RESEARCH PROJECTS

Our Current Focus

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GENERAL INTERESTS

We are interested in both method development using innovative approaches and statistics for reading genetic information, as well as learning about the evolution and phenotypic variation of diverse humans. We are interested in collaborating with investigators working on other natural populations, to understand the similarities and differences in the evolutionary process in humans compared to other species. Also trained in history, we have a keen awareness of, and continue to retain an interest in studying how societal norms affect the scientific process and enterprise and vice versa. We are committed to working towards making genomics and personalized medicine a universal phenomenon by helping to create genomic resources for underserved populations, and participating in the training of diverse scientists. We are also committed to participate in making genomic science an ethical and inclusionary pursuit. We enjoy working on science communication and outreach projects, using visual, audiovisual and written means. The Sohail lab considers all of the above important parts of a 21st century geneticist’s toolkit, and training and work in the lab aims to be multifaceted in this respect.

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USING GENOMICS DATA TO LEARN ABOUT HUMAN EVOLUTIONARY HISTORY, COMPLEX TRAIT VARIATION AND THEIR RELATIONSHIP

Population genetic history

We are interested in how genomics can inform historical inference, and vice versa, with a particular interest in Mexico and Pakistan (among the larger regions of central and south Asia and America), which present numerous parallels in their rich indigenous diversity, recent European colonization, and global positionality from being developing countries. We are interested in using identity-by-descent segments and other means of demographic inference to learn about the genetic histories of different regions and groups, and how these correlate with cultural histories and present-day cultural structure. We place an emphasis on developing relationships with participants and creating equitable and reciprocal frameworks for data generation and use for our studies. We are developing projects describing nation-wide genetic diversity and history, as well as projects focused on specific regional histories.


Complex trait variation

We are interested in investigating in the role that genetic ancestry and population history play in generating trait-relevant genetic variation. This involves combined analyses of identity-by-descent segments, runs of homozygosity, ancestry estimates, environmental variables and complex trait variation. We are also interested in developing methods for evaluating the role of gene-by-environment interactions in complex trait variation. Our general framework employs the correlations among fine-scale genetic, trait and cultural structure.


Prediction of traits in present-day and ancient humans

We are investigating the accuracy of trait prediction in ancient samples using present-day trait causing alleles by employing simulations under neutrality and under stabilizing selection. We are interested in learning the factors that are most relevant for lowering or improving trait prediction. We are also developing a project to evaluate deep leaning approaches (compared to polygenic scores) from artificial intelligence for trait prediction incorporating both genetic and environmental factors.


The evolutionary history of traits

We are interested in understanding the history of complex traits and disease by interrogating them through the contexts of our evolutionary past. Within this general agenda, we are developing a project on investigating relative contributions to complex trait architecture from sequence elements originating across multiple evolutionary time-scales.


Role of rare genetic variation

Rare genetic variants are relevant for understanding recent population structure, and have also been implicated in trait-relevant variants that are population-specific. We are interested in developing methods employing rare variants to interrogate recent history and variation in traits and disease incidence.


Projects


Mashaal Sohail, Alan Izarras-Gomez and Diego Ortega-Del Vecchyo. Populations, traits, and their spatial structure in humans. (Invited review article for Genome Biology and Evolution, in review)


Mashaal Sohail, Amanda Y. Chong, Maria Jose Palma, Consuelo Dayzu Quinto-Cortes, Aaron Ragsdale, Santiago Gerardo Medina, Andres Jimenez-Kaufmann, Carmina Barberena, Paulina Nunez, Guadalupe Delgado-Sánchez, Luis Pablo Cruz-Hervert, Leticia Ferreyra-Reyes, Hortensia Moreno-Macías, Carlos A. Aguilar-Salinas, Adrian Cortes, Selene L. Fernandez Valverde, Victor Acuña-Alonzo, Genevieve Wojcik, Christopher R. Gignoux, Carlos D. Bustamante, Adrian Hill, Maria Teresa Tusie Luna, Alexander J. Mentzer, John Novembre, Lourdes García-García, Andrés Moreno-Estrada. Nation-wide

biobank in Mexico unravels demographic history and complex trait architecture from 6,000 genomes. (In preparation). See The MX Biobank project


The Genome of the Netherlands Consortium. Whole-genome sequence variation, population structure and demographic history of the Dutch population. Nature Genetics (2014)


Mashaal Sohail*, Robert M. Maier*, Andrea Ganna, Alex Bloemendal, Alicia R. Martin, Michael C. Turchin,  Charleston W. K. Chiang, Joel N. Hirschhorn, Mark J. Daly, Nick Patterson, Benjamin M. Neale, Iain Mathieson, David Reich, Shamil R. Sunyaev. Signals of polygenic adaptation on height have been overestimated due to uncorrected population structure in genome-wide

association studies. eLife (2018) *equal contribution

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THE MECHANISMS OF EVOLUTION

Using linkage disequilibrium (two-locus dynamics) to learn about evolution.

