Journal ArticleDOI
Sequencing depth and coverage: key considerations in genomic analyses
TLDR
The issue of sequencing depth in the design of next-generation sequencing experiments is discussed and current guidelines and precedents on the issue of coverage are reviewed for four major study designs, including de novo genome sequencing, genome resequencing, transcriptome sequencing and genomic location analyses.Abstract:
Sequencing technologies have placed a wide range of genomic analyses within the capabilities of many laboratories. However, sequencing costs often set limits to the amount of sequences that can be generated and, consequently, the biological outcomes that can be achieved from an experimental design. In this Review, we discuss the issue of sequencing depth in the design of next-generation sequencing experiments. We review current guidelines and precedents on the issue of coverage, as well as their underlying considerations, for four major study designs, which include de novo genome sequencing, genome resequencing, transcriptome sequencing and genomic location analyses (for example, chromatin immunoprecipitation followed by sequencing (ChIP-seq) and chromosome conformation capture (3C)).read more
Citations
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Journal ArticleDOI
Simultaneous human platelet antigen genotyping and detection of novel single nucleotide polymorphisms by targeted next-generation sequencing.
TL;DR: A targeted next‐generation sequencing approach was designed to detect all known human platelet antigens with the additional capability of identifying novel mutations in the encoding genes.
Journal ArticleDOI
A PCR-Based Assay Targeting the Major Capsid Protein Gene of a Dinorna-Like ssRNA Virus That Infects Coral Photosymbionts.
Jose Montalvo-Proaño,Jose Montalvo-Proaño,Patrick Buerger,Patrick Buerger,Karen D. Weynberg,Madeleine J. H. van Oppen,Madeleine J. H. van Oppen +6 more
TL;DR: A novel PCR-based assay for examining the presence and diversity of a single-stranded RNA (ssRNA) virus by targeting its major capsid protein (MCP) gene, indicating that dinorna-like viruses are commonly associated with corals on the Great Barrier Reef.
Journal ArticleDOI
Application of next-generation sequencing technology to precision medicine in cancer: joint consensus of the Tumor Biomarker Committee of the Chinese Society of Clinical Oncology
Xu-Chao Zhang,Xu-Chao Zhang,Zhiyong Liang,Shengyue Wang,Shun Lu,Yong Song,Ying Cheng,Jianming Ying,Wei-ping Liu,Yingyong Hou,Yangqiu Li,Yi Liu,Jun Hou,Xiufeng Liu,Jian Yong Shao,Yanhong Tai,Zheng Wang,Li Fu,Hui Li,Xiaojun Zhou,Hua Bai,Mengzhao Wang,You Lu,Jin-Ji Yang,Wen-Zhao Zhong,Qing Zhou,Xue-Ning Yang,Jie Wang,Cheng Huang,Xiaoqing Liu,Xiaoyan Zhou,Shirong Zhang,Hong-Xia Tian,Hong-Xia Tian,Yu Chen,Yu Chen,Ruibao Ren,Ning Liao,Chunyan Wu,Zhongzheng Zhu,Hongming Pan,Yanhong Gu,Liwei Wang,Yunpeng Liu,Suzhan Zhang,Tianshu Liu,Gong Chen,Zhimin Shao,Binghe Xu,Qingyuan Zhang,Rui-Hua Xu,Lin Shen,Yi-Long Wu,Yi-Long Wu +53 more
TL;DR: The expert group has reached a preliminary consensus on the need of NGS in clinical diagnosis, its regulation, and compliance standards in clinical sample collection, and has prepared NGS criteria, the sequencing standard operation procedure (SOP), data analysis, report, and NGS platform certification and validation.
Journal ArticleDOI
Expanding the conservation genomics toolbox: incorporating structural variants to enhance genomic studies for species of conservation concern
Jana Wold,Klaus-Peter Koepfli,Klaus-Peter Koepfli,Stephanie J. Galla,Stephanie J. Galla,David Eccles,Carolyn J. Hogg,Marissa F. Le Lec,Joseph Guhlin,Anna W. Santure,Tammy E. Steeves +10 more
TL;DR: It is contended that characterizing SVs offers the conservation genomics community an exciting opportunity to complement SNP‐based approaches to enhance species recovery and leverage the existing literature–predominantly in human health, agriculture and ecoevolutionary biology–to identify approaches for readily characterization SVs.
Book ChapterDOI
Insertions and Deletions (Indels)
TL;DR: This chapter provides an overview of the mechanisms that generate indels and the impact these mechanisms have on detection, as well as technical factors of NGS assay design and specimen selection that impact indel detection.
References
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Journal ArticleDOI
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TL;DR: The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence.
Journal ArticleDOI
Differential expression analysis for sequence count data.
Simon Anders,Wolfgang Huber +1 more
TL;DR: A method based on the negative binomial distribution, with variance and mean linked by local regression, is proposed and an implementation, DESeq, as an R/Bioconductor package is presented.
Journal ArticleDOI
RNA-Seq: a revolutionary tool for transcriptomics
TL;DR: The RNA-Seq approach to transcriptome profiling that uses deep-sequencing technologies provides a far more precise measurement of levels of transcripts and their isoforms than other methods.
Journal ArticleDOI
TopHat: discovering splice junctions with RNA-Seq
TL;DR: The TopHat pipeline is much faster than previous systems, mapping nearly 2.2 million reads per CPU hour, which is sufficient to process an entire RNA-Seq experiment in less than a day on a standard desktop computer.