We develop and apply new software for identifying causal genetic variants in studies of rare familial disease. The University of Utah has a long history of expertise in this area and we work closely with many clinical collaborators to solve rare disease. Our GEMINI software is central to these efforts, and our laboratory collaborates with other members of the USTAR Center for Genetic Discovery to study familial disease among the large pedigrees in the Utah Genome Project.
Human chromosomes harbor hundreds of structural differences including deletions, insertions, duplications, inversions, and translocations. Collectively, these differences are known as "structural variation" (or, "SV"). Any two humans differ by thousands of structural variants which vary greatly in size and phenotypic consequence. However, we are just beginning to understand the contribution of SV to evolution, development, and complex disease. Our laboratory continues to develop new methods such as LUMPY for detecting and understanding structural variation using modern DNA sequencing techniques.
Massively parallel DNA sequencing has yielded detailed maps of clonal variation in human cancer, through an inference of clonal substructure by analysis of variant allele frequencies in bulk tumor cell populations and direct sequencing of single cells. Dynamic changes in clonal structure over time and under the selective pressure of treatment have been extensively studied in hematologic malignancies, but are less well characterized in solid cancers. Our understanding of the dynamics of clonal change and its role in therapeutic response and the emergence of resistance is in its infancy. However, deeper insight is accessible via significant advances in sequencing and new algorithms. We are developing new methods to identify genomic changes that are responsible for clonal evolution, chemoresistance, and relapse.
Broadly speaking, the research in my laboratory marries genetics with genomics technologies, computer science, and machine learning techniques to develop new strategies for gaining insight into genome biology. We try to tackle challenging problems with practical importance to understanding genome variation in the context of human disease. We actively maintain a broad range of widely used tools for genome research including: BEDTOOLS, GEMINI, LUMPY, VCFANNO, PEDAGREE, and GQT
.James M. Havrilla, Brent S. Pedersen, Ryan M. Layer, Aaron R. Quinlan
doi: https://doi.org/10.1101/220814
Donna M Werling, Harrison Brand, Joon-Yong An, Matthew R Stone, Joseph T Glessner, Lingxue Zhu, Ryan L Collins, Shan Dong, Ryan M Layer, Eiriene-Chloe Markenscoff-Papadimitriou, Andrew Farrell, Grace B Schwartz, Benjamin B Currall, Jeanselle Dea, Clif Duhn, Carolyn Erdman, Michael Gilson, Robert E Handsaker, Seva Kashin, Lambertus Klei, Jeffrey D Mandell, Tomasz J Nowakowski, Yuwen Liu, Sirisha Pochareddy, Louw Smith, Michael F Walker, Harold Z Wang, Mathew J Waterman, Xin He, Arnold R Kriegstein, John L Rubenstein, Nenad Sestan, Steven A McCarroll, Ben M Neale, Hilary Coon, A. Jeremy Willsey, Joseph D Buxbaum, Mark J Daly, Matthew W State, Aaron Quinlan, Gabor T Marth, Kathryn Roeder, Bernie Devlin, Michael E Talkowski, Stephan J Sanders
doi: https://doi.org/10.1101/127043
Miten Jain, Sergey Koren, Josh Quick, Arthur C Rand, Thomas A Sasani, John R Tyson, Andrew D Beggs, Alexander T Dilthey, Ian T Fiddes, Sunir Malla, Hannah Marriott, Karen H Miga, Tom Nieto, Justin O'Grady, Hugh E Olsen, Brent S Pedersen, Arang Rhie, Hollian Richardson, Aaron Quinlan, Terrance P Snutch, Louise Tee, Benedict Paten, Adam M. Phillippy, Jared T Simpson, Nicholas James Loman, View ORCID ProfileMatthew Loose
In press, Nature Biotechnology
Ryan M. Layer, Brent S. Pedersen, Tonya DiSera, Gabor T. Marth, Jason Gertz, Aaron R. Quinlan
In press, Nature Methods
Brent S. Pedersen and Aaron Quinlan
Bioinformatics doi.org/10.1093/bioinformatics/btx699
Brent S. Pedersen, Ryan L Collins, Michael E Talkowski, Aaron Quinlan
GigaScience doi.org/10.1093/gigascience/gix090
Karen Eilbeck*, Aaron Quinlan*, Mark Yandell
Nature Reviews Genetics doi:10.1038/nrg.2017.52
Andrea Bild, Samuel Brady, Jasmine McQuerry, Yi Qiao, Stephen Piccolo, Gajendra Shrestha, Ryan Layer, Brent Pedersen, David Jenkins, Ryan Miller, Amanda Esch, Sara Selitsky, Joel Parker, Layla Anderson, Chakravarthy Reddy, Jonathan Boltax, Dean Li, Philip Moos, Joe Gray, Laura Heiser, W. Evan Johnson, Saundra Buys, Adam Cohen, Quinlan AR, Gabor Marth, Theresa Werner, Brian Dalley, and Rachel Factor
Nature Communications, doi:10.1038/s41467-017-01174-3
Xiangfei Liu, Uma Devi Paila, Sharon N. Teraoka, Jocyndra A. Wright, Xin Huang, Quinlan AR, Richard A. Gatti and Patrick Concannon
International Journal of Radiation Oncology, doi:10.1016/j.ijrobp.2017.08.033
Pedersen BS, Quinlan AR†
AJHG doi: 10.1016/j.ajhg.2017.01.017
Pedersen BS, Quinlan AR†
Bioinformatics doi: 10.1093/bioinformatics/btx057
Pedersen BS, Layer RM, Quinlan AR†
Genome Biol. doi: 10.1186/s13059-016-0973-5
Ge Y, Onengut-Gumuscu S, Quinlan AR, Mackey AJ, Wright JA, Buckner JH, Habib T, Rich SS, Concannon P.
