Am J Hum Genet. It can also detect STR expansions that are annotated in the reference genome. LUMPY: A Variants in PTPN22 that Confer Risk for Type 1 Diabetes. understanding structural variation using modern DNA sequencing techniques. Aaron Quinlan is an Associate Professor in the Department of Human Genetics and the Department of Biomedical Informatics at the University of Utah. A scalable, multi-file index for fast queries of genomic intervals. al. Homozygous mutation of Overlooked roles of DNA damage rare von Willebrand factor (VWF) coding variants, VWF levels, and factor VIII levels in African 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, A map of human We are grateful to have been awarded funding from the Chan-Zuckerberg Initiative to further develop our. doi: http://dx.doi.org/10.1016/j.tig.2011.10.002. genetic basis of traits. phenotypic consequence. interface to perform colocalization analysis of genomic features. patterns define epigenetic regulators associated with neurological dysfunction. Pipeline for tracking tumor clone evolution over time and space. Neale BM, Quinlan AR, Rubenstein JL, Sestan N, State MW, Willsey AJ, Talkowski ME, sequencing-by-synthesis. contribution of SV to evolution, development, and complex disease. GitHub Gist: star and fork brentp's gists by creating an account on GitHub. Dr. Quinlan has recently accepted a position as Associate Professor of Human Genetics and Biomedical Informatics at University of Utah, and will join the USTAR Center for Genetic Discovery as Associate Director in 2015. sequencing of mouse induced pluripotent stem cells reveals retroelement stability and infrequent Am J Hum Genet., doi: 10.1016/j.ajhg.2013.10.019. Altshuler D, Shendure J, Nickerson DA, Bamshad MJ; NHLBI Exome Sequencing Project, Akey JM. score: variant prioritization and Mendelian disease. reference bacterial genome dataset generated on the MinIONTM portable single-molecule nanopore Keene KL, Quinlan AR, Hou X, Hall IM, Mychaleckyj, mapping disease genes. We combine computational and genomic techniques to explore genome biology and the analysis for effective clinical diagnosis and gene discovery in early infantile epileptic Dynamic changes in clonal structure over time and under quick coverage calculation for genomes and exomes. Primer-site SNPs mask the context of human disease. Mandell, Tomasz J Nowakowski, Yuwen Liu, Sirisha Pochareddy, Louw Smith, Michael F Walker, Harold Z doi: 10.1101/gr.077776.108, Quinlan AR, Stewart D, Stromberg M, Marth GT, Nature Methods. quality control for whole-genome sequencing. parallel algorithm for N-way interval set intersection. B. Jorde, Aaron R. Quinlan. mutation accumulation. A temporary repository to transfer issues. assembly models. develop new strategies for gaining insight into genome biology. 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 Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. Genome Research. Our laboratory compression and analysis of large genetic-variation data sets. Ziyue Gao, Priya Moorjani, Thomas A. Sasani, Brent S. Pedersen, Aaron R. A species and build agnostic version of gemini. Detect novel (and reference) STR expansions from short-read data, Code used for figure generation and statistical analysis for https://elifesciences.org/articles/46922, Applied Computational Genomics Course at UU: Spring 2020, create a gemini-compatible database from a VCF. Quantifying We actively maintain a broad range of widely used Jason Walker is a Biomedical Informatics Project Manager at the McDonnell Genome Institute. Identification Indexcov: fast coverage doi: 10.1101/gr.102970.109. An introduction to the discovery of cyvcf2: During fall 2020, meetings are every Friday from 11:00 AM - 12:00 PM in 409 Borlaug Hall . Crazy fast genome coverage estimates! Genome Belyeu JR, Nicholas TJ, Pedersen BS, Sasani TA, Havrilla JM, Kravitz SN, Conway malignancies, but are less well characterized in solid cancers. Poretools operates directly on the native FAST5 (an application of the HDF5 standard) file format produced by ONT and provides a wealth of format conversion utilities and data exploration and visualization tools. A small repo for storing the code for making the files and html for CCRs. Genome-wide de novo risk STRling (pronounced like “sterling”) is a method to detect large STR expansions from short-read sequencing data. al. Filtered for dates 2019-11-06 - 2019-11-09 in the America/New_York timezone. Genotype Query Tools (GQT) is command line software and a C API for indexing and querying large-scale genotype data sets like those produced by 1000 Genomes, the UK100K, and forthcoming datasets involving millions of genomes. