Digital quantification of chemical oligonucleotide synthesis errors

Chemically synthesized oligonucleotides are vital in most nucleic acids-based technologies and several applications are sensitive to oligonucleotide sequence errors. However, it is challenging to identify and quantify the type and amount of errors in chemically synthesized oligonucleotides.We applied SiMSen-Seq, a digital sequencing approach using unique molecular identifiers, to quantify errors in chemically synthesized oligonucleotides from multiple manufacturers with different sequence context, synthesis strategies and purity grades. Our data demonstrate that sequence context, manufacturer, synthesis strategy, purity and batch all contributed to errors in chemically synthesized oligonucleotides and need to be considered when choosing and evaluating oligonucleotides. High-performance oligonucleotides are essential in numerous molecular applications, including clinical diagnostics.