DKMS Life Science Lab - centre of innovations

Founded in 1997, DKMS Life Science Lab in Dresden (Germany) is part of the worldwide DKMS family. The lab is accredited by the EFI (European Federation of Immunogenetics) and the ASHI (American Society for Histocompatibility and Immunogenetics).

DKMS Life Science Lab provides genotyping services, currently focusing on a process called HLA typing. Here DNA extracted from blood or buccal swab (cheek smear) samples is analysed to determine the exact genetic profiles of the human compatibility genes. These profiles are essential for matching potential donors to patients needing stem cell transplantation. Only highly similar compatibility gene variants in both donor and patient can minimise the risk of complications following transplantation.

DKMS Life Science Lab employs the most advanced biotechnological methods to perform high resolution, high capacity HLA typing. In 2013, as the world’s first HLA typing lab, we started using novel sequencing technology, NGS, for HLA typing in a truly high throughput and highly parallelised fashion. Using this process, over 1 million potential stem cell donors are typed each year.

A clinical lab and a clinical search unit accredited by the German National Registry of Blood Stem Cell Donors (ZKRD) are affiliated with DKMS Life Science Lab. The clinical lab performs all patient-associated typings (patient, relatives and confirmatory typing of unrelated donors), while the search unit carries out donor searches for individual patients both among relatives and unrelated potential donors.

We are proud of our highly skilled and motivated employees. Our staff includes internationally recognised specialists in genotyping and related technologies.

To accommodate our growth, we are constantly looking for additional members to complement our team.

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Management team

Dr. Dr. Alexander Schmidt (CEO)

Dr. Dr. Alexander Schmidt

Chief Executive Officer (CEO)
Responsible for general medicine and science.

Dr. Vinzenz Lange (CTO)

Dr. Vinzenz Lange

Chief Technology Officer (CTO)
Responsible for laboratory technology and automation, bioinformatics, genotyping analysis, IT and R&D.

Thomas Schaefer (COO)

Thomas Schaefer

Chief Operating Officer (COO)
Responsible for administration, finances, laboratory management, quality management, customer service and business development.

Department heads

Dr. Monika Fuessel: Head of clinical laboratory and search unit, EFI and ASHI director
Irina Boehme: Head of quality and service, advanced projects
Carmen Schwarzelt: Head of laboratory management
Dr. Gerhard Schoefl: Head of bioinformatics and IT

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Departments

Laboratory management - High throughput lab

Our laboratory management department is the central platform for all incoming samples. It is the starting point for every stage of genotyping. Since 2013, we use Next Generation Sequencing for high throughput sequencing.

This new technique allows us to minimise sequencing costs and achieve a higher sample resolution.

Quality management and quality assurance

Our team of quality management and quality assurance experts with their high professional competence are responsible to ensure our performance. All reagents, equipment and software used at DKMS Life Science Lab are subject to stringent quality controls.

We participate in a number of external proficiency tests to independently confirm the high quality of our typings. The quality team ensures that the lab is performing according to highest quality standards. This is proven via internal audits or by on-the-spot inspection visits from professional associations like ASHI and EFI.

Laboratory technology

Our technology team is responsible for the technical infrastructure of the lab, especially for laboratory and IT equipment. They work on the technical implementation of new workflows, monitor the laboratory processes and initiate optimisation if troubleshooting is required.

In addition the department team also implements new procedures and methods into our lab processes. The aim is to ensure effective interaction between employees, equipment and IT to optimise results, minimise processing efforts and cut costs.

New methods have to be adapted to the needs of our laboratory, especially to achieve high throughput typing in short timeframes.

Research and development

Our laboratory generates DNA sequences using up-to-date methods and instruments. Our R&D staff develops new methods and processes to improve the efficiency and quality of standard methods.

The R&D department's main tasks are technology scouting, development and testing of new assays and development of inhouse reagents. They also conduct scientific projects and publish the findings in professional journals.

Genotyping analysis

Our team of highly trained analysts evaluates the DNA sequence data of tissue typing results, calculated by our inhouse analysis software. The analysis unit assures correct typing results by checking the gene sequences for accuracy and reliability. Our analysts also monitor the level of resolution and turnaround time of samples.

