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

Xiaobei Zhao, Anyou Wang, Vonn Walter, Nirali M. Patel, David A. Eberhard, Michele C. Hayward, Ashley H. Salazar, Heejoon Jo, Matthew G. Soloway, Matthew D. Wilkerson, Joel S. Parker, Xiaoying Yin, Guosheng Zhang, Marni B. Siegel, Gary B. Rosson, H. Shelton Earp, Norman E. Sharpless, Margaret L. Gulley, Karen E. Weck, D. Neil HayesStergios J. Moschos

Research output: Contribution to journalArticle

22 Citations (Scopus)

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.

Original languageEnglish (US)
Article numbere0129280
JournalPloS one
Volume10
Issue number6
DOIs
StatePublished - Jun 15 2015

Fingerprint

RNA Sequence Analysis
lung neoplasms
Aberrations
DNA Sequence Analysis
Non-Small Cell Lung Carcinoma
Assays
sequence analysis
Cells
RNA
neoplasms
DNA
assays
Tumors
germ cells
Nucleotides
nucleotides
Tissue
Single Nucleotide Polymorphism
cells
Lung Neoplasms

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

Cite this

Zhao, Xiaobei ; Wang, Anyou ; Walter, Vonn ; Patel, Nirali M. ; Eberhard, David A. ; Hayward, Michele C. ; Salazar, Ashley H. ; Jo, Heejoon ; Soloway, Matthew G. ; Wilkerson, Matthew D. ; Parker, Joel S. ; Yin, Xiaoying ; Zhang, Guosheng ; Siegel, Marni B. ; Rosson, Gary B. ; Earp, H. Shelton ; Sharpless, Norman E. ; Gulley, Margaret L. ; Weck, Karen E. ; Hayes, D. Neil ; Moschos, Stergios J. / 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. In: PloS one. 2015 ; Vol. 10, No. 6.
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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.",
author = "Xiaobei Zhao and Anyou Wang and Vonn Walter and Patel, {Nirali M.} and Eberhard, {David A.} and Hayward, {Michele C.} and Salazar, {Ashley H.} and Heejoon Jo and Soloway, {Matthew G.} and Wilkerson, {Matthew D.} and Parker, {Joel S.} and Xiaoying Yin and Guosheng Zhang and Siegel, {Marni B.} and Rosson, {Gary B.} and Earp, {H. Shelton} and Sharpless, {Norman E.} and Gulley, {Margaret L.} and Weck, {Karen E.} and Hayes, {D. Neil} and Moschos, {Stergios J.}",
year = "2015",
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language = "English (US)",
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Zhao, X, Wang, A, Walter, V, Patel, NM, Eberhard, DA, Hayward, MC, Salazar, AH, Jo, H, Soloway, MG, Wilkerson, MD, Parker, JS, Yin, X, Zhang, G, Siegel, MB, Rosson, GB, Earp, HS, Sharpless, NE, Gulley, ML, Weck, KE, Hayes, DN & Moschos, SJ 2015, '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', PloS one, vol. 10, no. 6, e0129280. https://doi.org/10.1371/journal.pone.0129280

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. / Zhao, Xiaobei; Wang, Anyou; Walter, Vonn; Patel, Nirali M.; Eberhard, David A.; Hayward, Michele C.; Salazar, Ashley H.; Jo, Heejoon; Soloway, Matthew G.; Wilkerson, Matthew D.; Parker, Joel S.; Yin, Xiaoying; Zhang, Guosheng; Siegel, Marni B.; Rosson, Gary B.; Earp, H. Shelton; Sharpless, Norman E.; Gulley, Margaret L.; Weck, Karen E.; Hayes, D. Neil; Moschos, Stergios J.

In: PloS one, Vol. 10, No. 6, e0129280, 15.06.2015.

Research output: Contribution to journalArticle

TY - JOUR

T1 - 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

AU - Zhao, Xiaobei

AU - Wang, Anyou

AU - Walter, Vonn

AU - Patel, Nirali M.

AU - Eberhard, David A.

AU - Hayward, Michele C.

AU - Salazar, Ashley H.

AU - Jo, Heejoon

AU - Soloway, Matthew G.

AU - Wilkerson, Matthew D.

AU - Parker, Joel S.

AU - Yin, Xiaoying

AU - Zhang, Guosheng

AU - Siegel, Marni B.

AU - Rosson, Gary B.

AU - Earp, H. Shelton

AU - Sharpless, Norman E.

AU - Gulley, Margaret L.

AU - Weck, Karen E.

AU - Hayes, D. Neil

AU - Moschos, Stergios J.

PY - 2015/6/15

Y1 - 2015/6/15

N2 - 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.

AB - 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.

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