Macarthur, Daniel

Daniel Macarthur, PhD

Daniel is a group leader at the ATGU, with a research program focusing on predicting the functional impact of genetic variants obtained from high-throughput sequencing data. Daniel coordinated the functional annotation of variation in protein-coding genes for the 1000 Genomes Project pilot study, which was published in Nature in 2010. His current focus is on genetic variants predicted to cause the complete loss of function of protein-coding genes, and their implications for human disease and the understanding of normal gene function. He recently led an analysis of loss-of-function variants in 185 sequenced human genomes, which was published in Science in February 2012.


More detail on Daniel’s team and loss-of-function variants can be found on his lab website.


Daniel is currently looking to fill positions for postdocs, bioinformatics specialists and graduate students – please see his jobs page for details.

Publications

Shaw ND, Brand H, Kupchinsky ZA, Bengani H, Plummer L, Jones TI, Erdin S, Williamson KA, Rainger J, Stortchevoi A, Samocha K, Currall BB, Dunican DS, Collins RL, Willer JR, Lek A, Lek M, Nassan M, Pereira S, Kammin T, Lucente D, Silva A, Seabra CM, Chiang C, An Y, Ansari M, Rainger JK, Joss S, Smith JC, Lippincott MF, Singh SS, Patel N, Jing JW, Law JR, Ferraro N, Verloes A, Rauch A, Steindl K, Zweier M, Scheer I, Sato D, Okamoto N, Jacobsen C, Tryggestad J, Chernausek S, Schimmenti LA, Brasseur B, Cesaretti C, García-Ortiz JE, Buitrago TP, Silva OP, Hoffman JD, Mühlbauer W, Ruprecht KW, Loeys BL, Shino M, Kaindl AM, Cho CH, Morton CC, Meehan RR, van Heyningen V, Liao EC, Balasubramanian R, Hall JE, Seminara SB, Macarthur D, Moore SA, Yoshiura KI, Gusella JF, Marsh JA, Graham JM, Lin AE, Katsanis N, Jones PL, Crowley WF, Davis EE, FitzPatrick DR, Talkowski ME
Corrigendum: SMCHD1 mutations associated with a rare muscular dystrophy can also cause isolated arhinia and Bosma arhinia microphthalmia syndrome.
Nat Genet. 2017;49(6):969 - PMID: 28546579
Cassa CA, Weghorn D, Balick DJ, Jordan DM, Nusinow D, Samocha KE, O'Donnell-Luria A, MacArthur DG, Daly MJ, Beier DR, Sunyaev SR
Estimating the selective effects of heterozygous protein-truncating variants from human exome data.
Nat Genet. 2017;:ePub - PMID: 28369035
Saleheen D, Natarajan P, Armean IM, Zhao W, Rasheed A, Khetarpal SA, Won HH, Karczewski KJ, O'Donnell-Luria AH, Samocha KE, Weisburd B, Gupta N, Zaidi M, Samuel M, Imran A, Abbas S, Majeed F, Ishaq M, Akhtar S, Trindade K, Mucksavage M, Qamar N, Zaman KS, Yaqoob Z, Saghir T, Rizvi SN, Memon A, Hayyat Mallick N, Ishaq M, Rasheed SZ, Memon FU, Mahmood K, Ahmed N, Do R, Krauss RM, MacArthur DG, Gabriel S, Lander ES, Daly MJ, Frossard P, Danesh J, Rader DJ, Kathiresan S
Human knockouts and phenotypic analysis in a cohort with a high rate of consanguinity.
Nature. 2017;544(7649):235-239 - PMID: 28406212
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
Refining the role of de novo protein-truncating variants in neurodevelopmental disorders by using population reference samples.
