Enabling Genomic-Phenomic Association Discovery without Sacrificing Anonymity
Publication Date
February 06, 2013
Journal
PLOS ONE
Authors
Raymond D. Heatherly, Grigorios Loukides, Joshua C. Denny, Jonathan L. Haines, et al
Volume
8
Issue
2
Pages
e53875
DOI
http://doi.org/10.1371/journal.pone.0053875
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0053875
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/23405076
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3566194
Europe PMC
http://europepmc.org/abstract/MED/23405076
Web of Science
000315153400020
Scopus
84873528324
Mendeley
http://www.mendeley.com/research/enabling-genomicphenomic-association-discovery-without-sacrificing-anonymity
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Mendeley | Further Information

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Scopus | Further Information

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  • {"files"=>["https://ndownloader.figshare.com/files/494405"], "description"=>"<p>Distribution of -value changes for associations between clinical conditions and SNP rs2476601 for left) , middle) , and right) .</p>", "links"=>[], "tags"=>["changes", "associations", "conditions", "snp", "rs2476601"], "article_id"=>164920, "categories"=>["Biological Sciences", "Medicine", "Genetics"], "users"=>["Raymond D. Heatherly", "Grigorios Loukides", "Joshua C. Denny", "Jonathan L. Haines", "Dan M. Roden", "Bradley A. Malin"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0053875.g009"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_value_changes_for_associations_between_clinical_conditions_and_SNP_rs2476601_for_left_middle_and_right_/164920", "title"=>"Distribution of -value changes for associations between clinical conditions and SNP rs2476601 for left) , middle) , and right) .", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-19 15:52:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/494516"], "description"=>"<p>Distribution of -value changes for associations between clinical conditions and SNP rs3135388 for left) , middle) , and right) .</p>", "links"=>[], "tags"=>["changes", "associations", "conditions", "snp", "rs3135388"], "article_id"=>165034, "categories"=>["Biological Sciences", "Medicine", "Genetics"], "users"=>["Raymond D. Heatherly", "Grigorios Loukides", "Joshua C. Denny", "Jonathan L. Haines", "Dan M. Roden", "Bradley A. Malin"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0053875.g010"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_value_changes_for_associations_between_clinical_conditions_and_SNP_rs3135388_for_left_middle_and_right_/165034", "title"=>"Distribution of -value changes for associations between clinical conditions and SNP rs3135388 for left) , middle) , and right) .", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-19 15:53:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/494612"], "description"=>"<p>Distribution of -value changes for associations between clinical conditions and SNP rs6457620 for left) , middle) , and right) .</p>", "links"=>[], "tags"=>["changes", "associations", "conditions", "snp", "rs6457620"], "article_id"=>165130, "categories"=>["Biological Sciences", "Medicine", "Genetics"], "users"=>["Raymond D. Heatherly", "Grigorios Loukides", "Joshua C. Denny", "Jonathan L. Haines", "Dan M. Roden", "Bradley A. Malin"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0053875.g011"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_value_changes_for_associations_between_clinical_conditions_and_SNP_rs6457620_for_left_middle_and_right_/165130", "title"=>"Distribution of -value changes for associations between clinical conditions and SNP rs6457620 for left) , middle) , and right) .", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-19 15:53:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/494689"], "description"=>"<p>Distribution of -value changes for associations between clinical conditions and SNP rs17234657 for left) , middle) , and right) .</p>", "links"=>[], "tags"=>["changes", "associations", "conditions", "snp", "rs17234657"], "article_id"=>165207, "categories"=>["Biological Sciences", "Medicine", "Genetics"], "users"=>["Raymond D. Heatherly", "Grigorios Loukides", "Joshua C. Denny", "Jonathan L. Haines", "Dan M. Roden", "Bradley A. Malin"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0053875.g012"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_value_changes_for_associations_between_clinical_conditions_and_SNP_rs17234657_for_left_middle_and_right_/165207", "title"=>"Distribution of -value changes for associations between clinical conditions and SNP rs17234657 for left) , middle) , and right) .", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-19 15:54:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/494788"], "description"=>"<p>The braces (“{ ldots }”) demarcate the set of diagnoses received in a visit to a healthcare provider, while the brackets (“”) denote codes that have been generalized in accordance with the anonymization discussed herein.</p>", "links"=>[], "tags"=>["fictional", "patient-specific", "records", "codes", "corresponding", "2-anonymized"], "article_id"=>165298, "categories"=>["Biological Sciences", "Medicine", "Genetics"], "users"=>["Raymond D. Heatherly", "Grigorios Loukides", "Joshua C. Denny", "Jonathan L. Haines", "Dan M. Roden", "Bradley A. Malin"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0053875.g013"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_fictional_example_of_patient_specific_records_of_diagnosis_codes_in_the_a_original_resource_and_b_corresponding_2_anonymized_result_/165298", "title"=>"A fictional example of patient-specific records of diagnosis codes in the a) original resource and b) corresponding 2-anonymized result.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-19 15:54:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/494856"], "description"=>"<p>The DATA SELECT process is an extraction of some records of the SD into a smaller, specific dataset, such as BioVU or a demonstration cohort. The ANONYMIZE process is the anonymization algorithm described in this manuscript. The DEMO EXTRACT process selects the remaining records associated with the Demonstration cohort from a larger, anonymized dataset. The resultant datasets are as follows: anonymized version of the Synthetic Derivative (SD-Anon); anonymized version of BioVU (BioVU-Anon); SD-Anon, from which the demonstration group is extracted (); BioVU-Anon, from which the demonstration group is extracted (); and the anonymized version of the demonstration cohort (). , , and each represent different anonymizations of the Demonstration group.