Our analysis team designs, creates and optimises evaluation directives according to laboratory best practices, the special workflow and our analysis software.

Bioinformatics

Our bioinformatics team works at the interface of complex data analysis, algorithmic development, and the implementation of specialised software to support the HLA typing workflow. Rapidly growing data volumes, evolving sequencing technologies and expanding typing profiles provide constant statistical and algorithmic challenges for the team to tackle.

Besides providing bioinformatics services to R&D and Quality Management, the team is engaged in research projects exploring upcoming sequencing technologies (e.g., PacBio or Oxford Nanopore sequencing) for their potential for HLA typing, the characterisation of novel alleles, or the use of machine learning as a means to enhance quality assurance.

Clinical lab

Any search for an unrelated donor should start with high resolution typing and all relevant loci. Our clinical department performs patient related and confirmatory typing. Our clinical lab employs the most up-to-date molecular genetics techniques.

The analytical spectrum ranges from confirmatory typing to typing disease-associated HLA antigens, antibody screening and crossmatch testing.

Customer service

Our customer service team is available to assist our customers from first contact onwards by helping to define the required service. As the main point of contact, they will assist with any subsequent questions about the ongoing partnership.

We support our customers to make the right choices with the right outcomes.

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Career - Jobs

Our expertise

High throughput tissue typing for stem cell donor registries and other medical purposes. As a subsidiary of the largest and most important global bone marrow donor centre (DKMS http://www.dkms.de/en), DKMS Life Science Lab currently employs around 100 people and has business relationships across multiple continents.

The lab is a pioneering organisation that regularly initiates or is involved in scientific projects. DKMS Life Science Lab is searching for highly qualified employees who call conventional practices into question, are open to new ideas and have ideals that motivate them.

Why you should apply

DKMS Life Science Lab is growing dynamically and has a management team which is keenly aware of employee value. We have a unique corporate team culture which places trust and confidence in our staff and their abilities. Every employee is assigned responsibilities from the outset. Our flexible working models actively support the balance between career and family life. We offer impressive social benefits.

Last but not least we have one of the most motivating business goals. We support new life chances for patients and their relatives.


Current job advertisements - aktuelle Stellenausschreibungen


Link to DKMS Family’s Careers Portal

Please choose for location 'Dresden'.


Deutsche Kurzinformation Bewerber-Info

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Publications

Please download your free copy of our ASHI-Posters:

KIR RESOLUTION POTENTIAL




Besides performing routine genotyping operations, our lab has always been proud to play an active role in the scientific field of HLA typing and beyond.


2017 - 2.7 million samples genotyped for HLA by next generation sequencing: lessons learned

Schöfl G, Lang K, Quenzel P, Böhme I, Sauter J, Hofmann JA, Pingel J, Schmidt AH, Lange V
BMC Genomics
, 18:161 [ DOI ]

Background: At the DKMS Life Science Lab, Next Generation Sequencing (NGS) has been used for ultra-high-volume high-resolution genotyping of HLA loci for the last three and a half years. Here, we report on our experiences in genotyping the HLA, CCR5, ABO, RHD and KIR genes using a direct amplicon sequencing approach on Illumina MiSeq and HiSeq 2500 instruments. Results: Between January 2013 and June 2016, 2,714,110 samples largely from German, Polish and UK-based potential stem cell donors have been processed. 98.9% of all alleles for the targeted HLA loci (HLA-A, -B, -C, -DRB1, -DQB1 and -DPB1) were typed at high resolution or better. Initially a simple three-step workflow based on nanofluidic chips in conjunction with 4-primer amplicon tagging was used. Over time, we found that this setup results in PCR artefacts such as primer dimers and PCR-mediated recombination, which may necessitate repeat typing. Split workflows for low- and high-DNA-concentration samples helped alleviate these problems and reduced average per-locus repeat rates from 3.1 to 1.3%. Further optimisations of the workflow included the use of phosphorothioate oligos to reduce primer degradation and primer dimer formation, and employing statistical models to predict read yield from initial template DNA concentration to avoid intermediate quantification of PCR products. Finally, despite the populations typed at DKMS Life Science Lab being relatively homogenous genetically, an analysis of 1.4 million donors processed between January 2015 and May 2016 led to the discovery of 1,919 distinct novel HLA alleles. Conclusions: Amplicon-based NGS HLA genotyping workflows have become the workhorse in high-volume tissue typing of registry donors. The optimisation of workflow practices over multiple years has led to insights and solutions that improve the efficiency and robustness of short amplicon based genotyping workflows.

