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J Appl Genet. 2018 Aug;59(3):269-277. doi: 10.1007/s13353-018-0439-4. Epub 2018 Mar 10.

Identification of novel mutations in FFPE lung adenocarcinomas using DEPArray sorting technology and next-generation sequencing.

Lee JW1,2,3, Shin JY2,4, Seo JS5,6,7,8.

Author information

1
Gongwu Genomic Medicine Institute (G2MI), Medical Research Center, Seoul National University Bundang Hospital, Seongnamsi, 13605, Republic of Korea.
2
Genomic Medicine Institute (GMI), Medical Research Center, Seoul National University, Seoul, 03080, Republic of Korea.
3
Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea.
4
Macrogen Genome Institute, Medical Research Center, Seoul National University Bundang Hospital, Seongnamsi, 13605, Republic of Korea.
5
Gongwu Genomic Medicine Institute (G2MI), Medical Research Center, Seoul National University Bundang Hospital, Seongnamsi, 13605, Republic of Korea. jeongsun@snu.ac.kr.
6
Genomic Medicine Institute (GMI), Medical Research Center, Seoul National University, Seoul, 03080, Republic of Korea. jeongsun@snu.ac.kr.
7
Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea. jeongsun@snu.ac.kr.
8
Macrogen Genome Institute, Medical Research Center, Seoul National University Bundang Hospital, Seongnamsi, 13605, Republic of Korea. jeongsun@snu.ac.kr.

Abstract

Formalin-fixed paraffin-embedded (FFPE) tissues are utilized as the standard diagnostic method in pathology laboratories. However, admixture of unwanted tissues and shortage of normal samples, which can be used to detect somatic mutation, are considered critical factors to accurately diagnose cancer. To explore these challenges, we sorted the pure tumor cells from 22 FFPE lung adenocarcinoma tissues via Di-Electro-Phoretic Array (DEPArray) technology, a new cell sorting technology, and analyzed the variants with next-generation sequencing (NGS) for the most accurate analysis. The allele frequencies of the all gene mutations were improved by 1.2 times in cells sorted via DEPArray (tumor suppressor genes, 1.3-10.1 times; oncogenes, 1.3-2.6 times). We identified 16 novel mutations using the sequencing from sorted cells via DEPArray technology, compared to detecting 4 novel mutation by the sequencing from unsorted cells. Using this analysis, we also revealed that five genes (TP53, EGFR, PTEN, RB1, KRAS, and CTNNB1) were somatically mutated in multiple homogeneous lung adenocarcinomas. Together, we sorted pure tumor cells from 22 FFPE lung adenocarcinomas by DEPArray technology and identified 16 novel somatic mutations. We also established the precise genomic landscape for more accurate diagnosis in 22 lung adenocarcinomas with mutations detected in pure tumor cells. The results obtained in this study could offer new avenues for the treatment and the diagnosis of squamous cell lung cancers.

KEYWORDS:

Heterogeneity of FFPE; Next-generation sequencing; Novel mutation; Pure cell sorting

PMID:
29525983
PMCID:
PMC6060994
DOI:
10.1007/s13353-018-0439-4
[Indexed for MEDLINE]
Free PMC Article

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