Abraham Palmer, Ph.D.
Associate Professor, Department of Human Genetics
Ph.D., Biomedical Sciences, University of California San Diego, 1999
A.B., Biology, The University of Chicago, 1992
920 E. 58th Street CLSC 507D Chicago, IL 60637
Phone: (773) 834-2897
Fax: (773) 834-0505
 

Research Description

We are interested in the relationship between genes and behavior. By identifying genes that influence behavior we hope to obtain fundamental mechanistic insights into the molecular basis of both health and disease. Our research uses mice, rats and humans in pursuit of these goals.

A major focus of our work is on refining methods for genome wide association studies (GWAS) in model organisms. Past efforts to identify chromosomal regions that are associated with behavioral and other traits have used intercrosses (F2s), recombinant inbred (RI) strains and related populations to identify quantitative trait loci (QTLs). While quite successful, these approaches have been unable to map QTLs to intervals that are small enough to permit gene identification. This is because the parental chromosomes have not been sufficiently recombined, so haplotypes are extremely large. To address this problem use we have focused our efforts on populations with greater numbers of recombinations.

An advanced intercross line (AIL) is produced by crossing two inbred strains beyond the F2 generation. Our lab maintains a 55th generation AIL that was produced by crossing LG/J and SM/J; we obtained these mice at the 33rd generation from Dr. James Chevrud. Because this population is comprised of only two inbred strains, all alleles are common and all markers that are identical-by-state are necessarily identical-by-descent. We created another AIL using the strains C57BL/6J and DBA/2J, that we have since transferred to several other labs.

Another population that we are using is a commercially available outbred mouse population called CFW. These mice are derived from a small number of outbred Swiss-Webster mice and have been maintained for several decades as an outbred population. While not as simple as an AIL, the offer even greater mapping resolution because they have a greater number of accumulated recombinations.

More recently we have expanded our research to include rats, primarily because of their greater behavioral repertoire. This research currently uses both Sprague Dawley rats, which are a commercially available outbred population that is analogous to CFW mice, and the N/NIH heterogeneous stock, which was created by crossing 8 inbred strains in the mid-1980s and is currently maintained by Dr. Leah Solberg Woods at the Medical College of Wisconsin and is analogous to the mouse Diversity Outcross (DO). We are currently seeking funding for NIDA National Center of Excellence (P50) grant that would support the phenotyping of approximately 5,000 and NIH rats.

A common challenge for the analysis of these populations is that all subjects have complex and varying levels of relationships to one another. Therefore, we have adapted and developed methods and software for this purpose, including the R package QTLRel.

The majority of our research is aimed at behavioral phenotypes. One component of our lab focuses on phenotypes with relevance to drug abuse. These phenotypes include acute and chronic responses to drugs of abuse and conditioned place preference. We are interested in phenotypes relevant to anxiety, PTSD and depression. Our work is also touched on schizophrenia. Genes of particular interest to the lab include casein kinase 1 epsilon (Csnk1e), CUB and Sushi multiple domains 1(Csmd1), Cadherin 13 (Cdh13) and glyoxalase 1 (Glo1). In addition to our behavioral phenotyping, we have formed numerous collaborations with to study physiological phenotypes in the animals; these collaborations are motivated by the fact that we can easily collect tissues at the conclusion of behavioral testing.

Finally, we are also interested in directly studying behavioral phenotypes in human populations. This is a multidisciplinary endeavor that uses the techniques of GWAS to study endophenotypes. We have performed significant research related to on genetic factors that influence the subjective response to psychoactive drugs, principally amphetamine. Ongoing work is aimed at examining the genetic basis of impulsive behavior. These projects are collaborations with Dr. Harriet de Wit. We are also collaborating with Dr. John Cacioppo to examine the genetic basis of loneliness.

Our laboratory is made up of undergraduates, graduate students and postdoctoral fellows. Research projects incorporate both wet and dry lab skills and draw on individuals with both neuroscience and statistical genetics backgrounds. Students interested in joining the Palmer lab should contact Dr. Abraham Palmer directly.