Diabetes. pii: db150322
Layer RM, Kindlon N, Karczewski K, Exome Aggregation Consortium, Quinlan AR†
Nature Methods. doi:10.1038/nmeth.3654
Chiang C, Layer RM, Faust GG, Lindberg MR, Rose DB, Garrison EP, Marth GT, Quinlan AR, Hall IM.
Nature Methods. doi:10.1038/nmeth.3505
Auer PL, et al.
JAMA Neurology. doi:10.1001/jamaneurol.2015.0582
Onengut-Gumuscu S, Chen WM, Burren O, Cooper NJ, Quinlan AR, et al.
Nature Genetics. doi:10.1038/ng.3245
Lindberg MR, Hall IM, Quinlan AR†, et al.
Bioinformatics. doi:10.1093/bioinformatics/btu771
Church DM, Schneider VA, Steinberg KM, Schatz MC, Quinlan AR, Chin CS, Kitts PA, Aken B, Marth GT, Hoffman MM, Herrero J, Mendoza ML, Durbin R, Flicek P.
Genome Biology. doi:10.1186/s13059-015-0587-3.
Do R, et al.
Nature. doi:10.1038/nature13917
Dai C, Deng Y, Quinlan AR, Gaskin F, Tsao B, Fu SM.
Current Opinion in Immunology. doi:10.1016/j.coi.2014.10.004
Quick J, Quinlan AR, Loman N.
GigaScience. doi: 10.1186/2047-217X-3-22
Loman N, Quinlan AR†, Loman N.
Bioinformatics. doi:10.1093/bioinformatics/btu555
Qiao Y, Quinlan AR, Jazaeri A, Verhaak R, Wheeler D, Marth G.
Genome Biology. doi:10.1186/s13059-014-0443-x
Quinlan AR†
Current Protocols in Bioinformatics. doi: 10.1002/0471250953.bi1112s47
Layer RM, Quinlan AR†, Hall IM.
Genome Biology. doi:10.1186/gb-2014-15-6-r84
Martin N, Nakamura K, Paila U, Woo J, Brown C, Wright J, Teraoka S, Haghayegh S, Mc- Curdy D, Schneider M, Hu H, Quinlan AR, Gatti R, and Concannon P.
Cell Death Dis. doi: 10.1038/cddis.2014.99
Farber CR, Reich A, Barnes AM, Becerra P, Rauch F, Cabral WA, Bae A, Quinlan AR, Glorieux FH, Clemens TL, and Marini JC.
J Bone Miner Res. doi: 10.1002/jbmr.2173
Tabor HK, Auer PL, Jamal SM, Chong JX, Yu JH, Gordon AS, Graubert TA, O’Donnell CJ, Rich SS, Nickerson DA; NHLBI Exome Sequencing Project, Bamshad MJ.
Am J Hum Genet. doi: 10.1016/j.ajhg.2014.07.006
Lange LA, Hu Y, Zhang H, NHLBI Grand Opportunity Exome Sequencing Project, et al.
Am J Hum Genet. doi: 10.1016/j.ajhg.2014.01.010
Gordon AS, Tabor HK, Johnson AD, Snively BM, NHLBI GO Exome Sequencing Project, et al.
Hum Mol Genet, doi: 10.1093/hmg/ddt588
Paila U, Chapman BA, Kirchner R, Quinlan AR†.
