Comparing Germany and Israel regarding debates on policy-making at the beginning of life: PGD, NIPT and their paths of routinization

Definition The routinization of prenatal diagnosis is the source of bioethical and policy debates regarding choice, autonomy, access, and protection. To understand these debates in the context of cultural diversity and moral pluralism, we compare Israel and Germany, focusing on two recent repro-genetic “hot spots” of such policy-making at the beginning of life: pre-implantation genetic diagnosis (PGD) and non-invasive prenatal genetic testing (NIPT), two cutting-edge repro-genetic technologies that are regulated and viewed very differently in Germany and Israel, reflecting different medicolegal policies as well as public and bioethical considerations. Arguments First, we compare policy-making in the context of PGD for HLA (human leukocyte antigen) typing, used to create sibling donors, approved in Israel under specific conditions while prohibited in Germany. Second, we compare policy-making in the context of NIPT, which came under fire in Germany, while in Israel there has been little public debate about it. Conclusion Both countries justify their contrasting policies as reflecting a concern for the well-being and care of the embryo/child, thus highlighting different concepts of embryo/child protection, (relational) autonomy, family relations, and the impact of religion and history on the promotion/protection of life. We use the juxtaposition of PGD and NIPT to highlight some inconsistencies in policies concerning the protection of extra- and intra-corporeal embryos. We conclude by drawing on the comparison to show how national variations exist alongside co-evolution.

Benchmarking the HLA typing performance of three HLA assays and seven NGS-based HLA algorithms

Background With the great progress made recently in NGS (Next Generation Sequencing) technology, sequencing accuracy and throughput have increased, while the cost for data has decreased. Various HLA (Human Leukocyte Antigen) typing algorithms and assays have been developed and have begun to be used in clinical practice. However, there is no systematic benchmarking to evaluate the HLA typing performance of different HLA assays and algorithms. In this study, we compared the HLA typing performance of three HLA assays and seven NGS-based HLA algorithms and assessed the impact of sequencing depth and length on HLA typing accuracy. Results Seven HLA typing algorithms at 4- and 6-digit allele levels were compared on three different assays in terms of accuracy, read depth and read length. The algorithms HLA-HD and HISAT-genotype showed the highest accuracy at both 2- and 4-digit resolution, followed by HLAscan. We designed a capture-based HLA assay, which showed comparable or even better performance compared with WES (Whole Exome Sequencing). In the depth evaluation, the sequencing data were down-sampled from 500X to 10X based on the depth of HLA genes. We found that the minimal depth was 100X for HLA-HD and HISAT-genotype to obtain more than 90% HLA typing accuracy at the 6-digit allele level. The accuracy of all three algorithms did not change when the read length decreased from 150 bp to 76 bp. Conclusion Although HISAT-genotype and HLA-HD may need more computing resources, we recommend using them for NGS-based HLA genotyping because of their higher accuracy and robustness to sequencing depth and read length. We propose that the minimal sequence depth for obtaining more than 90% HLA typing accuracy at the 6-digit allele level is 100X. Besides, targeting capture-based NGS HLA typing may be more suitable than WES in clinical practice due to its lower sequencing cost and higher HLA sequencing depth.

HLAssign 2.0: An advanced Graphical User Interface for the analysis of short and long read Human Leukocyte Antigen-typing data

Next Generation Sequencing (NGS) based Human Leukocyte Antigen (HLA) typing has been a challenge due to the polymorphism of the HLA region. Nevertheless, the method’s accuracy has increased during the last years and it is now routinely used by many large centers including bone marrow registries. However, challenging HLA genotype compositions exist, which hinder a fully automated analysis. Therefore, HLA typing results are still visually inspected in diagnostics, i.e. the underlying read mappings and phasing information is controlled. Here, we present HLAssign 2.0 that now includes a strict workflow, improved tools for visual inspection and read phasing analysis in the automatic caller. In collaboration with interface design researchers, biologists and informaticians we developed an elaborate graphical user interface for visual evaluation of automated HLA calls for Illumina NGS reads. We also provide tools to preprocess 10x Genomics and PacBio sequencing reads for HLAssign analysis. We benchmarked our automatic caller against STC-seq and xHLA, showing comparable automatic call rates. Additional manual inspection of the automatic results in our GUI assists the user to assign the correct HLA calls and to achieve diagnostic accuracy. HLAssign 2.0 is free for research and commercial use and is available for Windows and MacOS.