Genes and Addiction NIDA Center for GWAS in Outbred Rats

Datasets List
19 datasets

Publication name and date	Genotypes	Phenotypes	Omics Data	Sample size	Dataset access	Phenotype IDS	Publication link	Authors
Gunturkun et al., Genome-Wide Association Study on Three Behaviors Tested in an Open Field in Heterogeneous Stock Rats Identifies Multiple Loci Implicated in Psychiatric Disorders. Front Psychiatry. 2022 Feb 14;13:790566. doi: 10.3389/fpsyt.2022.790566. PMID: 35237186; PMCID: PMC8882588. 2022	3,513,494 Version R8	Locomotion Novel Object Interaction +1	None	1246	More details	ontology for behavior phenotypes		Hakan Gunturkun, Mustafa Chen, Hao Wang, Tengfei Chitre, Apurva St. Pierre, Celine Bimschleger, Hannah Cheng, Riyan Polesskaya, Oksana Solberg-Woods, Leah Palmer, Abraham Garcia Martinez, Angel Holl, Katie Gao, Jianjun
U01: Genetic Basis of Opioid Dependence Vulnerablility (U01DA045300) 9/30/2018	4,609,405, version R9	self- administration drug-seeking	RNA-Seq	Goal: 1000 Current: 655	More details		https://reporter.nih.gov/search/uklKYfh_tkGvcRicTWjt9w/project-details/10223254	Peter Kalivas W CHUNG, DONGJUN HARDIMAN, GERARD THOMAS SOLBERG WOODS,LEAH CICCOCIOPPO, ROBERTO
U01: Genomic analysis of avoidance learning in addiction (U01DA044468) 4/15/2018	4,609,405, version R9	Avoidance-Learning	RNA-Seq	Goal: 1200 Current: 1239	More details		https://reporter.nih.gov/search/QH2CQwXvTEiz41loh28b6A/project-details/10098021	Thomas Jhou
U01: Genetics of Compulsive Cocaine Intake in Rats (U01DA043799) 4/1/2017	4,609,405, version R9	Addiction Index Aggression Behavior Defensive Behavior +2	None	Goal: 1000 Current: 882	More details		https://reporter.nih.gov/search/UmvTCDBpc0qYTmrAE7ML_w/project-details/9873956	Olivier George Abraham Palmer
U01: Genetics of Compulsive Oxycodone Intake in HS Rats (U01DA044451) 8/13/2019	4,609,405, version R9	Oxycodone infusions Reward intake Tail immersion +1	None	Goal: 1000 Current: 619	More details	measure,trait_covariate,description 0,box,covariate,self administration box 1,cohort,covariate,batch 2,lga_12_age,covariate,age of animal on day 12 of long access session 3,pr_01_age,covariate,age of animal on day 1 of progressive ratio at breakpoint 4,pr_02_age,covariate,age of animal on day 2 of progressive ratio at breakpoint 5,room,covariate,experimental room 6,sex,covariate,sex of animal 7,sha_01_age,covariate,age of animal on day 1 of short access session 8,sha_04_age,covariate,age of animal on day 4 of short access session 9,weight_surgery,covariate,weight at surgery date 10,death_comment,metadata, 11,labanimalid,metadata,unique lab assigned id to animal 12,rfid,metadata,unique rfid assigned to animal 13,add_ind_olivier,trait,index calculated by Giordano's team 14,add_ind_sexcohort,trait,index calculated by Palmer team 15,add_ind_no_sex,trait,index calculated by Palmer team with no seperate Zscore of male and female 16,add_ind_no_sexcohort,trait,index calculated by Palmer team with no seperate Zscore of male and female or cohort 17,sha_mean_01_02,trait,average of the number of oxycodone infusions during the first three sessions of short access self administration (2 hours) 18,sha_mean_03_04,trait,average of the number of oxycodone infusions during the last three sessions of short access self administration (2 hours) 19,sha_mean_inactive_01_02,trait,average of the number of inactive during the first three sessions of short access self administration (2 hours) 20,sha_mean_inactive_03_04,trait,average of the number of inactive during the last three sessions of short access self administration (2 hours) 21,sha_mean_to_01_02,trait,average of the number of TO response during the first three sessions of short access self administration (2 hours) 22,sha_mean_to_03_04,trait,average of the number of TO response during the last three sessions of short access self administration (2 hours) 23,sha_iti_coefficient_of_variation_03_04,trait,standard deviation of ITI/mean of ITI within SHA (days 03-04) 24,sha_iti_coefficient_of_variation_01_02,trait,standard deviation of ITI/mean of ITI within SHA (days 01-02) 25,sha_iti_median_03_04,trait,Median of ITI (ITI