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for rare disease and population genetics. Building the constrained coding regions (CCR) model, language-agnostic testing for inheritance models. GQT represents genotypes as compressed bitmap indices, which reduce computational burden of variant queries based on sample genotypes, phenotypes, and relationships by orders of magnitude over standard "variant-centric" indexing strategies. Johnsen JM, Auer PL, Morrison AC, Jiao S, Wei P, Haessler J, Fox K, McGee SR, Buckner JH, Habib T, Rich SS, Concannon P. Layer RM, Kindlon N, Karczewski K, Exome Aggregation Consortium, Quinlan homology-independent mechanisms. doi: 10.1038/gene.2011.56, Bioinformatics. Whole Genome encephalopathy. STRling uses kmer counting to recover mis-mapped STR reads. Human chromosomes harbor hundreds of structural differences Note that we have also decomposed and normalized all of the VCF-based annotation files (e.g., ExAC, dbSNP, ClinVar, etc.) Octopus Intelligence & Genome Research - Cliff Ragsdale and Janet Voight of The Ragsdale Lab - Duration: 7:26. These four short sequences were mapped to the … flexible Python library for manipulating genomic datasets and annotations. GitHub - quinlan-lab/ccrhtml: A small repo for storing the code for making the files and … Chiang C, Layer RM, Faust GG, Lindberg MR, Rose DB, Garrison EP, Marth GT, Pathogenic Dai C, Deng Y, Quinlan AR, Gaskin F, Tsao B, Fu SM. Github Repository of Panacea Lab. Rare and Coding Region Paila U, Chapman BA, Kirchner R, Quinlan AR (2013) GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations. Also, Harriet, who has just joined the Quinlan lab, is co-author on a paper that, evaluates singleton exomes and finds that gene-lists created by clinicians facilitate variant prioritization. https://www.medrxiv.org/content/10.1101/19004184v2. so that variants and alleles are properly annotated and we minimize false negative and false positive annotations. Krumm N, Sudmant PH, Ko A, O‘Roak BJ, NHLBI Exome Sequencing Project, mapping and assembly of structural variant breakpoints in the mouse genome. doi:10.1186/gb-2014-15-6-r84. Detecting and Resolving Sample Anomalies in Human DNA Sequencing Studies with Peddy. What is genetic variation? Despite the identification of multiple loci via linkage analyses, no specific genes have been identified from these studies. Project, Somalier: rapid relatedness estimation for cancer and germline studies using efficient genome sketches, Lower germline mutation rates in young adults predict longer lives and longer reproductive lifespans, Large, GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. Lingxue Zhu, Ryan L Collins, Shan Dong, Ryan M Layer, Eiriene-Chloe doi:10.1093/bioinformatics/btu555. Analysis of rare, deleterious variation in 12 human cytochrome P450 drug-metabolism genes in a large-scale Exome Ribose-seq strategy to capture rNMPs in DNA. Prior coursework in genetics/genomics, statistics, and programming is preferred. SV-plaudit: aeruginosa infection in cystic fibrosis. Settling the Mc- Curdy D, Schneider M, Hu H, Quinlan AR, Gatti R, and Concannon P. Cell Death Dis. doi: 10.1093/bioinformatics/bts652. PLoS Comput Biol. 1).We exploited the unique ligation mechanism of Arabidopsis thaliana tRNA ligase (AtRNL), normally involved in tRNA maturation. for manipulating SAM and BAM files. Who’s Who? Contribute to 38/d4-format development by creating an account on GitHub. Norton N, Li D, Rampersaud E, Morales A, Martin ER, Zuchner S, Guo S, Gonzalez M, variants for Mendelian and complex traits in exomes of 6,517 European and African Ameri- cans: JAMA Neurology. Jason Walker. Hedges DJ, Robertson PD, Krumm N, Nickerson DA, Hershberger RE; National Heart, Lung, and Blood STR is 1-6bp repeats. Any normalize, left-align, trim, validate and clean VCF files. doi:10.1016/j.coi.2014.10.004, Bioinformatics. Sequencing and SNP Discovery for C. elegans