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- Nicolas, Aude, et al.
(författare)
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Genome-wide Analyses Identify KIF5A as a Novel ALS Gene
- 2018
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Ingår i: Neuron. - : Cell Press. - 0896-6273 .- 1097-4199. ; 97:6, s. 1268-1283.e6
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Tidskriftsartikel (refereegranskat)abstract
- To identify novel genes associated with ALS, we undertook two lines of investigation. We carried out a genome-wide association study comparing 20,806 ALS cases and 59,804 controls. Independently, we performed a rare variant burden analysis comparing 1,138 index familial ALS cases and 19,494 controls. Through both approaches, we identified kinesin family member 5A (KIF5A) as a novel gene associated with ALS. Interestingly, mutations predominantly in the N-terminal motor domain of KIF5A are causative for two neurodegenerative diseases: hereditary spastic paraplegia (SPG10) and Charcot-Marie-Tooth type 2 (CMT2). In contrast, ALS-associated mutations are primarily located at the C-terminal cargo-binding tail domain and patients harboring loss-of-function mutations displayed an extended survival relative to typical ALS cases. Taken together, these results broaden the phenotype spectrum resulting from mutations in KIF5A and strengthen the role of cytoskeletal defects in the pathogenesis of ALS.
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| 5. |
- Fogh, Isabella, et al.
(författare)
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Association of a Locus in the CAMTA1 Gene With Survival in Patients With Sporadic Amyotrophic Lateral Sclerosis
- 2016
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Ingår i: JAMA Neurology. - : American Medical Association (AMA). - 2168-6149 .- 2168-6157. ; 73:7, s. 812-820
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Tidskriftsartikel (refereegranskat)abstract
- IMPORTANCE Amyotrophic lateral sclerosis (ALS) is a devastating adult-onset neurodegenerative disorder with a poor prognosis and a median survival of 3 years. However, a significant proportion of patients survive more than 10 years from symptom onset. OBJECTIVE To identify gene variants influencing survival in ALS. DESIGN, SETTING, AND PARTICIPANTS This genome-wide association study (GWAS) analyzed survival in data sets from several European countries and the United States that were collected by the Italian Consortium for the Genetics of ALS and the International Consortium on Amyotrophic Lateral Sclerosis Genetics. The study population included 4256 patients with ALS (3125 [73.4%] deceased) with genotype data extended to 7 174 392 variants by imputation analysis. Samples of DNA were collected from January 1, 1993, to December 31, 2009, and analyzed from March 1, 2014, to February 28, 2015. MAIN OUTCOMES AND MEASURES Cox proportional hazards regression under an additive model with adjustment for age at onset, sex, and the first 4 principal components of ancestry, followed bymeta-analysis, were used to analyze data. Survival distributions for the most associated genetic variants were assessed by Kaplan-Meier analysis. RESULTS Among the 4256 patients included in the analysis (2589 male [60.8%] and 1667 female [39.2%]; mean [SD] age at onset, 59 [12] years), the following 2 novel loci were significantly associated with ALS survival: at 10q23 (rs139550538; P = 1.87 x 10(-9)) and in the CAMTA1 gene at 1p36 (rs2412208, P = 3.53 x 10(-8)). At locus 10q23, the adjusted hazard ratio for patients with the rs139550538 AA or AT genotype was 1.61 (95% CI, 1.38-1.89; P = 1.87 x 10(-9)), corresponding to an 8-month reduction in survival compared with TT carriers. For rs2412208 CAMTA1, the adjusted hazard ratio for patients with the GG or GT genotype was 1.17 (95% CI, 1.11-1.24; P = 3.53 x 10(-8)), corresponding to a 4-month reduction in survival compared with TT carriers. CONCLUSIONS AND RELEVANCE This GWAS robustly identified 2 loci at genome-wide levels of significance that influence survival in patients with ALS. Because ALS is a rare disease and prevention is not feasible, treatment that modifies survival is the most realistic strategy. Therefore, identification of modifier genes that might influence ALS survival could improve the understanding of the biology of the disease and suggest biological targets for pharmaceutical intervention. In addition, genetic risk scores for survival could be used as an adjunct to clinical trials to account for the genetic contribution to survival.
