Important Role of Deduplication Method in Next Generation Sequencing Data Analysis of Non-small Cell Lung Cancer
Objective To investigate the important role of deduplication method in next generation sequencing(NGS) data analysis by comparing the difference of indicators obtained from deduplication and duplication methods. Methods Tumor samples of a cohort of 58 NSCLC patients were collected. A panel of 286 ge...
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doaj-49361499b6cf4bc187ab908db5073ffe2020-11-25T02:18:26ZzhoMagazine House of Cancer Research on Prevention and TreatmentZhongliu Fangzhi Yanjiu1000-85781000-85782018-01-014511410.3971/j.issn.1000-8578.2018.17.09548578.2018.17.0954Important Role of Deduplication Method in Next Generation Sequencing Data Analysis of Non-small Cell Lung CancerCHEN Yu0ZHANG Xuchao1GUO Weibang2YAN Wenqing3XIE Zhi4LYU Zhiyi5LU Danxia6HUANG Ying7Guangdong Lung Cancer Institute, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, ChinaGuangdong Lung Cancer Institute, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, ChinaGuangdong Lung Cancer Institute, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, ChinaGuangdong Lung Cancer Institute, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, ChinaGuangdong Lung Cancer Institute, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, ChinaGuangdong Lung Cancer Institute, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, ChinaGuangdong Lung Cancer Institute, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, ChinaGuangdong Lung Cancer Institute, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, ChinaObjective To investigate the important role of deduplication method in next generation sequencing(NGS) data analysis by comparing the difference of indicators obtained from deduplication and duplication methods. Methods Tumor samples of a cohort of 58 NSCLC patients were collected. A panel of 286 genes was tested by NGS. The NGS data were analyzed by de-duplication method and common duplication method, respectively. Indicators of "Mapped Reads, On Target, Mean Depth and Uniformity" were compared. Results The differences of Mapped Reads, On Target, Mean Depth and Uniformity were statistically significant between two methods, respectively(P < 0.001). Mapped Reads and On Target and Mean Depth analyzed by de-duplication method were found significantly different between plasma sample and other three types of samples, ie., formalin fixed and paraffin embedded(FFPE) sample and puncture biopsy and surgical tissue sample; while Uniformity was generated without significant difference between the four types of samples. The results by duplication analysis were opposite. Conclusion Deduplication step plays an important role in NGS data analysis, which could improve the Uniformity and reflect the real DNA template amount and allele frequency of genomic alterations. Deduplication result is helpful for clinical decision.http://html.rhhz.net/ZLFZYJ/html/8578.2018.17.0954.htmnext generation sequencing(ngs)data analysisde-duplicationlung cancer |
collection |
DOAJ |
language |
zho |
format |
Article |
sources |
DOAJ |
author |
CHEN Yu ZHANG Xuchao GUO Weibang YAN Wenqing XIE Zhi LYU Zhiyi LU Danxia HUANG Ying |
spellingShingle |
CHEN Yu ZHANG Xuchao GUO Weibang YAN Wenqing XIE Zhi LYU Zhiyi LU Danxia HUANG Ying Important Role of Deduplication Method in Next Generation Sequencing Data Analysis of Non-small Cell Lung Cancer Zhongliu Fangzhi Yanjiu next generation sequencing(ngs) data analysis de-duplication lung cancer |
author_facet |
CHEN Yu ZHANG Xuchao GUO Weibang YAN Wenqing XIE Zhi LYU Zhiyi LU Danxia HUANG Ying |
author_sort |
CHEN Yu |
title |
Important Role of Deduplication Method in Next Generation Sequencing Data Analysis of Non-small Cell Lung Cancer |
title_short |
Important Role of Deduplication Method in Next Generation Sequencing Data Analysis of Non-small Cell Lung Cancer |
title_full |
Important Role of Deduplication Method in Next Generation Sequencing Data Analysis of Non-small Cell Lung Cancer |
title_fullStr |
Important Role of Deduplication Method in Next Generation Sequencing Data Analysis of Non-small Cell Lung Cancer |
title_full_unstemmed |
Important Role of Deduplication Method in Next Generation Sequencing Data Analysis of Non-small Cell Lung Cancer |
title_sort |
important role of deduplication method in next generation sequencing data analysis of non-small cell lung cancer |
publisher |
Magazine House of Cancer Research on Prevention and Treatment |
series |
Zhongliu Fangzhi Yanjiu |
issn |
1000-8578 1000-8578 |
publishDate |
2018-01-01 |
description |
Objective To investigate the important role of deduplication method in next generation sequencing(NGS) data analysis by comparing the difference of indicators obtained from deduplication and duplication methods. Methods Tumor samples of a cohort of 58 NSCLC patients were collected. A panel of 286 genes was tested by NGS. The NGS data were analyzed by de-duplication method and common duplication method, respectively. Indicators of "Mapped Reads, On Target, Mean Depth and Uniformity" were compared. Results The differences of Mapped Reads, On Target, Mean Depth and Uniformity were statistically significant between two methods, respectively(P < 0.001). Mapped Reads and On Target and Mean Depth analyzed by de-duplication method were found significantly different between plasma sample and other three types of samples, ie., formalin fixed and paraffin embedded(FFPE) sample and puncture biopsy and surgical tissue sample; while Uniformity was generated without significant difference between the four types of samples. The results by duplication analysis were opposite. Conclusion Deduplication step plays an important role in NGS data analysis, which could improve the Uniformity and reflect the real DNA template amount and allele frequency of genomic alterations. Deduplication result is helpful for clinical decision. |
topic |
next generation sequencing(ngs) data analysis de-duplication lung cancer |
url |
http://html.rhhz.net/ZLFZYJ/html/8578.2018.17.0954.htm |
work_keys_str_mv |
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1724882195582025728 |