Clinical next-generation sequencing in patients with non-small cell lung cancer.

Abstract

BACKGROUND:

A clinical assay was implemented to perform next-generation sequencing (NGS) of genes commonly mutated in multiple cancer types. This report describes the feasibility and diagnostic yield of this assay in 381 consecutive patients with non-small cell lung cancer (NSCLC).

METHODS:

Clinical targeted sequencing of 23 genes was performed with DNA from formalin-fixed, paraffin-embedded (FFPE) tumor tissue. The assay used Agilent SureSelect hybrid capture followed by Illumina HiSeq 2000, MiSeq, or HiSeq 2500 sequencing in a College of American Pathologists-accredited, Clinical Laboratory Improvement Amendments-certified laboratory. Single-nucleotide variants and insertion/deletion events were reported. This assay was performed before methods were developed to detect rearrangements by NGS.

RESULTS:

Two hundred nine of all requisitioned samples (55%) were successfully sequenced. The most common reason for not performing the sequencing was an insufficient quantity of tissue available in the blocks (29%). Excisional, endoscopic, and core biopsy specimens were sufficient for testing in 95%, 66%, and 40% of the cases, respectively. The median turnaround time (TAT) in the pathology laboratory was 21 days, and there was a trend of an improved TAT with more rapid sequencing platforms. Sequencing yielded a mean coverage of 1318×. Potentially actionable mutations (ie, predictive or prognostic) were identified in 46% of 209 samples and were most commonly found in KRAS (28%), epidermal growth factor receptor (14%), phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (4%), phosphatase and tensin homolog (1%), and BRAF (1%). Five percent of the samples had multiple actionable mutations. A targeted therapy was instituted on the basis of NGS in 11% of the sequenced patients or in 6% of all patients.

CONCLUSIONS:

NGS-based diagnostics are feasible in NSCLC and provide clinically relevant information from readily available FFPE tissue. The sample type is associated with the probability of successful testing.

• Authors: Ian S Hagemann, Siddhartha Devarakonda, Christina M Lockwood, David H Spencer, Kalin Guebert, Andrew J Bredemeyer, Hussam Al-Kateb, TuDung T Nguyen, Eric J Duncavage, Catherine E Cottrell, Shashikant Kulkarni, Rakesh Nagarajan, Karen Seibert, Maria Baggstrom, Saiama N Waqar, John D Pfeifer, Daniel Morgensztern, Ramaswamy Govindan
• Journal: Cancer (Cancer) Vol. 121 Issue 4 Pg. 631-9 (Feb 15 2015) ISSN: 1097-0142 [Electronic] United States
• PMID: 25345567 (Publication Type: Journal Article)
• Copyright: © 2014 American Cancer Society.

Chemical References

• DNA, Neoplasm
• Fixatives
• KRAS protein, human
• Proto-Oncogene Proteins
• Formaldehyde
• BRAF protein, human
• Proto-Oncogene Proteins B-raf
• Proto-Oncogene Proteins p21(ras)
• ras Proteins

Topics

• Adult
• Aged
• Carcinoma, Non-Small-Cell Lung (diagnosis, genetics)
• DNA, Neoplasm (analysis)
• Feasibility Studies
• Female
• Fixatives
• Formaldehyde
• Gene Deletion
• High-Throughput Nucleotide Sequencing
• Humans
• Lung Neoplasms (diagnosis, genetics)
• Male
• Middle Aged
• Mutagenesis, Insertional
• Paraffin Embedding
• Polymorphism, Single Nucleotide
• Proto-Oncogene Proteins (genetics)
• Proto-Oncogene Proteins B-raf (genetics)
• Proto-Oncogene Proteins p21(ras)
• Sequence Analysis, DNA (methods)
• ras Proteins (genetics)