being the time in sec between reward events using the timestamp data) 26,sha_loading_phase_intake_01_02,trait,number of rewards during the first ten minutes of SHA (days 01-02) 27,sha_loading_phase_intake_03_04,trait,number of rewards during the first ten minutes of SHA (days 03-04) 28,sha_titration_phase_01_02,trait,intake during the last 60 min in SHA (days 01-02) 29,sha_titration_phase_03_04,trait,intake during the last 60 min in SHA (days 03-04) 30,lga_mean_delta_esc,trait,average of the escalation values during the last three sessions of long access self administration (12 hours) 31,lga_mean_01_02,trait,average of the number of oxycodone infusions during the first 2 sessions of long access self administration (12 hours) 32,lga_mean_inactive_01_02,trait,average of the inactive during the first 2 sessions of long access self administration (12 hours) 33,lga_mean_active_01_02,trait,average of the active during the first 2 sessions of long access self administration (12 hours) 34,lga_mean_to_01_02,trait,average of the TO escalation values during the first 2 sessions of long access self administration (12 hours) 35,lga_iti_coefficient_of_variation_01_02,trait,standard deviation of ITI/mean of ITI wtihin LGA (days 01-02) 36,lga_iti_median_01_02,trait,Median of ITI (ITI being the time in sec between reward events using the timestamp data) first 2 sessions of LgA 37,lga_loading_phase_intake_01_02,trait,number of rewards during the first ten minutes of LGA (days 01-02) 38,lga_titration_phase_01_02,trait,intake during the last 6 * 60 min in LGA (days 01-02) (hour 5-11) 39,lga_mean_12_14,trait,average of the number of oxycodone infusions during the last three sessions of long access self administration (12 hours) 40,lga_mean_inactive_12_14,trait,average of the inactive during the last three sessions of long access self administration (12 hours) 41,lga_mean_active_12_14,trait,average of the active during the last three sessions of long access self administration (12 hours) 42,lga_mean_to_12_14,trait,average of the TO escalation values during the last three sessions of long access self administration (12 hours) 43,lga_iti_coefficient_of_variation_12_14,trait,standard deviation of ITI/mean of ITI wtihin LGA (days 12-14) 44,lga_iti_median_12_14,trait,Median of ITI (ITI being the time in sec between reward events using the timestamp data) 45,lga_loading_phase_intake_12_14,trait,number of rewards during the first ten minutes of LGA (days 12-14) 46,lga_titration_phase_12_14,trait,intake during the last 6 * 60 min in LGA (days 12-14) (hour 5-11) 47,tail_immersion_analgesia,trait,change in latency (tail imm 2 - tail imm BSL) note: positive number is more analgesia 48,tail_immersion_tolerance,trait,change in latency (tail imm 2 - tail imm 3) note: positive number is more tolerance 49,tail_immersion_baseline,trait,baseline latency (tail imm BSL) 50,tail_immersion_oxypresa,trait,tail imm 2 51,tail_immersion_oxypostsa,trait,tail imm 3 52,von_frey_force_bsl,trait,threshold force at baseline 53,von_frey_force_difference,trait,change in average force achieved (BSL - Withdrawal) 54,von_frey_force_percent,trait,percent change in average force achieved (BSL-Withdrawal) / BSL100 55,von_frey_force_withdrawal,trait,threshold force in withdrawal 56,von_frey_time_bsl,trait,threshold time at baseline 57,von_frey_time_difference,trait,change in average time achieved (BSL - Withdrawal) 58,von_frey_time_percent,trait,percent change in average time achieved (BSL-Withdrawal) / BSL100 59,von_frey_time_withdrawal,trait,threshold time in withdrawal 60,pr_01_sha,trait,number of oxycodone infusions received during day 1 (post-ShA) 61,pr_01_inactive,trait,number of inactive lever presses during day 1 (post-ShA) of progressive ratio session 62,pr_01_active,trait,number of active lever presses during day 1 (post-ShA) of progressive ratio session 63,pr_01_sha_breakpoint,trait,last completed number of oxycodone active lever presses during day 1 (post-ShA) of progressive ratio at breakpoint 64,pr_02_lga,trait,number of oxycodone infusions received during day 2 (post-LgA) 65,pr_02_inactive,trait,number of inactive