Important Role of Deduplication Method in Next Generation Sequencing Data Analysis of Non-small Cell Lung Cancer

CHEN Yu; ZHANG Xuchao; GUO Weibang; YAN Wenqing; XIE Zhi; LYU Zhiyi; LU Danxia; HUANG Ying

doi:10.3971/j.issn.1000-8578.2018.17.0954

Cancer Research on Prevention and Treatment > 2018 > 45(1): 1-4. > DOI: 10.3971/j.issn.1000-8578.2018.17.0954

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[J]. Cancer Research on Prevention and Treatment, 2018, 45(1): 1-4. DOI: 10.3971/j.issn.1000-8578.2018.17.0954

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Important Role of Deduplication Method in Next Generation Sequencing Data Analysis of Non-small Cell Lung Cancer

Guangdong Lung Cancer Institute, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China

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Corresponding author:
ZHANG Xuchao, E-mail:zhxuchao3000@126.com
Received Date: August 06, 2017
Revised Date: November 15, 2017
Available Online: January 12, 2024

Graphical Abstract

Abstract

Abstract

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.
- Next generation sequencing(NGS),
- Data analysis,
- De-duplication,
- Lung cancer

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References

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