We have been involved in developing methods to use linkage equilibrium to learn about non-additive natural selection (epistasis) and population structure (assortative mating). We are in interested in continuing to develop approaches using linkage disequilibrium to learn about evolutionary processes such as epistatic natural selection, non-random mating and adaptive introgression in humans and in other species. 


Genome-wide patterns of selection

We are interested in global patterns of selection genome-wide. We have previously found evidence for synergistic epistasis acting against deleterious variants genome-wide in human and in fruit flies. We have also done work on showing how balancing selection genome-wide correlates with genes that are mono-allelically expressed. Lastly, we have studied patterns of polygenic adaptation and how these are confounded by population stratification in genome-wide association studies. We are interested in continuing to develop approaches to interrogate different types of selection genome-wide and their relationship with modules of gene expression. We have been interested in the historiography of the concept of natural selection as a mechanism for evolution, and our major interest is in understanding how prevalent it is in living organisms, and in humans, using the plethora of genetic and phenotypic datasets now available.

Projects

Mashaal Sohail, Olga A Vakhrusheva, Jae Hoon Sul, Sara Pulit, Laurent Francioli, GoNL Consortium, Alzheimers Disease Neuroimaging Initiative, Leonard H van den Berg, Jan H Veldink, Paul de Bakker, Georgii A Bazykin, Alexey S Kondrashov, Shamil Sunyaev. Negative selection in humans and fruit flies involves synergistic epistasis. Science (2017)


Brian Arnold, Mashaal Sohail, Crista Wadsworth, Bill Hanage, Jukka Corander, Shamil Sunyaev, Yonatan Grad. Linkage reveals localized population structure and selection in Neisseria gonorrhoeae. bioRxiv (2019).


Virginia Savova*, Sung Chun*, Mashaal Sohail*,  Ruth B. McCole, Robert Witwicki, Lisa Gai, Tobias L. Lenz, C.-ting Wu, Shamil R. Sunyaev, Alexander A. Gimelbrant. Genes with monoallelic expression contribute disproportionately to genetic diversity in humans. Nature Genetics  (2016) *equal contribution


Mashaal Sohail*, Robert M. Maier*, Andrea Ganna, Alex Bloemendal, Alicia R. Martin, Michael C. Turchin,  Charleston W. K. Chiang, Joel N. Hirschhorn, Mark J. Daly, Nick Patterson, Benjamin M. Neale, Iain Mathieson, David Reich, Shamil R. Sunyaev. Polygenic adaptation on height has been overestimated due to uncorrected stratification in genome-wide association studies. eLife (2019) *equal contribution


AM history of science thesis paper (reach out for a copy!)

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USE SYSTEMS TRANSCRIPTOMICS TO STUDY TIME VARIATION IN GENE EXPRESSION DURING AND AFTER USE OF MEDICINAL PLANTS

While our genetic code is passed on to us, along with epigenetic marks, a remarkably understudied area is how global gene expression profiles vary under different environments and during and after specific interactions with the environment. A particular area of interest is the biological impact of use of plant medicines that have been used by indigenous groups in the Americas (among other places) for many millennia. While neuroscience research has identified both short-term and long-term impact of use on neural activity (using EEG and fMRI techniques), and in-vitro biological research is finding impact on proteomic activity, there are no studies that have assessed dynamic or sustained impact on global gene expression in humans. We are interested to begin work with yage (ayahuasca) and assess the impact on global gene expression following an intake of yage. We are further interested in investigating if there are long-term changes in global gene expression profiles of long-term users. We have and are establishing trans-disciplinary collaborations towards these studies. A long-term interest is in features of gene expression changes that are shared with and distinct from use of other medicinal plants such as certain mushrooms and peyote. We are excited to use transcriptional profiling along with systems approaches to identify up-regulated and down-regulated gene networks and network hubs that are modulated temporally or in a sustained manner on plant use.


Projects:

Reach out for more information!

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HISTORY OF RACE AND GENETICS

We believe that the 21st century geneticist’s toolkit should include a keen awareness of the history of race and genetics (to help understand how this legacy affects our thinking and practices today), and part of the work in our lab is continued participation in and organization of reading and study groups, invited seminars, courses, workshops and transdisciplinary teams towards this goal. Further, we read and consult broadly on our research themes to learn from our colleagues in history, science and technology studies, anthropology, archaeology and sociology to help contextualize and historicize our research questions, methods and the implications of our research results. We make an effort to apply what we are learning from these sources in every step of our research work from project motivation/design, sampling approach, analysis methods to interpretation, writing and communication of results. This is part of a general agenda of increasing our understanding and ability to think and communicate about issues at the intersection of genetics and society.

Projects:

History of race and genetics reading group at U Chicago. Website here: https://voices.uchicago.edu/geneticists-against-hate/


Member of Harvard University’s Edmond J. Safra Center for Ethics working group on ‘Understanding Variation: normative and analytical implications of using “population” and “ancestry” for generalization and comparison’

DEIA Systematic Bias in Science seminar. Video here:

https://www.dropbox.com/s/e63f1eckix5r35r/Sohail_DEIA_OBA_20201210.mp4?dl=0