| 1. |
- Brownstein, Catherine A., et al.
(författare)
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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
- 2014
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:3, s. R53-
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Tidskriftsartikel (refereegranskat)abstract
- Background: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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| 2. |
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| 3. |
- Sieberts, SK, et al.
(författare)
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Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis
- 2016
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 7, s. 12460-
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Tidskriftsartikel (refereegranskat)abstract
- Rheumatoid arthritis (RA) affects millions world-wide. While anti-TNF treatment is widely used to reduce disease progression, treatment fails in ∼one-third of patients. No biomarker currently exists that identifies non-responders before treatment. A rigorous community-based assessment of the utility of SNP data for predicting anti-TNF treatment efficacy in RA patients was performed in the context of a DREAM Challenge (http://www.synapse.org/RA_Challenge). An open challenge framework enabled the comparative evaluation of predictions developed by 73 research groups using the most comprehensive available data and covering a wide range of state-of-the-art modelling methodologies. Despite a significant genetic heritability estimate of treatment non-response trait (h2=0.18, P value=0.02), no significant genetic contribution to prediction accuracy is observed. Results formally confirm the expectations of the rheumatology community that SNP information does not significantly improve predictive performance relative to standard clinical traits, thereby justifying a refocusing of future efforts on collection of other data.
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| 4. |
- Dewan, Ramita, et al.
(författare)
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Pathogenic Huntingtin Repeat Expansions in Patients with Frontotemporal Dementia and Amyotrophic Lateral Sclerosis.
- 2021
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Ingår i: Neuron. - : Elsevier BV. - 1097-4199 .- 0896-6273. ; 109:3, s. 448-460.e4
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Tidskriftsartikel (refereegranskat)abstract
- We examined the role of repeat expansions in the pathogenesis of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) by analyzing whole-genome sequence data from 2,442 FTD/ALS patients, 2,599 Lewy body dementia (LBD) patients, and 3,158 neurologically healthy subjects. Pathogenic expansions (range, 40-64 CAG repeats) in the huntingtin (HTT) gene were found in three (0.12%) patients diagnosed with pure FTD/ALS syndromes but were not present in the LBD or healthy cohorts. We replicated our findings in an independent collection of 3,674 FTD/ALS patients. Postmortem evaluations of two patients revealed the classical TDP-43 pathology of FTD/ALS, as well as huntingtin-positive, ubiquitin-positive aggregates in the frontal cortex. The neostriatal atrophy that pathologically defines Huntington's disease was absent in both cases. Our findings reveal an etiological relationship between HTT repeat expansions and FTD/ALS syndromes and indicate that genetic screening of FTD/ALS patients for HTT repeat expansions should be considered.
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| 5. |
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| 6. |
- Zou, J, et al.
(författare)
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A primer on deep learning in genomics
- 2019
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Ingår i: Nature genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 51:1, s. 12-18
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Tidskriftsartikel (refereegranskat)
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| 7. |
- Hemati, N., et al.
(författare)
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Effect of Rare Earth Elements on the Microstructural and Mechanical Properties of ZK60 Alloy after T5 Treatment
- 2022
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Ingår i: Russian Journal of Non-Ferrous Metals = Izvestiya VUZ. Tsvetnaya Metallurgiya. - : Springer Nature. - 1067-8212 .- 1934-970X. ; 63:2, s. 223-236
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Tidskriftsartikel (refereegranskat)abstract
- In this study, the microstructure and mechanical properties of ZK60 extruded alloy were investigated after adding 3 wt % of Ce and Y and T5 operation. The microstructure of the base alloy consists of alpha-Mg and Mg7Zn3. In addition to these phases, MgZn2Ce and Mg3Y2Zn3 phases are formed by adding Ce and Y, respectively. The addition of rare earth elements reduces the grain size of the base alloy from 6.1 mu m to less than 3 mu m. The volume fraction of precipitates also increases because of the additions. After T5 operation for different times, it was observed that the hardness peak (88 HV) for the base alloy is achieved after 18 hours. However, the peak hardness of alloys containing rare earth elements occurred in 24 hours. Increasing the aging time results in an increase in the grain size of the base alloy, while it led to a slight increase in the grain size of alloys containing rare earth elements. The higher hardness at the peak age of all studied alloys is explained based on the increase in the volume fraction of precipitates during this operation. The delay in the peak age in alloys containing rare earth elements is due to the delay in the formation of beta(2’) precipitates. The shear punch test results of extruded alloys show that in alloys containing Ce and Y the shear strength is 156 and 160 MPa, respectively. While this value is about 148 MPa for the base alloy. At the peak age, this strength for ZK60-Ce and ZK60-Y alloys increases by 11% and 13%, respectively. Higher strength and hardness in Y-containing alloys are due to the simultaneous strengthening of solid solution and precipitates along with the formation of precipitates with high thermal stability.
