Publications

Preprints

Beryl B Cummings, Jamie L Marshall, Taru Tukiainen, Monkol Lek, Sandra Donkervoort, A. Reghan Foley, Veronique Bolduc, Leigh Waddell, Sarah Sandaradura, Gina L O’Grady, Elicia Estrella, Hemakumar Mutra Reddy, Fengmei Zhao, Ben Weisburd, Konrad Karczewski, Anne O’Donnell-Luria, Daniel Birnbaum, Anna Sarkozy, Ying Hu, Hernan Gonorazky, Kristl Claeys, Himanshu Joshi, Adam Bournazos, Emily Oates, Roula Ghaoui, Mark Davis, Nigel G Laing, Ana Topf, GTEx Consortium, Alan Beggs, Peter B Kang, Kathryn N North, Volker Straub, James Dowling, Francesco Muntoni, Nigel F Clarke, Sandra T Cooper, Carsten G Bonnemann, Daniel G MacArthur. (2016) Improving genetic diagnosis in Mendelian disease with transcriptome sequencing. bioRxiv doi: https://doi.org/10.1101/074153 (preprint)

Taru Tukiainen, Alexandra-Chloé Villani, Angela Yen, Manuel A. Rivas, Jamie L. Marshall, Rahul Satija, Matt Aguirre, Laura Gauthier, Mark Fleharty, Andrew Kirby, Beryl B. Cummings, Stephane E. Castel, Konrad J. Karczewski, François Aguet, Andrea Byrnes, GTEx Consortium, Tuuli Lappalainen, Aviv Regev, Kristin G. Ardlie, Nir Hacohen, Daniel G. MacArthur (2016) Landscape of X chromosome inactivation across human tissues. bioRxiv doi: https://doi.org/10.1101/073957 (preprint)

Selected publications

Cassa CA, Weghorn D, Balick DJ, Jordan DM, Nusinow D, Samocha KE, O’Donnell-Luria A, MacArthur DG, Daly MJ, Beier DR, Sunyaev SR. (2017) Estimating the selective effects of heterozygous protein-truncating variants from human exome data. Nature Genetics. [Epub ahead of print] (preprint)(full text)

Kosmicki JA, Samocha KE, Howrigan DP, Sanders SJ, Slowikowski K, Lek M, Karczewski KJ, Cutler DJ, Devlin B, Roeder K, Buxbaum JD, Neale BM, MacArthur DG, Wall DP, Robinson EB, Daly MJ. (2017) Refining the role of de novo protein-truncating variants in neurodevelopmental disorders by using population reference samples. Nature Genetics. 49(4):504-510. (preprint)(full text)

McCarthy MI, MacArthur DG. (2017) Human disease genomics: from variants to biology. Genome Biology.18(1):20. (full text)

Karczewski KJ, Weisburd B, Thomas B, Solomonson M, Ruderfer DM, Kavanagh D, Hamamsy T, Lek M, Samocha KE, Cummings BB, Birnbaum D; The Exome Aggregation Consortium., Daly MJ, MacArthur DG. (2017) The ExAC browser: displaying reference data information from over 60 000 exomes. Nucleic Acids Research. 45(D1):D840-D845. (preprint)(full text)

Zou J, Valiant G, Valiant P, Karczewski K, Chan SO, Samocha K, Lek M, Sunyaev S, Daly M, MacArthur DG. (2016) Quantifying unobserved protein-coding variants in human populations provides a roadmap for large-scale sequencing projects. Nature Communications 7:13293. (preprint)(full text)

Minikel EV, MacArthur DG. (2016) Publicly Available Data Provide Evidence against NR1H3 R415Q Causing Multiple Sclerosis. Neuron. 92(2):336-338. (full text)

Dickinson ME, Flenniken AM, Ji X, Teboul L, Wong MD, White JK, Meehan TF, Weninger WJ, Westerberg H, Adissu H, Baker CN, Bower L, Brown JM, Caddle LB, Chiani F, Clary D, Cleak J, Daly MJ, Denegre JM, Doe B, Dolan ME, Edie SM, Fuchs H, Gailus-Durner V, Galli A, Gambadoro A, Gallegos J, Guo S, Horner NR, Hsu CW, Johnson SJ, Kalaga S, Keith LC, Lanoue L, Lawson TN, Lek M, Mark M, Marschall S, Mason J, McElwee ML, Newbigging S, Nutter LM, Peterson KA, Ramirez-Solis R, Rowland DJ, Ryder E, Samocha KE, Seavitt JR, Selloum M, Szoke-Kovacs Z, Tamura M, Trainor AG, Tudose I, Wakana S, Warren J, Wendling O, West DB, Wong L, Yoshiki A; International Mouse Phenotyping Consortium.; Jackson Laboratory.; Infrastructure Nationale PHENOMIN, Institut Clinique de la Souris (ICS).; Charles River Laboratories.; MRC Harwell.; Toronto Centre for Phenogenomics.; Wellcome Trust Sanger Institute.; RIKEN BioResource Center., MacArthur DG, Tocchini-Valentini GP, Gao X, Flicek P, Bradley A, Skarnes WC, Justice MJ, Parkinson HE, Moore M, Wells S, Braun RE, Svenson KL, de Angelis MH, Herault Y, Mohun T, Mallon AM, Henkelman RM, Brown SD, Adams DJ, Lloyd KC, McKerlie C, Beaudet AL, Bućan M, Murray SA. (2016) High-throughput discovery of novel developmental phenotypes. Nature. 537(7621): 508-514. (full text)

Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O’Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB, Tukiainen T, Birnbaum DP, Kosmicki JA, Duncan LE, Estrada K, Zhao F, Zou J, Pierce-Hoffman E, Berghout J, Cooper DN, Deflaux N, DePristo M, Do R, Flannick J, Fromer M, Gauthier L, Goldstein J, Gupta N, Howrigan D, Kiezun A, Kurki MI, Moonshine AL, Natarajan P, Orozco L, Peloso GM, Poplin R, Rivas MA, Ruano-Rubio V, Rose SA, Ruderfer DM, Shakir K, Stenson PD, Stevens C, Thomas BP, Tiao G, Tusie-Luna MT, Weisburd B, Won HH, Yu D, Altshuler DM, Ardissino D, Boehnke M, Danesh J, Donnelly S, Elosua R, Florez JC, Gabriel SB, Getz G, Glatt SJ, Hultman CM, Kathiresan S, Laakso M, McCarroll S, McCarthy MI, McGovern D, McPherson R, Neale BM, Palotie A, Purcell SM, Saleheen D, Scharf JM, Sklar P, Sullivan PF, Tuomilehto J, Tsuang MT, Watkins HC, Wilson JG, Daly MJ, MacArthur DG, Exome Aggregation Consortium (2016) Analysis of protein-coding genetic variation in 60,706 humans. Nature. 536(7616):285-91. (preprint)(full text)

Ruderfer DM, Hamamsy T, Lek M, Karczewski KJ, Kavanagh D, Samocha KE; Exome Aggregation Consortium., Daly MJ, MacArthur DG, Fromer M, Purcell SM. (2016) Patterns of genic intolerance of rare copy number variation in 59,898 human exomes. Nature Genetics. 48(10):1107-11. (full text)

Narasimhan VM, Hunt KA, Mason D, Baker CL, Karczewski KJ, Barnes MR, Barnett AH, Bates C, Bellary S, Bockett NA, Giorda K, Griffiths CJ, Hemingway H, Jia Z, Kelly MA, Khawaja HA, Lek M, McCarthy S, McEachan R, O’Donnell-Luria A, Paigen K, Parisinos CA, Sheridan E, Southgate L, Tee L, Thomas M, Xue Y, Schnall-Levin M, Petkov PM, Tyler-Smith C, Maher ER, Trembath RC, MacArthur DG, Wright J, Durbin R, van Heel DA. (2016) Health and population effects of rare gene knockouts in adult humans with related parents. Science. (preprint)(full text)

Minikel EV, Vallabh SM, Lek M, Estrada K, Samocha KE, Sathirapongsasuti JF, McLean CY, Tung JY, Yu LP, Gambetti P, Blevins J, Zhang S, Cohen Y, Chen W, Yamada M, Hamaguchi T, Sanjo N, Mizusawa H, Nakamura Y, Kitamoto T, Collins SJ, Boyd A, Will RG, Knight R, Ponto C, Zerr I, Kraus TF, Eigenbrod S, Giese A, Calero M, de Pedro-Cuesta J, Haïk S, Laplanche JL, Bouaziz-Amar E, Brandel JP, Capellari S, Parchi P, Poleggi A, Ladogana A, O’Donnell-Luria AH, Karczewski KJ, Marshall JL, Boehnke M, Laakso M, Mohlke KL, Kähler A, Chambert K, McCarroll S, Sullivan PF, Hultman CM, Purcell SM, Sklar P, van der Lee SJ, Rozemuller A, Jansen C, Hofman A, Kraaij R, van Rooij JG, Ikram MA, Uitterlinden AG, van Duijn CM; Exome Aggregation Consortium (ExAC), Daly MJ, MacArthur DG. (2016) Quantifying prion disease penetrance using large population control cohorts. Science Translational Medicine. 8(322):322ra9 (full text)

Rivas MA, Pirinen M, Conrad DF, Lek M, Tsang EK, Karczewski KJ, Maller JB, Kukurba KR, DeLuca DS, Fromer M, Ferreira PG, Smith KS, Zhang R, Zhao F, Banks E, Poplin R, Ruderfer DM, Purcell SM, Tukiainen T, Minikel EV, Stenson PD, Cooper DN, Huang KH, Sullivan TJ, Nedzel J; GTEx Consortium; Geuvadis Consortium, Bustamante CD, Li JB, Daly MJ, Guigo R, Donnelly P, Ardlie K, Sammeth M, Dermitzakis ET, McCarthy MI, Montgomery SB, Lappalainen T, MacArthur DG. (2015) Effect of predicted protein-truncating genetic variants on the human transcriptome. Science. 348(6235):666-669. (full text)