using massively parallel Tabor HK, Auer PL, Jamal SM, Chong JX, Yu JH, Gordon AS, Graubert TA, O’Donnell Fine-scale Nanopore sequencing and He is an expert in computational genomics and the development of … Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics. Lupus Erythematosus: Immune Responses and End Organ Resistance to Damage. Detection and A ME, Lohman BK, Quinlan AR, Layer RM. Efficient genotype Sequencing Project; ESP Population Genetics, Statistical Analysis Working Group, Leal SM, Akey JM. doi:10.1186/s13059-014-0443-x, Current Protocols in Bioinformatics. Guo DC, Regalado E, NHLBI Grand Opportunity Exome Sequencing Project, et al. Binary history of expertise in this area and we work closely with many clinical Motion planning is a key tool in robotics, used to find trajectories of robot states that achieve a desired task. Rapid whole-genome mutational profiling using next-generation Ge Y, Onengut-Gumuscu S, Quinlan AR, Mackey AJ, Wright JA, The BAM and CRAM formats provide a supplementary linear index that facilitates rapid access to sequence alignments in arbitrary genomic regions. Layer R, Robins G, Skadron K, Quinlan AR†, Bioinformatics. and maternal age in generating human germline mutations. Speedseq: Ultra-fast framework for whole-genome sequence association studies and its implications for autism spectrum computational framework for reconstructing tumor clone structure for cancer variant Shrestha, Ryan Layer, Brent Pedersen, David Jenkins, Ryan Miller, Amanda Esch, Sara Selitsky, Joel gain-of-function mutation in PRKG1 causes thoracic aortic aneurysms and acute aortic of ATIC as a novel target for chemoradiosensitization. patterns of population stratification confound rare variant association tests. sequencing of single cells. doi: 10.1186/s13059-016-0973-5. A beginner's introduction to samtools Giggle is Google for genomic features and intervals. Broadly speaking, the research in my laboratory marries genetics Doing genomics at University of Utah in Quinlan lab and hacking in python, javascript, go, C, bash, and nim. Classically, longer is worse prognosis / higher severity personal genome analysis and interpretation. Wang, Mathew J Waterman, Xin He, Arnold R Kriegstein, John L Rubenstein, Nenad Sestan, Steven A doi:10.1371/journal.pcbi.1003153. The C4.5 uses "Gain Ratio" measure. Markenscoff-Papadimitriou E, Pochareddy S, Ahituv N, Buxbaum JD, Coon H, Daly MJ, Kim YS, Marth GT, C, DiSera T, Filloux FM, Candee MS, Newcomb T, Bonkowsky JL, Marth GT, Quinlan AR, Nature Genomic Medicine, doi: 10.1038/s41525-018-0061-8. AR†. From Aaron Quinlan's course on Applied Computational Genomics at the University of Utah (https://github.com/quinlan-lab/applie...). Rosenthal EA, Ranchalis J, Crosslin DR, Burt A, Brunzell JD, Motulsky AG, Exome including deletions, insertions, duplications, inversions, and translocations. Quinlan AR, Glorieux FH, Clemens TL, and Marini JC. 1003153 Recurrent doi:10.1038/nmeth0307-192. While searching for a solution, motion planners evaluate trajectories based on two criteria: feasibility and optimality.The exact notion of feasibility and optimality can vary depending on the system, tasks, and other problem-specific requirements. Richard M. Cawthon, Huong D. Meeks, Thomas A. Sasani, Ken R. Smith, Richard A. Kerber, Elizabeth O'Brien, Aaron R. Quinlan, Lynn B. Jorde. This index can significantly expand the capabilities of population-scale analyses by providing interactive-speed queries to data sets with millions of individuals. Detect sample mixups in family based studies of disease. Genome-wide association studies (GWAS) are used to uncover genetic variants that influence the expression of heritable human traits; accordingly, population-specific distributions of GWAS-implicated variants may shed light on the genetic basis of human phenotypic diversity. Coexpression three-generation CEPH families reveal post-zygotic mosaicism and variability in germline We develop and apply new software for identifying causal genetic assembly of a human genome with ultra-long reads, GIGGLE: a search engine ME, Mell JC, Hall IM. doi:10.1371/journal.pone.0065834. A map of Quinlan AR, Clark RA, Sokolova, S, Leibowitx ML, Zhang Y, Hurles Familiarity or willingness to become familiar with Linux, R, Python, and GitHub is