Christian-Albrechts-Universitaet zu Kiel (The Institute of Clinical Molecular Biology)

Short Name: CAU

Country: DE

Website: www.uni-kiel.de

Organization description:

The Institute of Clinical Molecular Biology (IKMB) is an institute of the Christian-Albrechts- University Kiel (CAU) and closely linked to the University Clinic of Schleswig-Holstein (UKSH), which drives interdisciplinary studies on innovative diagnostic and therapeutic principles with clinicians. Therefore, empowering physicians to direct therapies is a key commitment of the Institute. Research in biomedicine should enable new perspectives on disease processes and measurable advances for patients. Translation of the knowledge on genetic causations and markers to clinical decision-making algorithms is at the starting point for clinical use.

The institute employs scientists from different disciplines. An excellent infrastructure has been developed that allows them to choose their tools from a broad range of established cutting-edge technologies. Focusing on inflammatory diseases our approaches range from large-scale genome- wide association studies and whole genome sequencing to mechanistic studies and in vivo models.

The IKMB is the coordinating institute for several larger German projects: BMBF Systems Medicine application sysINFLAME (e:Med program, DFG Excellence Cluster Inflammation at Interfaces, DFG PhD Research Training Group “Genes, Environment and Inflammation”. The IKMB operates the Centre for Molecular Life Sciences at the CAU that hosts one of Germany’s largest academic sequencing (Sanger and NGS) and genotyping platforms. The associated Biobank PopGen covers the Northern part of Germany and is responsible for 20,000 individuals of the German National cohort.

The University Clinic of Schleswig-Holstein (UKSH) operates the second largest German university hospital center, including a comprehensive cancer center consisting of cancer centers that are accredited by OnkoZert. Next-Generation Sequencing based pre-clinical studies have been ongoing for many years between IKMB and most of the UKSH cancer centers. Routine diagnostic next- generation sequencing based testing for breast cancer and ovarian cancer is ongoing since 2016.

Expertise:

For the past 10 years, the IKMB has been involved in Next-Generation Sequencing (NGS) and the application and development of bioinformatic methods in various fields of human medical research, both in the field of inflammatory diseases and in immunology, microbial research (skin, oral cavity, stool) and cancer research. In cancer research, following GWAS studies on leukaemia risk genes, we also conducted the first large multi-omics study on the analysis of somatic changes in acute lymphoblastic leukaemia (Fischer, Forster et al 2016; Forster et al 2015; Kachroo et al 2017) and

subsequently conducted somatic multi-omics studies on gynecological (Meißner et al 2017) and other types of cancer (ongoing projects with the Women’s Hospital, the Central Laboratory, the Surgery and the Skin Clinic in Kiel). Since 2016 we are sequencing cell-free DNA (cfDNA) from blood plasma and urine of cancer patients using NGS (Streleckiene et al 2018).

The IKMB led work packages in the EU FP7 projects READNA and ESGI as well as in German clinical research projects. The IKMB leads the EU-H2020 project SYSCID (systems medicine) and several German research projects. Since 2016 we have been working together with the Avera Cancer Institute (USA) and in 2018 we joined the Nordic Alliance for Sequencing and Precision Medicine.

Since 2016, the IKMB has been operating NGS routine diagnostics for family members of the hereditary breast and ovarian cancer syndrom. Other cancer types will follow. In summer 2019, the IKMB will introduce NGS diagnostics for cardiomyopathy, pulmonary hypertension and immunodeficiencies at the University Hospital. The IKMB also operates Sanger- and TaqMan-based routine diagnostics for the University Hospital. All diagnostics are accredited based on the DIN EU ISO 15189 norm by the German National Accreditation Agency (DAkkS).

Non-routine FFPE-tissue sequencing with a large number of different NGS kits is also well established, and is performed on individual request for special patient cases.

 

Facilities:

The IKMB operates Germany’s largest high-throughput university platform for genotyping and sequencing, one of Germany’s four central competence centers for high-throughput sequencing: the Comprehensive Center for Genome Analysis (CCGA). This platform is based on a high-throughput pre-PCR platform with automated sample storage (Liconic). The sample warehouse has a capacity of 1 million samples at -80°C and 1 million samples at -20°C. All laboratory processes are controlled by a local laboratory information management system (LIMS). Where appropriate, standardized workflows (SOPs) and automated workflows (e.g. using Tecan, Hamilton and Perkin-Elmer pipetting robots) have been developed.