MacArthur DG, Manolio TA, Dimmock DP, Rehm HL, Shendure J, Abecasis GR, Adams DR, Altman RB, Antonarakis SE, Ashley EA, Barrett JC, Biesecker LG, Conrad DF, Cooper GM, Cox NJ, Daly MJ, Gerstein MB, Goldstein DB, Hirschhorn JN, Leal SM, Pennacchio LA, Stamatoyannopoulos JA, Sunyaev SR, Valle D, Voight BF, Winckler W, Gunter C. (2014) Guidelines for investigating causality of sequence variants in human disease. Nature. 508(7497):469-476. (full text)

SIGMA Type 2 Diabetes Consortium, Williams AL, Jacobs SB, Moreno-Macías H, Huerta-Chagoya A, Churchhouse C, Márquez-Luna C, García-Ortíz H, Gómez-Vázquez MJ, Burtt NP, Aguilar-Salinas CA, González-Villalpando C, Florez JC, Orozco L, Haiman CA, Tusié-Luna T, Altshuler D. (2014) Sequence variants in SLC16A11 are a common risk factor for type 2 diabetes in Mexico. Nature 506(7486):97-101. (full text)

Lappalainen T, Sammeth M, Friedländer MR, ‘t Hoen PA, Monlong J, Rivas MA, Gonzàlez-Porta M, Kurbatova N, Griebel T, Ferreira PG, Barann M, Wieland T, Greger L, van Iterson M, Almlöf J, Ribeca P, Pulyakhina I, Esser D, Giger T, Tikhonov A, Sultan M, Bertier G, MacArthur DG, Lek M, Lizano E, Buermans HP, Padioleau I, Schwarzmayr T, Karlberg O, Ongen H, Kilpinen H, Beltran S, Gut M, Kahlem K, Amstislavskiy V, Stegle O, Pirinen M, Montgomery SB, Donnelly P, McCarthy MI, Flicek P, Strom TM; Geuvadis Consortium, Lehrach H, Schreiber S, Sudbrak R, Carracedo A, Antonarakis SE, Häsler R, Syvänen AC, van Ommen GJ, Brazma A, Meitinger T, Rosenstiel P, Guigó R, Gut IG, Estivill X, Dermitzakis ET; Geuvadis Consortium. (2013) Transcriptome and genome sequencing uncovers functional variation in humans. Nature 501(7468):506-511. (full text)

Hunt KA, Mistry V, Bockett NA, Ahmad T, Ban M, Barker JN, Barrett JC, Blackburn H, Brand O, Burren O, Capon F, Compston A, Gough SC, Jostins L, Kong Y, Lee JC, Lek M, MacArthur DG, Mansfield JC, Mathew CG, Mein CA, Mirza M, Nutland S, Onengut-Gumuscu S, Papouli E, Parkes M, Rich SS, Sawcer S, Satsangi J, Simmonds MJ, Trembath RC, Walker NM, Wozniak E, Todd JA, Simpson MA, Plagnol V, van Heel DA. (2013) Negligible impact of rare autoimmune-locus coding-region variants on missing heritability. Nature 498(7453):232-235. (full text)

1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. (2012) An integrated map of genetic variation from 1,092 human genomes. Nature. 491(7422):56-65. (full text)

Macarthur D. (2012) Face up to false positives. Nature. 487(7408):427-428. (preprint)(full text)

MacArthur DG, Lek M. (2012) The uncertain road towards genomic medicine. Trends Genet. 28(7):303-305. (preprint)(full text)

MacArthur DG. (2012) Challenges in clinical genomics. Genome Med. 4:43. (preprint)(full text)

MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, Montgomery SB, Albers CA, Zhang Z, Conrad DF, Lunter G, Zheng H, Ayub Q, DePristo MA, Banks E, Hu M, Handsaker R, Habegger L, Fromer M, Jin M, Mu X, Khurana E, Ye K, Kay M, Saunders GI, Suner M.-M., Hunt T, Barnes IHA, Amid C, Carvalho-Silva DR, Bignell AH, Snow C, Yngvadottir B, Bumpstead S, Cooper DN, Xue Y, Gallego Romero I, 1000 Genomes Project Consortium, Wang J, Li Y, Gibbs RA, McCarroll SA, Dermitzakis ET, Pritchard JK, Barrett JC, Harrow J, Hurles ME, Gerstein M, Tyler-Smith C. (2012) A systematic survey of loss-of-function polymorphisms in human protein-coding genes.Science. 335(6070):823-828. (preprint and additional data)(full text)