Nat Genet. 2017;:ePub - PMID: 28191890
Shaw ND, Brand H, Kupchinsky ZA, Bengani H, Plummer L, Jones TI, Erdin S, Williamson KA, Rainger J, Stortchevoi A, Samocha K, Currall BB, Dunican DS, Collins RL, Willer JR, Lek A, Lek M, Nassan M, Pereira S, Kammin T, Lucente D, Silva A, Seabra CM, Chiang C, An Y, Ansari M, Rainger JK, Joss S, Smith JC, Lippincott MF, Singh SS, Patel N, Jing JW, Law JR, Ferraro N, Verloes A, Rauch A, Steindl K, Zweier M, Scheer I, Sato D, Okamoto N, Jacobsen C, Tryggestad J, Chernausek S, Schimmenti LA, Brasseur B, Cesaretti C, García-Ortiz JE, Buitrago TP, Silva OP, Hoffman JD, Mühlbauer W, Ruprecht KW, Loeys BL, Shino M, Kaindl AM, Cho CH, Morton CC, Meehan RR, van Heyningen V, Liao EC, Balasubramanian R, Hall JE, Seminara SB, Macarthur D, Moore SA, Yoshiura KI, Gusella JF, Marsh JA, Graham JM, Lin AE, Katsanis N, Jones PL, Crowley WF, Davis EE, FitzPatrick DR, Talkowski ME
SMCHD1 mutations associated with a rare muscular dystrophy can also cause isolated arhinia and Bosma arhinia microphthalmia syndrome.
Nat Genet. 2017;:ePub - PMID: 28067909
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
The ExAC browser: displaying reference data information from over 60 000 exomes.
Nucleic Acids Res. 2016;:ePub - PMID: 27899611
Zou J, Valiant G, Valiant P, Karczewski K, Chan SO, Samocha K, Lek M, Sunyaev S, Daly M, MacArthur DG
Quantifying unobserved protein-coding variants in human populations provides a roadmap for large-scale sequencing projects.
Nat Commun. 2016;7:13293 - PMID: 27796292 - PMCID: PMC5095512
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
High-throughput discovery of novel developmental phenotypes.
Nature. 2016;:ePub - PMID: 27626380
Rivas MA, Graham D, Sulem P, Stevens C, Desch AN, Goyette P, Gudbjartsson D, Jonsdottir I, Thorsteinsdottir U, Degenhardt F, Mucha S, Kurki MI, Li D, D'Amato M, Annese V, Vermeire S, Weersma RK, Halfvarson J, Paavola-Sakki P, Lappalainen M, Lek M, Cummings B, Tukiainen T, Haritunians T, Halme L, Koskinen LL, Ananthakrishnan AN, Luo Y, Heap GA, Visschedijk MC, UK IBD Genetics Consortium, NIDDK IBD Genetics Consortium, MacArthur DG, Neale BM, Ahmad T, Anderson CA, Brant SR, Duerr RH, Silverberg MS, Cho JH, Palotie A, Saavalainen P, Kontula K, Färkkilä M, McGovern DP, Franke A, Stefansson K, Rioux JD, Xavier RJ, Daly MJ
Erratum: A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis.
Nat Commun. 2016;7:12869 - PMID: 27619887
Ruderfer DM, Hamamsy T, Lek M, Karczewski KJ, Kavanagh D, Samocha KE, Exome Aggregation Consortium, Daly MJ, MacArthur DG, Fromer M, Purcell SM
Patterns of genic intolerance of rare copy number variation in 59,898 human exomes.
Nat Genet. 2016;:ePub - PMID: 27533299
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
Analysis of protein-coding genetic variation in 60,706 humans.
