Clinical application of amplicon-based next-generation sequencing in cancer

Chang, Fengqi; Li, Marilyn M.

doi:10.1016/j.cancergen.2013.10.003

Cited by 97 publications

(77 citation statements)

References 44 publications

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“…This analysis consist of a primary analysis, in which the base pairs are called and quality score are generated; a secondary analysis, numerous reads are aligned to the human reference sequence; and a tertiary analysis which consists of variant calling and annotation [117]. Many databases are useful for helping the variant annotation, such as the 1000 Genome Project [118], dbSNP database [119], Clinvar-NCBI [120], LOVD-Leiden Open Variation Database [121], The Cancer Genome Atlas (TCGA) [122] and others.…”

Section: Discussionmentioning

confidence: 99%

“…However, information from these sources can contain ambiguous and insuicient information. Variants detected should be reported according to Human Genome Variation Society (HGVS) recommendations, with information of the human reference genome version and transcript information used to variant description [117]. The reference coding sequence should be preferably from the RefSeq database [123].…”

Section: Discussionmentioning

confidence: 99%

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Application of Next-Generation Sequencing in the Era of Precision Medicine

Pereira¹,

Malta²,

Freire³

et al. 2017

Applications of RNA-Seq and Omics Strategies - From Microorganisms to Human Health

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Next-generation sequencing (NGS) technologies represented the next step in the evolution of DNA sequencing, through the generation of thousands to millions of DNA sequences in a short time. The relatively fast emergence and success of NGS in research revolutionized the ield of genomics and medical diagnosis. The traditional medicine model of diagnosis has changed to one precision medicine model, leading to a more accurate diagnosis of human diseases and allowing the selection of molecular target drugs for individual treatment. This chapter atempts to review the main features of NGS technique (concepts, data analysis, applications, advances and challenges), starting with a brief history of DNA sequencing followed by a comprehensive description of most used NGS platforms. Further topics will highlight the application of NGS towards routine practice, including variant detection, whole-exome sequencing (WES), whole-genome sequencing (WGS), custom panels (multi-gene), RNA-seq and epigenetic. The potential use of NGS in precision medicine is vast and a beter knowledge of this technique is necessary for an eicacious implementation in the clinical workplace. A centralized chapter describing the main NGS aspects in the clinic could help beginners, scientists, researchers and health care professionals, as they will be responsible for translating genomic data into genomic medicine.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Application of Next-Generation Sequencing in the Era of Precision Medicine

Pereira¹,

Malta²,

Freire³

et al. 2017

Applications of RNA-Seq and Omics Strategies - From Microorganisms to Human Health

View full text Add to dashboard Cite

show abstract

“…The output of sequencing data per run is 600 Gb, the read lengths are ~100 bp, the cost is lower, and the run times are 3-10 days which are much longer than most other systems. However, this system has some disadvantages including complex data analysis and higher cost of data generation 8,10 .…”

Section: Illumina/solexamentioning

confidence: 99%

“…Furthermore, the current error rate of this system is relatively high (3-5%). The main error type is deletion which probably results from detection errors and/or incorporation of unlabeled nucleotides 10 . Other SMS technologies with higher sequencing speed, longer read lengths, or lower overall cost are also emerging.…”

Section: Emerging Technologiesmentioning

confidence: 99%

“…This system presently offers a throughput of approximately 50-100 Mb/run, which is much lower than current NGS platforms. Moreover, the single-read error rate is typically 15%, exceeding the error tolerance of many applications 5,10 . Nano-technology has long been considered a cutting-edge equipment for single-molecule DNA sequencing.…”

Section: Emerging Technologiesmentioning

confidence: 99%

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