The use of FNA samples for whole-exome sequencing and detection of somatic mutations in breast cancer surgical specimens.
BACKGROUND
The availability of suitable biospecimens is critical to the success of advanced genomic analyses. The objective of this study was to assess the sensitivity of fine-needle aspiration (FNA) compared with gross surgical sampling (GSS) from surgical specimens for the detection of somatic mutations in breast cancer using whole-exome sequencing (WES).


METHODS
DNA was extracted from paired GSS tissues and FNA samples of surgically resected breast cancer from 12 patients and was used for WES. Sanger sequencing was performed to validate selected somatic mutations. Tumor purity was calculated for each sample using sequencing data.


RESULTS
There was no difference in the total amount of DNA extracted from GSS tissues and FNA samples. WES was successfully performed for all 12 pairs of samples. The median number of somatic mutations identified in individual samples was higher in FNA samples than in GSS tissues (39.5 vs 18.5; P = .036). The somatic mutation profiles from both sampling methods were well correlated for samples that had GSS tissues with high tumor content, as indicated by hematoxylin and eosin staining. Nineteen mutations that were identified exclusively in FNA samples were subjected to Sanger sequencing, and 13 of those mutations (68.4%) were validated. The mean estimated tumor purity was higher in FNA samples than in GSS tissues (55.87% vs 25.76%), and FNA samples were estimated to have a consistently higher proportion of malignant cells.


CONCLUSIONS
The current results suggest that FNA is feasible for the collection of tumor samples sufficient for WES analysis and that the higher purity obtained using this method may make it more reliable for genomic studies.
Department of Surgery, Seoul National University College of Medicine, Seoul, Republic of Korea.
Han-Byoel
HB
Lee
Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea.
Je-Gun
JG
Joung
Department of Surgery, Asan Medical Center, Seoul, Republic of Korea.
Jisun
J
Kim
Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
Kyung-Min
KM
Lee
Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea.
Han Suk
HS
Ryu
Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea.
Hae-Ock
HO
Lee
Department of Surgery, Seoul National University College of Medicine, Seoul, Republic of Korea.|Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
Hyeong-Gon
HG
Moon
Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea.|Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
Woong-Yang
WY
Park
Department of Surgery, Seoul National University College of Medicine, Seoul, Republic of Korea.|Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
Dong-Young
DY
Noh
Department of Surgery, Seoul National University College of Medicine, Seoul, Republic of Korea.|Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
Wonshik
W
Han
D000368:Aged; D044963:Biopsy, Fine-Needle / Q000379:methods; D001943:Breast Neoplasms / Q000235:genetics* / Q000473:pathology* / Q000601:surgery; D004273:DNA, Neoplasm / Q000235:genetics; D059472:Exome / Q000235:genetics*; D005260:Female; D060005:Genotyping Techniques; D006801:Humans; D008408:Mastectomy / Q000379:methods; D008875:Middle Aged; D009154:Mutation; D015203:Reproducibility of Results; D056910:Republic of Korea; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA; D046509:Tissue Culture Techniques
D004273:DNA, Neoplasm
breast cancer; fine-needle aspiration; high-throughput DNA sequencing; mutation