lever presses during day 2 (post-LgA) of progressive ratio session 66,pr_02_active,trait,number of active lever presses during day 2 (post-LgA) of progressive ratio session 67,pr_02_lga_breakpoint,trait,last completed number of oxycodone active lever presses during day 2 (post-ShA) of progressive ratio at breakpoint 68,treatments_pr_vehicle,trait,percent of vehicle for each pharmacological treatment ( (treatment PR - PR02) / PR02 x 100% ) (vehicle) 69,treatments_pr_buprenorphine,trait,percent of vehicle for each pharmacological treatment ( (treatment PR - PR02) / PR02 x 100% ) (buprenorphine) 70,treatments_pr_methadone,trait,percent of vehicle for each pharmacological treatment ( (treatment PR - PR02) / PR02 x 100% ) (methadone) 71,treatments_pr_naltrexone,trait,percent of vehicle for each pharmacological treatment ( (ttreatment PR - PR02) / PR02 x 100% ) (naltrexone) 72,pr_saline_active,trait,number of active lever presses during saline treatment 73,pr_saline_breakpoint,trait,breakpoint (last completed ratio) during saline treatment 74,pr_saline_inactive,trait,number of inactive lever presses during saline treatment 75,pr_saline_rewards,trait,number of oxycodone infusions received during saline treatment 76,pr_buprenorphine_active,trait,number of active lever presses during buprenorphine treatment 77,pr_buprenorphine_breakpoint,trait,breakpoint (last completed ratio) during buprenorphine treatment 78,pr_buprenorphine_inactive,trait,number of inactive lever presses during buprenorphine treatment 79,pr_buprenorphine_rewards,trait,number of oxycodone infusions received during buprenorphine treatment 80,pr_methadone_active,trait,number of active lever presses during methadone treatment 81,pr_methadone_breakpoint,trait,breakpoint (last completed ratio) during methadone treatment 82,pr_methadone_inactive,trait,number of inactive lever presses during methadone treatment 83,pr_methadone_rewards,trait,number of oxycodone infusions received during methadone treatment 84,pr_naltrexone_active,trait,number of active lever presses during naltrexone treatment 85,pr_naltrexone_breakpoint,trait,breakpoint (last completed ratio) during naltrexone treatment 86,pr_naltrexone_inactive,trait,number of inactive lever presses during naltrexone treatment 87,pr_naltrexone_rewards,trait,number of oxycodone infusions received during naltrexone treatment 88,sha_iti_mode_03_04,trait,most frequent ITI for last 2 days 89,sha_iti_numburst_03_04,trait,number of bursts (= grouped rewards that are seperated by max 120 sec) in a session for last 2 days 90,sha_iti_maxburst_03_04,trait,maximum number of rewards contain in a single burst in one session for last 2 days 91,sha_iti_meannumrewards_03_04,trait,average number of rewards in a burst over all bursts in the session for last 2 days 92,sha_iti_pctrewards_03_04,trait,percantage of rewards that fall in a burst of total rewards for the session for last 2 days 93,sha_iti_mode_01_02,trait,most frequent ITI for first 2 days 94,sha_iti_numburst_01_02,trait,number of bursts (= grouped rewards that are seperated by max 120 sec) in a session for first 2 days 95,sha_iti_maxburst_01_02,trait,maximum number of rewards contain in a single burst in one session for first 2 days 96,sha_iti_meannumrewards_01_02,trait,average number of rewards in a burst over all bursts in the session for first 2 days 97,sha_iti_pctrewards_01_02,trait,percantage of rewards that fall in a burst of total rewards for the session for first 2 days 98,lga_iti_mode_12_14,trait,most frequent ITI for last 3 days 99,lga_iti_numburst_12_14,trait,number of bursts (= grouped rewards that are seperated by max 120 sec) in a session for last 3 days 100,lga_iti_maxburst_12_14,trait,maximum number of rewards contain in a single burst in one session for last 3 days 101,lga_iti_meannumrewards_12_14,trait,average number of rewards in a burst over all bursts in the session for last 3 days 102,lga_iti_pctrewards_12_14,trait,percantage of rewards that fall in a burst of total rewards for the session for last 3 days 103,lga_iti_mode_01_02,trait,most frequent ITI for first 2 days 104,lga_iti_numburst_01_02,trait,number of bursts (= grouped rewards that are seperated by max 120 sec) in a session for first 2 days 105,lga_iti_maxburst_01_02,trait,maximum number of rewards contain in a single burst in one session for first 2 days 106,lga_iti_meannumrewards_01_02,trait,average number of rewards in a burst over all bursts in the session for first 2 days 107,lga_iti_pctrewards_01_02,trait,percantage of rewards that fall in a burst of total rewards for the session for first 2 days	https://reporter.nih.gov/search/f6C7xo1EpESCW4neFmUNOg/project-details/10356094	Olivier George Abraham Palmer