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- Lindblad-Toh, Kerstin, et al.
(författare)
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Genome sequence, comparative analysis and haplotype structure of the domestic dog.
- 2005
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 438:7069, s. 803-19
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Tidskriftsartikel (refereegranskat)abstract
- Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.
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- Xu, Kerui, et al.
(författare)
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Isolation of a Low Number of Sperm Cells from Female DNA in a Glass-PDMS-Glass Microchip via Bead-Assisted Acoustic Differential Extraction
- 2019
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Ingår i: Analytical Chemistry. - : American Chemical Society (ACS). - 0003-2700 .- 1520-6882. ; 91:3, s. 2186-2191
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Tidskriftsartikel (refereegranskat)abstract
- We report an improved separation method for the isolation of sperm cells from dilute, "large volume" samples containing female DNA using bead-assisted acoustic trapping. In an enclosed glass-PDMS-glass (GPG) resonator, we exploit a three-layer microfluidic architecture to generate "trapping nodes" in ultrasonic standing waves. We investigate the dependence of trapping efficiency on particle concentration for both sperm cells and polymeric beads. After determination of the critical concentration of polymeric beads required to seed the trapping event, sperm cells in dilute solution are trapped as a result of the enhanced secondary radiation force (SRF). Sperm-cell-containing samples with volumes up to 300 μL and cell concentrations as low as ∼10 cells/μL are amenable to effective trapping in the presence of an abundance of female DNA in solution. Complete processing of samples is accomplished with separation of the female and male fractions within 15 min. We demonstrate that the collected fractions are amenable to subsequent DNA extraction, short tandem repeat PCR, and the generation of STR profiles for the isolated sperm cells.
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| 8. |
- Evander, Mikael, et al.
(författare)
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Acoustic Differential Extraction - ultrasonic DNA-extraction from sexual assault evidence
- 2007
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Ingår i: International Congress on Ultrasonics. ; 1, s. 151-151
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Konferensbidrag (refereegranskat)abstract
- Isolation of the male and female DNA is one of the most important steps in obtaining the DNA profile of the perpetrator in sexual assault cases. The sample is obtained by taking a vaginal swab containing both epithelial cells from the female and sperm cells from the male from the victim. The purity of the extracted male fraction decides whether or not a single-source DNA profile of the suspect will be obtained or not. The existing techniques are have poor separation efficiency, time-consuming, labour-intensive and are neither easily automated nor integrated with further analysis steps. A novel method of DNA extraction based on ultrasonic trapping, Acoustic Differential Extraction, has been developed. A microfluidic device using laminar flow valving and miniature PZT transducers retains the sperm cells while mobilizing the female fraction into a separate outlet. The device was evaluated using a mock sexual assault sample and the separated fractions were analyzed using quantitative PCR and STR-profiling. A 16-fold enrichment of the male fraction, making an originally hard-to-detect-male DNA profile readily profiled, has been demonstrated. The STR-profiling of the male and female fractions showed a male fraction purity of up to 99 % making it possible to obtain a single-source DNA-profile of the suspect. The microfluidic format of the device makes it possible to downscale the sample time from 4-8 hours to 10 minutes. It is also possible to integrate this method with further downstream analysis steps necessarey for the full forensic DNA analysis.
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| 9. |
- Evander, Mikael, et al.
