Clinical mutational profiling of bone metastases of lung and colon carcinoma and malignant melanoma using next-generation sequencing.
BACKGROUND
Bone is a common metastatic site for solid tumors and is often the only source for molecular testing. Current routine decalcification protocols for the processing of bone specimens damage nucleic acids, leading to a high failure rate.


METHODS
In this retrospective quality-assessment analysis, preanalytic factors that contributed to the failure of mutational profiling in metastatic bone specimens were evaluated using a next-generation sequencing assay.


RESULTS
Mutational profiling was conducted in 33 formalin-fixed, paraffin-embedded bone lesions that were submitted to a clinical laboratory. Adequate depth of coverage was obtained in 21 specimens, of which, 16 had mutations detected. "No results" were reported in 12 specimens because the NGS assay failed. There was a significantly higher failure rate in bone specimens compared with nonbone specimens (36% vs 2.3%, respectively). Although nonbone specimens had a higher failure rate in biopsy/fine-needle aspiration (FNA) specimens, in-house bone biopsy/FNA specimens with or without short-duration surface decalcification had a lower failure rate than resected bone specimens (11% vs 60%, respectively). The high failure rate in resected metastatic bone specimens was associated with regular decalcification but not with low DNA input.


CONCLUSIONS
Next-generation sequencing assays demonstrated clinical utility in metastatic bone specimens. FNA (smear and cell block) and core-biopsy specimens provided adequate resources of nucleic acids for molecular profiling of metastatic bone lesions. The current findings suggest the need for developing specific tissue procurement and processing protocols for bone metastases and greater use of small biopsy and FNA specimens. Cancer Cytopathol 2016;124:744-53. © 2016 American Cancer Society.
Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
Gang
G
Zheng
Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
Ming-Tseh
MT
Lin
Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
Parvez M
PM
Lokhandwala
Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
Katie
K
Beierl
Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.|Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
George J
GJ
Netto
Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.|Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
Christopher D
CD
Gocke
Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.|Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
James R
JR
Eshleman
Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
Edward
E
McCarthy
Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland. pillei1@jhmi.edu.|Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland. pillei1@jhmi.edu.
Peter B
PB
Illei
D000465:Algorithms; D001859:Bone Neoplasms / Q000235:genetics* / Q000556:secondary*; D015179:Colorectal Neoplasms / Q000235:genetics* / Q000473:pathology; D004252:DNA Mutational Analysis / Q000379:methods; D046152:Gastrointestinal Stromal Tumors / Q000235:genetics / Q000473:pathology; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics* / Q000473:pathology; D008297:Male; D008545:Melanoma / Q000235:genetics* / Q000473:pathology; D012189:Retrospective Studies
bone metastasis; core biopsy; decalcification; fine-needle aspiration; mutation detection; next-generation sequencing