Nature. 2016;536(7616):285-91 - PMID: 27535533
Rivas MA, Graham D, Sulem P, Stevens C, Desch AN, Goyette P, Gudbjartsson D, Jonsdottir I, Thorsteinsdottir U, Degenhardt F, Mucha S, Kurki MI, Li D, D'Amato M, Annese V, Vermeire S, Weersma RK, Halfvarson J, Paavola-Sakki P, Lappalainen M, Lek M, Cummings B, Tukiainen T, Haritunians T, Halme L, Koskinen LL, Ananthakrishnan AN, Luo Y, Heap GA, Visschedijk MC, UK IBD Genetics Consortium, NIDDK IBD Genetics Consortium, MacArthur DG, Neale BM, Ahmad T, Anderson CA, Brant SR, Duerr RH, Silverberg MS, Cho JH, Palotie A, Saavalainen P, Kontula K, Färkkilä M, McGovern DP, Franke A, Stefansson K, Rioux JD, Xavier RJ, Daly MJ, Barrett J, de Lane K, Edwards C, Hart A, Hawkey C, Jostins L, Kennedy N, Lamb C, Lee J, Lees C, Mansfield J, Mathew C, Mowatt C, Newman B, Nimmo E, Parkes M, Pollard M, Prescott N, Randall J, Rice D, Satsangi J, Simmons A, Tremelling M, Uhlig H, Wilson D, Abraham C, Achkar JP, Bitton A, Boucher G, Croitoru K, Fleshner P, Glas J, Kugathasan S, Limbergen JV, Milgrom R, Proctor D, Regueiro M, Schumm PL, Sharma Y, Stempak JM, Targan SR, Wang MH
A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis.
Nat Commun. 2016;7:12342 - PMID: 27503255
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
Quantifying prion disease penetrance using large population control cohorts.
Sci Transl Med. 2016;8(322):322ra9 - PMID: 26791950
Baran Y, Subramaniam M, Biton A, Tukiainen T, Tsang EK, Rivas MA, Pirinen M, Gutierrez-Arcelus M, Smith KS, Kukurba KR, Zhang R, Eng C, Torgerson DG, Urbanek C, , Li JB, Rodriguez-Santana JR, Burchard EG, Seibold MA, MacArthur DG, Montgomery SB, Zaitlen NA, Lappalainen T
The landscape of genomic imprinting across diverse adult human tissues.
Genome Res. 2015;:ePub - PMID: 25953952
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, , , Bustamante CD, Li JB, Daly MJ, Guigo R, Donnelly P, Ardlie K, Sammeth M, Dermitzakis ET, McCarthy MI, Montgomery SB, Lappalainen T, MacArthur DG
Effect of predicted protein-truncating genetic variants on the human transcriptome.
Science. 2015;348(6235):666-9 - PMID: 25954003
Grimm DG, Azencott CA, Aicheler F, Gieraths U, MacArthur DG, Samocha KE, Cooper DN, Stenson PD, Daly MJ, Smoller JW, Duncan LE, Borgwardt KM
The evaluation of tools used to predict the impact of missense variants is hindered by two types of circularity.
Hum Mutat. 2015;:ePub - PMID: 25684150
Yuen M, Sandaradura SA, Dowling JJ, Kostyukova AS, Moroz N, Quinlan KG, Lehtokari VL, Ravenscroft G, Todd EJ, Ceyhan-Birsoy O, Gokhin DS, Maluenda J, Lek M, Nolent F, Pappas CT, Novak SM, D'Amico A, Malfatti E, Thomas BP, Gabriel SB, Gupta N, Daly MJ, Ilkovski B, Houweling PJ, Davidson AE, Swanson LC, Brownstein CA, Gupta VA, Medne L, Shannon P, Martin N, Bick DP, Flisberg A, Holmberg E, Van den Bergh P, Lapunzina P, Waddell LB, Sloboda DD, Bertini E, Chitayat D, Telfer WR, Laquerrière A, Gregorio CC, Ottenheijm CA, Bönnemann CG, Pelin K, Beggs AH, Hayashi YK, Romero NB, Laing NG, Nishino I, Wallgren-Pettersson C, Melki J, Fowler VM, MacArthur DG, North KN, Clarke NF
Leiomodin-3 dysfunction results in thin filament disorganization and nemaline myopathy.