The IKMB genotyping and sequencing platform includes TaqMan, Illumina iScan, Agena MassARRAY, Sanger (4 ABI 3730XL) and Illumina-NGS (two NovaSeq, one each of HiSeq 2500, 3000, 4000, NextSeq 500 and two MiSeqs) as well as one PacBio (Sequel) and one 10X genomics device. An Affymetrix platform is available for expression typing. For single-cell sequencing a microfluidics library preparation instrument has been developed in-house. Approximately 46000 samples are processed on the capillary Sanger sequencers per year, and in the first 10 months of 2017 approximately 15900 samples were processed on the NGS platforms. These machines are used for research and for DAkkS accredited clinical diagnostics. The operation of the DNA/biobanking, genotyping, Sanger-sequencing and next-generation sequencing labs is certified according to DIN EU ISO 15189.

To cope with the vast increase in data production and subsequent data processing, large investments were made into the IT infrastructure. For data analysis, the IKMB has highly redundant, scalable EMC Isilon storage servers, a total of 2.9 petabytes of hard disk storage capacity, a classic Linux cluster which comprises over a thousand cores and a scalable local high-performance computer cloud (OpenStack) at its disposal. For data archiving, the IKMB has invested in high-performance tape systems administered by the computer center of Kiel University. A field programmable gate array (FPGA) supercomputer is integrated into the linux cluster, to enable e.g. sensitive virus detection (Vy-PER). A hybrid FPGA-and-GPU supercomputer was designed and built in-house for virus detection and genome wide association testing.

Other European projects:

• ESGI (European Sequencing and Genotyping Infrastructure; 262055), 2011-2015
• SYSCID (A systems medicine approach to chronic inflammatory disease; 733100) 2017-2021
• EASI-Genomics (European Advanced infraStructure for Innovative Genomics; 824110), 2019- 2023

Role in the project:

IKMB will be involved in WP2, WP3, WP4, WP5 and WP7 Pharmacogenomics and e-reporting

 

Key personnel:

Prof. Dr. Andre Franke

Prof. Dr. Andre Franke (male), director of the IKMB since 2011, Group leader Genetics and Bioinformatics, over 13 years of experience in research and genomics. Author of more than 412 publications with a cumulative impact factor >4647. H-Index = 84 (Scopus). Headed work packages in the EU-funded FP7 project READNA and ESGI. Heads DFG-funded doctoral training program DFG Research Training Group (ID: GRK1743/2) “Genes, Environment and Inflammation” (2017- 2021, € 3,172,000)

Dipl.-Ing. Michael Forster

Dipl.-Ing. Michael Forster (male), group leader Oncology, 9 years of experience in NGS research, translation into clinic, accreditation. Research includes clinical bioinformatics and “difficult” nucleic acids from FFPE tissue and liquid biopsies. Participated in the EU-funded FP7 projects READNA, ESGI, and ongoing H2020 project EASI-Genomics, and coordinated the EU-funded FP5 High-Level Scientific Conference ECITTT (HPCF-CT-2000- 00118).

 

Dr. Britt-Sabina Petersen

Dr. Britt-Sabina Petersen (female), head of Sanger sequencing, 9 years of experience in NGS research, clinical translation and bioinformatics. Research focus: clinical exome sequencing for diagnostic purposes.

 

Dr. Sandra May

Dr. Sandra May (female), head of the clinical diagnostics accredited high-throughput DNA platform and IKMB biobank, key Person at intersection to clinics (sample entry), 10 years of experience with Sanger sequencing, cfDNA and ELSI.

 

Prof. Dr. Norbert Arnold

Prof. Dr. Norbert Arnold (male), head of oncological testing, spokesperson for the Center Kiel in the German Consortium for Hereditary Breast-/Ovarian Cancer, heading research laboratory in the woman’s hospital, expert auditor for genetic testing for the German National Accreditation Agency (DAkkS), over 20 years of experience in translational research of gynecological malignancies esp. performing genetic screening of family members with Hereditary Breast-/Ovarian Cancer.

 

Main publications and patents:

Publications:

Genomics and drug profiling of fatal TCF3-HLF-positive acute lymphoblastic leukemia identifies recurrent mutation patterns and therapeutic options. Fischer U, Forster M*, Rinaldi A, Risch T, Sungalee S, Warnatz HJ, Bornhauser B, Gombert M, Kratsch C, Stütz AM, Sultan M, Tchinda J,

Worth CL, Amstislavskiy V, Badarinarayan N, Baruchel A, Bartram T, Basso G, Canpolat C, Cario G, Cavé H, Dakaj D, Delorenzi M, Dobay MP, Eckert C, Ellinghaus E, Eugster S, Frismantas V, Ginzel S, Haas OA, Heidenreich O, Hemmrich-Stanisak G, Hezaveh K, Höll JI, Hornhardt S, Husemann P, Kachroo P, Kratz CP, Kronnie GT, Marovca B, Niggli F, McHardy AC, Moorman AV, Panzer-Grümayer R, Petersen B-S, Raeder B, Ralser M, Rosenstiel P, Schäfer D, Schrappe M, Schreiber S, Schütte M, Stade B, Thiele R, Weid Nv, Vora A, Zaliova M, Zhang L, Zichner T, Zimmermann M, Lehrach H, Borkhardt A, Bourquin JP, Franke A*, Korbel JO, Stanulla M, Yaspo ML. Nat Genet. 2015 Sep;47(9):1020-9. doi: 10.1038/ng.3362. Epub 2015 Jul 27. PMID: 26214592

 coordination of a national consortium for multi-omics analyses of a rare leukemia subtype

