| 1. |
- Fresard, Laure, et al.
(författare)
-
Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts
- 2019
-
Ingår i: Nature Medicine. - : NATURE PUBLISHING GROUP. - 1078-8956 .- 1546-170X. ; 25:6, s. 911-919
-
Tidskriftsartikel (refereegranskat)abstract
- It is estimated that 350 million individuals worldwide suffer from rare diseases, which are predominantly caused by mutation in a single gene(1). The current molecular diagnostic rate is estimated at 50%, with whole-exome sequencing (WES) among the most successful approaches(2-5). For patients in whom WES is uninformative, RNA sequencing (RNA-seq) has shown diagnostic utility in specific tissues and diseases(6-8). This includes muscle biopsies from patients with undiagnosed rare muscle disorders(6,9), and cultured fibroblasts from patients with mitochondrial disorders(7). However, for many individuals, biopsies are not performed for clinical care, and tissues are difficult to access. We sought to assess the utility of RNA-seq from blood as a diagnostic tool for rare diseases of different pathophysiologies. We generated whole-blood RNA-seq from 94 individuals with undiagnosed rare diseases spanning 16 diverse disease categories. We developed a robust approach to compare data from these individuals with large sets of RNA-seq data for controls (n = 1,594 unrelated controls and n = 49 family members) and demonstrated the impacts of expression, splicing, gene and variant filtering strategies on disease gene identification. Across our cohort, we observed that RNA-seq yields a 7.5% diagnostic rate, and an additional 16.7% with improved candidate gene resolution.
|
|
| 2. |
- Jones, Lesley, et al.
(författare)
-
Convergent genetic and expression data implicate immunity in Alzheimer's disease
- 2015
-
Ingår i: Alzheimer's & Dementia. - : Wiley. - 1552-5260 .- 1552-5279. ; 11:6, s. 658-671
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Late-onset Alzheimer's disease (AD) is heritable with 20 genes showing genome-wide association in the International Genomics of Alzheimer's Project (IGAP). To identify the biology underlying the disease, we extended these genetic data in a pathway analysis. Methods: The ALIGATOR and GSEA algorithms were used in the IGAP data to identify associated functional pathways and correlated gene expression networks in human brain. Results: ALIGATOR identified an excess of curated biological pathways showing enrichment of association. Enriched areas of biology included the immune response (P = 3.27 X 10(-12) after multiple testing correction for pathways), regulation of endocytosis (P = 1.31 X 10(-11)), cholesterol transport (P = 2.96 X 10(-9)), and proteasome-ubiquitin activity (P = 1.34 X 10(-6)). Correlated gene expression analysis identified four significant network modules, all related to the immune response (corrected P = .002-.05). Conclusions: The immime response, regulation of endocytosis, cholesterol transport, and protein ubiquitination represent prime targets for AD therapeutics.
|
|
| 3. |
- Escott-Price, Valentina, et al.
(författare)
-
Gene-Wide Analysis Detects Two New Susceptibility Genes for Alzheimer's Disease
- 2014
-
Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:6, s. e94661-
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Alzheimer's disease is a common debilitating dementia with known heritability, for which 20 late onset susceptibility loci have been identified, but more remain to be discovered. This study sought to identify new susceptibility genes, using an alternative gene-wide analytical approach which tests for patterns of association within genes, in the powerful genome-wide association dataset of the International Genomics of Alzheimer's Project Consortium, comprising over 7 m genotypes from 25,580 Alzheimer's cases and 48,466 controls. Principal Findings: In addition to earlier reported genes, we detected genome-wide significant loci on chromosomes 8 (TP53INP1, p = 1.4x10(-6)) and 14 (IGHV1-67 p = 7.9x10(-8)) which indexed novel susceptibility loci. Significance: The additional genes identified in this study, have an array of functions previously implicated in Alzheimer's disease, including aspects of energy metabolism, protein degradation and the immune system and add further weight to these pathways as potential therapeutic targets in Alzheimer's disease.
|
|
| 4. |
- Schoch, Conrad L., et al.
