Welcome to the Atkinson Lab at Baylor College of Medicine!


The primary goal of my lab is to reduce the disparity in genomics research across ancestries. We accomplish this by using diverse genomic datasets and cutting-edge computational techniques to study human populations that genomics has so far underserved. Our work is centered around complex neuropsychiatric traits with particular focus on populations of African and Latinx descent, though many of the tools we build are broadly applicable across phenotypes and populations, giving them the potential for widespread impact on human health. We also work on better understanding the demographic and evolutionary history of diverse human groups.

The Atkinson lab is recruiting a postdoc!
[Postdoc listing]



What We Work On


Our lab investigates a range of topics in statistical and human genetics to improve the inclusion of diverse participants in genomics studies. We have three primary tracks in the group spanning 1) basic research in applied/analytic statistical genetics, 2) investigations into population structure and evolution, and 3) methods/computational tool development.

Statistical Genetics

Population Genetics

Psychiatric Genetics

Collaborative Research

Research Areas




Tractor

Improving statistical genomics for diverse ancestries

Nearly 80% of all GWAS studies have been conducted on European cohorts. In particular, “admixed” people – those whose DNA contains more than one ancestral component, including African American and Latino individuals – are systemically excluded from studies due to the lack of available methods to appropriately handle their complex genomes. We bridge this concerning gap in research space by developing novel methods and tools to enable the study of complex traits in admixed people, bettering our understanding of mental health genetics in these diverse populations who have so far been underserved.





FOXP2

Understanding human evolution and population structure with globally representative data

A necessary precursor to accounting for global diversity in genomics research is a thorough understanding of population history and evolution, which shapes the naturally occurring patterns of genetic variation. Therefore, a second line of inquiry my research group explores is characterizing key aspects of human evolution with ancestrally-tuned evolutionary statistics using global DNA collections. Elucidating the forces shaping the genetic variation of key (brain) genes in modern populations is not only of significant academic interest, but is vital for determining the appropriate methods for statistical and medical genomic analyses of diverse datasets.



Characterizing the genetics of mental health within and across populations

Psychiatric disorders are the leading global cause of years lived with disability and affect all societies, yet there are major disparities in mental health research and treatment across ancestry groups. In partnership with both local and international colleagues and consortia, we lead efforts to optimize and apply ancestry informed analyses for psychiatric disorders to improve the understanding of the genetic contributors to mental health across populations.



Building globally representative datasets for equitable clinical genomics

Driving for equitable genomics is a team effort, and requires large sample sizes attainable only through aggregation of data. We are in the leadership of multiple international consortia, including the Psychiatric Genomics Consortium (PTSD working group), Neuropsychiatric Genetics in African Populations (NeuroGAP), and the Latin American Genomics Consortium (LAGC), affording trainees access to a wealth of diverse genetic datasets containing a wide range of phenotypes for potential study




Select Publications


For the most complete and up to date list, see Dr. Atkinson's Google scholar page.




  • Atkinson EG, Maihofer AX, Kanai M, Martin AR, Karczewski KJ, Santoro ML, et al. (2021) Tractor uses local ancestry to enable the inclusion of admixed individuals in GWAS and to boost power. Nature Genetics, 53:195–204. [Online][Press release][In the news]
  • Atkinson EG, Audesse AJ, Palacios J, Smith GT, Bobo DM, Webb AE, Ramachandran S, Henn BM (2018). No Evidence for Recent Selection at FOXP2 among Diverse Human Populations. Cell, 174(6): 1424-1435. PMC6128738. [Online][In the news] [In popular press]
  • Camarena B, Atkinson EG, Baker M, Becerra-Palars C, Chibnik LB, Escamilla-Orozco R, Jiménez-Pavón J, Koenig Z, Márquez-Luna C, Martin AR, Morales-Cedillo IP, Olivares AM, Ortega-Ortiz H, Rodriguez-Ramírez AM, Saracco-Alvarez R, Basaldua RE, Sena BF, Koenen K.C. (2021) Neuropsychiatric Genetics of Psychosis in the Mexican Population: A Genome-Wide Association Study Protocol for Schizophrenia, Schizoaffective, and Bipolar Disorder Patients and Controls. Complex Psychiatry. https://www.karger.com/Article/Abstract/518926. [Online]
  • Gopalan S, Atkinson EG, Buck LT, Weaver TD, Henn BM. (2021) Inferring archaic introgression from hominin genetic data. Evolutionary Anthropology. https://doi.org/10.1002/evan.21895. [Online]
  • Martin AR, Atkinson EG, Chapman SB, Stevenson A, Stroud RE, et al. (2021) Low-coverage sequencing cost-effectively detects known and novel variation in underrepresented populations. Am. J. Hum. Genet., 108:656-668. [Online]
  • The COVID-19 Host Genetics Initiative. Mapping the human genetic architecture of COVID-19 by worldwide meta-analysis. (2021) Nature. [Online]
  • Wendt FR, Pathak GA, Overstreet C, Tylee DS, Gelernter J, Atkinson EG, Polimanti, R. (2021) Characterizing the effect of background selection on the polygenicity of brain-related traits. Genomics, 113:111–119.[Online]
  • Guindo-Martínez M, Amela R, Bonàs-Guarch S, Puiggròs M, Salvoro C, Miguel-Escalada I, et al. (2021) The impact of non-additive genetic associations on age-related complex diseases. Nature Communications, 12:2436.[Online]
  • Scelza BA, Atkinson EG, Prall S, McElreath R, Sheehama J, Henn BM. (2020) The ethics and logistics of field-based genetic paternity studies. Evol Hum Sci 2020;2:1–36. [Online]
  • Scelza BA, Prall SP, Swinford N, Gopalan S, Atkinson EG, McElreath R, et al. (2020) High rate of extrapair paternity in a human population demonstrates diversity in human reproductive strategies.Science Advances 6:eaay6195. [Online]
  • Nievergelt CM, Maihofer AX, Klengel T, Atkinson EG, et al. (2019). International meta-analysis of PTSD genome-wide association studies identifies sex- and ancestry-specific genetic risk loci. Nature Communications, 10:4558. [Online]
  • Sugden LA, Atkinson EG, Fischer AP, Rong S, Henn BM, Ramachandran S. Localization of adaptive variants in human genomes using averaged one-dependence estimation. (2018) Nature Communications 9:703. [Online]
  • Martin, A.R., Lin, M., Granka, J.M., Myrick, J.W., Liu, X., Sockell, A., Atkinson, EG, Werely, C.J., Möller, M., Sandhu, M.S., et al. (2017). An Unexpectedly Complex Architecture for Skin Pigmentation in Africans. Cell 171, 1340–1353.e14. [Online] [In the media] [Related popular press]
  • Monzón JD*, Atkinson EG*, Henn BM, Benach JL. (2016) Population and Evolutionary Genomics of Amblyomma americanum, an Expanding Arthropod Disease Vector. 8:5, 1351–1360. Genome Biology and Evolution [Online]
  • Atkinson EG, Rogers J, Cheverud JM. Evolutionary and developmental implications of asymmetric brain folding in a large primate pedigree. Evolution. 2016;70:707–15. [Online]
  • Atkinson EG Rogers J, Mahaney MC, Cox LA, Cheverud JM. Cortical Folding of the Primate Brain: An Interdisciplinary Examination of the Genetic Architecture, Modularity, and Evolvability of a Significant Neurological Trait in Pedigreed Baboons (Genus Papio). Genetics (2015) 200:651–65. [Online] [In popular press]




