Technological limitations have hindered the large-scale genetic investigation of tandem repeats in disease. We show that long-read sequencing with a single Oxford Nanopore Technologies PromethION flow cell per individual achieves 30× human genome coverage and enables accurate assessment of tandem repeats including the 10,000-bp Alzheimer’s disease-associated ABCA7 VNTR. The Guppy “flip-flop” base caller and tandem-genotypes tandem repeat caller are efficient for large-scale tandem repeat assessment, but base calling and alignment challenges persist. We present NanoSatellite, which analyzes tandem repeats directly on electric current data and improves calling of GC-rich tandem repeats, expanded alleles, and motif interruptions.

Aims The aim of this study was to determine if computed tomography (CT) psoas muscular attenuation measurements may predict all-cause mortality in patients undergoing TAVI.Methods Ninety-four consecutive patients undergoing TAVI were analysed. The CT axial slice at the level of the fourth lumbar vertebra was selected. The psoas muscle areas were manually contoured. The circumferential surface area (CSA) of both psoas muscles was determined by selecting the voxels with attenuation values, ranging from 0 to 100 Hounsfield Units (HU). The mean CT attenuation coefficient of the psoas muscle (Psoas mean HU) was measured. The muscle was subdivided into a low-density muscle (LDM) (0-29 HU) and high-density muscle (HDM) (30-100 HU) portion. The HDM/LDM ratio was calculated. We searched for a correlation between HDM/LDM, CSA LDM (%), Psoas mean HU and all-cause mortality. ResultsThe mean age was 81.2 W 7.5 years. Thirty patients had adverse outcome (all-cause mortality). Compared with patients with the lowest CSA LDM (%), patients in the third and second tertiles had an increased hazard ratio for mortality (2.871; 95% confidence interval 0.880-9.371 and 5.044; 95% confidence interval 1. 641-15.795, respectively) in a multivariable model with EuroSCORE II, Barthel frailty index and CSA LDM (%) (P U 0.231, 0.097 and 0.019, respectively). HDM/LDM and Psoas mean HU (as continuous variable) were also independent predictors of all-cause mortality (P U 0.019, P U 0.013, respectively) Conclusion CSA LDM (%), Psoas mean HU and HDM/LDM are independent and incremental predictors of all-cause mortality in patients undergoing TAVI.

Background Alzheimer’s disease (AD) is the leading cause of dementia, clinically characterized by memory deficits and progressive cognitive decline. Despite decades of research effective therapies are lacking, and a large part of the genetic heritability remains unidentified. ABCA7 and ABCA1, members of the ATP-binding cassette subfamily A (ABCA), were identified as AD risk genes in genome-wide association studies. Nevertheless, genetic and/or functional studies propose a link between AD and two other members of the ABCA subclass, i.e., ABCA2 and ABCA5. Main body Changes in expression or dysfunction of these transporters were found to increase amyloid β levels. This might be related to the common role of ABCA transporters in cellular cholesterol homeostasis, for which a prominent role in AD development has been suggested. In this review, we provide a comprehensive overview and discussion on the contribution of the ABCA subfamily to the etiopathogenesis of AD. Conclusions A better understanding of the function and identification of disease-associated genetic variants in ABCA transporters can contribute to the development of novel therapeutic strategies for AD.

De Roeck et al., PromethION sequencing and tandem repeat characterization 2 Abstract Tandem repeats (TRs) can cause disease through their length, sequence motif interruptions, and nucleotide modifications. For many TRs, however, these features are very difficult -if not impossible -to assess, requiring low-throughput and labor-intensive assays. One example is a VNTR in ABCA7 for which we recently discovered that expanded alleles strongly increase risk of Alzheimer's disease. Here, we investigated the potential of long-read whole genome sequencing to surmount these challenges, using the high-throughput PromethION platform from Oxford Nanopore Technologies. To overcome the limitations of conventional base calling and alignment, we developed an algorithm to study the TR size and sequence directly on raw PromethION current data.We report the long-read sequencing of multiple human genomes (n = 11) using only a single sequencing run and flow cell per individual. With the use of fresh DNA extractions, DNA shearing to approximately 20kb and size selection, we obtained an average output of 70 gigabases (Gb) per flow cell, corresponding to a 21x genome coverage, and a maximum yield of 98 Gb (30x genome coverage). All ABCA7 VNTR alleles, including expansions up to 10,000 bases, were spanned by long sequencing reads, validated by Southern blotting. Classical approaches of TR length estimation suffered from low accuracy, low precision, DNA strand effects and/or inability to call pathogenic repeat expansions. In contrast, our novel NanoSatellite algorithm, which circumvents base calling by using dynamic time warping on raw PromethION current data, achieved more than 90% accuracy and high precision (5.6% relative standard deviation) of TR length estimation, and detected all clinically relevant repeat expansions. In addition, we identified alternative TR sequence motifs with high consistency, allowing determination of TR sequence and distinction of VNTR alleles with homozygous length.In conclusion, we validated the robustness of single-experiment whole genome long-read sequencing on PromethION, a prerequisite for application of long-read sequencing in the clinic. In addition, we outperformed Southern blotting, enabling improved characterization of the role of expanded ABCA7 VNTR alleles in Alzheimer's disease, and opening new opportunities for TR research.