J Clin Invest. 2015;125(1):456-457 - PMID: 25654555
Yuen M, Sandaradura SA, Dowling JJ, Kostyukova AS, Moroz N, Quinlan KG, Lehtokari VL, Ravenscroft G, Todd EJ, Ceyhan-Birsoy O, Gokhin DS, Maluenda J, Lek M, Nolent F, Pappas CT, Novak SM, D'Amico A, Malfatti E, Thomas BP, Gabriel SB, Gupta N, Daly MJ, Ilkovski B, Houweling PJ, Davidson AE, Swanson LC, Brownstein CA, Gupta VA, Medne L, Shannon P, Martin N, Bick DP, Flisberg A, Holmberg E, Van den Bergh P, Lapunzina P, Waddell LB, Sloboda DD, Bertini E, Chitayat D, Telfer WR, Laquerrière A, Gregorio CC, Ottenheijm CA, Bönnemann CG, Pelin K, Beggs AH, Hayashi YK, Romero NB, Laing NG, Nishino I, Wallgren-Pettersson C, Melki J, Fowler VM, MacArthur DG, North KN, Clarke NF
Leiomodin-3 dysfunction results in thin filament disorganization and nemaline myopathy.
J Clin Invest. 2014;:ePub - PMID: 25250574
Samocha KE, Robinson EB, Sanders SJ, Stevens C, Sabo A, McGrath LM, Kosmicki JA, Rehnström K, Mallick S, Kirby A, Wall DP, MacArthur DG, Gabriel SB, DePristo M, Purcell SM, Palotie A, Boerwinkle E, Buxbaum JD, Cook EH, Gibbs RA, Schellenberg GD, Sutcliffe JS, Devlin B, Roeder K, Neale BM, Daly MJ
A framework for the interpretation of de novo mutation in human disease.
Nat Genet. 2014;:ePub - PMID: 25086666
Lim ET, Würtz P, Havulinna AS, Palta P, Tukiainen T, Rehnström K, Esko T, Mägi R, Inouye M, Lappalainen T, Chan Y, Salem RM, Lek M, Flannick J, Sim X, Manning A, Ladenvall C, Bumpstead S, Hämäläinen E, Aalto K, Maksimow M, Salmi M, Blankenberg S, Ardissino D, Shah S, Horne B, McPherson R, Hovingh GK, Reilly MP, Watkins H, Goel A, Farrall M, Girelli D, Reiner AP, Stitziel NO, Kathiresan S, Gabriel S, Barrett JC, Lehtimäki T, Laakso M, Groop L, Kaprio J, Perola M, McCarthy MI, Boehnke M, Altshuler DM, Lindgren CM, Hirschhorn JN, Metspalu A, Freimer NB, Zeller T, Jalkanen S, Koskinen S, Raitakari O, Durbin R, MacArthur DG, Salomaa V, Ripatti S, Daly MJ, Palotie A,
Distribution and Medical Impact of Loss-of-Function Variants in the Finnish Founder Population.
PLoS Genet. 2014;10(7):e1004494 - PMID: 25078778
Delaneau O, Marchini J, 1000 Genomes Project Consortium.
Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel.
Nat Commun. 2014;5:3934 - PMID: 25653097
SIGMA Type 2 Diabetes Consortium, Estrada K, Aukrust I, Bjørkhaug L, Burtt NP, Mercader JM, García-Ortiz H, Huerta-Chagoya A, Moreno-Macías H, Walford G, Flannick J, Williams AL, Gómez-Vázquez MJ, Fernandez-Lopez JC, Martínez-Hernández A, Centeno-Cruz F, Mendoza-Caamal E, Revilla-Monsalve C, Islas-Andrade S, Córdova EJ, Soberón X, González-Villalpando ME, Henderson E, Wilkens LR, Le Marchand L, Arellano-Campos O, Ordóñez-Sánchez ML, Rodríguez-Torres M, Rodríguez-Guillén R, Riba L, Najmi LA, Jacobs SB, Fennell T, Gabriel S, Fontanillas P, Hanis CL, Lehman DM, Jenkinson CP, Abboud HE, Bell GI, Cortes ML, Boehnke M, González-Villalpando C, Orozco L, Haiman CA, Tusié-Luna T, Aguilar-Salinas CA, Altshuler D, Njølstad PR, Florez JC, MacArthur DG
Association of a Low-Frequency Variant in HNF1A With Type 2 Diabetes in a Latino Population.
