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Biases in the SMART-DNA library preparation method associated with genomic poly dA/dT sequences
Oriya Vardi1, Inbal Shamir1, Elisheva Javasky1
1Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Hadassah Medical School, Jerusalem, Israel.
Plos One
|February 25, 2017
Summary
The SMART library preparation method for next-generation sequencing (NGS) introduces a bias toward poly dA/dT genomic regions. This bias affects both single-end and paired-end sequencing data, impacting reliability.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Next-generation sequencing (NGS) library preparation requires minimizing biases for reliable data.
- The SMART (switching mechanism at the 5' end of the RNA transcript) method offers ligation-free library preparation.
- Systematic analysis of biases introduced by SMART methodology has been lacking.
Purpose of the Study:
- To systematically analyze biases introduced by the SMART library preparation method.
- To investigate the genomic distribution of sequenced reads prepared using SMART methodology.
Main Methods:
- Analysis of genomic distribution of sequenced reads from DNA libraries prepared with SMART methodology.
- Comparison with conventional ligation-based library preparation methods.
Main Results:
- SMART library preparation exhibits a strong bias toward long (≥12bp) poly dA/dT containing genomic loci.
- This bias is specific to SMART-based methods and not observed in ligation-based methods.
- The bias affects both single-end and paired-end sequencing data.
Conclusions:
- SMART-based DNA library preparation introduces a significant bias towards poly dA/dT tracts.
- This bias must be considered when utilizing SMART technology for library preparation to ensure data accuracy.
