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
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
Lyndal Henden, Liam G. Fearnley, Natalie Grima, Emily P. McCann, Carol Dobson-Stone, Lauren Fitzpatrick, Kathryn Friend, Lynne Hobson, Sandrine Chan Moi Fat, Dominic B. Rowe, Susan D'Silva, John B. Kwok, Glenda M. Halliday, Matthew C. Kiernan, Srestha Mazumder, Hannah C. Timmins, Margaret Zoing, Roger Pamphlett, Lorel Adams, Melanie Bahlo, Ian P. Blair, Kelly L. Williams
Summary: In this study, we analyzed whole-genome sequencing data from 608 patients with sporadic ALS, 68 patients with sporadic FTD, and 4703 matched controls using three tools. We found that 17.6% of clinically diagnosed ALS and FTD cases had expanded STR alleles reported to be pathogenic or intermediate for other neurodegenerative diseases, providing evidence for their contribution to the development of these diseases. We also identified multiple disease-relevant STR expansions associated with neurodegenerative diseases, highlighting the clinical and pathological pleiotropy of neurodegenerative disease genes and their importance in ALS and FTD.
Article
Neurosciences
Yiting Wu, Tingwei Song, Qian Xu
Summary: Expansions of short tandem repeats (STRs) are associated with over 50 diseases, particularly neurodegenerative diseases. Several potential molecular mechanisms, including transcriptional silencing, R-LOOP formation, sequestration of RNA-binding proteins, gain-of-function proteins, and repeat-associated non-AUG translation, contribute to STR expansion disorders. R-LOOP, a three-stranded nucleic acid structure formed during transcription, plays a crucial role in inducing DNA damage and genome instability. This review provides a comprehensive discussion on the recent advancements in understanding R-LOOP and its genetic destabilizing effects in neurodegenerative diseases, offering potential targets for drug design and therapeutic advancements.
MOLECULAR NEUROBIOLOGY
(2023)
Article
Oncology
Paola Visconti, Federica Parodi, Barbara Parodi, Lucia Casarino, Paolo Romano, Mariachiara Buccarelli, Roberto Pallini, Quintino Giorgio D'Alessandris, Andrea Montori, Emanuela Pilozzi, Lucia Ricci-Vitiani
Summary: Colorectal and glioblastoma cancer stem-like cells are crucial for translational research, and their authentication through STR profiling ensures research reproducibility. This study provides a reference dataset for a panel of CSCs, allowing comparison with a large number of tumor cell lines, along with clinical data and mutation information. The STR profiles and information of CSCs are available in databases for further research.
INTERNATIONAL JOURNAL OF CANCER
(2021)
Article
Biochemical Research Methods
Shinichi Morishita, Kazuki Ichikawa, Eugene W. Myers
Summary: This study presents an efficient algorithm that utilizes the characteristics of repetitive sequences to address the issue of high error rates in long-read sequencing technologies. The algorithm first estimates regions that may contain tandem repeats, and then assembles the k-mers of these regions into a consensus repeat unit by greedily traversing a de Bruijn graph. Experimental results demonstrate that the proposed algorithm outperforms the widely used Tandem Repeats Finder in terms of sensitivity.
Article
Microbiology
Bram Spruijtenburg, Cynthea C. S. Z. Baqueiro, Arnaldo L. Colombo, Eelco F. J. Meijer, Joao N. de Almeida, Indira Berrio, Norma B. Fernandez, Guilherme M. Chaves, Jacques F. Meis, Theun de Groot
Summary: Candida tropicalis is a common opportunistic pathogen causing infections in Latin America, and the rise of antifungal-resistant isolates is becoming a concern. This study utilized short tandem repeat (STR) genotyping and antifungal susceptibility testing (AFST) to investigate the population genomics and resistance patterns of 230 C. tropicalis isolates. The results revealed outbreak events, the presence of anidulafungin-resistant isolates, and azole resistance-associated substitutions. The findings highlight the importance of this STR genotyping scheme for identifying outbreaks and understanding the spread of antifungal-resistant C. tropicalis isolates.
Article
Genetics & Heredity
Indhu-Shree Rajan-Babu, Junran J. Pen, Readman Chiu, Chenkai Li, Arezoo Mohajeri, Egor Dolzhenko, Michael A. Eberle, Inanc Birol, Jan M. Friedman
Summary: The study developed an efficient computational workflow for detecting STR expansions in next-generation sequencing data, successfully identifying individuals with repeat expansion disorders in genetic testing of families.
