title: Combined Targeted DNA Sequencing in Non-Small Cell Lung Cancer (NSCLC) Using UNCseq and NGScopy, and RNA Sequencing Using UNCqeR for the Detection of Genetic Aberrations in NSCLC.
abstract: The recent FDA approval of the MiSeqDx platform provides a unique opportunity to develop targeted next generation sequencing (NGS) panels for human disease, including cancer. We have developed a scalable, targeted panel-based assay termed UNCseq, which involves a NGS panel of over 200 cancer-associated genes and a standardized downstream bioinformatics pipeline for detection of single nucleotide variations (SNV) as well as small insertions and deletions (indel). In addition, we developed a novel algorithm, NGScopy, designed for samples with sparse sequencing coverage to detect large-scale copy number variations (CNV), similar to human SNP Array 6.0 as well as small-scale intragenic CNV. Overall, we applied this assay to 100 snap-frozen lung cancer specimens lacking same-patient germline DNA (07-0120 tissue cohort) and validated our results against Sanger sequencing, SNP Array, and our recently published integrated DNA-seq/RNA-seq assay, UNCqeR, where RNA-seq of same-patient tumor specimens confirmed SNV detected by DNA-seq, if RNA-seq coverage depth was adequate. In addition, we applied the UNCseq assay on an independent lung cancer tumor tissue collection with available same-patient germline DNA (11-1115 tissue cohort) and confirmed mutations using assays performed in a CLIA-certified laboratory. We conclude that UNCseq can identify SNV, indel, and CNV in tumor specimens lacking germline DNA in a cost-efficient fashion.
authors.affiliation: Lineberger Comprehensive Cancer Center, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States of America.
authors.forename: Xiaobei
authors.initials: X
authors.lastname: Zhao
authors.affiliation: Lineberger Comprehensive Cancer Center, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States of America.
authors.forename: Anyou
authors.initials: A
authors.lastname: Wang
authors.affiliation: Lineberger Comprehensive Cancer Center, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States of America.
authors.forename: Vonn
authors.initials: V
authors.lastname: Walter
authors.affiliation: Lineberger Comprehensive Cancer Center, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States of America; Department of Pathology and Laboratory Medicine, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States of America.
authors.forename: Nirali M
authors.initials: NM
authors.lastname: Patel
authors.affiliation: Lineberger Comprehensive Cancer Center, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States of America; Department of Pathology and Laboratory Medicine, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States of America.
authors.forename: David A
authors.initials: DA
authors.lastname: Eberhard
authors.affiliation: Lineberger Comprehensive Cancer Center, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States of America.
authors.forename: Michele C
authors.initials: MC
authors.lastname: Hayward
authors.affiliation: Lineberger Comprehensive Cancer Center, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States of America.
authors.forename: Ashley H
authors.initials: AH
authors.lastname: Salazar
authors.affiliation: Lineberger Comprehensive Cancer Center, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States of America; Department of Biostatistics, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States of America.
authors.forename: Heejoon
authors.initials: H
authors.lastname: Jo
authors.affiliation: Lineberger Comprehensive Cancer Center, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States of America.
authors.forename: Matthew G
authors.initials: MG
authors.lastname: Soloway
authors.affiliation: Lineberger Comprehensive Cancer Center, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States of America; Department of Genetics, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States of America.
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Wilkerson
authors.affiliation: Lineberger Comprehensive Cancer Center, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States of America.
authors.forename: Joel S
authors.initials: JS
authors.lastname: Parker
authors.affiliation: Lineberger Comprehensive Cancer Center, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States of America.
authors.forename: Xiaoying
authors.initials: X
authors.lastname: Yin
authors.affiliation: Lineberger Comprehensive Cancer Center, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States of America.
authors.forename: Guosheng
authors.initials: G
authors.lastname: Zhang
authors.affiliation: The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, United States of America.
authors.forename: Marni B
authors.initials: MB
authors.lastname: Siegel
authors.affiliation: Lineberger Comprehensive Cancer Center, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States of America; The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, United States of America.
authors.forename: Gary B
authors.initials: GB
authors.lastname: Rosson
authors.affiliation: Lineberger Comprehensive Cancer Center, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States of America; Department of Medicine, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States of America; Department of Pharmacology, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States of America.
authors.forename: H Shelton
authors.initials: HS
authors.lastname: Earp
authors.affiliation: Lineberger Comprehensive Cancer Center, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States of America; Department of Genetics, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States of America; Department of Medicine, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States of America.
authors.forename: Norman E
authors.initials: NE
authors.lastname: Sharpless
authors.affiliation: Lineberger Comprehensive Cancer Center, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States of America; Department of Pathology and Laboratory Medicine, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States of America.
authors.forename: Margaret L
authors.initials: ML
authors.lastname: Gulley
authors.affiliation: Lineberger Comprehensive Cancer Center, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States of America; Department of Pathology and Laboratory Medicine, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States of America.
authors.forename: Karen E
authors.initials: KE
authors.lastname: Weck
authors.affiliation: Lineberger Comprehensive Cancer Center, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States of America; Department of Genetics, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States of America; Department of Medicine, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States of America.
authors.forename: D Neil
authors.initials: DN
authors.lastname: Hayes
authors.affiliation: Lineberger Comprehensive Cancer Center, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States of America; Department of Medicine, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States of America.
authors.forename: Stergios J
authors.initials: SJ
authors.lastname: Moschos
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D002289:Carcinoma, Non-Small-Cell Lung / Q000235:genetics* / Q000473:pathology; D019295:Computational Biology; D056915:DNA Copy Number Variations; D005260:Female; D056726:Genetic Association Studies; D014644:Genetic Variation; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics* / Q000473:pathology; D008297:Male; D008875:Middle Aged; D009154:Mutation; D060787:Neoplasm Grading; D009367:Neoplasm Staging; D016283:Proto-Oncogene Proteins p21(ras) / Q000235:genetics; D015203:Reproducibility of Results
chemical_list: C117307:KRAS protein, human; D016283:Proto-Oncogene Proteins p21(ras)