Industrial-grade NGS Oligos

High quality oligos optimised for excellent performance in industrial NGS applications

Optimal-synthesis process to minimize the risk of data interpretation errors.

Introduction

Quality requirements for NGS oligonucleotides are necessarily very high, but Index Adapter oligonucleotides stand out in particular, because they must meet the highest quality requirements.

It is essential that they consist of near non-truncated, full-length oligo and contain an absolute minimum of other adaptor primers that will be used in the same sequencing run.

Cross-contamination can cause mis-assignments of sequencing reads to other samples. Consequently, this can lead to data interpretation errors, for example when your experiment includes the identification of rare genomic variants.

Industrial-grade NGS Oligos

To comply with these requirements, Eurofins Genomics has developed a new synthesis process to produce high quality NGS oligos. Benefit from NGS oligos with a market leading cross-contamination rate:

Typical cross-contamination rate of 0.01 - 0.05%
High flexibility with three different minimum yield options: 4 nmol, 10 nmol & 25 nmol
High quality ESI-MS analytics and reporting
Oligos that are used in the Eurofins Genomics NGS service laboratory
Various customization options to comply with your industry requirements

Related Information

Specifications

What you can expect from our industrial-grade NGS Oligos

Typical cross contamination rate of 0.01 - 0.05% determined by our NGS lab (see cross-contamination rate)
Available minimum quantities of 4 nmol, 10 nmol and 25 nmol
DNA sequence length from 15 - 120 bases
Available modifications are PTO bounds, 2’-Desoxyinosine, 2’-Desoxyuridine and 5’-Phosphate
Quality is ensured by OD measurement and ESI-MS (electrospray ionization mass spectrometry)
A quality report, including the ESI-MS spectra, is provided online free of charge
Selectable solvents are bidest water, TE buffer (10 mM Tris, 1 mM EDTA; pH=8) or Low EDTA Puffer (10 mM Tris, 0.1 mM EDTA pH = 8)
Various customization options to comply with your industry requirements are available upon request:
- Custom normalization
- Mixing or pooling
- Verification of cross-contamination rate by NGS
- Production of oligos > 120 bases
- Fast delivery times from 8 working days

For delivery in tubes:

Oligos are supplied in 2ml screw cap tubes either lyophilized or in liquid form at the selected concentration
Oligo tube labels can be defined with personal customer barcodes

For delivery in plates:

Oligos are supplied in the selected 96well plate in liquid form at the defined concentration
A minimum of 12 oligos per 96-well plate is required

Cross-Contamination Rate

The cross-contamination rate of 0.01 – 0.05% was determined by sequencing representative sets of Unique Dual Index (UDI) primer pairs using Illumina instruments at Eurofins Genomics’ European NGS sequencing facility. The rate given represents the typical total percentage of read pairs not matching the expected UDI combinations for a set of 96 UDI primer pairs. The corresponding Application Note shows a cross-contamination rate of 0.0014% for a set of 14 UDI primer pairs.

Please note that the total cross-contamination rate (percentage of incorrectly assigned read pairs) is influenced by the total amount of UDI primer pairs analysed in parallel. The more UDI primers are analysed, the higher the total cross-contamination can get, as more unexpected index combinations can be attributed.

In all cases, the actual cross-contamination of primers would be even lower as stated above. This is because the association of reads with other unexpected UDI primer pairs is a result of primer cross-contamination and index hopping during sequencing. Discriminating between these causes is not possible in this analysis setup.

Please note that Eurofins Genomics does not determine the cross-contamination rate for each individual set of NGS oligonucleotides produced and shipped.

	Total cross-contamination rate per UDI set (% total read pairs not matching the expected UDI combinations	Lowest measured cross-contamination per UDI combination	Reference
Eurofins Genomics NGSgrade Oligos	Typically 0.01 - 0.05%	0.00446%	Set of 96 UDI primer pairs
Eurofins Genomics NGSgrade Oligos	0.0014% (see application note)	0.00045%	Set of 14 UDI primer pairs
Other supplier	0.0208% (see application note)	0.00767%	Set of 14 UDI primer pairs

Purity and Coupling Rate

Product Data

Eurofins Genomics uses a new and proprietary synthesis device to produce high performance NGS grade oligonucleotides. This equipment enables best-in-class coupling efficiencies, resulting in a high percentage of non-truncated, full-length oligonucleotides.

Figure 1. Theoretical purities for NGSgrade 2.0 oligonucleotides. (A) Plot of theoretical purities for different lengths of oligos applying a coupling rate of 99.6%. This average coupling rate was determined based on a large and representative sample of data points. (B) Example IP-RP-HPLC-chromatogram for a UDI adapter primer of 72 nucleotides, recorded at λ = 260 nm. A purity of 74.0% was measured for the target product. Analytical IP-RP UHPLC was performed on a Vanquish Horizon Duo system from ThermoFisher Scientific.