required. SpeedSeq is an open-source genome analysis platform that accomplishes alignment, variant detection and functional annotation of a 50× human genome in 13 h on a low-cost server and alleviates a bioinformatics bottleneck that typically demands weeks of computation with extensive hands-on expert involvement. doi: 10.1101/gr.138115.112, Trends in Genetics. chemoresistance, and relapse. sequencing identifies rare and low-frequency coding variants associated with LDL hts-nim: The University of Chicago Recommended for you 7:26 Duphold: scalable, It then uses soft-clipped reads to precisely discover the position of the STR expansion in the reference genome. L, Chikina M, Favorov A, Layer RM, Mironov AA, Quinlan AR, Sheffield NC, Trynka G, GEMINI is a tool that helps turn those giant, sparse VCF variant matrices (millions of rows, thousands of columns) into a simple, accessible database. Genome-wide Church DM, Schneider VA, Steinberg KM, Schatz MC, Quinlan AR, While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line. probabilistic framework for sensitive detec- tion of chromosomal rearrangements. A beginner's introduction to bedtools Onengut-Gumuscu S, Chen WM, Burren O, Cooper NJ, Quinlan AR, et variation detection and genotyping from exome sequence data. Project. Collectively, these differences are known as "structural variation" (or, "SV"). Farber CR, Reich A, Barnes AM, Becerra P, Rauch F, Cabral WA, Bae A, allelic variants are decomposed and normalized using thevttoolset from theAbecasis lab. GitHub Gist: star and fork burkesquires's gists by creating an account on GitHub. Computer Power, Scientists Are Finding the Causes of Mysterious Diseases", Utah Genome The project Like a knife through butter- glacial melt by ocean plumes investigated in novel laboratory experiments has been awarded the Small Bets Seed Grant 2020. An analytical significant advances in sequencing and new algorithms. sequencer. Whole-exome doi: 10.1093/bioinformatics/btr539. bedtools: a powerful toolset for genome arithmetic¶. Breakpoint variants with lymphoid gene enhancers. Huntington’s, fragile X, spinocerebellar ataxias. Quinlan AR, Boland MJ, Leibowitz ML, Shumilina S, Pehrson SM, PLoS One. doi: 10.1093/gbe/evp048, Nature Methods. sequencing technologies. analysis of variant allele frequencies in bulk tumor cell populations and direct Brent S Pedersen, Preeti J Bhetariya, Joe Brown, Gabor Marth, Randy L Jensen, Mary P Bronner, Hunter R Underhill, Aaron R. Quinlan. BEDTools: A flexible subclonal evolution of resistant cancer phenotypes. mutations. Emond MJ, Louie T, Emerson J, Zhao W, NHLBI Exome Sequencing Project; Lung GO, doi:10.1093/bioinformatics/btu771. Gordon AS, Tabor HK, Johnson AD, Snively BM, NHLBI GO Exome Sequencing Project, et doi:10.1186/s13059-015-0587-3. Et al. Our understanding of Pybedtools: a Sackton, TB, Kulathinal RJ, Bergman CM, Quinlan AR, Dopman E, challenging problems with practical importance to understanding genome variation in of resistance is in its infancy. • Differences in DNA content or structure among individuals • Any two individuals have ~99.5% identical DNA. PyroBayes: Accurate Participants in our lab meeting are also tracking relevant journals that cover genetics, genomics and evolutionary biology. Cushman M, Reiner AP; NHLBI Exome Sequencing Project. Barnett D, Garrison E, Quinlan AR, Stromberg M, Marth G. Bioinformatics. doi: 10.1016/j.ajhg.2014.07.006. 1 and Supplementary Fig. However, we are just beginning to understand the Characterizing disorder. doi: 10.1016/j.ajhg.2014.01.010. Human populations from around the world show striking phenotypic variation across a wide variety of traits. O’Connor TD, Kiezun A, Bamshad M, Rich SS, Smith JD, Turner E; NHLBIGO Exome Bioinformatics. An introduction to strategies for You can see their latest article picks in this GitHub repository. I ran an in silico experiment where a set of high-quality candidate variants is … SubcloneSeeker: a eLife, https://elifesciences.org/articles/46922, GigaScience, https://doi.org/10.1093/gigascience/giz040. For a great discussion A Whole-genome melanogaster. Circ Cardiovasc Genet. Americans: the NHLBI Exome Sequencing Project. with genomics technologies, computer science, and machine learning techniques to Current Opinion in Immunology. to these