Genomics Research. May 31, Malvika Pillai

Transcription

1 Genomics Research May 31, 2018 Malvika Pillai

2 Outline for Research Discussion Why Informatics Read journal articles! Example Paper Presentation Research Pipeline

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4 How To Read A Paper If I m aiming to just get the main points, I ll read the abstract, hop to the figures, and scan the discussion for important points. I think the figures are the most important part of the paper, because the abstract and body of the paper can be manipulated and shaped to tell a compelling story. Then anything I m unclear about, I head to the methodology. If I want to delve deeper into the paper, I typically read it in its entirety and then also read a few of the previous papers from that group or other articles on the same topic. If there is a reference after a statement that I find particularly interesting or controversial, I also look it up. Should I need more detail, I access any provided data repositories or supplemental information. Then, if the authors' research is similar to my own, I see if their relevant data match our findings or if there are any inconsistencies. If there are, I think about what could be causing them. Additionally, I think about what would happen in our model if we used the same methods as they did and what we could learn from that. Sometimes, it is also important to pay attention to why the authors decided to conduct an experiment in a certain way. Did the authors use an obscure test instead of a routine assay, and why would they do this? - Jeremy C. Borniger, doctoral candidate in neuroscience at Ohio State University, Columbus

5 Example Presentation

6 Objectives Estimate the heritability and familial environmental patterns of 149 diseases Infer the genetic and environmental correlations for disease pairs from a set of 29 complex diseases

7 Dataset Truven Health MarketScan Commercial Claims and Encounters Database 115,805,687 individuals 56,003,690 policies Subset: 481,657 unique individuals 128,989 families

8 Definitions Trait s narrow-sense heritability!""#$#%& (&)&$#* %!+#!)*& $,$!-./&),$0.#* %!+#!)*& Environmental trait.+&%&)$!1#-#$0 $,$!- "#2&!2&32.&*#4#*./&),$0.#* %!+#!)*&

9 Population Characteristics

10 Model Selection DIC = Deviance Information Criterion G = additive genetics F = common family environment S = common sibling environment C = environment common for parental couples

11 Heritability & Preventability Estimates

12 Prevalence vs. Heritability

13 Methods Multivariate, generalized, linear mixed model Infer: Genetic effects associated with pedigree Environmental effects shared by couples Environmental effects shared by siblings Environmental effects shared within families Unique environmental effects

14 Methods MCMCglmm package in R MCMC = Markov chain Monte Carlo Pedigree Simulation Heritability Comparison Comparison with GWAS genetic correlations

15 Takeaways Examine genetic and environmental determinants in disease classification Improved results in comparison to that of previously published work 84 first-time estimates

16 Any Questions?

17 Research Pipeline: Hands-On Exploration Next Class

18 Group Discussion Group 1: Paris + Kerani Group 2: Lapresha + Joseph Group 3: Dara + Miguel + Kashley 2017 Monitoring biomedical literature for post-market safety purposes by analyzing networks of text-based coded information PMID: Surveillance of Peripheral Arterial Disease Cases Using Natural Language Processing of Clinical Notes PMID: Development of a Framework for Large Scale Three-Dimensional Pathology and Biomarker Imaging and Spatial Analytics PMID:

19 Present Introduction Background on the topic Methods What they did (whiteboard it or draw it out) Results How successful were they Conclusions/Takeaways Interesting references Something interesting in the paper Something you want to learn more about / didn t understand