Dr. Palmer is the director of the course “Genetic Analysis of Model Organisms” which is taught to both graduate and undergraduate students.  Dr. Palmer is also the program director of the NIMH funded T32 training grant called “Training in Emerging Multidisciplinary Approaches to Mental Health and Disease”. In addition Dr. Palmer is one of the co-organizers of the “Short Course on the Genetics of Addiction” which is held each summer at the Jackson laboratory in Bar Harbor, Maine.

Selected Publications

Annexin A6 modifies muscular dystrophy by mediating sarcolemmal repair.
Swaggart KA, Demonbreun AR, Vo AH, Swanson KE, Kim EY, Fahrenbach JP, Holley-Cuthrell J, Eskin A, Chen Z, Squire K, Heydemann A, Palmer AA, Nelson SF, McNally EM
(2014 Apr) Proc Natl Acad Sci U S A. 2014 Apr 9. 24717843


Genetic variation associated with euphorigenic effects of d-amphetamine is associated with diminished risk for schizophrenia and attention deficit hyperactivity disorder.
Hart AB, Gamazon ER, Engelhardt BE, Sklar P, Kahler AK, Hultman CM, Sullivan PF, Neale BM, Faraone SV, de Wit H, Cox NJ, Palmer AA
(2014 Apr) Proc Natl Acad Sci U S A. 2014 Apr 7. 24711425


A locus on mouse Ch10 influences susceptibility to limbic seizure severity: fine mapping and in silico candidate gene analysis.
Winawer MR, Klassen TL, Teed S, Shipman M, Leung EH, Palmer AA
(2014 Mar) Genes Brain Behav. 2014 Mar;13(3):341-9. doi: 10.1111/gbb.12116. Epub 2014 Jan 27. 24373497 ( Full Text )


Genetic variation for life history sensitivity to seasonal warming in Arabidopsis thaliana.
Li Y, Cheng R, Spokas KA, Palmer AA, Borevitz JO
(2014 Feb) Genetics. 2014 Feb;196(2):569-77. doi: 10.1534/genetics.113.157628. Epub 2013 Nov 26. 24281156 ( Full Text )


Propensity for social interaction predicts nicotine-reinforced behaviors in outbred rats.
Wang T, Han W, Wang B, Jiang Q, Solberg-Woods LC, Palmer AA, Chen H
(2014 Feb) Genes Brain Behav. 2014 Feb;13(2):202-12. doi: 10.1111/gbb.12112. Epub 2013 Dec 27. 24289793 ( Full Text )


Rats are the smart choice: Rationale for a renewed focus on rats in behavioral genetics.
Parker CC, Chen H, Flagel SB, Geurts AM, Richards JB, Robinson TE, Solberg Woods LC, Palmer AA
(2014 Jan) Neuropharmacology. 2014 Jan;76 Pt B:250-8. doi: 10.1016/j.neuropharm.2013.05.047. Epub 2013 Jun 18. 23791960 ( Full Text )


Traits of fear resistance and susceptibility in an advanced intercross line.
McGuire JL, Bergstrom HC, Parker CC, Le T, Morgan M, Tang H, Selwyn RG, Silva AC, Choi K, Ursano RJ, Palmer AA, Johnson LR
(2013 Nov) Eur J Neurosci. 2013 Nov;38(9):3314-24. doi: 10.1111/ejn.12337. Epub 2013 Aug 22. 23968228


Practical considerations regarding the use of genotype and pedigree data to model relatedness in the context of genome-wide association studies.
Cheng R, Parker CC, Abney M, Palmer AA
(2013 Oct) G3 (Bethesda). 2013 Oct 3;3(10):1861-7. doi: 10.1534/g3.113.007948. 23979941 ( Full Text )


The circadian clock gene Csnk1e regulates REM sleep amount and NREM sleep architecture in mice.

Zhou L, Bryant CD, Loudon A, Palmer AA, Vitaterna MH, Turek FW.