</p>", "links"=>[], "tags"=>["anonymization"], "article_id"=>165376, "categories"=>["Biological Sciences", "Medicine", "Genetics"], "users"=>["Raymond D. Heatherly", "Grigorios Loukides", "Joshua C. Denny", "Jonathan L. Haines", "Dan M. Roden", "Bradley A. Malin"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0053875.g014"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Datasets_used_for_comparison_of_anonymization_strategies_/165376", "title"=>"Datasets used for comparison of anonymization strategies.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-19 15:55:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/494906"], "description"=>"<p>The table to the left illustrates if a record contained a condition (green “Y”) or did not (grey “N”) in the original dataset before anonymization. The table to the right illustrates if a record lost a diagnosis (red “N”). Notice that the second record lost one diagnosis, which resulted in both the Code Count and Diagnosis Count to be lowered by a score of 1.</p>", "links"=>[], "tags"=>["computation"], "article_id"=>165430, "categories"=>["Biological Sciences", "Medicine", "Genetics"], "users"=>["Raymond D. Heatherly", "Grigorios Loukides", "Joshua C. Denny", "Jonathan L. Haines", "Dan M. Roden", "Bradley A. Malin"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0053875.g015"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_An_illustration_of_the_computation_for_Code_Count_and_Diagnosis_Count_/165430", "title"=>"An illustration of the computation for Code Count and Diagnosis Count.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-19 15:55:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/494961"], "description"=>"<p>, , and are the Demonstration group when anonymized, extracted from the BioVU anonymization, and extracted from the SD anonymization, respectively. Original is the number of significant associations (p 0.05) found in the PheWAS when conducted on pre-anonymized data. Identical is the number of associations which were the same between studies. Lost is the number of associations that were lost in the anonymized study. False is the number of associations that were determined as significant in the new study but were not in the original.</p>", "links"=>[], "tags"=>["anonymization", "phewas"], "article_id"=>165480, "categories"=>["Biological Sciences", "Medicine", "Genetics"], "users"=>["Raymond D. Heatherly", "Grigorios Loukides", "Joshua C. Denny", "Jonathan L. Haines", "Dan M. Roden", "Bradley A. Malin"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0053875.t004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Results_of_anonymization_on_PheWAS_Analysis_for_six_SNPs_/165480", "title"=>"Results of anonymization on PheWAS Analysis for six SNPs.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-19 15:55:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/494984"], "description"=>"<p>Descriptions for the condition codes presented in the QQ-plots.</p>", "links"=>[], "tags"=>["codes", "presented"], "article_id"=>165503, "categories"=>["Biological Sciences", "Medicine", "Genetics"], "users"=>["Raymond D. Heatherly", "Grigorios Loukides", "Joshua C. Denny", "Jonathan L. Haines", "Dan M. Roden", "Bradley A. Malin"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0053875.t005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Descriptions_for_the_condition_codes_presented_in_the_QQ_plots_/165503", "title"=>"Descriptions for the condition codes presented in the QQ-plots.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-19 15:55:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/495013"], "description"=>"<p>Code Count and Diagnosis Count are the number of unique ICD-9 (or generalized set of ICD-9 codes) and total number of diagnoses for all records in the anonymized dataset, respectively. In this table, *corresponds to the original (i.e., non-anonymized) datasets.</p>", "links"=>[], "tags"=>["retention", "datasets"], "article_id"=>165538, "categories"=>["Biological Sciences", "Medicine", "Genetics"], "users"=>["Raymond D. Heatherly", "Grigorios Loukides", "Joshua C. Denny", "Jonathan L. Haines", "Dan M. Roden", "Bradley A. Malin"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0053875.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_statistics_and_information_retention_for_the_datasets_in_this_study_/165538", "title"=>"Summary statistics and information retention for the datasets in this study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-19 15:56:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/495060"], "description"=>"<p>Full Diagnosis Count information retained.</p>", "links"=>[], "tags"=>["genetics and genomics", "Computational biology", "Non-clinical medicine"], "article_id"=>165578, "categories"=>["Biological Sciences", "Medicine", "Genetics"], "users"=>["Raymond D. Heatherly", "Grigorios Loukides", "Joshua C. Denny", "Jonathan L. Haines", "Dan M. Roden", "Bradley A. Malin"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0053875.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Full_Diagnosis_Count_information_retained_/165578", "title"=>"Full Diagnosis Count information retained.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-19 15:56:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/495097"], "description"=>"<p>Full Code Count information retained.</p>", "links"=>[], "tags"=>["genetics and genomics", "Computational biology", "Non-clinical medicine"], "article_id"=>165616, "categories"=>["Biological Sciences", "Medicine", "Genetics"], "users"=>["Raymond D. Heatherly", "Grigorios Loukides", "Joshua C. Denny", "Jonathan L. Haines", "Dan M. Roden", "Bradley A. Malin"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0053875.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Full_Code_Count_information_retained_/165616", "title"=>"Full Code Count information retained.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-19 15:56:23"}

PMC Usage Stats | Further Information

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Relative Metric

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