R01: Identification of Genes Regulating Bone Matrix Composition and Quality 9/15/2016	None	Bone density	None	Goal = 4800	More details			Douglas Adams
U01:Characterization of Tandem Repeat and Structural Variants Contributing to Addictive Behaviors in Mice and Rats Not available	4,609,405, version R9		None	None	More details			Abraham Palmer Melissa Gymrek Jonathan Sebat
U01: Decoding the grammar of transcriptional enhancers regulating different stages of opioid use disorder 9/30/2020	4,609,405, version R9	RNA-Seq ATAC-seq	RNA-Seq	None	More details			Francesca Telese
Genetic basis for unilateral renal agenesis in heterogenous stock rats TBD	Version R8	Unilateral renal agenesis	None	5585	More details			Joel D. Leal-Gutiérrez Apurva S. Chitre Oksana Polesskaya Riyan Cheng Alexander F. Gileta Keita Ishiwari Christopher P. King Alexander Lamparelli Tengfei Wang Hao Chen Shelly B. Flagel Paul Meyer Terry E. Robinson Leah C. Solberg Woods Abraham A. Palmer Denghui Chen Michael Garrett Jerry Richards Cassandra L. Versaggi Connor Martin Celine L. St. Pierre, Jordan A. Tripi Wenyan Han Aidan Horvath Alesa Hughson Milad Mortazavi Hannah Bimschleger, Angel Garcia Martinez Tony George Katie Holl Jianjun Gao Bonnie Lin Daniel Munro
Structural equation modeling for understanding the genetic architecture of cocaine contextual conditioning and cocaine conditioned cue preference in heterogeneous stock rats undercover candidate genes for behavioral variation caused by cocaine exposure TBD	Version R8	Cocaine contextual conditioning cocaine conditioned cue preference		3050	More details			Joel D. Leal-Gutiérrez Apurva S. Chitre Oksana Polesskaya Riyan Cheng Alexander F. Gileta Keita Ishiwari Christopher P. King Alexander Lamparelli Tengfei Wang Hao Chen Shelly B. Flagel Paul Meyer Terry E. Robinson Leah C. Solberg Woods Abraham A. Palmer Denghui Chen Michael Garrett Jerry Richards Cassandra L. Versaggi Connor Martin Celine L. St. Pierre, Jordan A. Tripi Wenyan Han Aidan Horvath Alesa Hughson Milad Mortazavi Hannah Bimschleger, Angel Garcia Martinez Tony George Katie Holl Jianjun Gao Bonnie Lin Daniel Munro
Genetic architecture for cecum metabolomics of heterogeneous stock rats undercover candidate genes for metabolome abundance and presence TBD	Version R8	Cocaine Contextual Conditioning Cocaine Conditioned cue Preference	Metabolomics	1000	More details			Joel D. Leal-Gutiérrez Apurva S. Chitre Oksana Polesskaya Riyan Cheng Alexander F. Gileta Keita Ishiwari Christopher P. King Alexander Lamparelli Tengfei Wang Hao Chen Shelly B. Flagel Paul Meyer Terry E. Robinson Leah C. Solberg Woods Abraham A. Palmer Denghui Chen Wenyan Han Michael Garrett Jerry Richards Cassandra L. Versaggi Connor Martin Celine L. St. Pierre, Jordan A. Tripi Aidan Horvath Alesa Hughson Milad Mortazavi Hannah Bimschleger, Angel Garcia Martinez Tony George Katie Holl Jianjun Gao Bonnie Lin Daniel Munro
Chitre AS et al. Genome-Wide Association Study in 3,173 Outbred Rats Identifies Multiple Loci for Body Weight, Adiposity, and Fasting Glucose. Obesity (Silver Spring). 2020 Oct;28(10):1964-1973. doi: 10.1002/oby.22927. Epub 2020 AUG 29. PMID: 32860487; PMCID: PMC7511439. 2022	3,400,759 SNPs Version 2018	Body length with no tail body length with tail body weight +5	None	3173	UCSD library	parametrial-fat-weight-g_UBERON_UBERON:0010413 parametrial-fat-weight-g_MGI_MP:0005375 Body length with no tail CMO_0002804 (ontobee/PATO) Body length with tail CMO_0000078 (ontobee/PATO) Body weight CMO_0000079 (ontobee/PATO) Body Mass Index NoTail CMO_0002781 (ontobee/PATO) Retroperitoneal fat pad UBERON:0010411 Epididymal fat pad UBERON:0010412	https://pubmed.ncbi.nlm.nih.gov/32860487/	Apurva S Chitre Oksana Polesskaya Riyan Cheng Hannah Bimschleger Hao Chen Shelly B Flagel Paul Meyer Terry E Robinson Abraham A Palmer Leah C Solberg Woods Alexander F Gileta Keita Ishiwari Christopher P King Alexander Lamparelli Angel Garcia Martinez Tony George Katie Holl Jianjun Gao Cassandra L Versaggi Celine L St Pierre Jordan A Tripi Tengfei Wang Wenyan Han Jerry Richards Alesa Hughson