2016 - ABO allele-level frequency estimation based on population-scale genotyping by next generation sequencing

Lang K, Wagner I, Schöne B, Schöfl G, Birkner K, Hofmann JA, Sauter J, Pingel J, Böhme I, Schmidt AH, Lange V
BMC Genomics
, 17:374 [ DOI ]

BACKGROUND: The characterization of the ABO blood group status is vital for blood transfusion and solid organ transplantation. Several methods for the molecular characterization of the ABO gene, which encodes the alleles that give rise to the different ABO blood groups, have been described. However, the application of those methods has so far been restricted to selected samples and not been applied to population-scale analysis. RESULTS: We describe a cost-effective method for high-throughput genotyping of the ABO system by next generation sequencing. Sample specific barcodes and sequencing adaptors are introduced during PCR, rendering the products suitable for direct sequencing on Illumina MiSeq or HiSeq instruments. Complete sequence coverage of exons 6 and 7 enables molecular discrimination of the ABO subgroups and many alleles. The workflow was applied to ABO genotype more than a million samples. We report the allele group frequencies calculated on a subset of more than 110,000 sampled individuals of German origin. Further we discuss the potential of the workflow for high resolution genotyping taking the observed allele group frequencies into account. Finally, sequence analysis revealed 287 distinct so far not described alleles of which the most abundant one was identified in 174 samples. CONCLUSIONS: The described workflow delivers high resolution ABO genotyping at low cost enabling population-scale molecular ABO characterization.

2016 - Prediction of spurious HLA class II typing results using probabilistic classification

Schöfl G, Schmidt AH, Lange V
Human Immunology
, 77:264-272 [ DOI ]

While modern high-throughput sequence-based HLA genotyping methods generally provide highly accurate typing results, artefacts may nonetheless arise for numerous reasons, such as sample contamination, sequencing errors, read misalignments, or PCR amplification biases. To help detecting spurious typing results, we tested the performance of two probabilistic classifiers (binary logistic regression and random forest models) based on population-specific genotype frequencies. We trained the model using high-resolution typing results for HLA-DRB1, DQB1, and DPB1 from large samples of German, Polish and UK-based donors. The high predictive capacity of the best models replicated both in 10-fold cross-validation for each gene and in using independent evaluation data (AUC 0.820–0.893). While genotype frequencies alone provide enough predictive power to render the model generally useful for highlighting potentially spurious typing results, the inclusion of workflow-specific predictors substantially increases prediction specificity. Low initial DNA concentrations in combination with low-volume PCR reactions form a major source of stochastic error specific to the Fluidigm chip-based workflow at DKMS Life Science Lab. The addition of DNA concentrations as a predictor variable thus substantially increased AUC (0.947–0.959) over purely frequency-based models.

2014 - High density FTA plates serve as efficient long-term sample storage for HLA genotyping

Lange V, Arndt K, Schwarzelt C, Boehme I, Giani AS, Schmidt AH, Ehninger G, Wassmuth R
Tissue Antigens
, 83:101-105 [ DOI ]

Storage of dried blood spots (DBS) on high-density FTA({textregistered}) plates could constitute an appealing alternative to frozen storage. However, it remains controversial whether DBS are suitable for high-resolution sequencing of human leukocyte antigen (HLA) alleles. Therefore, we extracted DNA from DBS that had been stored for up to 4 years, using six different methods. We identified those extraction methods that recovered sufficient high-quality DNA for reliable high-resolution HLA sequencing. Further, we confirmed that frozen whole blood samples that had been stored for several years can be transferred to filter paper without compromising HLA genotyping upon extraction. Concluding, DNA derived from high-density FTA({textregistered}) plates is suitable for high-resolution HLA sequencing, provided that appropriate extraction protocols are employed.

