Review
Genetics & Heredity
Francesco Kumara Mastrorosa, Danny E. Miller, Evan E. Eichler
Summary: Advances in clinical genetic testing, especially long-read sequencing (LRS), have greatly improved the diagnosis rate for rare and previously unsolved genetic disorders. LRS technology has been used to evaluate complex genetic variations, identify missing variants, and has the potential to revolutionize clinical practice in the future.
Review
Clinical Neurology
Yun Su, Liyuan Fan, Changhe Shi, Tai Wang, Huimin Zheng, Haiyang Luo, Shuo Zhang, Zhengwei Hu, Yu Fan, Yali Dong, Jing Yang, Chengyuan Mao, Yuming Xu
Summary: The emergence of long-read single-molecule DNA sequencing technologies has opened up new possibilities for studying neurodegenerative diseases, aiding in the discovery of novel pathogenic mutations and resolving unresolved disorders. Comparing the two prevailing long-read sequencing technologies, Pacific Biosciences and Oxford Nanopore Technologies, and discussing their applications in neurodegenerative diseases.
Review
Clinical Neurology
Yun Su, Liyuan Fan, Changhe Shi, Tai Wang, Huimin Zheng, Haiyang Luo, Shuo Zhang, Zhengwei Hu, Yu Fan, Yali Dong, Jing Yang, Chengyuan Mao, Yuming Xu
Summary: Emerging long-read single-molecule DNA sequencing technologies provide unprecedented resolutions for studying genomes, transcriptomes, and metagenomes, thus expanding our understanding of unresolved issues in neurodegenerative diseases.
Article
Genetics & Heredity
Christopher Mark Watson, Lucy Jackson, Laura A. Crinnion, David T. Bonthron, Eamonn Sheridan
Summary: Long-read nanopore sequencing has significant clinical utility in determining the parental origin of de novo variants.
JOURNAL OF MEDICAL GENETICS
(2022)
Article
Biochemical Research Methods
Christian Clappier, Dennis Boettner, Daniel Heinzelmann, Anna Stadermann, Patrick Schulz, Moritz Schmidt, Benjamin Lindner
Summary: The complete integration locus of two Chinese hamster ovary (CHO) cell lines was reconstructed using CRISPR/Cas9 target enrichment, nanopore sequencing, and the Canu de novo assembly pipeline. The study revealed that one CHO cell line integrated three near full-length vector copies, while another CHO cell line integrated seven highly fragmented vector copies. Comparison with TLA-seq data showed that TLA-seq missed most of the breakpoints of the vector-vector fusions.
Article
Biochemical Research Methods
Xue Zhang, Chen-Guang Liu, Shi-Hui Yang, Xia Wang, Feng-Wu Bai, Zhuo Wang
Summary: The quality of genome construction depends on the sequencing platform, depth, and tools used, with Flye being superior for low-depth datasets according to C_score evaluation.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Mengfei Liu, Linlin Hao, Sien Yang, Xiaohui Wu
Summary: Poly(A) tails play an essential role in regulating gene expression, and there is currently a lack of easy-to-use tools for measuring poly(A) tails in different sequencing protocols. In this study, we developed PolyAtailor, a unified and efficient framework for identifying and analyzing poly(A) tails, and compared its performance with other methods.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Yoshitaka Sakamoto, Suzuko Zaha, Yutaka Suzuki, Masahide Seki, Ayako Suzuki
Summary: Long-read sequencing technologies have significantly advanced cancer genomics research by enabling precise detection of structural variants (SVs) and unveiling their complex structures, as well as revealing epigenomic information surrounding SV loci. This provides a new opportunity for better understanding disease development and drug development.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Review
Biochemical Research Methods
Jiadong Lin, Peng Jia, Songbo Wang, Walter Kosters, Kai Ye
Summary: Structural variant (SV) detection is essential for genomic studies, and comparing read-based and assembly-based strategies is important. This study investigated the factors that influence the two strategies and assessed their performance using well-curated SVs. It was found that a majority of SVs could be detected by both strategies, but discordance was mainly caused by complex SVs and inversions.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Genetics & Heredity
Marilena Melas, Esko A. Kautto, Samuel J. Franklin, Mari Mori, Kim L. McBride, Theresa Mihalic Mosher, Ruthann B. Pfau, Maria Elena Hernandez-Gonzalez, Sean D. McGrath, Vincent J. Magrini, Peter White, Julie Balch Samora, Daniel C. Koboldt, Richard K. Wilson
Summary: Synpolydactyly 1, or syndactyly type II (SDTY2), is a genetic limb malformation characterized by polydactyly with syndactyly. The study identified heterozygous alterations in the HOXD13 gene associated with the disease, and highlighted the value of long-read whole-genome sequencing in elucidating the molecular etiology of congenital limb malformation disorders.
Article
Biology
Shanika L. Amarasinghe, Matthew E. Ritchie, Quentin Gouil
Summary: The long-read Tools database provides researchers with an essential resource to keep track of the expanding collection of long-read data analysis tools and choose the most relevant tool for their analysis needs.
