1. Ethnic and region-specific genetic risk variants of stroke and its comorbid conditions can define the variations in the burden of stroke and its phenotypic traits

    This article has 3 authors:
    1. Rashmi Sukumaran
    2. Achuthsankar S Nair
    3. Moinak Banerjee
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This paper provides a useful analysis of the variation of the burden of strokes across geographic regions, finding differences in the relationship between strokes and their comorbidities. This dataset and the correlations found within will be a resource for directing the focus of future investigations. The results are technically solid, but there are cases where statistical analyses are yet to be carried out to support statements of statistical significance.

    Reviewed by eLife

    This article has 7 evaluationsAppears in 1 listLatest version Latest activity
  2. Risk factors affecting polygenic score performance across diverse cohorts

    This article has 22 authors:
    1. Daniel Hui
    2. Scott Dudek
    3. Krzysztof Kiryluk
    4. Theresa L Walunas
    5. Iftikhar J Kullo
    6. Wei-Qi Wei
    7. Hemant Tiwari
    8. Josh F Peterson
    9. Wendy K Chung
    10. Brittney H Davis
    11. Atlas Khan
    12. Leah C Kottyan
    13. Nita A Limdi
    14. Qiping Feng
    15. Megan J Puckelwartz
    16. Chunhua Weng
    17. Johanna L Smith
    18. Elizabeth W Karlson
    19. Regeneron Genetics Center
    20. Penn Medicine BioBank
    21. Gail P Jarvik
    22. Marylyn D Ritchie
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This study presents a convincing analysis of the effects of covariates, such as age, sex, socio-economic status, or biomarker levels, on the predictive accuracy of polygenic scores for body mass index; The work is further supported by important approaches for improving prediction accuracy by accounting for such covariates across a variety of association studies. The authors did a commendable job addressing reviewer suggestions and comments. The work will be of interest to colleagues using and developing methods for phenotypic prediction based on polygenic scores.

    Reviewed by eLife

    This article has 8 evaluationsAppears in 1 listLatest version Latest activity
  3. De novo variants in PLCG1 are associated with hearing impairment, ocular pathology, and cardiac defects

    This article has 23 authors:
    1. Mengqi Ma
    2. Yiming Zheng
    3. Shenzhao Lu
    4. Xueyang Pan
    5. Kim C. Worley
    6. Lindsay C. Burrage
    7. Lauren S. Blieden
    8. Aimee Allworth
    9. Wei-Liang Chen
    10. Giuseppe Merla
    11. Barbara Mandriani
    12. Jill A. Rosenfeld
    13. David Li-Kroeger
    14. Debdeep Dutta
    15. Shinya Yamamoto
    16. Michael F. Wangler
    17. Undiagnosed Diseases Network
    18. Ian A. Glass
    19. Sam Strohbehn
    20. Elizabeth Blue
    21. Paolo Prontera
    22. Seema R. Lalani
    23. Hugo J. Bellen
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This important study reveals how Drosophila may be used to investigate the role of missense variants in the gene PLCG1 related to human disease in case studies. The evidence that most of these variants have a gain-of-function effect in the fly is convincing and supportive of their pathogenic effect. With some additional control experiments to assess overexpression toxicity, this work would be of relevance to human and Drosophila geneticists alike.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  4. Discovery of runs-of-homozygosity diplotype clusters and their associations with diseases in UK Biobank

    This article has 3 authors:
    1. Ardalan Naseri
    2. Degui Zhi
    3. Shaojie Zhang
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This study is of potential interest to readers in human genetics and quantitative genetics, as it presents a new method for homozygosity mapping in population-scale datasets, based on an innovative computational algorithm that efficiently identifies runs-of-homozygosity (ROH) segments shared by many individuals. Although the method is innovative and has the potential to be broadly useful, its power and limitations have not yet been adequately evaluated. The application of this new method to the UK Biobank dataset identifies several interesting associations, but it remains currently unclear under what conditions the new approach can provide additional power over existing genome-wide association study methods.

    Reviewed by eLife

    This article has 5 evaluationsAppears in 1 listLatest version Latest activity
  5. Explaining the counter-intuitive effectiveness of trophectoderm biopsy for PGT-A using computational modelling

    This article has 5 authors:
    1. Benjamin M Skinner
    2. Manuel Viotti
    3. International Registry of Mosaic Embryo Transfers (IRMET)
    4. Darren K Griffin
    5. Peter JI Ellis
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This study presents a valuable computational model for elaborating on the interpretation of chromosomal mosaicism in preimplantation embryos. The evidence supporting the claims of the authors is incomplete due to the assumption that is possible to quantify the cells in the embryo, oversimplification of mitotic errors, and the inclusion of the self-correction premise. The work will be of interest to embryologists, and geneticists working on reproductive medicine.