PLoS Comput Biol. doi:10.1371/journal.pcbi.1003153
Rosenthal EA, Ranchalis J, Crosslin DR, Burt A, Brunzell JD, Motulsky AG, Nickerson DA; NHLBI GO Exome Sequencing Project, Wijsman EM, Jarvik GP.
Am J Hum Genet., doi: 10.1016/j.ajhg.2013.10.019
Guo DC, Regalado E, NHLBI Grand Opportunity Exome Sequencing Project, et al.
Am J Hum Genet., doi: 10.1016/j.ajhg.2013.06.019
O’Connor TD, Kiezun A, Bamshad M, Rich SS, Smith JD, Turner E; NHLBIGO Exome Sequencing Project; ESP Population Genetics, Statistical Analysis Working Group, Leal SM, Akey JM.
PLoS One. doi:10.1371/journal.pone.0065834
Johnsen JM, Auer PL, Morrison AC, Jiao S, Wei P, Haessler J, Fox K, McGee SR, Smith JD, Carlson CS, Smith N, Boerwinkle E, Kooperberg C, Nickerson DA, Rich SS, Green D, Peters U, Cushman M, Reiner AP; NHLBI Exome Sequencing Project.
Blood. doi:10.1182/blood-2013-02-485094
Norton N, Li D, Rampersaud E, Morales A, Martin ER, Zuchner S, Guo S, Gonzalez M, Hedges DJ, Robertson PD, Krumm N, Nickerson DA, Hershberger RE; National Heart, Lung, and Blood Institute GO Exome Sequencing Project and the Exome Sequencing Project Family Studies Project Team.
Circ Cardiovasc Genet. doi:10.1161/CIRCGENETICS.111.000062
Malhotra A, Lindberg M, Leibowitz M, Clark R, Faust G, Layer R, Quinlan AR†, and Hall IM†.
Genome Research, doi:10.1101/gr.143677.112
Fu W, O’Connor TD, Jun G, Kang HM, Abecasis G, Leal SM, Gabriel S, Rieder MJ, Altshuler D, Shendure J, Nickerson DA, Bamshad MJ; NHLBI Exome Sequencing Project, Akey JM.
Nature. doi:10.1038/nature11690
Layer R, Robins G, Skadron K, Quinlan AR†
Bioinformatics. doi: 10.1093/bioinformatics/bts652
Boileau C, Guo DC, Hanna N, Regalado ES, D, NHLBI Go Exome Sequencing Project, et al.
Nature Genetics. doi:10.1038/ng.2348
Emond MJ, Louie T, Emerson J, Zhao W, NHLBI Exome Sequencing Project; Lung GO, Gibson RL, Bamshad MJ.
Nature Genetics. doi:10.1038/ng.2344
Krumm N, Sudmant PH, Ko A, O‘Roak BJ, NHLBI Exome Sequencing Project, Quinlan AR, Nickerson DA, Eichler EE.
Genome Research. doi: 10.1101/gr.138115.112
Quinlan AR and Hall IM.
Trends in Genetics. doi: http://dx.doi.org/10.1016/j.tig.2011.10.002
Quinlan AR and Hall IM.
Methods in Molecular Biology
Quinlan AR, Boland MJ, Leibowitz ML, Shumilina S, Pehrson SM, Baldwin KK, Hall IM.
Cell Stem Cell. doi: 10.1016/j.stem.2011.07.018
Keene KL, Quinlan AR, Hou X, Hall IM, Mychaleckyj, Onengut-Gumuscu S, Concannon P.
Genes and Immunity. doi: 10.1038/gene.2011.56
Dale R, Pedersen B, Quinlan AR†.
Bioinformatics. doi: 10.1093/bioinformatics/btr539
Barnett D, Garrison E, Quinlan AR, Stromberg M, Marth G.
Bioinformatics. doi: 10.1093/bioinformatics/btr174
1000 Genomes Project Consortium.
Nature. doi: 10.1038/nature09534
Quinlan AR and Hall IM.
Bioinformatics. doi: 10.1093/bioinformatics/btq033
Quinlan AR, Clark RA, Sokolova, S, Leibowitx ML, Zhang Y, Hurles ME, Mell JC, Hall IM.
Genome Research. doi: 10.1101/gr.102970.109
Sackton, TB, Kulathinal RJ, Bergman CM, Quinlan AR, Dopman E, Marth GT, Hartl DL, Clark AG.
Genome Biol Evol. doi: 10.1093/gbe/evp048
Smith D, Quinlan AR, Peckham HR, et al.
Genome Research
Hillier LW, Marth GT, Quinlan AR, et al.
Nature Methods. doi: 10.1101/gr.077776.108
Quinlan AR, Stewart D, Stromberg M, Marth GT
Nature Methods. doi:10.1038/nmeth.1172
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