(författare)
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Using Acoustic Differential Extraction to enhance analysis of sexual assualt evidence on a valveless glass microdevice
- 2006
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Ingår i: Proceedings of µTAS 2006 Conference. ; 2, s. 1055-1057
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Konferensbidrag (refereegranskat)abstract
- The isolation of male and female DNA is an important step in the analysis of sexual assault evidence. A vaginal swab with female epithelial cells and male sperm cells is obtained from the female, and it is vital to separate the male and female fractions in order to obtain a single-source DNA profile of the suspect. In the case of a low abundance of sperm cells, it is very important that no cells are lost in the isolation step. The conventional isolation method used in the forensic DNA laboratories, differential extraction, is a time-consuming step, requiring up to 24 hours. It is neither highly amenable to automation, nor can it be easily integrated with other steps of the analysis. Therefore, a novel method of performing the isolation of male and female fractions of biological material from sexual assault evidence has been developed, termed acoustic differential extraction (ADE). After selectively lysing the female epithelial cells while keeping the sperm cells intact, the sample, now containing sperm cells and female cell lysate, is infused in a 900 μm wide and 70 μm deep microfabricated glass channel with miniature piezoelectric transducers mounted at the bottom of the channel, as shown in Figure 1. Upon activation of the ultrasound, the sperm cells will be trapped in a standing wave1 while free DNA will not be retained. The sperm cells, levitated in the 3D fluidic space above the transducer, can be washed with buffer and the unretained biological material directed to an output reservoir. Using laminar flow valving2, the sperm cells can be released and directed into a separate output reservoir in anticipation of DNA analysis, see Figure 2. With the purpose of evaluating the ADE microdevice for the collection of the two output fractions (male and female), preliminary work used a mock sexual assault sample created with polystyrene microparticles as sperm cells and Evan's Blue dye as female cell lysate. The particles were trapped over the transducer and the dye was directed to the female outlet reservoir as shown in Figure 3. After washing the particles, the ultrasound was deactivated and the flow redirected in order to collect the particles in the male outlet reservoir. A biological sample consisting of sperm cells and lysed female epithelial cells was subsequently tested by infusion into the device for five minutes while trapping the sperm cells over the transducer (Figure 4). The trapped sperm cells were washed with PBS for five minutes, then released and collected for analysis off-chip. DNA from the isolated cells was extracted with a commercial DNA extraction kit and analyzed with a duplex quantitative PCR assay3 to show the sample purity. An example of the qPCR data obtained is provided in Table 1. The results show that a highly-enriched sperm cell fraction can be obtained with the ADE technique. It is reasonable to expect that this technique can be integrated with on-chip downstream sample processing, e.g. DNA extraction and amplification. This would greatly diminish the analysis time from 24 hours to approximately 60 minutes. The time savings, in combination with the possibility to create a fully automated system, gives the ADE technique the potential to significantly alter the means by which sexual assault evidence is processed in crime laboratories today.
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| 10. |
- Norris, Jessica Voorhees, et al.
(författare)
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Acoustic differential extraction for forensic analysis of sexual assault evidence.
- 2009
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Ingår i: Analytical Chemistry. - : American Chemical Society (ACS). - 1520-6882 .- 0003-2700. ; 81:15, s. 6089-6095
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Tidskriftsartikel (refereegranskat)abstract
- Forensic DNA analysis of samples obtained from sexual assault evidence relies on separation of male and female components of the recovered genetic material. The conventional separation method used by crime laboratories, differential extraction (DE), is one of the most time-consuming sample preparation steps, requires extensive sample handling, is difficult to automate, and often results in inefficient separation of female DNA from the male sample components. To circumvent conventional DE, acoustic differential extraction (ADE) analysis was developed on a microfluidic device. The ADE method relies on acoustic trapping of sperm cells in the presence of epithelial cell lysate (which is unretained), and laminar flow valving to direct the male and female fractions to separate outlets. Following the separation of sperm from epithelial cell lysate, DNA extraction, quantitation, amplification, and separation were performed using conventional laboratory methods. The results show that highly purified male and female fractions can be obtained with the ADE microdevice from mock sexual assault samples in 14 min. ADE analysis provides the potential to significantly alter the means by which sexual assault evidence is processed in crime laboratories.
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