Sleep - in press



Psychopharmacology of theobromine in healthy volunteers.
Baggott MJ, Childs E, Hart AB, de Bruin E, Palmer AA, Wilkinson JE, de Wit H
(2013 Jul) Psychopharmacology (Berl). 2013 Jul;228(1):109-18. doi: 10.1007/s00213-013-3021-0. Epub 2013 Feb 19. 23420115 ( Full Text )


Mice selectively bred for High and Low fear behavior show differences in the number of pMAPK (p44/42 ERK) expressing neurons in lateral amygdala following Pavlovian fear conditioning.
Coyner J, McGuire JL, Parker CC, Ursano RJ, Palmer AA, Johnson LR
(2013 Jun) Neurobiol Learn Mem. 2013 Jun 28. pii: S1074-7427(13)00102-0. doi: 10.1016/j.nlm.2013.06.010. 23811025


Variation in the form of Pavlovian conditioned approach behavior among outbred male Sprague-Dawley rats from different vendors and colonies: sign-tracking vs. goal-tracking.
Fitzpatrick CJ, Gopalakrishnan S, Cogan ES, Yager LM, Meyer PJ, Lovic V, Saunders BT, Parker CC, Gonzales NM, Aryee E, Flagel SB, Palmer AA, Robinson TE, Morrow JD
(2013) PLoS One. 2013 Oct 1;8(10):e75042. doi: 10.1371/journal.pone.0075042. eCollection 2013. 24098363 ( Full Text )


Candidate gene studies of a promising intermediate phenotype: failure to replicate.
Hart AB, de Wit H, Palmer AA
(2013 Apr) Neuropsychopharmacology. 2013 Apr;38(5):802-16. doi: 10.1038/npp.2012.245. Epub 2012 Dec 3. 23303064 ( Full Text )


Glyoxalase 1 and its substrate methylglyoxal are novel regulators of seizure susceptibility.
Distler MG, Gorfinkle N, Papale LA, Wuenschell GE, Termini J, Escayg A, Winawer MR, Palmer AA
(2013 Apr) Epilepsia. 2013 Apr;54(4):649-57. doi: 10.1111/epi.12121. Epub 2013 Feb 14. 23409935 ( Full Text )


A simulation study of permutation, bootstrap, and gene dropping for assessing statistical significance in the case of unequal relatedness.
Cheng R, Palmer AA
(2013 Mar) Genetics. 2013 Mar;193(3):1015-8. doi: 10.1534/genetics.112.146332. Epub 2012 Dec 24. 23267053 ( Full Text )


Does COMT genotype influence the effects of d-amphetamine on executive functioning?
Wardle MC, Hart AB, Palmer AA, de Wit H
(2013 Feb) Genes Brain Behav. 2013 Feb;12(1):13-20. doi: 10.1111/gbb.12012. Epub 2012 Dec 29. 23231539 ( Full Text )


Congenic dissection of a major QTL for methamphetamine sensitivity implicates epistasis.
Bryant CD, Kole LA, Guido MA, Sokoloff G, Palmer AA
(2012 Jul) Genes Brain Behav. 2012 Jul;11(5):623-32. doi: 10.1111/j.1601-183X.2012.00795.x. Epub 2012 May 2. 22487465 ( Full Text )


QTLs for murine red blood cell parameters in LG/J and SM/J F(2) and advanced intercross lines.
Bartnikas TB, Parker CC, Cheng R, Campagna DR, Lim JE, Palmer AA, Fleming MD
(2012 Jun) Mamm Genome. 2012 Jun;23(5-6):356-66. doi: 10.1007/s00335-012-9393-3. Epub 2012 Feb 10. 22322356 ( Full Text )


Translational genetic approaches to substance use disorders: bridging the gap between mice and humans.
Palmer AA, de Wit H
(2012 Jun) Hum Genet. 2012 Jun;131(6):931-9. doi: 10.1007/s00439-011-1123-5. Epub 2011 Dec 15. 22170288 ( Full Text )


Glyoxalase 1 increases anxiety by reducing GABAA receptor agonist methylglyoxal.
Distler MG, Plant LD, Sokoloff G, Hawk AJ, Aneas I, Wuenschell GE, Termini J, Meredith SC, Nobrega MA, Palmer AA
(2012 Jun) J Clin Invest. 2012 Jun 1;122(6):2306-15. doi: 10.1172/JCI61319. Epub 2012 May 15. 22585572 ( Full Text )


