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StaGe (statistical genetics)

AP (StaGE) Journal Club

A new journal club, started in Nov 2018, focusing broadly on topics in statistical genetics. The aim is to provide a inter-departmental forum where researchers and students from different groups can meet to discuss recent stat gen publications (both methods and/or applications). Anybody who is interested is welcome.

 

The journal club will be held on Wednesdays at 10 am in the lunch room at BiRC, building 1110.

Meetings

2020

January 22, 2020: Jakob will lead the discussion on the paper by Yin et al. titled: “Integrating Clinical Data and Imputed Transcriptome from GWAS to Uncover Complex Disease Subtypes: Applications in Psychiatry and Cardiology” -> https://www.cell.com/ajhg/fulltext/S0002-9297(19)30400-8?dgcid=raven_jbs_etoc_email#.XemY0eMkqv4.twitter

Jan 8, 2020: Aguirre et al. (bioRxiv, 2019)


2019

Nov 20, 2019: Florian: "Efficient toolkit implementing best practices for principal component analysis of population genetic data". www.biorxiv.org/content/10.1101/841452v1

 

Nov 13, 2019: Maria Izabel: Shi et al. (bioRxiv, 2019). "Population-specific causal disease effect sizes in functionally important regions impacted by selection". www.biorxiv.org/content/10.1101/803452v2

Oct 23, 2019: Zeynep Yilmaz will lead a discussion on Watson et al., titled: “Genome-wide association study identifies eight risk loci and implicates metabo-psychiatric origins for anorexia nervosa”.   

Oct 9, 2019: Yengo et al. (Nat Comm, 2019)

 

Oct 2, 2019: Hujoel et al. (bioRxiv, 2019)

Sep 25, 2019: Kalle will discuss the paper by Vattikuti et al. (GigaScience, 2014) titled: “Applying compressed sensing to genome-wide association studies”.

 

Sep 18, 2019: Ganna et al. (Science, 2019)

Sep 2, 2019: Doug Speed: : Zhang et al. (Genome Medicine, 2019). https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-019-0667-1

July 3, 2019: Clara: the paper by Hakhamanesh et al. (bioRxiv, 2019) titled: Variable prediction accuracy of polygenic scores within an ancestry group.

June 26, 2019: two presenters and two papers: Kalle and Bjarni will present two similar papers in eLIFE:

  • Berg et al. (eLIFE). Reduced signal for polygenic adaptation of height in UK Biobank.
  • Sohail et al. (eLIFE). Polygenic adaptation on height is overestimated due to uncorrected stratification in genome-wide association studies.

June 12, 2019: Florian: paper by Chung et al. (Nat Commun, 2019) titled "Efficient cross-trait penalized regression increases prediction accuracy in large cohorts using secondary phenotypes".

May 29, 2019: Doug Speed: paper by Dahl et al. (bioRxiv, 2019) titled "GxEMM: Extending linear mixed models to general gene-environment interactions".

May 8, 2019: Kalle L.: paper by Li et al. (Nat Genet, 2019) titled "Dynamic Scan Procedure for Detecting  Rare-Variant Association Regions in Whole-Genome Sequencing Studies".

April 24, 2019: Thomas Als: paper by Martin et al. (Nat Genet, 2019) titled "Clinical use of current polygenic risk scores may exacerbate health disparities".

April 3, 2019: Jakob Grove: paper by Wainschtein et al. (bioRxiv, 2019) titled "Recovery of trait heritability from whole genome sequence data".  

March 20, 2019: Emil Maag: paper by Zhou et al. (Nat Genet, 2018) titled "Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies".  

March 6, 2019: Clara Albiñana: paper by Schork et al. (bioRxiv, 2019) titled "A genome-wide association study of shared risk across psychiatric disorders implicates gene regulation during fetal neurodevelopment." 

Feb 20, 2019: Qianqian Zhang: a paper by Lloyd-Jones et al. (bioRxiv, 2019) titled "Improved polygenic prediction by Bayesian multiple regression on summary statistics”

Jan 30, 2019: Doug Speed: a paper by Hou et al. (bioRxiv, 2018) titled "Accurate estimation of SNP-heritability from biobank-scale data irrespective of genetic architecture”.

Jan 16, 2019: Bjarni Vilhjalmsson: a paper by Moore et al. (Nat Genet, 2018) titled "A linear mixed-model approach to study multivariate gene-environment interactions”.

Jan 9, 2019: Clara Albiñana: "Analysis of shared heritability in common disorders of the brain" by the Brainstorm Consortium

2018

Dec 19, 2018: Thomas Bataillon: a paper by Stephens (Biostatistics, 2017) titled "False discovery rates: a new deal”.

Dec 5, 2018: Maria Izabel Alves: paper by Urbut et al. (Nat Genet, 2018) titled "Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions”.

Nov. 28, 2018: Doug Speed: Disease heritability enrichment of regulatory elements is concentrated in elements with ancient sequence age and conserved function across species by Hujoel et al.
https://www.biorxiv.org/content/biorxiv/early/2018/09/18/420166.full.pdf

Nov. 14, 2018: Kalle Leppälä: paper by O’Conner et al.(bioRxiv, 2018) titled "Polygenicity of complex traits is explained by negative selection”.

Nov 7, 2018: Bjarni Vilhjalmsson: a paper by O’Connor and Price (Nat Genet 2018), titled “Distinguishing genetic correlation from causation across 52 diseases and complex traits”.