Lab news



  • 10/11/21: Genetics and Genomics gradute students David Quispe and Grace Tietz will be rotating in the Atkinson lab for term 2. Welcome!

  • 09/27/21: Our NeuroMex protocol paper is published in Complex Psychiatry!

    Details/link in Publications tab.


  • 8/30/21: The Atkinson lab is hiring a postdoc and bioinformatics analyst!

    Candidates with training and interest in diverse population genomics or psychiatric genetics please email Dr. Atkinson and/or apply directly to the relevant BCM job listing. [Postdoc listing] [Analyst listing]

  • 7/13/21: The COVID-19 Host Genetics Initiative manuscript is published in Nature Genetics!

    Details/link in Publications tab. It's great to see the efforts of the Pan-UKB project helping include more ancestries in large-scale analyses.


  • 6/1/21: Genetics and Genomics gradute student Nirav Shah has started a rotation in the Atkinson lab. Welcome Nirav!

  • 5/23/21: Our ethnolinguistic analysis of the NeuroGAP pilot genotype arrays is up on bioRxiv! Check it out to learn more about the complex structure of genetics and cultural affiliations in eastern and southern africa:

    Atkinson EG, Dalvie S, Pichkar Y, Kalungi A, Majara L, Injera WE, et al. Genetic structure correlates with ethnolinguistic diversity in eastern and southern Africa. BioRxiv 2021. [Online]


  • 4/24/21: The MAMA method paper is up on bioRxiv! Check it out to learn more about improving meta-analysis for diverse cohorts:

    Turley P, Martin AR, Goldman G, Li H, Kanai M, Walters RK, et al. Multi-Ancestry Meta-Analysis yields novel genetic discoveries and ancestry-specific associations. 23 Michelle N Meyer 2021;12:26. BioRxiv 2021. [Online]


  • 4/20/21: Renovations are complete in the Atkinson lab. Come check out our freshly updated lab space in Taub 619/621!

  • 3/12/21: Our collaborative effort doing a pan-ancestry gene discovery effort for COVID is up on medRxiv!

    The COVID-19 Host Genetics Initiative. Mapping the human genetic architecture of COVID-19 by worldwide meta-analysis. 2021:2021.03.10.21252820. MedRxiv. [Online]


  • 1/14/21: GINGER fellow Lerato Majara wrote her first first author paper, now on bioRxiv:

    Majara L, Kalungi A, Koen N, … Atkinson EG, Martin AR. Low generalizability of polygenic scores in African populations due to genetic and environmental diversity. BioRxiv 2021:2021.01.12.426453. [Online]


  • 1/05/21: Our work with the New Haven Lexinome Project is up on bioRxiv!

    Adams AK, Guertin EL, Truong DT, Atkinson EG, DeMille MMC, Bosson-Heenan JM, et al. Genome Wide Association Study in the New Haven Lexinome Project Identifies GARRE1 as a Novel Gene for Reading Performance. 2021. bioRxiv. [Online]


  • 6/16/20: The pan-ukb website is live! Stay tuned for a preprint on our work generating GWAS summary statistics for 6 global ancestry groups and over 7,200 phenotypes (+phecodes, +prescriptions). Check it out at: pan.ukbb.broadinstitute.org





Contact


Interested in joining our group?

We are recruiting trainees! Candidates with training and interest in diverse population genomics or psychiatric genetics please email Dr. Atkinson and/or apply directly to the BCM job listing. [Postdoc listing]





Elizabeth Atkinson

1 Baylor Plaza
Taub Research Building, Rooms 621 (office) and 619 (lab)
Department of Molecular and Human Genetics
Baylor College of Medicine
Houston, TX 77030