Allele-Level KIR Genotyping of More Than a Million Samples: Workflow, Algorithm, and Observations

The killer-cell immunoglobulin-like receptor (KIR) genes regulate natural killer cell activity, influencing predisposition to immune mediated disease, and affecting hematopoietic stem cell transplantation (HSCT) outcome. Owing to the complexity of the KIR locus, with extensive gene copy number variation (CNV) and allelic diversity, high-resolution characterization of KIR has so far been applied only to relatively small cohorts. Here, we present a comprehensive high-throughput KIR genotyping approach based on next generation sequencing. Through PCR amplification of specific exons, our approach delivers both copy numbers of the individual genes and allelic information for every KIR gene. Ten-fold replicate analysis of a set of 190 samples revealed a precision of 99.9%. Genotyping of an independent set of 360 samples resulted in an accuracy of more than 99% taking into account consistent copy number prediction. We applied the workflow to genotype 1.8 million stem cell donor registry samples. We report on the observed KIR allele diversity and relative abundance of alleles based on a subset of more than 300,000 samples. Furthermore, we identified more than 2,000 previously unreported KIR variants repeatedly in independent samples, underscoring the large diversity of the KIR region that awaits discovery. This cost-efficient high-resolution KIR genotyping approach is now applied to samples of volunteers registering as potential donors for HSCT. This will facilitate the utilization of KIR as additional selection criterion to improve unrelated donor stem cell transplantation outcome. In addition, the approach may serve studies requiring high-resolution KIR genotyping, like population genetics and disease association studies.

Anatomically weighted second-order total variation reconstruction of 23Na MRI using prior information from 1H MRI

Sodium ((23)Na) MRI is a noninvasive tool to assess cell viability, which is linked to the total tissue sodium concentration (TSC). However, due to low in vivo concentrations, (23)Na MRI suffers from low signal-to-noise ratio (SNR) and limited spatial resolution. As a result, image quality is compromised by Gibbs ringing artifacts and partial volume effects. An iterative reconstruction algorithm that incorporates prior information from (1)H MRI is developed to reduce partial volume effects and to increase the SNR in non-proton MRI. Anatomically weighted second-order total variation (AnaWeTV) is proposed as a constraint for compressed sensing reconstruction of 3D projection reconstruction (3DPR) data. The method is evaluated in simulations and a MR measurement of a multiple sclerosis (MS) patient by comparing it to gridding and other reconstruction techniques. AnaWeTV increases resolution of known structures and reduces partial volume effects. In simulated MR brain data (nominal resolution Δx(3) = 3 × 3 × 3 mm(3)), the intensity error of four small MS lesions was reduced from (6.9 ± 3.8)% (gridding) to (2.8 ± 1.4)% (AnaWeTV with T2-weighted reference images). Compared to gridding, a substantial SNR increase of 130% was found in the white matter of the MS patient. The algorithm is robust against misalignment of the prior information on the order of the (23)Na image resolution. Features without prior information are still reconstructed with high contrast. AnaWeTV allows a more precise quantification of TSC in structures with prior knowledge. Thus, the AnaWeTV algorithm is in particular beneficial for the assessment of tissue structures that are visible in both (23)Na and (1)H MRI.

Cavity-controlled collective scattering at the recoil limit

We study collective scattering with Bose-Einstein condensates interacting with a high-finesse ring cavity. The condensate scatters the light of a transverse pump beam superradiantly into modes which, in contrast to previous experiments, are not determined by the geometrical shape of the condensate, but specified by a resonant cavity mode. Moreover, since the recoil-shifted frequency of the scattered light depends on the initial momentum of the scattered fraction of the condensate, we show that it is possible to employ the good resolution of the cavity as a filter selecting particular quantized momentum states.