Use of dried blood spots for the determination of genetic variation of interleukin-10, killer immunoglobulin-like receptor and HLA class I genes

Development and validation of a sample sparing strategy for HLA typing utilizing next generation sequencing

We report the development of a general methodology to genotype HLA class I and class II loci. A Whole Genome Amplification (WGA) step was used as a sample sparing methodology. HLA typing data could be obtained with as few as 300 cells, underlining the usefulness of the methodology for studies for which limited cells are available. The next generation sequencing platform was validated using a panel of cell lines from the International Histocompatibility Working Group (IHWG) for HLA-A, -B, and -C. Concordance with the known, previously determined HLA types was 99%. We next developed a panel of primers to allow HLA typing of alpha and beta chains of the HLA DQ and DP loci and the beta chain of the DRB1 locus. For the beta chain genes, we employed a novel strategy using primers in the intron regions surrounding exon 2, and the introns surrounding exons 3 through 4 (DRB1) or 5 (DQB1 and DPB1). Concordance with previously determined HLA Class II types was also 99%. To increase throughput and decrease cost, we developed strategies combining multiple loci from each donor. Multiplexing of 96 samples per run resulted in increases in throughput of approximately 8-fold. The pipeline developed for this analysis (HLATyphon) is available for download at https://github.com/LJI-Bioinformatics/HLATyphon.

Whole Genome Amplification from Blood Spot Samples

Whole genome amplification is an invaluable technique when working with DNA extracted from blood spots, as the DNA obtained from this source often is too limited for extensive genetic analysis. Two techniques that amplify the entire genome are common. Here, both are described with focus on the benefits and drawbacks of each system. However, in order to obtain the best possible WGA result the quality of input DNA extracted from the blood spot is essential, but also time consumption, flexibility in format and elution volume and price of the technology are factors influencing system choice. Here, three DNA extraction techniques are described and the above aspects are compared between the systems.

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

Storage of dried blood spots (DBS) on high-density FTA(®) 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(®) plates is suitable for high-resolution HLA sequencing, provided that appropriate extraction protocols are employed.

Natural killer cells and killer-cell immunoglobulin-like receptor polymorphisms: their role in hematopoietic stem cell transplantation

Natural killer (NK) cells are important effector cells in the early control of infected, malignant, and "nonself" cells. Various receptor families are involved in enabling NK cells to detect and efficiently eliminate these target cells. The killer-cell immunoglobulin-like receptor (KIR) family is a set of receptors that are very polymorphic with regard to gene content, expression level, and expression pattern. KIRs are responsible for the induction of a NK cell alloreactive response through their interaction with HLA class I molecules. The role of NK cells in hematopoietic stem cell transplantation (HSCT) has been studied for many years, and induction of antileukemic responses by donor NK cells has been reported. Conflicting data still exist on the exact circumstances in which the KIR repertoire affects and influences clinical outcome after HSCT. More large-scale studies are needed on well-defined cohorts to unravel the mechanism of action of the NK cell-mediated alloresponse in an HSCT setting.