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
Multidisciplinary Sciences
WenHui Fu, Hualian Pei, Nitin Shivappa, James R. Hebert, Tao Luo, Tian Tian, Dilibaier Alimu, Zewen Zhang, Jianghong Dai
Summary: This study found an association between a pro-inflammatory diet and an increased risk of type 2 diabetes mellitus in Chinese adults.
Article
Genetics & Heredity
Solip Lee, Heesang You, Songhee Lee, Yeongju Lee, Hee-Gyoo Kang, Ho-Joong Sung, Jiwon Choi, Sunghee Hyun
Summary: Forensic investigation is crucial for analyzing evidence and finding key individuals in criminal cases. This study explores the potential of using next-generation sequencing to analyze human evidence and microbial genome communities. The results demonstrate the feasibility of obtaining anthropological and microbiological evidence using these techniques.
Article
Biochemistry & Molecular Biology
Yujie Huang, Cong Liu, Chao Xiao, Xiaoying Chen, Xueli Han, Shaohua Yi, Daixin Huang
Summary: This study investigated the mutation rates of 28 autosomal STRs in the Chinese Han population, revealing relationships between STR mutation rates and factors such as population, sex, age, allele length, and heterozygosity. The results showed a higher frequency of paternal mutations compared to maternal mutations, an increase in mutation rate with paternal age, a bias towards contraction mutations for long alleles, and expansion mutations for short alleles, with no overall bias in mutation direction. Additionally, loci with higher expected heterozygosity tended to have higher mutation rates, providing valuable information for further research on STR mutations in forensic genetics.
MOLECULAR BIOLOGY REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Yimin Wang, Yunchao Ling, Jiao Gong, Xiaohan Zhao, Hanwen Zhou, Bo Xie, Haiyi Lou, Xinhao Zhuang, Li Jin, Shaohua Fan, Guoqing Zhang, Shuhua Xu
Summary: PGG.SV is a practical platform that provides large-scale structural variation data, including 1030 long-read sequencing genomes representing 177 global populations. The database offers high-quality SVs with precise genomic locations, estimates of SV prevalence in different geographical populations, informative annotations of related genes, and an analysis platform and visualization tools for association studies.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Rheumatology
Fangyi Wu, Xuling Han, Jing Liu, Zhenghua Zhang, Kexiang Yan, Beilan Wang, Lin Yang, Hejian Zou, Chengde Yang, Wei Huang, Li Jin, Jiucun Wang, Feng Qian, Zhenmin Niu
Summary: This study explores the association between variants in non MHC proteasome gene and AS, and finds that the rs12717 SNP in PSMB1 gene is significantly associated with AS. The study also discovers that PSMB1 regulates the RANK/RANKL signaling pathway and affects bone formation by inhibiting osteoclast differentiation.
Letter
Biochemistry & Molecular Biology
Shixiong Tian, Ziqi Wang, Liting Liu, Yiling Zhou, Yue Lv, Dongdong Tang, Jiaxiong Wang, Jing Jiang, Huan Wu, Shuyan Tang, Guanxiong Wang, Hao Geng, Fangbiao Tao, Hongbin Liu, Xiaojin He, Feng Zhang, Jinsong Li, Li Jin, Tao Huang, Chunyu Liu, Yunxia Cao
JOURNAL OF GENETICS AND GENOMICS
(2023)
Article
Dermatology
Qianqian Peng, Yu Liu, Anke Huels, Canfeng Zhang, Yao Yu, Wenqing Qiu, Xiyang Cai, Yuepu Zhao, Tamara Schikowski, Katja Merches, Yun Liu, Yajun Yang, Jiucun Wang, Yong Zhao, Li Jin, Liang Zhang, Jean Krutmann, Sijia Wang
Summary: Solar lentigines (SLs) are a common sign of aging skin caused by chronic exposure to sunlight and environmental stressors. Recent studies have suggested a possible genetic component, but the findings are inconsistent. Through a multi-trait analysis, researchers discovered that genetic variants in the telomerase reverse transcriptase gene are significantly associated with non-facial SLs in East Asian and Caucasian populations. These variants are also related to facial SLs but not other skin aging or pigmentation traits, highlighting a previously unrecognized role of telomerase reverse transcriptase in lentigines formation.