Genome-wide association for fear conditioning in an advanced intercross mouse line.
Parker CC, Sokoloff G, Cheng R, Palmer AA
(2012 May) Behav Genet. 2012 May;42(3):437-48. doi: 10.1007/s10519-011-9524-8. Epub 2012 Jan 12. 22237917 ( Full Text )


Methamphetamine-induced conditioned place preference in LG/J and SM/J mouse strains and an F45/F46 advanced intercross line.
Bryant CD, Kole LA, Guido MA, Cheng R, Palmer AA
(2012) Front Genet. 2012 Jul 11;3:126. doi: 10.3389/fgene.2012.00126. eCollection 2012. 22798962 ( Full Text )


Genome-wide association study of d-amphetamine response in healthy volunteers identifies putative associations, including cadherin 13 (CDH13).
Hart AB, Engelhardt BE, Wardle MC, Sokoloff G, Stephens M, de Wit H, Palmer AA
(2012) PLoS One. 2012;7(8):e42646. doi: 10.1371/journal.pone.0042646. Epub 2012 Aug 28. 22952603 ( Full Text )


Role of Glyoxalase 1 (Glo1) and methylglyoxal (MG) in behavior: recent advances and mechanistic insights.
Distler MG, Palmer AA
(2012) Front Genet. 2012 Nov 19;3:250. doi: 10.3389/fgene.2012.00250. eCollection 2012. 23181072 ( Full Text )


Assessment of behaviors modeling aspects of schizophrenia in Csmd1 mutant mice.
Distler MG, Opal MD, Dulawa SC, Palmer AA
(2012) PLoS One. 2012;7(12):e51235. doi: 10.1371/journal.pone.0051235. Epub 2012 Dec 17. 23284669 ( Full Text )


Csnk1e is a genetic regulator of sensitivity to psychostimulants and opioids.
Bryant CD, Parker CC, Zhou L, Olker C, Chandrasekaran RY, Wager TT, Bolivar VJ, Loudon AS, Vitaterna MH, Turek FW, Palmer AA
(2012 Mar) Neuropsychopharmacology. 2012 Mar;37(4):1026-35. doi: 10.1038/npp.2011.287. Epub 2011 Nov 16. 22089318 ( Full Text )


High-resolution genetic mapping using the Mouse Diversity outbred population.
Svenson KL, Gatti DM, Valdar W, Welsh CE, Cheng R, Chesler EJ, Palmer AA, McMillan L, Churchill GA
(2012 Feb) Genetics. 2012 Feb;190(2):437-47. doi: 10.1534/genetics.111.132597. 22345611 ( Full Text )


Pavlovian fear memory circuits and phenotype models of PTSD.
Johnson LR, McGuire J, Lazarus R, Palmer AA
(2012 Feb) Neuropharmacology. 2012 Feb;62(2):638-46. doi: 10.1016/j.neuropharm.2011.07.004. Epub 2011 Jul 19. 21782833


Genome-wide association for methamphetamine sensitivity in an advanced intercross mouse line.
Parker CC, Cheng R, Sokoloff G, Palmer AA
(2012 Feb) Genes Brain Behav. 2012 Feb;11(1):52-61. doi: 10.1111/j.1601-183X.2011.00747.x. Epub 2011 Nov 23. 22032291 ( Full Text )


Mapping a mouse limbic seizure susceptibility locus on chromosome 10.
Winawer MR, Gildersleeve SS, Phillips AG, Rabinowitz D, Palmer AA
(2011 Nov) Epilepsia. 2011 Nov;52(11):2076-83. doi: 10.1111/j.1528-1167.2011.03256.x. Epub 2011 Sep 11. 21906048 ( Full Text )


Genetic determinants for intramuscular fat content and water-holding capacity in mice selected for high muscle mass.
Karst S, Cheng R, Schmitt AO, Yang H, de Villena FP, Palmer AA, Brockmann GA
(2011 Oct) Mamm Genome. 2011 Oct;22(9-10):530-43. doi: 10.1007/s00335-011-9342-6. Epub 2011 Jul 6. 21732194 ( Full Text )


