Literature DB >> 30963077

Leveraging summary statistics to make inferences about complex phenotypes in large biobanks.

Angela Gasdaska1, Derek Friend2, Rachel Chen3, Jason Westra4, Matthew Zawistowski5, William Lindsey6, Nathan Tintle7.   

Abstract

As genetic sequencing becomes less expensive and data sets linking genetic data and medical records (e.g., Biobanks) become larger and more common, issues of data privacy and computational challenges become more necessary to address in order to realize the benefits of these datasets. One possibility for alleviating these issues is through the use of already-computed summary statistics (e.g., slopes and standard errors from a regression model of a phenotype on a genotype). If groups share summary statistics from their analyses of biobanks, many of the privacy issues and computational challenges concerning the access of these data could be bypassed. In this paper we explore the possibility of using summary statistics from simple linear models of phenotype on genotype in order to make inferences about more complex phenotypes (those that are derived from two or more simple phenotypes). We provide exact formulas for the slope, intercept, and standard error of the slope for linear regressions when combining phenotypes. Derived equations are validated via simulation and tested on a real data set exploring the genetics of fatty acids.

Entities:  

Keywords:  biobank; computational challenges; data security; genetics; genome-wide association study; phenotypes; privacy; single nucleotide variant

Mesh:

Substances:

Year:  2019        PMID: 30963077      PMCID: PMC6417828     

Source DB:  PubMed          Journal:  Pac Symp Biocomput        ISSN: 2335-6928


  6 in total

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Authors:  William S Harris; James V Pottala; Sean M Lacey; Ramachandran S Vasan; Martin G Larson; Sander J Robins
Journal:  Atherosclerosis       Date:  2012-06-07       Impact factor: 5.162

2.  From genotypes to genes: doubling the sample size.

Authors:  P D Sasieni
Journal:  Biometrics       Date:  1997-12       Impact factor: 2.571

3.  Privacy and Security within Biobanking: The Role of Information Technology.

Authors:  Raymond Heatherly
Journal:  J Law Med Ethics       Date:  2016-03       Impact factor: 1.718

4.  A genome-wide association study of saturated, mono- and polyunsaturated red blood cell fatty acids in the Framingham Heart Offspring Study.

Authors:  N L Tintle; J V Pottala; S Lacey; V Ramachandran; J Westra; A Rogers; J Clark; B Olthoff; M Larson; W Harris; G C Shearer
Journal:  Prostaglandins Leukot Essent Fatty Acids       Date:  2014-12-02       Impact factor: 4.006

5.  UK biobank: an open access resource for identifying the causes of a wide range of complex diseases of middle and old age.

Authors:  Cathie Sudlow; John Gallacher; Naomi Allen; Valerie Beral; Paul Burton; John Danesh; Paul Downey; Paul Elliott; Jane Green; Martin Landray; Bette Liu; Paul Matthews; Giok Ong; Jill Pell; Alan Silman; Alan Young; Tim Sprosen; Tim Peakman; Rory Collins
Journal:  PLoS Med       Date:  2015-03-31       Impact factor: 11.069

6.  A genome-wide association study of red-blood cell fatty acids and ratios incorporating dietary covariates: Framingham Heart Study Offspring Cohort.

Authors:  Anya Kalsbeek; Jenna Veenstra; Jason Westra; Craig Disselkoen; Kristin Koch; Katelyn A McKenzie; Jacob O'Bott; Jason Vander Woude; Karen Fischer; Greg C Shearer; William S Harris; Nathan L Tintle
Journal:  PLoS One       Date:  2018-04-13       Impact factor: 3.240

  6 in total
  2 in total

1.  When Biology Gets Personal: Hidden Challenges of Privacy and Ethics in Biological Big Data.

Authors:  Gamze Gürsoy; Arif Harmanci; Haixu Tang; Erman Ayday; Steven E Brenner
Journal:  Pac Symp Biocomput       Date:  2019

2.  Computationally efficient, exact, covariate-adjusted genetic principal component analysis by leveraging individual marker summary statistics from large biobanks.

Authors:  Jack M Wolf; Martha Barnard; Xueting Xia; Nathan Ryder; Jason Westra; Nathan Tintle
Journal:  Pac Symp Biocomput       Date:  2020
  2 in total

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