NGS-based methylation profiling differentiates TCF3-HLF and TCF3-PBX1 positive B-cell acute lymphoblastic leukemia. Kachroo P, Szymczak S, Heinsen F-A, Forster F, Bethune J, Hemmrich- Stanisak G, Baker L, Schrappe M, Stanulla M, Franke A. Epigenomics. 2018. doi: 10.2217/epi-2017- 0080. PMID: 29334255. methylation profiling for differentiation of ALL types

IKZF1plus defines a new minimal residual disease-dependent very-poor prognostic profile in pediatric B-cell Precursor Acute Lymphoblastic Leukemia. Stanulla M, Dagdan E, Zaliova M, Möricke A, Palmi C, Cazzaniga G, Eckert C, Te Kronnie G, Bourquin J-P, Bornhauser B, Koehler R, Bartram CR, Ludwig W-D, Bleckmann K, Groeneveld-Krentz S, Schewe D, Junk SV, Hinze L, Klein N, Kratz CP, Biondi A, Borkhardt A, Kulozik A, Muckenthaler MU, Basso G, Valsecchi MG, Izraeli S, Petersen B-S, Franke A, Dörge P, Steinemann D, Haas OA, Panzer-Grümayer R, Cave H, Houlston RS, Cario G, Schrappe M, Zimmermann M. J. Clin. Oncol. 2018. doi: 10.1200/jco.2017.74.3617. PMID: 29498923.

 refinement of the prognostic strength of IKZF1 deletions in ALL patients

Development of a high-resolution NGS-based HLA-typing and analysis pipeline. Wittig M, Anmarkrud JA, Kässens JC, Koch S, Forster M, Ellinghaus E, Hov JR, Sauer S, Schimmler M, Ziemann M, Görg S, Jacob F, Karlsen TH, Franke A. Nucleic Acids Res. 2015 Jun 23;43(11):e70. doi: 10.1093/nar/gkv184. Epub 2015 Mar 9. PMID: 25753671 development of an accurate HLA typing approach including an intuitive analysis software

From next-generation sequencing alignments to accurate comparison and validation of single- nucleotide variants: the pibase software. Forster M, Forster P, Elsharawy A, Hemmrich G, Kreck B, Wittig M, Thomsen I, Stade B, Barann M, Ellinghaus D, Petersen B-S, May S, Melum E, Schilhabel MB, Keller A, Schreiber S, Rosenstiel P, Franke A. Nucleic Acids Res. 2013. doi: 10.1093/nar/gks836. PMID: 22965131 new software for diagnostic analysis of known variants in NGS data

Metastatic triple-negative breast cancer patient with TP53 tumor mutation experienced 11 months progression-free survival on bortezomib monotherapy without adverse events after ending standard treatments with grade 3 adverse events. Meißner T, Mark A, Williams C, Berdel WE, Wiebe S, Kerkhoff A, Wardelmann E, Gaiser T, Müller-Tidow C, Rosenstiel P, Arnold N, Leyland-Jones B,

Franke A, Stanulla M, Forster M. Cold Spring Harb Mol Case Stud. 2017 Jul 5;3(4). pii: a001677. doi: 10.1101/mcs.a001677. PMID: 28679691 NGS-based molecular retrospective case study of cancer patient who received multiple lines of treatment

RNA based individualized drug selection in breast cancer patients without patient-matched normal tissue. Forster M, Mark A, Egberts F, Rosati E, Rodriguez E, Stanulla M, Bauerschlag D, Schem C, Maass N, Amallraja A, Murphy KK, Prouse BR, Sulaiman RA, Young BM, Mathiak M, Hemmrich- Stanisak G, Ellinghaus D, Weidinger S, Rosenstiel P, Arnold N, Leyland-Jones B, Williams CB, Franke A, Meißner T. ONCOTARGET. 2018. doi: 10.18632/oncotarget.25981. PMID: 30190792.

 individualized drug selection in breast cancer patients using RNA

Quantifying cell free DNA in urine: comparison between commercial kits, impact of gender and inter- individual variation. Streleckiene G, Reid HM, Arnold N, Bauerschlag D, Forster M. Biotechniques. 2018 May;64(5):225-230. doi: 10.2144/btn-2018-0003. PMID: 29793362 cell free DNA in blood and urine