Article
Genetics & Heredity
Shuaibing Yang, Qianqian Zhao, Lihua Tang, Zejia Chen, Zhaoting Wu, Kaixin Li, Ruoru Lin, Yang Chen, Danlin Ou, Li Zhou, Jianzhen Xu, Qingsong Qin
Summary: This study used Oxford nanopore sequencing technology to complete whole-genome sequencing of cervical cancer tissue and CaSki cell line, successfully assembling HPV35 and HPV16 genomic sequences. Nanopore sequencing also revealed integration breakpoints and concatemeric genomic sequences.
FRONTIERS IN GENETICS
(2022)
Review
Genetics & Heredity
Yuta Suzuki, Shinichi Morishita
Summary: The complete sequencing of human centromeres has long been difficult due to the presence of highly repetitive HOR units, which hamper sequence assembly. However, the recent availability of longer reads is expected to enable better observation of individual HOR occurrences.
Article
Gastroenterology & Hepatology
Liuyang Zhao, Yu Shi, Harry Cheuk-Hay Lau, Weixin Liu, Guangwen Luo, Guoping Wang, Changan Liu, Yasi Pan, Qiming Zhou, Yanqiang Ding, Joseph Jao-Yiu Sung, Jun Yu
Summary: Through ultra-deep metagenomic sequencing, we discovered 1058 novel human gut viruses, including some viral genomes longer than the largest bacteriophage found in humans. Our study also demonstrated that a biomarker panel of 14 novel viruses can differentiate patients with colorectal cancer from controls in a training cohort.
Review
Biochemical Research Methods
Tianjiao Zhang, Jie Zhou, Wentao Gao, Yuran Jia, Yanan Wei, Guohua Wang
Summary: High-quality genome chromosome-scale sequences are crucial for genomics downstream analysis, especially in the construction of haplotype-resolved and complete genomes. The emergence of long-read sequencing technology has greatly improved complex genome assembly. Among various computational methods, uncollapsed assembly is the most accurate and complete way to represent genomes. Genome assembly is closely related to haplotype reconstruction.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Infectious Diseases
Raja Polavarapu, Potshangbam Angamba Meetei, Mohit Midha, Dhammapal Bharne, Vaibhav Vindal
INFECTION GENETICS AND EVOLUTION
(2015)
Article
Multidisciplinary Sciences
Hong-Sen Chen, Shin-Chen Hou, Jhih-Wei Jian, King-Siang Goh, San-Tai Shen, Yu-Ching Lee, Jhong-Jhe You, Hung-Pin Peng, Wen-Chih Kuo, Shui-Tsung Chen, Ming-Chi Peng, Andrew H. -J. Wang, Chung-Ming Yu, Ing-Chien Chen, Chao-Ping Tung, Tzu-Han Chen, Kuo Ping Chiu, Che Ma, Chih Yuan Wu, Sheng-Wei Lin, An-Suei Yang
SCIENTIFIC REPORTS
(2015)
Article
Multidisciplinary Sciences
Yu-Shin Nai, Tzu-Han Chen, Yu-Feng Huang, Mohit K. Midha, Hsin-Chieh Shiau, Chen-Yang Shen, Chien-Jen Chen, Alice L. Yu, Kuo Ping Chiu
SCIENTIFIC REPORTS
(2017)
Article
Genetics & Heredity
Yu-Feng Huang, Yen-Ju Chen, Tan-Chi Fan, Nai-Chuan Chang, Yi-Jie Chen, Mohit K. Midha, Tzu-Han Chen, Hsiao-Hsiang Yang, Yu-Tai Wang, Alice L. Yu, Kuo-Ping Chiu
BMC MEDICAL GENOMICS
(2018)
Article
Multidisciplinary Sciences
Yih-Shien Chiang, Yu-Feng Huang, Mohit K. Midha, Tzu-Han Chen, Hsin-Chieh Shiau, Kuo-Ping Chiu
Article
Multidisciplinary Sciences
Yu-Feng Huang, Mohit Midha, Tzu-Han Chen, Yu-Tai Wang, David Glenn Smith, Kurtis Jai-Chyi Pei, Kuo Ping Chiu
Article
Biotechnology & Applied Microbiology
Yu-Feng Huang, Tzu-Han Chen, Zih-Ting Chang, Tai-Chuan Wang, Se Jin Lee, Jong Cheol Kim, Jae Su Kim, Kuo-Ping Chiu, Yu-Shin Nai
Article
Multidisciplinary Sciences
Kuo-Ping Chiu, Alice L. Yu
Article
Oncology
Mohit K. Midha, Yu-Feng Huang, Hsiao-Hsiang Yang, Tan-Chi Fan, Nai-Chuan Chang, Tzu-Han Chen, Yu-Tai Wang, Wen-Hung Kuo, King-Jen Chang, Chen-Yang Shen, Alice L. Yu, Kuo-Ping Chiu, Chien-Jen Chen