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Ultra Deep Amplicon Sequencing

Ultra Deep Sequencing of Amplicons

Profit from our expertise for amplicon sequencing.

Amplicon sequencing refers to ultra deep sequencing of PCR products for analysing genetic variations.

Sequencing of amplicons using the Illumina technology comes with shorter reads but much higher outputs compared to Roche sequencing. A single run on the MiSeq provides 20-30 fold the amount of reads of a full Roche 454 plate and therefore offers a much higher depth of analysis.

On the other hand the Illumina technology makes greater demands on the primer design than the Roche 454 technology does. As a consequence, Eurofins developed a proprietary primer design that offers several advantages compared to published designs:

  • Flexible design suitable for different sample numbers
  • Higher data outputs due to less “spiking in” of control DNA
  • Higher read qualities
  • Shorter primers that reduce the overall project costs

We offer you our amplicon service on the MiSeq with different service lines, ranging from a full service package starting with DNA extraction to sequencing of ready-to-seq amplicon pools.

NEW: 16S Microbiome profiling from only 6 samples.

Are you interested in an individual quote or need more information? We would be happy to consult you about the most convenient strategy for your specific aimsmplicon project. Just contact us!

Selected publications about ultra deep amplicon sequencing


Amplicon analysis (MiSeq): Lange, A., Schilling E., Strittmatter A. et al., AmpliconDuo: A split-sample filtering protocol for high-throughput amplicon sequencing of microbial communities. PLOS One 10(11)

Amplicon analysis (MiSeq): Köberl, M. et al., Agroforestry leads to shifts within the gammaproteobacterial microbiome of banana plants cultivated in Central America. Frontiers in microbiology 6

Amplicon analysis: Tambadou, F. et al., Characterization of the colistin (polymyxin E1 and E2) biosynthetic gene cluster. Archives of Microbiology



Amplicon analysis: Schiml, S. et al., The CRISPR/Cas system can be used as nuclease for in planta gene targeting and as paired nickases for directed mutagenesis in Arabidopsis resulting in heritable progeny. Plant J. 80 (6)

Amplicon analysis: Zozomová-Lihová, J. et al., When fathers are instant losers: homogenization of rDNA loci in recently formed Cardamine schulzii trigenomic allopolyploid. New Phytologist

Amplicon analysis: Schmidt, R. et al., Effects of bacterial inoculants on the indigenous microbiome and secondary metabolites of chamomile plants. Frontiers in microbiology 5

Fish-Project: Roche 454 & MiSeq: Haase et al. Species identification by DNA sequencing (Application of Next Generation Sequencing on Food and Feed Analysis). eFOOD-Lab International (2)

Amplicon analysis: Chaillou et al. Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage. The ISME Journal

Amplicon analysis: Holler et al. Metagenomic analysis of the stool microbiome in patients receiving allogeneic SCT: Loss of diversity is associated with use of systemic antibiotics and more pronounced in gastrointestinal GvHD. BBMT 01.030

Amplicon analysis: Wunderlin et al. Endospore-enriched sequencing approach reveals unprecedented diversity of Firmicutes in sediments. Environ. Microbio. Reports

Amplicon analysis: Fauser et al. Both CRISPR/Cas-based nucleases and nickases can be used efficiently for genome engineering in Arabidopsis thaliana. The Plant Journal, 79 (2)

Amplicon analysis: Gomathi et al. Screening of Indigenous Oxalate Degrading Lactic Acid Bacteria from Human Faeces and South Indian Fermented Foods: Assessment of Probiotic Potential. The Scientific World Journal, 648059

Amplicon analysis: Sugiyama et al. Changes in the Bacterial Community of Soybean Rhizospheres during Growth in the Field. PLOS One 9(6)



Amplicon analysis: Wunderlin et al. Stage 0 sporulation gene A as a molecular marker to study diversity of endospore-forming Firmicutes. environmental microbiology reports 10.1111

Amplicon analysis: Sauvain et al. Bacterial communities in trace metal contaminated lake sediments are dominated by endospore-forming bacteria. Aquat Sci, 10.1007

Amplicon analysis: Bueche et al. Quantification of Endospore-Forming Firmingcutes by Quantitative PCR with the Functional Gene spo0A. Appl. Environ.Microbiol. 79(17)

Amplicon analysis: Sedlácek et al. Enterococcus ureilyticus sp. nov and Enterococcus rotai sp. nov., two urease-producing enterococci from the environment. IJSEM 63(Pt 2)

Amplicon analysis: Heinrichs et al. Analysis of Black Fungal Biofilms Occurring at Domestic Water Taps (I): Compositional Analysis Using Tag-Encoded FLX Amplicon Pyrosequencing. Mycopathologia 1-11



Amplicon analysis: Matyasek R et al. Next generation sequencing analysis reveals a relationship between rDNA unit diversity and locus number in Nicotiana diploids. BMC Genomics 13:722

Amplicon analysis: Jacoby et al. Interindividual variability and co-regulation of DNA methylation differ among blood cell populations. Epigenetics 7:12

Amplicon analysis: Håkansson Å et al. Blueberry Husks and Probiotics Attenuate Colorectal Inflammation and Oncogenesis, and Liver Injuries in Rats Exposed to Cycling DSS-Treatment. PLoS ONE 7(3)



Amplicon analysis: Medinger, R., Ottenwälder, B. et al. Diversity in a hidden world: potential and limitation of next generation sequencing for surveys of molecular diversity of Eukaryotic microorganisms. Molecular Ecology, 19 Suppl. 1: 32-40

Amplicon analysis: Nolte, V., Ottenwälder, B. et al. Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity. Molecular Ecology; 19(14):2908-2915

Bold = Eurofins employee