P50 Project 1: Neurogenetic Substrates of Cocaine Addiction 2019-2024	4,609,405, version R9	Intermittent access to cocaine	RNA-Seq	Goal: 1600 Current: 1911	More details	None	https://ratgenes.org/research-projects/rp1new/	Paul Meyer Chris King
P50 Project 2: Socially-acquired nicotine self-administration	4,609,405, Version R9	Open Field Novel Object Interaction Test Nicotine self-administration +1	None	Goal: 4800 Current: 2600	More details	trait,InterLex ID novel_object_age,ILX:0793285 novel_object_arena,ILX:0793286 novel_object_batchnumber,ILX:0793287 novel_object_cntrdurat,ILX:0793288 novel_object_cntrfreq,ILX:0793289 novel_object_cntrlate,ILX:0793290 novel_object_color,ILX:0793291 novel_object_dist2ctrmean,ILX:0793292 novel_object_dist2ctrtotal,ILX:0793293 novel_object_sex,ILX:0793294 novel_object_totaldistance,ILX:0793295 open_field_age,ILX:0793296 open_field_arena,ILX:0793297 open_field_batchnumber,ILX:0793298 open_field_cntrdurat,ILX:0793299 open_field_cntrfreq,ILX:0793300 open_field_cntrlate,ILX:0793301 open_field_color,ILX:0793302 open_field_dist2ctrmean,ILX:0793303 open_field_dist2ctrtotal,ILX:0793304 open_field_sex,ILX:0793305 open_field_totaldistance,ILX:0793306 rfid,ILX:0793307 social_interaction_age,ILX:0793308 social_interaction_arena,ILX:0793309 social_interaction_batchnumber,ILX:0793310 social_interaction_color,ILX:0793311 social_interaction_dist2objzonemean,ILX:0793312 social_interaction_dist2objzonetotal,ILX:0793313 social_interaction_dist2socmean,ILX:0793314 social_interaction_dist2soctotal,ILX:0793315 social_interaction_inobjzonedura,ILX:0793316 social_interaction_inobjzonefreq,ILX:0793317 social_interaction_inobjzonelate,ILX:0793318 social_interaction_insoczonedura,ILX:0793319 social_interaction_insoczonefreq,ILX:0793320 social_interaction_insoczonelate,ILX:0793321 social_interaction_sex,ILX:0793322 social_interaction_totaldistance,ILX:0793323 bmi_wo_tail,ILX:0793324 bmi_w_tail,ILX:0793325 body_weight_g,ILX:0793326 epididymis_fat_weight_g,ILX:0793327 glucose_reading_mg_dl,ILX:0793328 length_wo_tail_cm,ILX:0793329 length_w_tail_cm,ILX:0793330 parametrial_fat_weight_g,ILX:0793331 retroperitoneal_fat_weight_g,ILX:0793332 tail_length,ILX:0793333		Hao Chen
P50 Project 3: Association between behavioral regulation and cocaine cue preference 2014-2024	4,609,405, version R9.1	Locomotor Response Delay Discounting Light Reinforcement +5	None	Goal: 1600 Current: 1066	More details		https://ratgenes.org/research-projects/rp3/	David Dietz Keita Ishiwari Paul Meyer Suzanne Mitchell Jerry Richards
P50 Project 4, P50: Network-based analysis 2019-2024	4,609,405, version R9	N/A	None	various	More details		https://ratgenes.org/research-projects-rp4-networks/	Trey Ideker
P50 Project 1, P50: Genetic Studies of Incentive Salience 2014-2019	4,609,405, Version R9	Cocaine Contextual Conditioning Novelty seeking Pavlovian Conditioned Approach	None	1600	More details		https://ratgenes.org/research-projects/rp1/	Shelly Flagel Terry Robinson
U01: Single-cell resolution analysis of chromatin accessibility and gene expression (U01DA050239) 5/1/2020	4,609,405, version R9	RNA-Seq ATAC-seq H3K27Ac +1	RNA-seq, ATAC-seq, H3K27Ac, PLAC-seq	Goal: 96 Current: 96	More details		https://reporter.nih.gov/search/4O2ekcqX80yU0a3FTHylnw/project-details/10360680	Francesca Telese
U01: Genetic Features of Delay Discounting in an HS Rat Model (U01DA046077) 7/1/2018	4,609,405, version R9	Delay Discounting impulsivity 5-choice serial reaction time task	RNA-Seq	Goal: 1560 Current: 901	More details		https://reporter.nih.gov/search/a5pMHTPdZkyjaaOw8MpZZA/project-details/10146324	Suzanne Mitchell

