Sequencing & Genomics

Every cell in the human body contains that person’s entire genomic information encoded in the DNA. This also applies to tumor cells, in which external influences can drive the occurrence of small or large variations in the genome. Identifying these unique changes in each patient may help determine the underlying cause of disease and support the development of personalized therapies.

TRON operates a suite of the latest Next Generation Sequencing (NGS) technologies that enable high throughput DNA- and RNA-sequencing. Our sequencing capabilities include exome sequencing, RNA-Seq, whole genome sequencing, miRNA-Seq, targeted resequencing and T-cell receptor sequencing.

Our scientists have developed specifically adapted sample preparation protocols (e.g. formalin-fixed and paraffin-embedded tissue samples) for sequencing on our Illumina platforms (NovaSeq6000, HiSeq2500, MiSeq) and Oxford Nanopore Technologies (MinIon).

In addition to traditional bulk sequencing approaches, we have adapted the technologies to high throughput single-cell sequencing with the 10x Genomics® Chromium™ system. Single-cell sequencing has the advantage of detecting heterogeneity among individual cells, revealing complex and rare cell populations and can provide a better understanding of the disease state at the cellular level.

All methods are established as standard operating procedures (SOPs) as a component of our internal quality management system.

 

Tools & Platforms

  • Illumina NovaSeq6000

    ©Illumina

  • Illumina MiSeq

    ©Illumina

  • Illumina HiSeq2500

    ©Illumina

  • Oxford Nanopore MinION

    ©Oxford Nanopore

  • 10x Genomics® Chromium™ Controller

    ©10x Genomics

Key publications

  • Sethi R, Becker J, de Graaf J, Löwer M, Suchan M, Sahin U, Weber D. (2020) Integrative analysis of structural variations using short-reads and linked-reads yields highly specific and sensitive predictionsPLoS. Comput. Biol. 16(11):e100839.  DOI; PMID
  • Sahin U, Derhovanessian E, Miller M, Kloke BP, Simon P, Löwer M, Bukur V, Tadmor AD, Luxemburger U, Schrörs B, Omokoko T, Vormehr M, Albrecht C, Paruzynski A, Kuhn AN, Buck J, Heesch S, Schreeb KH, Müller F, Ortseifer I, Vogler I, Godehardt E, Attig S, Rae R, Breitkreuz A, Tolliver C, Suchan M, Martic G, Hohberger A, Sorn P, Diekmann J, Ciesla J, Waksmann O, Kemmer-Brück A, Witt M, Zillgen M, Rothermel A, Kasemann B, Langer D, Bolte S, Diken M, Kreiter S, Nemecek R, Gebhardt C, Grabbe S, Höller C, Utikal J, Huber C, Loquai C, Türeci Ö. (2017) Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer. Nature. 547(7662):222-226. DOI; PUBMED
  • Castle JC, Loewer M, Boegel S, Graaf J de, Bender C, Tadmor AD, Boisguerin V, Bukur T, Sorn P, Paret C, Diken M, Kreiter S, Türeci Ö, Sahin U. (2014) Immunomic, genomic and transcriptomic characterization of CT26 colorectal carcinoma. BMC Genomics. 15:190.  DOI; PUBMED
  • Boegel S, Löwer M, Schäfer M, Bukur T, Graaf J de, Boisguérin V, Türeci O, Diken M, Castle JC, Sahin U. (2012) HLA typing from RNA-Seq sequence reads. Genome Medicine. 4:102. DOI; PUBMED
  • Castle JC, Kreiter S, Diekmann J, Löwer M, van de Roemer, Niels, Graaf J de, Selmi A, Diken M, Boegel S, Paret C, Koslowski M, Kuhn AN, Britten CM, Huber C, Türeci O, Sahin U. (2012) Exploiting the mutanome for tumor vaccination. Cancer Research. 72:1081-1091. DOI; PUBMED

More Technologies and Platforms