An intronic VNTR affects splicing of ABCA7 and increases risk of Alzheimer’s disease

Roeck, Arne De; Duchateau, Lena; Dongen, Jasper Van; Cacace, Rita; Bjerke, Maria; Bossche, Tobi Van den; Cras, Patrick; Vandenberghe, Rik; Deyn, Peter Paul De; Engelborghs, Sebastiaan; Broeckhoven, Christine Van; Sleegers, Kristel

doi:10.1007/s00401-018-1841-z

Cited by 80 publications

(117 citation statements)

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“…ABCA7 VNTR expansions result in a > 4-fold increased risk of Alzheimer's disease 22 , yet the technological challenges of investigating TR sequences have so far precluded further research and large-scale screening. Long-read sequencing has the potential to overcome these issues on the condition that sufficient yield and read lengths are consistently obtained to traverse tandem repeats, and algorithms exist that can accurately size even the largest alleles.…”

Section: Discussionmentioning

confidence: 99%

“…We performed long-read whole genome sequencing on DNA from eleven individuals (Table 1), using the PromethION sequencing platform (Oxford Nanopore Technologies (ONT), Oxford, United Kingdom). Ten individuals (Subject01 till Subject10) were recruited in the context of the Belgian Neurology (BELNEU) Consortium 22,23 and consisted of AD patients (n = 6), an FTLD patient, a family member at risk of developing dementia, and healthy elderly control individuals (n = 2). All participants and/or their legal guardian provided written informed consent for participation in genetic studies.…”

Section: Study Populationmentioning

confidence: 99%

“…In addition, we included the previously described NA19240 PromethION sequencing dataset 24 . ABCA7 VNTR lengths were determined in all individuals with Southern blotting as previously described 22 .…”

Section: Study Populationmentioning

confidence: 99%

“…Second, we evaluated the use of this data to characterize TR length, sequence, and nucleotide modifications. We focused our analyses on an ABCA7 VNTR, for which we recently discovered that expanded alleles are a strong risk factor for Alzheimer's disease 22 . This VNTR (chr19:1049437-1050028, hg19) has a high GC-content, a 25bp repeat unit with frequent nucleotide substitutions and insertions (consensus motif embedded in Figure 1), and the total repeat size can reach more than 10,000 bp.…”

Section: Introductionmentioning

confidence: 99%

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Accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION

Roeck

Coster

Bossaerts

et al. 2018

Preprint

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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.

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Section: Discussionmentioning

confidence: 99%

Section: Study Populationmentioning

confidence: 99%

Section: Study Populationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION

Roeck

Coster

Bossaerts

et al. 2018

Preprint

Self Cite

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“…The sQTL is hypothesized to be the causal signal, as it is associated with the production of a nonfunctional transcript. 11,12 Functional studies of eQTLs have been hindered by the time and energy required to identify and then mechanistically characterize the QTLs in model systems. QTL discovery efforts in primary tissues have been highly productive, but have several important drawbacks, such as the reliance on heterogeneous post-mortem tissue collection and the difficulty of interrogating phenotypes in tissues.…”

Section: Introductionmentioning

confidence: 99%

Evaluating the contribution of cell-type specific alternative splicing to variation in lipid levels

Gawronski

Bone

Park

et al. 2019

Preprint

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Background: Genome-wide association studies have identified 150+ loci associated with lipid levels. However, the genetic mechanisms underlying most of these loci are not well-understood. Recent work indicates that changes in the abundance of alternatively spliced transcripts contributes to complex trait variation. Consequently, identifying genetic loci that associate with alternative splicing in disease-relevant cell types and determining the degree to which these loci are informative for lipid biology is of broad interest. Methods and Results:We analyze gene splicing in 83 sample-matched induced pluripotent stem cell (iPSC) and hepatocyte-like cell (HLC) lines (n=166), as well as in an independent collection of primary liver tissues (n=96). We observe that transcript splicing is highly cell-type specific, and the genes that are differentially spliced between iPSCs and HLCs are enriched for metabolism pathway annotations. We identify 1,381 HLC splicing quantitative trait loci (sQTLs) and 1,462 iPSC sQTLs and find that sQTLs are often shared across cell types. To evaluate the contribution of sQTLs to variation in lipid levels, we conduct colocalization analysis using lipid genome-wide association data. We identify 19 lipid-associated loci that colocalize either with an HLC expression quantitative trait locus (eQTL) or sQTL. Only one locus colocalizes with both an sQTL and eQTL, indicating that sQTLs contribute information about GWAS loci that cannot be obtained by analysis of steady-state gene expression alone. Conclusions: These results provide an important foundation for future efforts that use iPSC and iPSC-derived cells to evaluate genetic mechanisms influencing both cardiovascular disease risk and complex traits in general. phenotype via SORT1 at the 1p13 cholesterol locus. Nature. 2010;466(7307):714-719. 6. Fadista J, Vikman P, Laakso EO, et al. Global genomic and transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolism. 7. Li M, Jaffe AE, Straub RE, et al. A human-specific AS3MT isoform and BORCS7 are molecular risk factors in the 10q24.32 schizophrenia-associated locus. Nat Med. 2016;22(6):649-656.

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Alternative splicing in a presenilin 2 variant associated with Alzheimer disease

Braggin

Bucks

Course

et al. 2019

Ann Clin Transl Neurol

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Objective Autosomal‐dominant familial Alzheimer disease ( AD ) is caused by by variants in presenilin 1 ( PSEN 1 ), presenilin 2 ( PSEN 2 ), and amyloid precursor protein ( APP ). Previously, we reported a rare PSEN 2 frameshift variant in an early‐onset AD case ( PSEN 2 p.K115Efs*11). In this study, we characterize a second family with the same variant and analyze cellular transcripts from both patient fibroblasts and brain lysates. Methods We combined genomic, neuropathological, clinical, and molecular techniques to characterize the PSEN 2 K115Efs*11 variant in two families. Results Neuropathological and clinical evaluation confirmed the AD diagnosis in two individuals carrying the PSEN 2 K115Efs*11 variant. A truncated transcript from the variant allele is detectable in patient fibroblasts while levels of wild‐type PSEN 2 transcript and protein are reduced compared to controls. Functional studies to assess biological consequences of the variant demonstrated that PSEN 2 K115Efs*11 fibroblasts secrete less A β 1–40 compared to controls, indicating abnormal γ ‐secretase activity. Analysis of PSEN 2 transcript levels in brain tissue revealed alternatively spliced PSEN 2 products in patient brain as well as in sporadic AD and age‐matched control brain. Interpretation These data suggest that PSEN 2 K115Efs*11 is a likely pathogenic variant associated with AD . We uncovered novel PSEN 2 alternative transcripts in addition to previously reported PSEN 2 splice isoforms associated with sporadic AD . In the context of a frameshift, these alternative transcripts return to the canonical reading frame with potential to generate deleterious protein products. Our findings suggest novel potential mechanisms by which PSEN variants may influence AD pathogenesis, highlighting the complexity underlying genetic contribution to disease risk.

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An intronic VNTR affects splicing of ABCA7 and increases risk of Alzheimer’s disease

Cited by 80 publications

References 52 publications

Accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION

Accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION

Evaluating the contribution of cell-type specific alternative splicing to variation in lipid levels

Alternative splicing in a presenilin 2 variant associated with Alzheimer disease

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