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2023)
Article
Genetics & Heredity
Shixiong Tian, Chaofeng Tu, Xiaojin He, Lanlan Meng, Jiaxiong Wang, Shuyan Tang, Yang Gao, Chunyu Liu, Huan Wu, Yiling Zhou, Mingrong Lv, Ge Lin, Li Jin, Yunxia Cao, Dongdong Tang, Feng Zhang, Yue-Qiu Tan
Summary: This study identified biallelic deleterious mutations of CFAP54 in three unrelated men with severe MMAF or NOA. These mutations were associated with abnormal sperm morphology, reduced sperm concentration and motility. Immunofluorescence assays showed reduced staining of four flagellar assembly-associated proteins in the spermatozoa of CFAP54-deficient men.
JOURNAL OF MEDICAL GENETICS
(2023)
Letter
Plant Sciences
Xiao-Min Yang, Hai-Liang Meng, Jian-Lin Zhang, Yao Yu, Edward Allen, Zi-Yang Xia, Kong-Yang Zhu, Pan-Xin Du, Xiao-Ying Ren, Jian-Xue Xiong, Xiao-Yu Lu, Yi Ding, Sheng Han, Wei-Peng Liu, Li Jin, Chuan-Chao Wang, Shao-Qing Wen
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Hanni Ke, Shuyan Tang, Ting Guo, Dong Hou, Xue Jiao, Shan Li, Wei Luo, Bingying Xu, Shidou Zhao, Guangyu Li, Xiaoxi Zhang, Shuhua Xu, Lingbo Wang, Yanhua Wu, Jiucun Wang, Feng Zhang, Yingying Qin, Li Jin, Zi-Jiang Chen
Summary: Whole-exome sequencing in a cohort of 1,030 patients with POI identified new likely pathogenic variants and revealed different genetic architectures between primary and secondary amenorrhea. This study expands our understanding of the genetic landscape underlying POI and provides insights that have the potential to improve diagnostic genetic screenings.
Article
Genetics & Heredity
Chunyu Liu, Wei Si, Chaofeng Tu, Shixiong Tian, Xiaojin He, Shengnan Wang, Xiaoyu Yang, Chencheng Yao, Cong Li, Zine-Eddine Kherraf, Maosen Ye, Zixue Zhou, Yuhua Ma, Yang Gao, Yu Li, Qiwei Liu, Shuyan Tang, Jiaxiong Wang, Hexige Saiyin, Liangyu Zhao, Liqun Yang, Lanlan Meng, Bingbing Chen, Dongdong Tang, Yiling Zhou, Huan Wu, Mingrong Lv, Chen Tan, Ge Lin, Qingpeng Kong, Hong Shi, Zhixi Su, Zheng Li, Yong-Gang Yao, Li Jin, Ping Zheng, Pierre F. Ray, Yue-Qiu Tan, Yunxia Cao, Feng Zhang
Summary: Primate-specific genes (PSGs) expressed in the brain and testis are consistent with brain evolution in primates. The identification of deleterious variants of the X-linked SSX1 gene in men with asthenoteratozoospermia highlights its crucial role in spermatogenesis. Knocking down Ssx1 expression in non-human primate and tree shrew models resulted in reduced sperm motility and abnormal sperm morphology, reflecting the phenotype observed in humans. This study has important implications for genetic counseling and clinical diagnosis, and provides insights into the functions of testis-enriched PSGs in spermatogenesis.
AMERICAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Environmental Sciences
Tongchao Zhang, Xiaolin Yin, Xiaorong Yang, Ziyu Yuan, Qiyun Wu, Li Jin, Xingdong Chen, Ming Lu, Weimin Ye
Summary: This study investigated the association between 12 trace elements and gastroesophageal cancers (GOC) using hair and fingernail samples collected from GOC cases and controls in Taixing, China. The results showed that higher levels of Ca, Zn, Fe, Al, Cr, Pb, Se, and V were positively associated with increased GOC, while higher levels of Mg, Mn, Sr, and As were inversely associated with GOC. Interaction effects between hair level of Cr and smoking or alcohol drinking were also observed.
