Literature DB >> 23393026

Critical role of bioinformatics in translating huge amounts of next-generation sequencing data into personalized medicine.

Huixiao Hong1, Wenqian Zhang, Jie Shen, Zhenqiang Su, Baitang Ning, Tao Han, Roger Perkins, Leming Shi, Weida Tong.   

Abstract

Realizing personalized medicine requires integrating diverse data types with bioinformatics. The most vital data are genomic information for individuals that are from advanced next-generation sequencing (NGS) technologies at present. The technologies continue to advance in terms of both decreasing cost and sequencing speed with concomitant increase in the amount and complexity of the data. The prodigious data together with the requisite computational pipelines for data analysis and interpretation are stressors to IT infrastructure and the scientists conducting the work alike. Bioinformatics is increasingly becoming the rate-limiting step with numerous challenges to be overcome for translating NGS data for personalized medicine. We review some key bioinformatics tasks, issues, and challenges in contexts of IT requirements, data quality, analysis tools and pipelines, and validation of biomarkers.

Mesh:

Year:  2013        PMID: 23393026     DOI: 10.1007/s11427-013-4439-7

Source DB:  PubMed          Journal:  Sci China Life Sci        ISSN: 1674-7305            Impact factor:   6.038


  11 in total

Review 1.  The long tail and rare disease research: the impact of next-generation sequencing for rare Mendelian disorders.

Authors:  Tony Shen; Ariel Lee; Carol Shen; C Jimmy Lin
Journal:  Genet Res (Camb)       Date:  2015-09-14       Impact factor: 1.588

2.  Comparing genetic variants detected in the 1000 genomes project with SNPs determined by the International HapMap Consortium.

Authors:  Wenqian Zhang; Hui Wen Ng; Mao Shu; Heng Luo; ZhenQiang Su; Weigong Ge; Roger Perkins; Weida Tong; Huixiao Hong
Journal:  J Genet       Date:  2015-12       Impact factor: 1.166

3.  Quality control metrics improve repeatability and reproducibility of single-nucleotide variants derived from whole-genome sequencing.

Authors:  W Zhang; V Soika; J Meehan; Z Su; W Ge; H W Ng; R Perkins; V Simonyan; W Tong; H Hong
Journal:  Pharmacogenomics J       Date:  2014-11-11       Impact factor: 3.550

4.  Comparison of library construction kits for mRNA sequencing in the Illumina platform.

Authors:  Yong-Soo Park; Songmi Kim; Dong-Guk Park; Dong Hee Kim; Kyeong-Wook Yoon; Wonseok Shin; Kyudong Han
Journal:  Genes Genomics       Date:  2019-07-26       Impact factor: 1.839

5.  An integrative computational approach for prioritization of genomic variants.

Authors:  Inna Dubchak; Sandhya Balasubramanian; Sheng Wang; Meydan Cem; Cem Meyden; Dinanath Sulakhe; Alexander Poliakov; Daniela Börnigen; Bingqing Xie; Andrew Taylor; Jianzhu Ma; Alex R Paciorkowski; Ghayda M Mirzaa; Paul Dave; Gady Agam; Jinbo Xu; Lihadh Al-Gazali; Christopher E Mason; M Elizabeth Ross; Natalia Maltsev; T Conrad Gilliam
Journal:  PLoS One       Date:  2014-12-15       Impact factor: 3.240

Review 6.  High-Throughput Sequencing, a VersatileWeapon to Support Genome-Based Diagnosis in Infectious Diseases: Applications to Clinical Bacteriology.

Authors:  Ségolène Caboche; Christophe Audebert; David Hot
Journal:  Pathogens       Date:  2014-04-02

7.  Whole genome sequencing of 35 individuals provides insights into the genetic architecture of Korean population.

Authors:  Wenqian Zhang; Joe Meehan; Zhenqiang Su; Hui Wen Ng; Mao Shu; Heng Luo; Weigong Ge; Roger Perkins; Weida Tong; Huixiao Hong
Journal:  BMC Bioinformatics       Date:  2014-10-21       Impact factor: 3.169

Review 8.  Genomic Discoveries and Personalized Medicine in Neurological Diseases.

Authors:  Li Zhang; Huixiao Hong
Journal:  Pharmaceutics       Date:  2015-12-07       Impact factor: 6.321

9.  A quick guide to genomics and bioinformatics training for clinical and public audiences.

Authors:  Michelle D Brazas; Fran Lewitter; Maria Victoria Schneider; Celia W G van Gelder; Patricia M Palagi
Journal:  PLoS Comput Biol       Date:  2014-04-10       Impact factor: 4.475

Review 10.  Alignment of Short Reads: A Crucial Step for Application of Next-Generation Sequencing Data in Precision Medicine.

Authors:  Hao Ye; Joe Meehan; Weida Tong; Huixiao Hong
Journal:  Pharmaceutics       Date:  2015-11-23       Impact factor: 6.321

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