@article{e77b4cd65fff4b37876249633908be4b,
title = "A Clinician's Guide to Bioinformatics for Next-Generation Sequencing",
abstract = "Next-generation sequencing (NGS) technologies are high-throughput methods for DNA sequencing and have become a widely adopted tool in cancer research. The sheer amount and variety of data generated by NGS assays require sophisticated computational methods and bioinformatics expertise. In this review, we provide background details of NGS technology and basic bioinformatics concepts for the clinician investigator interested in cancer research applications, with a focus on DNA-based approaches. We introduce the general principles of presequencing library preparation, postsequencing alignment, and variant calling. We also highlight the common variant annotations and NGS applications for other molecular data types. Finally, we briefly discuss the revealed utility of NGS methods in NSCLC research and study design considerations for research studies that aim to leverage NGS technologies for clinical care.",
keywords = "Bioinformatics, DNA, Next-generation sequencing, Review",
author = "Larson, {Nicholas Bradley} and Oberg, {Ann L.} and Adjei, {Alex A.} and Liguo Wang",
note = "Funding Information: This work was supported by the National Cancer Institute (grant numbers U10CA180882, P50CA136393, P50CA102701, and P30CA15083). COSMIC: https://cancer.sanger.ac.uk/cosmic, HGMD: http://www.hgmd.cf.ac.uk/ac/index.php, ClinVar: https://www.ncbi.nlm.nih.gov/clinvar/, gnomAD: https://gnomad.broadinstitute.org/, OncoKB: https://www.oncokb.org/, 1000 Genomes: https://www.internationalgenome.org/, GWAS Catalog: https://www.ebi.ac.uk/gwas/, SNPnexus: https://www.snp-nexus.org/v4/, SNPsnap: https://data.broadinstitute.org/mpg/snpsnap/about.ht, VEP: https://useast.ensembl.org/info/docs/tools/vep/index.html, Variant Annotation Integrator: https://genome.ucsc.edu/cgi-bin/hgVai, GVS: https://gvs.gs.washington.edu/GVS150/, NCI Genomic Data Commons (GDC): https://gdc.cancer.gov/, dbGaP: https://www.ncbi.nlm.nih.gov/gap/, EGA: https://ega-archive.org/, GEO: https://www.ncbi.nlm.nih.gov/geo/, SRA: https://www.ncbi.nlm.nih.gov/sra/, cBioPortal: https://www.cbioportal.org/, NIH GDC Portal: https://portal.gdc.cancer.gov/, Integrative Genomics Viewer (IGV): https://software.broadinstitute.org/software/igv/ Funding Information: This work was supported by the National Cancer Institute (grant numbers U10CA180882, P50CA136393, P50CA102701, and P30CA15083). Publisher Copyright: {\textcopyright} 2022 International Association for the Study of Lung Cancer",
year = "2022",
doi = "10.1016/j.jtho.2022.11.006",
language = "English (US)",
journal = "Journal of Thoracic Oncology",
issn = "1556-0864",
publisher = "International Association for the Study of Lung Cancer",
}