Fine-mapping alleles for body weight in LG/J x SM/J F(2) and F(34) advanced intercross lines.
Parker CC, Cheng R, Sokoloff G, Lim JE, Skol AD, Abney M, Palmer AA
(2011 Oct) Mamm Genome. 2011 Oct;22(9-10):563-71. doi: 10.1007/s00335-011-9349-z. Epub 2011 Jul 15. 21761260 ( Full Text )


Genetic analysis in the Collaborative Cross breeding population.
Philip VM, Sokoloff G, Ackert-Bicknell CL, Striz M, Branstetter L, Beckmann MA, Spence JS, Jackson BL, Galloway LD, Barker P, Wymore AM, Hunsicker PR, Durtschi DC, Shaw GS, Shinpock S, Manly KF, Miller DR, Donohue KD, Culiat CT, Churchill GA, Lariviere WR, Palmer AA, O'Hara BF, Voy BH, Chesler EJ
(2011 Aug) Genome Res. 2011 Aug;21(8):1223-38. doi: 10.1101/gr.113886.110. Epub 2011 Jul 6. 21734011 ( Full Text )


Casein kinase 1 enables nucleus accumbens amphetamine-induced locomotion by regulating AMPA receptor phosphorylation.
Li D, Herrera S, Bubula N, Nikitina E, Palmer AA, Hanck DA, Loweth JA, Vezina P
(2011 Jul) J Neurochem. 2011 Jul;118(2):237-47. doi: 10.1111/j.1471-4159.2011.07308.x. Epub 2011 Jun 6. 21564097 ( Full Text )


Anxiety and fear in a cross of C57BL/6J and DBA/2J mice: mapping overlapping and independent QTL for related traits.
Sokoloff G, Parker CC, Lim JE, Palmer AA
(2011 Jul) Genes Brain Behav. 2011 Jul;10(5):604-14. doi: 10.1111/j.1601-183X.2011.00699.x. Epub 2011 May 31. 21554534 ( Full Text )


Dark matter: are mice the solution to missing heritability?
Parker CC, Palmer AA
(2011) Front Genet. 2011 Jun 13;2:32. doi: 10.3389/fgene.2011.00032. eCollection 2011. 22303328 ( Full Text )


QTL Analysis of Type I and Type IIA Fibers in Soleus Muscle in a Cross between LG/J and SM/J Mouse Strains.
Carroll AM, Palmer AA, Lionikas A
(2011) Front Genet. 2012 Jan 6;2:99. doi: 10.3389/fgene.2011.00099. eCollection 2011. 22303393 ( Full Text )


QTLRel: an R package for genome-wide association studies in which relatedness is a concern.
Cheng R, Abney M, Palmer AA, Skol AD
(2011) BMC Genet. 2011 Jul 27;12:66. doi: 10.1186/1471-2156-12-66. 21794153 ( Full Text )


Modulation ofTcf7l2 expression alters behavior in mice.
Savic D, Distler MG, Sokoloff G, Shanahan NA, Dulawa SC, Palmer AA, Nobrega MA
(2011) PLoS One. 2011;6(10):e26897. doi: 10.1371/journal.pone.0026897. Epub 2011 Oct 27. 22046400 ( Full Text )


 

Animal Models of Prenatal Protein Malnutrition Relevant for Schizophrenia(Patterson, Paul, Brown, Alan, Eds.)

Tarantino LM, Reyes TM, Palmer AA.

(PDF)

OPRM1 gene variants modulate amphetamine-induced euphoria in humans.
Dlugos AM, Hamidovic A, Hodgkinson C, Shen PH, Goldman D, Palmer AA, de Wit H
(2011 Mar) Genes Brain Behav. 2011 Mar;10(2):199-209. doi: 10.1111/j.1601-183X.2010.00655.x. Epub 2010 Nov 2. 21029375 ( Full Text )


Distinct genetic regions modify specific muscle groups in muscular dystrophy.
Swaggart KA, Heydemann A, Palmer AA, McNally EM
(2011 Jan) Physiol Genomics. 2011 Jan 7;43(1):24-31. doi: 10.1152/physiolgenomics.00172.2010. Epub 2010 Oct 19. 20959497 ( Full Text )