2014 - Cost-efficient high-throughput HLA typing by MiSeq amplicon sequencing

Lange V, Böhme I, Hofmann J, Lang K, Sauter J, Schöne B, Paul P, Albrecht V, Andreas JM, Baier DM, Nething J, Ehninger U, Schwarzelt C, Pingel J, Ehninger G, Schmidt AH
BMC Genomics
, 15:63 [ DOI ]

BACKGROUND: A close match of the HLA alleles between donor and recipient is an important prerequisite for successful unrelated hematopoietic stem cell transplantation. To increase the chances of finding an unrelated donor, registries recruit many hundred thousands of volunteers each year. Many registries with limited resources have had to find a trade-off between cost and resolution and extent of typing for newly recruited donors in the past. Therefore, we have taken advantage of recent improvements in NGS to develop a workflow for low-cost, high-resolution HLA typing. RESULTS: We have established a straightforward three-step workflow for high-throughput HLA typing: Exons 2 and 3 of HLA-A, -B, -C, -DRB1, -DQB1 and -DPB1 are amplified by PCR on Fluidigm Access Array microfluidic chips. Illumina sequencing adapters and sample specific tags are directly incorporated during PCR. Upon pooling and cleanup, 384 samples are sequenced in a single Illumina MiSeq run. We developed 'neXtype' for streamlined data analysis and HLA allele assignment. The workflow was validated with 1140 samples typed at 6 loci. All neXtype results were concordant with the Sanger sequences, demonstrating error-free typing of more than 6000 HLA loci. Current capacity in routine operation is 12,000 samples per week. CONCLUSIONS: The workflow presented proved to be a cost-efficient alternative to Sanger sequencing for high-throughput HLA typing. Despite the focus on cost efficiency, resolution exceeds the current standards of Sanger typing for donor registration.

2013 - High-resolution HLA haplotype frequencies of stem cell donors in Germany with foreign parentage: How can they be used to improve unrelated donor searches?

Pingel J, Solloch UV, Hofmann JA, Lange V, Ehninger G, Schmidt AH
Human Immunology
, 74:330-340 [ DOI ]

In hematopoietic stem cell transplantation, human leukocyte antigens (HLA), usually HLA loci A, B, C, DRB1 and DQB1, are required to check histocompatibility between a potential donor and the recipient suffering from a malignant or non-malignant blood disease. As databases of potential unrelated donors are very heterogeneous with respect to typing resolution and number of typed loci, donor registries make use of haplotype frequency-based algorithms to provide matching probabilities for each potentially matching recipient/donor pair. However, it is well known that HLA allele and haplotype frequencies differ significantly between populations. We estimated high-resolution HLA-A, -B, -C, -DRB1 haplotype and allele frequencies of donors within DKMS German Bone Marrow Donor Center with parentage from 17 different countries: Turkey, Poland, Italy, Russian Federation, Croatia, Greece, Austria, Kazakhstan, France, The Netherlands, Republic of China, Romania, Portugal, USA, Spain, United Kingdom and Bosnia and Herzegovina. 5-locus haplotypes including HLA-DQB1 are presented for Turkey, Poland, Italy and Russian Federation. We calculated linkage disequilibria for each sample. Genetic distances between included countries could be shown to reflect geography. We further demonstrate how genetic differences between populations are reflected in matching probabilities of recipient/donor pairs and how they influence the search for unrelated donors as well as strategic donor center typings.

2013 - Regional HLA Differences in Poland and Their Effect on Stem Cell Donor Registry Planning

Schmidt AH, Solloch UV, Pingel J, Sauter J, Böhme I, Cereb N, Dubicka K, Schumacher S, Wachowiak J, Ehninger G
PLoS ONE
, 8:e73835 [ DOI ]

Regional HLA frequency differences are of potential relevance for the optimization of stem cell donor recruitment. We analyzed a very large sample (n = 123,749) of registered Polish stem cell donors. Donor figures by 1-digit postal code regions ranged from n = 5,243 (region 9) to n = 19,661 (region 8). Simulations based on region-specific haplotype frequencies showed that donor recruitment in regions 0, 2, 3 and 4 (mainly located in the south-eastern part of Poland) resulted in an above-average increase of matching probabilities for Polish patients. Regions 1, 7, 8, 9 (mainly located in the northern part of Poland) showed an opposite behavior. However, HLA frequency differences between regions were generally small. A strong indication for regionally focused donor recruitment efforts can, therefore, not be derived from our analyses. Results of haplotype frequency estimations showed sample size effects even for sizes between n≈5,000 and n≈20,000. This observation deserves further attention as most published haplotype frequency estimations are based on much smaller samples.