JAMA. 2014;311(22):2305-2314 - PMID: 24915262
Sergouniotis PI, Chakarova C, Murphy C, Becker M, Lenassi E, Arno G, Lek M, Macarthur DG, , Bhattacharya SS, Moore AT, Holder GE, Robson AG, Wolfrum U, Webster AR, Plagnol V
Biallelic Variants in TTLL5, Encoding a Tubulin Glutamylase, Cause Retinal Dystrophy.
Am J Hum Genet. 2014;94(5):760-9 - PMID: 24791901
Kukurba KR, Zhang R, Li X, Smith KS, Knowles DA, How Tan M, Piskol R, Lek M, Snyder M, Macarthur DG, Li JB, Montgomery SB
Allelic Expression of Deleterious Protein-Coding Variants across Human Tissues.
PLoS Genet. 2014;10(5):e1004304 - PMID: 24786518 - PMCID: PMC4006732
Brownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, Dechene ET, Towne MC, Savage SK, Price EN, Holm IA, Luquette LJ, Lyon E, Majzoub J, Neupert P, McCallie D, Szolovits P, Willard HF, Mendelsohn NJ, Temme R, Finkel RS, Yum SW, Medne L, Sunyaev SR, Adzhubey I, Cassa CA, de Bakker PI, Duzkale H, Dworzy Ski P, Fairbrother W, Francioli L, Funke BH, Giovanni MA, Handsaker RE, Lage K, Lebo MS, Lek M, Leshchiner I, Macarthur DG, McLaughlin HM, Murray MF, Pers TH, Polak PP, Raychaudhuri S, Rehm HL, Soemedi R, Stitziel NO, Vestecka S, Supper J, Gugenmus C, Klocke B, Hahn A, Schubach M, Menzel M, Biskup S, Freisinger P, Deng M, Braun M, Perner S, Smith RJ, Andorf JL, Huang J, Ryckman K, Sheffield VC, Stone EM, Bair T, Black-Ziegelbein EA, Braun TA, Darbro B, Deluca AP, Kolbe DL, Scheetz TE, Shearer AE, Sompallae R, Wang K, Bassuk AG, Edens E, Mathews K, Moore SA, Shchelochkov OA, Trapane P, Bossler A, Campbell CA, Heusel JW, Kwitek A, Maga T, Panzer K, Wassink T, Van Daele D, Azaiez H, Booth K, Meyer N, Segal MM, Williams MS, Tromp G, White P, Corsmeier D, Fitzgerald-Butt S, Herman G, Lamb-Thrush D, McBride KL, Newsom D, Pierson CR, Rakowsky AT, Maver A, Lovre I L, Palanda I A, Peterlin B, Torkamani A, Wedell A, Huss M, Alexeyenko A, Lindvall JM, Magnusson M, Nilsson D, Stranneheim H, Taylan F, Gilissen C, Hoischen A, van Bon B, Yntema H, Nelen M, Zhang W, Sager J, Zhang L, Blair K, Kural D, Cariaso M, Lennon GG, Javed A, Agrawal S, Ng PC, Sandhu KS, Krishna S, Veeramachaneni V, Isakov O, Halperin E, Friedman E, Shomron N, Glusman G, Roach JC, Caballero J, Cox HC, Mauldin D, Ament SA, Rowen L, Richards DR, Lucas FA, Gonzalez-Garay ML, Caskey CT, Bai Y, Huang Y, Fang F, Zhang Y, Wang Z, Barrera J, Garcia-Lobo JM, González-Lamuño D, Llorca J, Rodriguez MC, Varela I, Reese MG, De La Vega FM, Kiruluta E, Cargill M, Hart RK, Sorenson JM, Lyon GJ, Stevenson DA, Bray BE, Moore BM, Eilbeck K, Yandell M, Zhao H, Hou L, Chen X, Yan X, Chen M, Li C, Yang C, Gunel M, Li P, Kong Y, Alexander AC, Albertyn ZI, Boycott KM, Bulman DE, Gordon PM, Innes AM, Knoppers BM, Majewski J, Marshall CR, Parboosingh JS, Sawyer SL, Samuels ME, Schwartzentruber J, Kohane IS, Margulies DM
An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.