    Reviewed by eLife

    This article has 5 evaluationsAppears in 1 listLatest version Latest activity
  6. Allelic strengths of encephalopathy-associated UBA5 variants correlate between in vivo and in vitro assays

    This article has 13 authors:
    1. Xueyang Pan
    2. Albert N Alvarez
    3. Mengqi Ma
    4. Shenzhao Lu
    5. Michael W Crawford
    6. Lauren C Briere
    7. Oguz Kanca
    8. Shinya Yamamoto
    9. David A Sweetser
    10. Jenny L Wilson
    11. Ruth J Napier
    12. Jonathan N Pruneda
    13. Hugo J Bellen
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      The authors establish a Drosophila model to assess the severity of disease-linked alleles of Uba5. Using both in vivo and in vitro experiments, this valuable study demonstrates the alleles fall into mild, intermediate, and severe classes, with convincing evidence to support their conclusion. This well-executed study establishes a model for further characterization of Uba5-related phenotypes in a powerful model system.

    Reviewed by eLife

    This article has 10 evaluationsAppears in 1 listLatest version Latest activity
  7. Novel discoveries and enhanced genomic prediction from modelling genetic risk of cancer age-at-onset

    This article has 7 authors:
    1. Ekaterina S. Maksimova
    2. Sven E. Ojavee
    3. Kristi Läll
    4. Marie C. Sadler
    5. Reedik Mägi
    6. Zoltan Kutalik
    7. Matthew R. Robinson
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This manuscript is a useful contribution to the field of complex trait genomics. The study does have some real strengths, such as focusing on cancer age-of-onset, developing methods for this unusual trait and using two cohorts. However, the significance of findings is difficult to evaluate without further comparisons and validations, leaving the work in its current form incomplete.

    Reviewed by eLife

    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  8. Multi-omics analysis in human retina uncovers ultraconserved cis -regulatory elements at rare eye disease loci

    This article has 8 authors:
    1. Victor Lopez Soriano
    2. Alfredo Dueñas Rey
    3. Rajarshi Mukherjee
    4. Genomics England Research Consortium
    5. Frauke Coppieters
    6. Miriam Bauwens
    7. Andy Willaert
    8. Elfride De Baere

    Reviewed by Review Commons

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  9. Trumpet plots: Visualizing The Relationship Between Allele Frequency And Effect Size In Genetic Association Studies

    This article has 4 authors:
    1. Lucia Corte
    2. Lathan Liou
    3. Paul F. O’Reilly
    4. Judit García-González
    This article has been curated by 1 group:
    • Curated by GigaByte

      **Editors Assessment: **

      This work presents a new standardized graphical approach for visualizing genetic associations across a wide range of allele frequencies. These proposed TrumpetPlots have a distinctive trumpet shape, hence the proposed name. With the majority of variants having low frequency and small effects, while a small number of variants have higher frequency and larger effects, this view can help to provide new and valuable insights into the genetic basis of traits and diseases, and also help prioritize efforts to discover new risk variants. The tool is provided as a novel R package and R Shiny application and to demonstrate its use the article illustrates the distribution of variant effect sizes across the allele frequency range for over 100 continuous traits available in the UK Biobank. After some problems in testing the package is now available and easy to deploy via CRAN.

      *This assessment refers to version 1 of this preprint. *

    Reviewed by GigaByte

    This article has 3 evaluationsAppears in 2 listsLatest version Latest activity
  10. Genetic inactivation of zinc transporter SLC39A5 improves liver function and hyperglycemia in obesogenic settings

    This article has 27 authors:
    1. Shek Man Chim
    2. Kristen Howell
    3. John Dronzek
    4. Weizhen Wu
    5. Cristopher Van Hout
    6. Manuel AR Ferreira
    7. Bin Ye
    8. Alexander Li
    9. Susannah Brydges
    10. Vinayagam Arunachalam
    11. Anthony Marcketta
    12. Adam E Locke
    13. Jonas Bovijn
    14. Niek Verweij
    15. Tanima De
    16. Luca Lotta
    17. Lyndon Mitnaul
    18. Michelle LeBlanc
    19. Regeneron Genetics Center
    20. David J Carey
    21. Olle Melander
    22. Alan Shuldiner
    23. Katia Karalis
    24. Aris N Economides
    25. Harikiran Nistala
    26. DiscovEHR collaboration
    27. Regeneron Genetics Center
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This fundamental study substantially advances our understanding of the role of zinc in metabolism, specifically a newly established clinical link between mutations in the zinc transporter SLC39A5, elevated serum zinc levels, and a reduction in the risk of Type 2 Diabetes. The provided evidence is solid with state-of-the-art genetic analysis of large human cohorts followed by a comprehensive analysis of a mouse SLC39A5 knockout mutant, establishing that SLC39A5 plays a role in hepatic lipid handling through AMPK signaling, although the limited analysis of a pancreatic phenotype that has previously been described constitutes a weakness. This study will be of relevance to researchers interested in metabolism, fatty liver disease, and the biology of trace elements.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
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