More on ADORA.
Yang A, Childs E, Palmer AA, de Wit H
(2010 Dec) Psychopharmacology (Berl). 2010 Dec;212(4):699-700. doi: 10.1007/s00213-010-2003-8. Epub 2010 Aug 28. 20802997


Fine mapping of QTL for prepulse inhibition in LG/J and SM/J mice using F(2) and advanced intercross lines.
Samocha KE, Lim JE, Cheng R, Sokoloff G, Palmer AA
(2010 Oct) Genes Brain Behav. 2010 Oct;9(7):759-67. doi: 10.1111/j.1601-183X.2010.00613.x. Epub 2010 Jul 20. 20597988 ( Full Text )


Fine-mapping of muscle weight QTL in LG/J and SM/J intercrosses.
Lionikas A, Cheng R, Lim JE, Palmer AA, Blizard DA
(2010 Sep) Physiol Genomics. 2010 Sep;42A(1):33-8. doi: 10.1152/physiolgenomics.00100.2010. Epub 2010 Jul 13. 20627939 ( Full Text )


Genetics of caffeine consumption and responses to caffeine.
Yang A, Palmer AA, de Wit H
(2010 Aug) Psychopharmacology (Berl). 2010 Aug;211(3):245-57. doi: 10.1007/s00213-010-1900-1. Epub 2010 Jun 9. 20532872


Genome-wide association studies and the problem of relatedness among advanced intercross lines and other highly recombinant populations.
Cheng R, Lim JE, Samocha KE, Sokoloff G, Abney M, Skol AD, Palmer AA
(2010 Jul) Genetics. 2010 Jul;185(3):1033-44. doi: 10.1534/genetics.110.116863. Epub 2010 May 3. 20439773 ( Full Text )


Catechol-O-methyltransferase val158met genotype modulates sustained attention in both the drug-free state and in response to amphetamine.
Hamidovic A, Dlugos A, Palmer AA, de Wit H
(2010 Jun) Psychiatr Genet. 2010 Jun;20(3):85-92. doi: 10.1097/YPG.0b013e32833a1f3c. 20414144 ( Full Text )


Murine Warriors or Worriers: The Saga of Comt1, B2 SINE Elements, and the Future of Translational Genetics.
Palmer AA, Dulawa SC
(2010) Front Neurosci. 2010 Oct 8;4:177. doi: 10.3389/fnins.2010.00177. eCollection 2010. 20976038 ( Full Text )


Role of Genetics in Caffeine Response and Its Implications for Health

Yang A, Palmer AA, de Wit H.

(2010) 211:245. Psychopharmacology (PDF)

Differences in aggressive behavior and DNA copy number variants between BALB/cJ and BALB/cByJ substrains.
Velez L, Sokoloff G, Miczek KA, Palmer AA, Dulawa SC
(2010 Mar) Behav Genet. 2010 Mar;40(2):201-10. doi: 10.1007/s10519-009-9325-5. Epub 2009 Dec 23. 20033273 ( Full Text )


Polymorphisms in dopamine transporter (SLC6A3) are associated with stimulant effects of D-amphetamine: an exploratory pharmacogenetic study using healthy volunteers.
Hamidovic A, Dlugos A, Palmer AA, de Wit H
(2010 Mar) Behav Genet. 2010 Mar;40(2):255-61. doi: 10.1007/s10519-009-9331-7. Epub 2010 Jan 21. 20091113


Are attention lapses related to d-amphetamine liking?
McCloskey M, Palmer AA, de Wit H
(2010 Feb) Psychopharmacology (Berl). 2010 Feb;208(2):201-9. doi: 10.1007/s00213-009-1719-9. Epub 2009 Nov 21. 19936714


More aroused, less fatigued: fatty acid amide hydrolase gene polymorphisms influence acute response to amphetamine.
Dlugos AM, Hamidovic A, Hodgkinson CA, Goldman D, Palmer AA, de Wit H
(2010 Feb) Neuropsychopharmacology. 2010 Feb;35(3):613-22. doi: 10.1038/npp.2009.166. Epub 2009 Nov 4. 19890266 ( Full Text )