2011 - A multi-site study using high-resolution HLA genotyping by next generation sequencing

Holcomb CL, Höglund B, Anderson MW, Blake LA, Böhme I, Egholm M, Ferriola D, Gabriel C, Gelber SE, Goodridge D, Hawbecker S, Klein R, Ladner M, Lind C, Monos D, Pando MJ, Pröll J, Sayer DC, Schmitz-Agheguian G, Simen BB, Thiele B, Trachtenberg EA, Tyan DB, Wassmuth R, White S, Erlich HA
Tissue Antigens
, 77:206-217 [ DOI ]

The high degree of polymorphism at human leukocyte antigen (HLA) class I and class II loci makes high-resolution HLA typing challenging. Current typing methods, including Sanger sequencing, yield ambiguous typing results because of incomplete genomic coverage and inability to set phase for HLA allele determination. The 454 Life Sciences Genome Sequencer (GS FLX) next generation sequencing system coupled with conexio atf software can provide very high-resolution HLA genotyping. High-throughput genotyping can be achieved by use of primers with multiplex identifier (MID) tags to allow pooling of the amplicons generated from different individuals prior to sequencing. We have conducted a double-blind study in which eight laboratory sites performed amplicon sequencing using GS FLX standard chemistry and genotyped the same 20 samples for HLA-A, -B, -C, DPB1, DQA1, DQB1, DRB1, DRB3, DRB4, and DRB5 (DRB3/4/5) in a single sequencing run. The average sequence read length was 250 base pairs and the average number of sequence reads per amplicon was 672, providing confidence in the allele assignments. Of the 1280 genotypes considered, assignment was possible in 95% of the cases. Failure to assign genotypes was the result of researcher procedural error or the presence of a novel allele rather than a failure of sequencing technology. Concordance with known genotypes, in cases where assignment was possible, ranged from 95.3% to 99.4% for the eight sites, with overall concordance of 97.2%. We conclude that clonal pyrosequencing using the GS FLX platform and CONEXIO ATF software allows reliable identification of HLA genotypes at high resolution.

2011 - High-resolution human leukocyte antigen allele and haplotype frequencies of the Polish population based on 20,653 stem cell donors

Schmidt AH, Solloch UV, Pingel J, Baier D, Böhme I, Dubicka K, Schumacher S, Rutt C, Skotnicki AB, Wachowiak J, Ehninger G
Human Immunology
, 72:558-565 [ DOI ]

We present high-resolution allele and haplotype frequency (HF) estimations of the Polish population based on more than 20,000 registered stem cell donors. Sequencing-based donor human leukocyte antigen (HLA) typing led to unambiguous typing results in most cases (between 94.3% for HLA-DRB1 and 96.9% for HLA-B). HF estimations were carried out with a new, validated implementation of the expectation-maximization algorithm that allowed processing of data with ambiguities. Our results confirm several earlier results, for example, the relative commonness of the haplotype A*25:01 g, B*18:01 g, C*12:03, DRB1*04:01 in the Polish population. Because of the large sample size, we were able to obtain results of unprecedented accuracy. The estimated population-specific HFs were then used to analyze questions of strategic donor registry planning. Simulated matching probabilities by donor file size suggest that there is a need for intense donor recruitment efforts in Poland despite the large German donor registry and the genetic relatedness of both populations. Based on the current German registry size of approximately 4 million donors, the recruitment of 100,000 Polish donors would produce a stronger increase in matching probabilities for Polish patients than the recruitment of 3.3 million additional German donors.

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Software

Produced at DKMS Life Science as part of our scientific projects.

TypeLoader

TypeLoader is an automated workflow to aid in the curation and submission of new alleles identified from genotyping immunogenetics samples using second and third generation sequencing technologies to the IMGT/HLA repository.

GitHub



HLAsim - Simulating HLA locus allelic dropout

Simulation code and data associated with the article G Schoefl , AH Schmidt, V Lange (2016) Prediction of spurious HLA class II typing results using probabilistic classification.
Human Immunology, doi:10.1016/j.humimm.2016.01.012

GitHub

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