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Advantages of Single-Stranded DNA Over Double-Stranded DNA Library Preparation for Capturing Cell-Free Tumor DNA in Plasma

  • Jing ZhuEmail author
  • Jinyong Huang
  • Peng Zhang
  • Qianxia Li
  • Manish Kohli
  • Chiang-Ching Huang
  • Liang WangEmail author
Short Communication

Abstract

Background

Single-stranded DNA (ssDNA) libraries have been shown to enrich shorter and more degraded DNA fragments than double-stranded DNA (dsDNA) libraries.

Objective

In this study, we evaluated whether ssDNA libraries captured more circulating tumor DNA (ctDNA) in plasma cell-free DNA (cfDNA).

Methods

We prepared dsDNA, ssDNA and pure-ssDNA (capture the preexisting ssDNA) libraries using ten plasma cfDNA samples. After low-pass whole genome sequencing, we calculated a duplicate rate to estimate library complexity and compared the library insert sizes between the different library methods. Finally, we estimated the ctDNA content and plasma genomic abnormality (PGA) score, an indicator of ctDNA burden.

Results

27 libraries were prepared and sequenced from the ten cfDNA samples. The duplicate rate in the ssDNA and pure-ssDNA libraries was significantly lower than in the dsDNA libraries (p < 0.001 and p < 0.01, respectively). ctDNA content and PGA scores were consistently higher in the ssDNA and pure-ssDNA libraries than in the matched dsDNA libraries (p < 0.005). The higher ctDNA content in ssDNA libraries was associated with smaller library insert size.

Conclusions

ssDNA libraries preserve more diversity and capture more ctDNA than dsDNA libraries. The ssDNA library method is preferred when performing genomic analysis of ctDNA.

Notes

Acknowledgments

The authors thank Molecular Pathology Core in Medical College of Wisconsin for timely sequencing service. We acknowledge the scholarship from the China Scholarship Council (CSC) (201508230031 to JZ).

Compliance with Ethical Standards

Funding

This research was supported by the National Institute of Health (R01CA212097) to LW; the University Nursing Program for Young Scholars with Creative Talents in Heilongjiang Province (UNPYSCT-2017056), Natural Science Foundation of Heilongjiang Province (YQ2019H002) and the Fund Program of Heilongjiang Province for Selected Returned Overseas Professionals to JZ.

Conflict of Interest

JZ, JH, PZ, QL, MK, CH and LW have no conflicts of interest.

Supplementary material

40291_2019_429_MOESM1_ESM.tif (4 mb)
Supplementary Figure S1 Correlation between insert size difference and ctDNA burden difference. For ssDNA and their matched dsDNA libraries, a positive correlation (r = 0.673, p = 0.017) was found between insert size difference and ctDNA burden difference
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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Laboratory of Medical GeneticsHarbin Medical University, and The Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Chinese Ministry of EducationHarbinChina
  2. 2.Department of Pathology and MCW Cancer CenterMedical College of WisconsinMilwaukeeUSA
  3. 3.Department of Genitourinary OncologyH. Lee Moffitt Cancer Center and Research InstituteTampaUSA
  4. 4.Joseph J. Zilber School of Public HealthUniversity of WisconsinMilwaukeeUSA
  5. 5.Department of Tumor BiologyH. Lee Moffitt Cancer Center and Research InstituteTampaUSA

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