepeat is a method that converts ionic current signals into image channels for accurate detection and quantification of long tandem repeats. In experiments, DeepRepeat outperforms other methods in repeat detection and quantification, and has been validated on multiple datasets.
Article
Multidisciplinary Sciences
Tan A. Ince, Aurea D. Sousa, Michelle A. Jones, J. Chuck Harrell, Elin S. Agoston, Marit Krohn, Laura M. Selfors, Wenbin Liu, Ken Chen, Mao Yong, Peter Buchwald, Bin Wang, Katherine S. Hale, Evan Cohick, Petra Sergent, Abigail Witt, Zhanna Kozhekbaeva, Sizhen Gao, Agoston T. Agoston, Melissa A. Merritt, Rosemary Foster, Bo R. Rueda, Christopher P. Crum, Joan S. Brugge, Gordon B. Mills
NATURE COMMUNICATIONS
(2015)
Article
Biochemical Research Methods
Sangjo Shim, Katherine Stemke-Hale, Jamileh Noshari, Frederick F. Becker, Peter R. C. Gascoyne
Article
Biochemical Research Methods
Sangjo Shim, Katherine Stemke-Hale, Apostolia M. Tsimberidou, Jamileh Noshari, Thomas E. Anderson, Peter R. C. Gascoyne
Article
Oncology
Kimberly C. Wiegand, Bryan T. Hennessy, Samuel Leung, Yemin Wang, Zhenlin Ju, Mollianne McGahren, Steve E. Kalloger, Sarah Finlayson, Katherine Stemke-Hale, Yiling Lu, Fan Zhang, Michael S. Anglesio, Blake Gilks, Gordon B. Mills, David G. Huntsman, Mark S. Carey
Article
Oncology
K. M. Britton, R. Eyre, I. J. Harvey, K. Stemke-Hale, D. Browell, T. W. J. Lennard, A. P. Meeson
Meeting Abstract
Oncology
Violeta Serra, Jordi Rodon, Ludmila Prudkin, Claudia Aura, Ana Vivancos, Yasir H. Ibrahim, Mathew Maurer, Hanina Hibshoosh, Katherine Stemke-Hale, Jose Jimenez, Yuker Wang, Vicente Peg, Javier Hernandez, Santiago Ramon Y Cajal, Rodrigo Dienstmann, Cristina Saura, Gessami Sanchez, Josep Tabernero, Ramon Parsons, Gordon Mills, Jose Baselga
Meeting Abstract
Oncology
Banibrata Sen, Tuhina Mazumdar, Shaohua Peng, Katherine S. Hale, Bonnie S. Glisson, Faye M. Johnson
Article
Oncology
Ian R. Watson, Liren Li, Peter K. Cabeceiras, Mozhdeh Mahdavi, Tony Gutschner, Giannicola Genovese, Guocan Wang, Zhuangna Fang, James M. Tepper, Katherine Stemke-Hale, Kenneth Y. Tsai, Michael A. Davies, Gordon B. Mills, Lynda Chin
Article
Biochemical Research Methods
Peter R. C. Gascoyne, Sangjo Shim, Jamileh Noshari, Frederick F. Becker, Katherine Stemke-Hale
Article
Pathology
Katherine Stemke-Hale, Kristy Shipman, Isidora Kitsou-Mylona, David G. de Castro, Vicky Hird, Robert Brown, James Flanagan, Hani Gabra, Gordon B. Mills, Roshan Agarwal, Mona El-Bahrawy
Article
Oncology
Tuhina Mazumdar, Lauren A. Byers, Patrick Kwok Shing Ng, Gordon B. Mills, Shaohua Peng, Lixia Diao, You-Hong Fan, Katherine Stemke-Hale, John V. Heymach, Jeffrey N. Myers, Bonnie S. Glisson, Faye M. Johnson
MOLECULAR CANCER THERAPEUTICS
(2014)
Article
Biochemistry & Molecular Biology
Manal M. Hassan, Ahmed Kaseb, Carol J. Etzel, Hashem El-Serag, Margaret R. Spitz, Ping Chang, Katherine S. Hale, Mei Liu, Asif Rashid, Mohamed Shama, James L. Abbruzzese, Evelyne M. Loyer, Harmeet Kaur, Hesham M. Hassabo, Jean-Nicolas Vauthey, Curtis J. Wray, Basmah S. Hassan, Yehuda Z. Patt, Ernest Hawk, Khalid M. Soliman, Donghui Li
MOLECULAR CARCINOGENESIS
(2013)
Article
Multidisciplinary Sciences
Michael J. Overman, Jiexin Zhang, Scott Kopetz, Michael Davies, Jiang Zhi-Qin, Katherine Stemke-Hale, Petra Ruemmele, Christian Pilarsky, Robert Gruetzmann, Stanley Hamilton, Rosa Hwang, James L. Abbruzzese, Gauri Varadhachary, Bradley Broom, Huamin Wang
Article
Oncology
Rachel Eyre, Ian Harvey, Katherine Stemke-Hale, Thomas W. J. Lennard, Alison Tyson-Capper, Annette P. Meeson
Article
Multidisciplinary Sciences
Kosuke Yoshihara, Maria Shahmoradgoli, Emmanuel Martinez, Rahulsimham Vegesna, Hoon Kim, Wandaliz Torres-Garcia, Victor Trevino, Hui Shen, Peter W. Laird, Douglas A. Levine, Scott L. Carter, Gad Getz, Katherine Stemke-Hale, Gordon B. Mills, Roel G. W. Verhaak
NATURE COMMUNICATIONS
(2013)
Article
Oncology
Yuxin Liu, Swati Bhardwaj, Keith Sigel, John Winters, Joseph Terlizzi, Michael M. Gaisa
Summary: This study investigated the prevalence and severity of anal HPV disease among MSM LWH under the age of 35, finding a high prevalence of HPV infection and precancer but no cases of invasive anal cancer. This supports the adoption of age-based anal cancer screening for this population.
INTERNATIONAL JOURNAL OF CANCER
(2024)
Correction
Oncology
J. Gu, S. Xie, S. Wang
INTERNATIONAL JOURNAL OF CANCER
(2024)