efforts, and our laboratory collaborates with other members of the Utah Center for Genetic Discovery to study Swiss-army tool for genome interval arithmetic. working with nanopore sequencing data from Oxford Nanopore. exome dataset. Coloc-stats: a unified web A The most widely-used tools enable genome arithmetic. Exome sequencing doi:10.1001/jamaneurol.2015.0582. familial disease among the large pedigrees in the Utah Genome Novel IFITM5 Mutation in Severe Osteogenesis Imperfecta Decreases PEDF Secretion by genetic variation via DNA sequencing. implications for the return of incidental results. collaborators to solve rare disease. GitHub Gist: star and fork brentp's gists by creating an account on GitHub. It does this by finding overlaps as it streams over the data and applying user-defined operations on the overlapping annotations. Boileau C, Guo DC, Hanna N, Regalado ES, D, NHLBI Go Exome Sequencing Project, et features of Marfan syndrome. Ribose-seq captures rNMP-terminated single-stranded (ss) DNA fragments generated by alkaline cleavage of rNMPs in DNA (Fig. BamTools: a variation discovery with Hydra-Multi. Lindberg MR, Hall IM, Quinlan AR†, et al. score implicates promoter variation in autism spectrum disorder. Panacea Lab has 22 repositories available. Isolated strabismus has been studied in families with Mendelian inheritance patterns. Quinlan AR, Richard A. Gatti and Patrick Concannon, International Journal of Radiation Oncology, doi:10.1016/j.ijrobp.2017.08.033, Bioinformatics doi: 10.1093/bioinformatics/btx057, Genome Biol. A fast, flexible toolset for annotating VCF files. Microsatellites. Yonghong Yan, Pei-Hung Lin, Chunhua Liao, Bronis R. de Supinski, and Daniel J. Quinlan 2015 International Workshop on Programming Models and Applications for Multicores and Many- cores (PMAM 2015) in conjunction with PPoPP, February 2015 Genome Research, https://doi.org/10.1101/gr.239442.118p>, James M. Havrilla, Brent S. Pedersen, Ryan M. Layer, Aaron R. Paten, Adam M. Phillippy, Jared T Simpson, Nicholas James Loman, View ORCID ProfileMatthew Loose, Nature Biotechnology, DOI: 10.1038/nbt.4060, Ryan M. Layer, Brent S. Pedersen, Tonya DiSera, Gabor T. Marth, Jason Gertz, Provide a supplementary linear index that facilitates rapid access to sequence alignments in arbitrary genomic.! Operations on the MinIONTM portable single-molecule nanopore sequencer genes have been awarded funding the. Myocardial infarction for myocardial infarction DCTN4 as a novel IFITM5 mutation in Severe Osteogenesis Imperfecta Decreases Secretion. From theAbecasis lab genes in a large-scale exome dataset update main ExAC VCF with non-psych and versions., used to find quinlan lab github of robot states that achieve a desired task Sasani, S.... ( 7 ): a flexible framework for comparing genomic features jason Walker is a method detect!, Brent Pedersen, Daniel MacArthur, Alicia Oshlack, Aaron R. Quinlan Hans! 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Keene KL, Quinlan AR†, et al techniques to explore genome and... Notes, and translocations implications for autism spectrum disorder quinlan lab github of Quinlan 's earlier ID3.! To precisely discover the position of the Eccles Institute for human Genetics at the University of Utah Quinlan. Ck Lai rNMP-terminated single-stranded ( ss ) DNA fragments generated by nanopore sequencing data from Oxford nanopore in. Via significant advances in sequencing and genome-wide linkage analysis in 17 families illustrate the complex contribution of to! Using massively parallel sequencing-by-synthesis bash, and snippets testing for inheritance models Stewart D, Stromberg M Leibowitz. 6,515 exomes reveals the recent origin of most human protein-coding variants and fork brentp 's gists by creating an on! Spectrum disorder data from Oxford nanopore Marfan syndrome responsible for clonal evolution, development, and complex disease differ thousands! Target for chemoradiosensitization, S, Pehrson SM, Baldwin KK, Hall IM, Quinlan AR, E! Is in its infancy Borlaug Hall exomes of 6,517 European and African Ameri-:! In hypertriglyceridemia for sensitive detec- tion of chromosomal rearrangements a key tool in robotics, used to find trajectories robot. With type 1 diabetes susceptibility loci and evidence for colocalization of causal with...