JOURNAL OF EXPOSURE SCIENCE AND ENVIRONMENTAL EPIDEMIOLOGY
(2023)
Article
Multidisciplinary Sciences
Yang Gao, Xiaofei Yang, Hao Chen, Xinjiang Tan, Zhaoqing Yang, Lian Deng, Baonan Wang, Shuang Kong, Songyang Li, Yuhang Cui, Chang Lei, Yimin Wang, Yuwen Pan, Sen Ma, Hao Sun, Xiaohan Zhao, Yingbing Shi, Ziyi Yang, Dongdong Wu, Shaoyuan Wu, Xingming Zhao, Binyin Shi, Li Jin, Zhibin Hu, Yan Lu, Jiayou Chu, Kai Ye, Shuhua Xu
Summary: The data from the Chinese Pangenome Consortium's first phase reveals a substantial increase in the discovery of novel and missing sequences when individuals from underrepresented minority ethnic groups are included. The missing reference sequences contain archaic-derived alleles and genes related to keratinization, response to ultraviolet radiation, DNA repair, immunological responses, and lifespan, suggesting great potential for understanding human evolution and filling in missing heritability in complex diseases.
Article
Neurosciences
Jincheng Li, Sibo Zhu, Yingzhe Wang, Min Fan, Jiacheng Dai, Chengkai Zhu, Kelin Xu, Mei Cui, Chen Suo, Li Jin, Yanfeng Jiang, Xingdong Chen
Summary: By comparing the gut microbiota in a community-based cohort, it was found that bacteria capable of producing SCFAs were positively associated with better cognitive performance. In addition, specific bacterial strains were more abundant in individuals with MCI or CN groups and were correlated with cognitive performance.
NEUROBIOLOGY OF DISEASE
(2023)
Article
Chemistry, Applied
Junyu Luo, Qili Qian, Wenxin Zheng, Ieva Gripkauskaite, Sijie Wu, Min Zhang, Jinxi Li, Bingfei Fu, Ranjit Bhogal, Peter Murray, Matthew Rowson, Bin Li, Xiangyang Xue, Xuelan Gu, Yajun Yang, Li Jin, David Andrew Gunn, Sijia Wang
Summary: This study investigated the extent to which scalp hair parameters change with age in Chinese men and women. The number of hairs per follicular unit was found to have a negative correlation with age in both men and women. Men had a greater number of hairs and follicular units than women on average, but experienced a greater decrease in the number of hairs per follicular unit with age, particularly in multi-hair follicular units. Hair loss was not random across follicular units, and a higher number of hairs per follicular unit increased the risk of hair loss. The results suggest that the presence of multi-hair follicular units on the scalp contributes to the greater susceptibility of scalp hair to hair loss compared to other body sites.
INTERNATIONAL JOURNAL OF COSMETIC SCIENCE
(2023)
Editorial Material
Multidisciplinary Sciences
Yi Li, Meng Hao, Zixin Hu, Yanyun Ma, Kun Wang, Xiaoyu Liu, Xianhong Yin, Menghan Zhang, Yi Wang, Meng Liang, Yuan Guo, Lei Bao, Shixuan Zhang, Shiguan Le, Chenyuan Wu, Dayan Sun, Yang Wei, Fei Wu, Rui Zhang, Lingxian Zhu, Hui Zhang, Shuai Jiang, Xingdong Chen, Xiaofeng Wang, Yao Zhang, Longli Kang, Wenyuan Duan, Bin Qiao, Jiucun Wang, Li Jin
NATIONAL SCIENCE REVIEW
(2023)
Article
Medicine, Research & Experimental
Wenjing Wang, Yoichi Miyamoto, Biaobang Chen, Juanzi Shi, Feiyang Diao, Wei Zheng, Qun Li, Lan Yu, Lin Li, Yao Xu, Ling Wu, Xiaoyan Mao, Jing Fu, Bin Li, Zheng Yan, Rong Shi, Xia Xue, Jian Mu, Zhihua Zhang, Tianyu Wu, Lin Zhao, Weijie Wang, Zhou Zhou, Jie Dong, Qiaoli Li, Li Jin, Lin He, Xiaoxi Sun, Ge Lin, Yanping Kuang, Lei Wang, Qing Sang
Summary: By analyzing whole-exome sequencing data of 606 women with PREMBA, researchers have identified a candidate gene KPNA7, which may contribute to the development of PREMBA. The study further revealed that KPNA7 mutations reduce protein levels, impair its binding capacity to substrate RSL1D1, and affect nuclear transport activity. Furthermore, the study found that mouse KPNA2 plays a critical role in embryonic development and its deficiency leads to embryo arrest, similar to human PREMBA cases. These findings provide a mechanistic understanding of PREMBA and a diagnostic marker for PREMBA patients.