Genome Biol. 2014;15(3):R53 - PMID: 24667040
The SIGMA Type 2 Diabetes Consortium; Writing team, Williams AL, Jacobs SB, Moreno-Macías H, Huerta-Chagoya A, Churchhouse C, Márquez-Luna C, García-Ortíz H, José Gómez-Vázquez M, Burtt NP, Aguilar-Salinas CA, González-Villalpando C, Florez JC, Orozco L, Haiman CA, Tusié-Luna T, Altshuler D, , Williams AL, Márquez-Luna C, Huerta-Chagoya A, Ripke S, José Gómez-Vázquez M, Manning AK, Moreno-Macías H, García-Ortíz H, Neale B, Burtt NP, Aguilar-Salinas CA, Reich D, Stram DO, Fernández-López JC, Romero-Hidalgo S, Altshuler D, Florez JC, Tusié-Luna T, Patterson N, Haiman CA, , Aguilar-Delfín I, Martínez-Hernández A, Centeno-Cruz F, Mendoza-Caamal E, Revilla-Monsalve C, Islas-Andrade S, Córdova E, Rodríguez-Arellano E, Soberón X, Orozco L, , Florez JC, , González-Villalpando C, González-Villalpando ME, , Haiman CA, Henderson BE, Monroe K, Wilkens L, Kolonel LN, Le Marchand L, , Riba L, Ordóñez-Sánchez ML, Rodríguez-Guillén R, Cruz-Bautista I, Rodríguez-Torres M, Muñoz-Hernández LL, Sáenz T, Gómez D, Alvirde U, , Burtt NP, Onofrio RC, Brodeur WM, Gage D, Murphy J, Franklin J, Mahan S, Ardlie K, Crenshaw AT, Winckler W, , Prüfer K, Shunkov MV, Sawyer S, Stenzel U, Kelso J, Lek M, Sankararaman S, Williams AL, Patterson N, Macarthur DG, Reich D, Derevianko AP, Pääbo S, , Jacobs SB, Churchhouse C, Gopal S, Grammatikos JA, Smith IC, Bullock KH, Deik AA, Souza AL, Pierce KA, Clish CB, Altshuler D, , Fennell T, Farjoun Y, Genomics Platform B, Gabriel S, , Stram DO, Gross MD, Pereira MA, Seielstad M, Koh WP, Tai ES, , Flannick J, Fontanillas P, Morris A, Teslovich TM, Burtt NP, Atzmon G, Blangero J, Bowden DW, Chambers J, Shin Cho Y, Duggirala R, Glaser B, Hanis C, Kooner J, Laakso M, Lee JY, Tai ES, Ying Teo Y, Wilson JG, , Haiman CA, Henderson BE, Monroe K, Wilkens L, Kolonel LN, Le Marchand L, , Puppala S, Farook VS, Thameem F, Abboud HE, Defronzo RA, Jenkinson CP, Lehman DM, Curran JE, Blangero J, Duggirala R, , Burtt NP, Cortes ML, , Altshuler D, Florez JC, Haiman CA, Henderson BE, Aguilar-Salinas CA, González-Villalpando C, Orozco L, Tusié-Luna T
Sequence variants in SLC16A11 are a common risk factor for type 2 diabetes in Mexico.
Nature. 2013;506(7486):97-101 - PMID: 24390345
Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüs ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GR, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F, , Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M
Integrative annotation of variants from 1092 humans: application to cancer genomics.
Science. 2013;342(6154):1235587 - PMID: 24092746 - PMCID: PMC3947637
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, , 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,
Transcriptome and genome sequencing uncovers functional variation in humans.
Nature. 2013;501(7468):506-11 - PMID: 24037378 - PMCID: PMC3918453
Kasippillai T, Macarthur DG, Kirby A, Thomas B, Lambalk CB, Daly MJ, Welt CK
Mutations in eIF4ENIF1 Are Associated With Primary Ovarian Insufficiency.
J Clin Endocrinol Metab. 2013;98(9):E1534-9 - PMID: 23902945