(författare)
-
Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
- 2014
-
Ingår i: Database: The Journal of Biological Databases and Curation. - : Oxford University Press (OUP). - 1758-0463. ; 2014:bau061, s. 1-21
-
Tidskriftsartikel (refereegranskat)abstract
- DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
|
|
| 5. |
- Johnston, Janet A
(författare)
-
A molecular biological study of Alzheimer's disease : investigation of amyloid precursor protein, amyloid precursor-like protein 2 and presenilin-1
- 1997
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The devastating symptoms of Alzheimer's disease result from a progressive regional neurodegenerative process, the cause of which is unknown. Current research suggests that several different mechanisms may be involved, perhaps acting at different points in a common pathological pathway. This thesis explores potential levels of involvement of three molecules likely to be important in this pathway, namely amyloid precursor protein (APP), amyloid precursor-like protein 2 (APLP2) and presenilin-1 (PS- 1). A metabolite of APP, B-amyloid (AB), is found aggregated in abnormal extracellular amyloid plaques in Alzheimer's disease brains. APP missense mutations which can cause Alzheimer's disease have been identified. To investigate the prevalence of such mutations in Sweden, APP exons 16 and 17 were sequenced in 46 individuals affected by Alzheimer's disease (Paper I). The previously identified APP670/671 double mutation was the only abnormality present, demonstrating that these mutations are a not a major cause of Alzheimer's disease in Sweden. Although relatively rare, the APP mutations opened up an important new line of inquiry into the aetiology of Alzheimer's disease. In order to investigate the mechanism(s) of action of the APP670/671 mutation, we determined APP mRNA, protein and AB levels in fibroblast cell lines from 6 mutation-bearing and 6 control family members (Paper II). Mutation-bearing cells released approximately threefold more AB than controls, suggesting a mechanism by which this mutation could lead to the increased AB deposition characteristic of Alzheimer's disease. In order to investigate whether altered mRNA expression of APP or the homologous protein, APLP2, could be involved in the pathogenesis of Alzheimer's disease, quantitative solution hybridisation assays were developed for these mRNAs (Paper III). These assays were characterised and shown to quantify the target mRNAs reproducibly in tissue samples and cell culture systems, before they were used to determine APP and APLP2 mRNA levels in post mortem brains (mid-temporal and superior frontal cortices) from a series of 14 Apolipoprotein E (APOE) genotyped sporadic Alzheimer's disease and 14 control individuals (Paper IV). Inheritance of the APOE 4 allele increases susceptibility to Alzheimer's disease by an unknown mechanism and we wished to determine whether it affected APP or APLP2 mRNA levels. Total APP and APLP2 mRNA levels were reduced in mid-temporal cortex, while the proportion of APP splice forms containing a kunitz-type protease inhibitor insert increased significantly in both brain regions studied. APOE genotype had no effect on target mRNA levels. The accumulation of AB in sporadic Alzheimer's disease cannot therefore be attributed to over-expression of the precursor protein, although APP splicing may be altered in the disease. The PS-I gene, identified in 1995, also carries mutations which are pathogenic for Alzheimer's disease. A quantitative solution hybridisation assay was established and used to determine PS-I mRNA levels in the series of post mortem brains described above, to determine whether the expression of this gene was altered in sporadic Alzheimer's disease (Paper V). There were no significant differences between the levels of PS- I mRNA in the Alzheimer's disease and control groups. PS-I mRNA levels were around 10% that of APP and 30% that of APLP2 mRNA in both cortical regions studied. Significant positive correlations between the levels of PS- I mRNA, APP and APLP2 mRNAs were identified, perhaps indicating that the expression of these genes is co-regulated, or that they are expressed in similar neuronal populations. There is evidence that cerebral cortex affected by Alzheimer's disease is subjected to levels of stress sufficient to induce a heat shock response. Since APP expression is increased in response to heat shock, an altered APP stress response could predispose to AB accumulation. Several PS-I mutations increase AB42/43 production, and we investigated whether they also affected basal APP levels or response to stress by studying the APP heat shock response in Iymphoblastoid cell lines from 8 PS-I mutation-bearing and 9 control members of Alzheimer's disease families (Paper VI). APP mRNA levels increased reversibly following heat shock, followed by a similar increase in APP protein levels. No significant differences were observed between cell lines derived from mutation-bearers and controls, indicating that the five PS-I mutations studied did not affect the normal APP stress response in these cell lines. The studies presented in this thesis indicate that APP mutations causing Alzheimer's disease are rare and that their effects are exerted at the level of protein processing so as to increase the accumulation and deposition of AB. Accumulation of AB in sporadic Alzheimer's disease could not be attributed to over expression of APP or APLP2 mRNA, although APP RNA splicing was altered in affected post mortem brain. PS-I mRNA levels, which were unchanged in Alzheimer's disease post mortem brain, showed positive correlations with cortical APP and APLP2 mRNA levels. PS-I mutations which are pathogenic for Alzheimer's disease did not affect the normal APP stress response in Iymphoblastoid cell lines.
|
|