Improving our understanding of genetic susceptibility

NIDA center for genetic studies of drug abuse in outbred rats (P50DA037844)

There are few effective therapies to treat drug abuse and dependence, despite the urgent need to develop more effective treatments. A major impediment to the development of such treatments is our extremely limited understanding of the biological basis of drug abuse.

While human genome-wide association studies (GWAS) have begun to elucidate genes that influence various traits relevant to drug abuse, they are still unable to attribute more than a small fraction of the heritable variance to specific genes. NIDA center for genetic studies of drug abuse in outbred rats (P50DA037844) was created in 2014 to perform GWAS on numerous behavioral traits that have well-established relevance to drug abuse using outbred rats. The Center was successfully renewed in 2019. We expect to discover new genes that can influence drug abuse-related behaviors in rats, therefore improving our understanding of genetic susceptibility to drug abuse in humans. Our results will help to identify new opportunities to treat psychiatric disorders, including addiction.

Abraham Palmer, PHD
Maryann Martone
Paul Meyer

Trey Ideker
Oksana Polesskaya
Leah Solberg-Woods

Anita Bandrowski
Hao Chen
Shelly Flagel

Jerry Richards
David Dietz
Jeffrey Grethe

Request access to secured data and get started now.

Fill out the form to let us know you’re interested in using the data and please indicate which dataset(s). Once your request is submitted, we’ll review it and get in touch to send you the necessary credentials in order to access the requested dataset(s). By requesting access to the data, you agree to our license.