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| 8. |
- Banijamali, S. M., et al.
(författare)
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Effect of Ce Addition on the Tribological Behavior of ZK60 Mg-Alloy
- 2021
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Ingår i: Metals and Materials International. - : Springer. - 1598-9623 .- 2005-4149. ; 27:8, s. 2732-2742
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Tidskriftsartikel (refereegranskat)abstract
- The present work aims to study the tribological behavior of an extruded ZK60 alloy in the presence of Ce; in a previous study, among ZK60 alloys with different Ce addition rates, an alloy with 3 wt% of Ce was found to exhibit the most promising mechanical (e.g., hardness and strengths) properties, while its wear behavior remained unknown. The results of microstructural examinations by optical and electron microscopes show that Ce addition reduces the grain size from 6.1 to 2.0 μm. Besides, in addition to the precipitates already distributed in the base alloy (Mg7Zn3), Ce could promote the formation of a new precipitate (MgZn2Ce), increasing the total fraction of the precipitates. These microstructural evolutions enhance the strengths of the studied ZK60 alloy, as the yield and tensile strengths increase from 212 to 308 MPa and from 297 to 354 MPa, respectively. A pin on disc tribometer was employed to study the wear behavior of the developed alloy under different normal loads (5, 20, 40, and 60 N). The results show that the base and Ce-added alloys exhibit almost a similar frictional behavior, while the wear resistance of the Ce-added alloy is higher within the load ranges applied: (i) in low load conditions (5 and 20 N), where the abrasive wear is the active mechanism, the precipitates in the Ce-added alloy could enhance the wear resistance. (ii) Under the load of 40 N, oxidative wear is also an operative wear mechanism, leading to a sharp increase in the wear rate of the alloys. In this condition, Ce could provide a protective oxide layer, which could improve the wear resistance of the alloy. (iii) At a load of 60 N, both studied alloys exhibit a similar wear rate due to a severe oxidation condition. Therefore, beyond this loading condition, the microstructural evolutions (e.g., change in precipitation behavior) caused by Ce addition can no longer contribute to the enhancement of wear resistance.
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| 9. |
- Schork, Andrew J, et al.
(författare)
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All SNPs are not created equal: genome-wide association studies reveal a consistent pattern of enrichment among functionally annotated SNPs.
- 2013
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Ingår i: PLoS genetics. - : Public Library of Science (PLoS). - 1553-7404. ; 9:4
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Tidskriftsartikel (refereegranskat)abstract
- Recent results indicate that genome-wide association studies (GWAS) have the potential to explain much of the heritability of common complex phenotypes, but methods are lacking to reliably identify the remaining associated single nucleotide polymorphisms (SNPs). We applied stratified False Discovery Rate (sFDR) methods to leverage genic enrichment in GWAS summary statistics data to uncover new loci likely to replicate in independent samples. Specifically, we use linkage disequilibrium-weighted annotations for each SNP in combination with nominal p-values to estimate the True Discovery Rate (TDR = 1-FDR) for strata determined by different genic categories. We show a consistent pattern of enrichment of polygenic effects in specific annotation categories across diverse phenotypes, with the greatest enrichment for SNPs tagging regulatory and coding genic elements, little enrichment in introns, and negative enrichment for intergenic SNPs. Stratified enrichment directly leads to increased TDR for a given p-value, mirrored by increased replication rates in independent samples. We show this in independent Crohn's disease GWAS, where we find a hundredfold variation in replication rate across genic categories. Applying a well-established sFDR methodology we demonstrate the utility of stratification for improving power of GWAS in complex phenotypes, with increased rejection rates from 20% in height to 300% in schizophrenia with traditional FDR and sFDR both fixed at 0.05. Our analyses demonstrate an inherent stratification among GWAS SNPs with important conceptual implications that can be leveraged by statistical methods to improve the discovery of loci.
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