High-density mapping of the MHC identifies a shared role for HLA-DRB1*01:03 in inflammatory bowel diseases and heterozygous advantage in ulcerative colitis. Goyette P, Boucher G, Mallon D, Ellinghaus E, Jostins L, Huang H, Ripke S, Gusareva ES, Annese V, Hauser SL, Oksenberg JR, Thomsen I, Leslie S; International Inflammatory Bowel Disease Genetics Consortium; Australia and New Zealand IBDGC; Belgium IBD Genetics Consortium; Italian Group for IBD Genetic Consortium; NIDDK Inflammatory Bowel Disease Genetics Consortium; United Kingdom IBDGC; Wellcome Trust Case Control Consortium; Quebec IBD Genetics Consortium, Daly MJ, Van Steen K, Duerr RH, Barrett JC, McGovern DP, Schumm LP, Traherne JA, Carrington MN, Kosmoliaptsis V, Karlsen TH, Franke A*, Rioux JD. Nat Genet. 2015 Feb;47(2):172-9. doi: 10.1038/ng.3176. Epub 2015 Jan 5. PMID: 25559196 Immunogenetics analysis of the HLA region in inflammatory bowel disease; project co- coordination

Genome-wide association analysis identifies variation in vitamin D receptor and other host factors influencing the gut microbiota. Wang J, Thingholm LB, Skiecevičienė J, Rausch P, Kummen M, Hov JR, Degenhardt F, Heinsen FA, Rühlemann MC, Szymczak S, Holm K, Esko T, Sun J, Pricop- Jeckstadt M, Al-Dury S, Bohov P, Bethune J, Sommer F, Ellinghaus D, Berge RK, Hübenthal M, Koch M, Schwarz K, Rimbach G, Hübbe P, Pan WH, Sheibani-Tezerji R, Häsler R, Rosenstiel P, D’Amato M, Cloppenborg-Schmidt K, Künzel S, Laudes M, Marschall HU, Lieb W, Nöthlings U, Karlsen TH, Baines JF, Franke A. Nat Genet. 2016 Nov;48(11):1396-1406. doi: 10.1038/ng.3695. PMID: 27723756

One of the first genome-wide microbiome QTL analyses that identified several hits including variants at the Vitamin D receptor locus.

Identification of 12 new susceptibility loci for different histotypes of epithelial ovarian cancer.

Phelan CM, Kuchenbaecker KB, Tyrer JP, ….Arnold N et al. Nat Genet. 2017 May;49(5):680-691. doi: 10.1038/ng.3826.

International collaborative GWAS study to decipher new susceptibility regions for ovarian cancer Mutational spectrum in a worldwide study of 29,700 families with BRCA1 or BRCA2 mutations.

Rebbeck TR, Friebel TM, Friedman E, ……Arnold N et al.

Hum Mutat 2018 May; 39(5):593-620. doi:10.1002/humu.23406 PMID: 29446198

International collaborative study to describe mutation type and frequency by geographical region and race/ethnicity

Gene panel testing of 5589 BRCA1/2-negative index patients with breast cancer in a routine diagnostic setting: results of the German Consortium for Hereditary Breast and Ovarian Cancer. Hauke J, Horvath J, Groß E,…..Arnold N et al.

Cancer Med. 2018 Apr;7(4):1349-1358. doi: 10.1002/cam4.1376 PMID:29522266

 National collaborative study to elaborate the frequency of additional breast cancer predisposition genes in hereditary breast and ovarian cancer families in Germany

Prevalence of pathogenic BRCA1/2 germline mutations among 802 women with unilateral triple- negative breast cancer without family cancer history.

Engel C, Rhiem K, Hahnen E,……Arnold N et al.

BMC Cancer. 2018 Mar 7;18(1):265. doi: 10.1186/s12885-018-4029-y PMID 29514593

National collaborative study to elaborate the frequency of the mutation frequency in single unilateral triple-negativ breast cancer cases in Germany. This study lead to the acceptance of diagnostic cost reimbursement by the German health care system for this patients

Prevalence of BRCA1/2 germline mutations in 21 401 families with breast and ovarian cancer.

Kast K, Rhiem K, Wappenschmidt B,……Arnold N et al.

J Med Genet. 2016 Jul;53(7):465-71. doi: 10.1136/jmedgenet-2015-103672 PMID 26928436

National collaborative study to elaborate the BRCA1/2 mutation frequency in hereditary breast and ovarian cancer families in Germany

*shared first/last authors

Awards:

 

Prof. Andre Franke:

2017: Schleswig-Holstein Excellence Chair 2017: Thannhauser Prize (10k EUR)

2012: DCCV Ludwig-Demling Research Prize (25k EUR) 2011: Jannssen Prize Dermatology

2011: W2 Peter Hans-Hofschneider professorship of Foundation of Experimental Biomedicine (Zurich, Switzerland)

2008: Award: Hensel Research Prize for Excellent Research (100k EUR)