[DEBUG-WINDOW 처리영역 보기]
즐겨찾기  |  뉴스레터  |  오늘의 정보  |  e브릭몰e브릭몰 회원가입   로그인
BRIC홈 한국을 빛내는 사람들
랩박스 - Neuroscience
스폰서배너광고 안내  배너1 배너2 배너3 배너4
전체보기 한빛사논문 상위피인용논문 인터뷰 그이후 한빛사통계
신영기
신영기 (Young Kee Shin) 저자 이메일 보기
서울대학교
 
조회 889  인쇄하기 주소복사 트위터 공유 페이스북 공유 
Comparison of Accuracy of Whole-Exome Sequencing with Formalin-Fixed Paraffin-Embedded and Fresh Frozen Tissue Samples

Ensel Oh1,2,3, Yoon-La Choi1,2,4,5, Mi Jeong Kwon6,7, Ryong Nam Kim3, Yu Jin Kim1,2, Ji-Young Song1,2, Kyung Soo Jung1,5, Young Kee Shin3*

1 Laboratory of Cancer Genomics and Molecular Pathology, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea, 2 Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, Korea, 3 Department of Pharmacy, College of Pharmacy, Seoul National University, Seoul, Korea, 4 Department of Pathology, Samsung Medical Center, Sungkyunkwan University College of Medicine, Seoul, Korea, 5 Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University School of Medicine, Seoul, Korea, 6 College of Pharmacy, Kyungpook National University, Daegu, Korea, 7 Research Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, Daegu, Korea

Abstract
Formalin fixing with paraffin embedding (FFPE) has been a standard sample preparation method for decades, and archival FFPE samples are still very useful resources. Nonetheless, the use of FFPE samples in cancer genome analysis using next-generation sequencing, which is a powerful technique for the identification of genomic alterations at the nucleotide level, has been challenging due to poor DNA quality and artificial sequence alterations. In this study, we performed whole-exome sequencing of matched frozen samples and FFPE samples of tissues from 4 cancer patients and compared the next-generation sequencing data obtained from these samples. The major differences between data obtained from the 2 types of sample were the shorter insert size and artificial base alterations in the FFPE samples. A high proportion of short inserts in the FFPE samples resulted in overlapping paired reads, which could lead to overestimation of certain variants; >20% of the inserts in the FFPE samples were double sequenced. A large number of soft clipped reads was found in the sequencing data of the FFPE samples, and about 30% of total bases were soft clipped. The artificial base alterations, C>T and G>A, were observed in FFPE samples only, and the alteration rate ranged from 200 to 1,200 per 1M bases when sequencing errors were removed. Although high-confidence mutation calls in the FFPE samples were compatible to that in the frozen samples, caution should be exercised in terms of the artifacts, especially for low-confidence calls. Despite the clearly observed artifacts, archival FFPE samples can be a good resource for discovery or validation of biomarkers in cancer research based on whole-exome sequencing.

논문정보 F1000선정
- 형식: Research article
- 게재일: 2015년 12월 (BRIC 등록일 2017-01-31)
- 연구진: 국내연구진태극기
- 분야: Pharmacology, Bioinformatics
- 추천: Faculty of 1000 Biology
- 추천사유: F1000Prime Recommendations, Dissents and Comments for [Oh E et al., PLoS ONE 2015, 10(12):e0144162]. In F1000Prime, 31 Jan 2017; F1000Prime.com/725996494
m6A 변형에 의해 유도되는 RNA의 내부적 붕괴[Mol. Cell]
박옥현
발표: 박옥현 (고려대학교)
일자: 2019년 6월 21일 (금) 오후 02시 (한국시간)
언어: 한국어
참석자 접수신청하기
CRISPR-BetaBinomial(CB2) 기법을 이용한 CRISPR pooled screen data 분석[Genome Res.]
정현환
발표: 정현환 (Baylor College of Medicine, Texas C...)
일자: 2019년 6월 26일 (수) 오전 10시 (한국시간)
언어:
참석자 접수신청하기

  댓글 0
등록
 
동일바이오테크
관련링크
신영기 님 전체논문보기 >
관련인물
오은설 ((주)엔젠바이오)
최윤라 (성균관대학교 삼성융합의과...)
관련분야 논문보기
Pharmacology

Bioinformatics

외부링크
Google (by Young Kee Shin)
Pubmed (by Young Kee Shin)
프리미엄 Bio일정 Bio일정 프리미엄 안내
[BRIC Webinar]초짜 대학원생을 위한 연구방법론-배현진 (울산대학교 의과대학)
생물정보 빅데이터 분석 UCC 공모전
생물정보 빅데이터 분석 UCC 공모전
날짜: 2019.08.22
주관: K-Genome 유전체빅데..
[BRIC Webinar]CRISPR-BetaBinomial(CB2) 기법을 이용한 CRISPR pooled screen data 분석-정현환 (Baylor College of Medicine, Texas Children’s Hospital)
대구경북과학기술원(DGIST) 뇌·인지과학전공 3-DAY INTENSE BRAIN BOOTCAMP
대구경북과학기술원(DGIST) 뇌·인지과학전공 3-DAY INTENSE BRAIN BOOTCAMP
사전접수: ~2019.06.30
날짜: 2019.07.10~12
장소: 대구경북과학기술원 (DGIST) 뇌·인지과학전공
[BRIC Webinar]m6A변형에 의해 유도되는 RNA의 내부적 붕괴-박옥현(고려대학교)
[대졸 미취업자]바이오QC 실무과정 7기 모집
[대졸 미취업자]바이오QC 실무과정 7기 모집
날짜: 2019.09.02~06.12
장소: 성남시 분당구 황새울로 329번길 5
위로가기
한빛사 홈  |  한빛사FAQ  |  한빛사 문의 및 제안
 |  BRIC소개  |  이용안내  |  이용약관  |  개인정보처리방침  |  이메일무단수집거부
Copyright © BRIC. All rights reserved.  |  문의 member@ibric.org
트위터 트위터    페이스북 페이스북   유튜브 유튜브    RSS서비스 RSS
에펜도르프코리아