JOURNAL OF CLINICAL INVESTIGATION
(2023)
Article
Genetics & Heredity
Jialin Li, Qingxia Huang, Yingzhe Wang, Mei Cui, Kelin Xu, Chen Suo, Zhenqiu Liu, Yanpeng An, Li Jin, Huiru Tang, Xingdong Chen, Yanfeng Jiang
Summary: Cardiovascular health is linked to a lower risk of cognitive decline, and this association may be mediated by metabolic perturbations. The study found that better cardiovascular health was associated with a lower risk of concentration and orientation decline. Certain blood components, such as apolipoprotein-A1 and high-density lipoprotein cholesterol, were also associated with a lower risk of memory and orientation decline. Mediation analysis suggested that cholesterol ester and total lipids in medium-size HDL may partially mediate the negative association between health status and the risk of orientation decline. These findings highlight the potential of using lipoproteins as targets for early stage dementia screening and intervention.
Article
Genetics & Heredity
Amy H. J. Chan, Michael G. Gardner, Adrian Linacre
Summary: We report the detection and visualisation of latent DNA from pangolin scales using a nucleic acid staining dye, and propose that this method is invaluable in wildlife forensic science.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2024)
Article
Genetics & Heredity
Fernanda M. Garcia, Raquel S. R. Trabach, Victor S. Stange, Bruno Cancian, Alexia S. S. Zetum, Matheus C. Casotti, Flavia I. V. Errera, Elizeu F. de Carvalho, Debora D. Meira, Iuri D. Louro
Summary: This study found that the population of Espirito Santo, Brazil is genetically closer to the Italian population based on the analysis of STR markers on the X chromosome.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2024)
Article
Genetics & Heredity
Zhiyong Liu, Jiajun Liu, Jiaojiao Geng, Enlin Wu, Jianzhang Zhu, Bin Cong, Riga Wu, Hongyu Sun
Summary: Microorganisms can serve as potential markers for identifying body fluids and tissues in forensic genetics. This study explored the use of metatranscriptomics to characterize common forensic samples and investigated the potential application of metatranscriptomics in forensic science. The results demonstrated high alpha diversity in saliva and skin samples, and the use of machine learning models showed that microbial RNA-based methods could be applied for forensic body fluid/tissue identification. Overall, this study provides insights into the role of metatranscriptomics in forensic science and its potential for microbe-based individual identification.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2024)
Article
Genetics & Heredity
Guro Dorum, Nadescha Viviane Haenggi, Dario Burri, Yael Marti, Regine Banemann, Galina Kulstein, Cornelius Courts, Annica Gosch, Thorsten Hadrys, Cordula Haas, Jacqueline Neubauer
Summary: RNA has gained attention in forensic field for predicting biological age. This study used RNA-Seq data to search for markers associated with age and presented two candidate marker lists.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2024)
Article
Genetics & Heredity
Michele Di Nunzio, Carme Barrot-Feixat, David Gangitano
Summary: This study developed five SNaPshotTM assays for nine chloroplast markers to differentiate between marijuana crop type and hemp crop type. The testing of 122 cannabis samples successfully distinguished between marijuana and hemp, and genetic differences between different groups based on biogeographical origin and crop type were observed. Phylogenetic analysis and principal component analysis provided valuable information about the genetic relationship and differentiation between different cannabis samples.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2024)
Article
Genetics & Heredity
Katherine B. Gettings, Martin Bodner, Lisa A. Borsuk, Jonathan L. King, David Ballard, Walther Parson, Corina C. G. Benschop, Claus Borsting, Bruce Budowle, John M. Butler, Kristiaan J. van der Gaag, Peter Gill, Leonor Gusmao, Douglas R. Hares, Jerry Hoogenboom, Jodi Irwin, Lourdes Prieto, Peter M. Schneider, Marielle Vennemann, Christopher Phillips
Summary: The DNA Commission of the ISFG has developed nomenclature recommendations for STR sequences, incorporating research findings and providing guidance for interlaboratory comparisons and the integration of new markers into investigative databases.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2024)
