Samocha, Kaitlin

Kaitlin Samocha, PhD

Publications

Weiner DJ, Wigdor EM, Ripke S, Walters RK, Kosmicki JA, Grove J, Samocha KE, Goldstein JI, Okbay A, Bybjerg-Grauholm J, Werge T, Hougaard DM, Taylor J, iPSYCH-Broad Autism Group, Psychiatric Genomics Consortium Autism Group, Skuse D, Devlin B, Anney R, Sanders SJ, Bishop S, Mortensen PB, Børglum AD, Smith GD, Daly MJ, Robinson EB
Polygenic transmission disequilibrium confirms that common and rare variation act additively to create risk for autism spectrum disorders.
Nat Genet. 2017;:ePub - PMID: 28504703
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
Willsey AJ, Fernandez TV, Yu D, King RA, Dietrich A, Xing J, Sanders SJ, Mandell JD, Huang AY, Richer P, Smith L, Dong S, Samocha KE, Tourette International Collaborative Genetics (TIC Genetics), Tourette Syndrome Association International Consortium for Genetics (TSAICG), Neale BM, Coppola G, Mathews CA, Tischfield JA, Scharf JM, State MW, Heiman GA
De Novo Coding Variants Are Strongly Associated with Tourette Disorder.
Neuron. 2017;94(3):486-499.e9 - PMID: 28472652
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
Francioli LC, Cretu-Stancu M, Garimella KV, Fromer M, Kloosterman WP, Samocha KE, Neale BM, Daly MJ, Banks E, DePristo MA, de Bakker PI, Genome of the Netherlands consortium
A framework for the detection of de novo mutations in family-based sequencing data.
Eur J Hum Genet. 2016;:ePub - PMID: 27876817
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
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
Choi J, Shooshtari P, Samocha KE, Daly MJ, Cotsapas C
Network Analysis of Genome-Wide Selective Constraint Reveals a Gene Network Active in Early Fetal Brain Intolerant of Mutation.
PLoS Genet. 2016;12(6):e1006121 - PMID: 27305007
Robinson EB, St Pourcain B, Anttila V, Kosmicki JA, Bulik-Sullivan B, Grove J, Maller J, Samocha KE, Sanders SJ, Ripke S, Martin J, Hollegaard MV, Werge T, Hougaard DM, iPSYCH-SSI-Broad Autism Group, Neale BM, Evans DM, Skuse D, Mortensen PB, Børglum AD, Ronald A, Smith GD, Daly MJ
Genetic risk for autism spectrum disorders and neuropsychiatric variation in the general population.
Nat Genet. 2016;:ePub - PMID: 26998691
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
Kryukov GV, Bielski C, Samocha K, Fromer M, Seepo S, Gentry C, Neale B, Garraway LA, Sweeney CJ, Taplin ME, Van Allen EM
Genetic effect of chemotherapy exposure in children of testicular cancer survivors.
Clin Cancer Res. 2015;:ePub - PMID: 26631610
Ware JS, Samocha KE, Homsy J, Daly MJ
Interpreting de novo Variation in Human Disease Using denovolyzeR.
Curr Protoc Hum Genet. 2015;87:7.25.1-7.25.15 - PMID: 26439716
Sanders SJ, He X, Willsey AJ, Ercan-Sencicek AG, Samocha KE, Cicek AE, Murtha MT, Bal VH, Bishop SL, Dong S, Goldberg AP, Jinlu C, Keaney JF, Klei L, Mandell JD, Moreno-De-Luca D, Poultney CS, Robinson EB, Smith L, Solli-Nowlan T, Su MY, Teran NA, Walker MF, Werling DM, Beaudet AL, Cantor RM, Fombonne E, Geschwind DH, Grice DE, Lord C, Lowe JK, Mane SM, Martin DM, Morrow EM, Talkowski ME, Sutcliffe JS, Walsh CA, Yu TW, , Ledbetter DH, Martin CL, Cook EH, Buxbaum JD, Daly MJ, Devlin B, Roeder K, State MW
Insights into Autism Spectrum Disorder Genomic Architecture and Biology from 71 Risk Loci.
Neuron. 2015;87(6):1215-1233 - PMID: 26402605
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
Muona M, Berkovic SF, Dibbens LM, Oliver KL, Maljevic S, Bayly MA, Joensuu T, Canafoglia L, Franceschetti S, Michelucci R, Markkinen S, Heron SE, Hildebrand MS, Andermann E, Andermann F, Gambardella A, Tinuper P, Licchetta L, Scheffer IE, Criscuolo C, Filla A, Ferlazzo E, Ahmad J, Ahmad A, Baykan B, Said E, Topcu M, Riguzzi P, King MD, Ozkara C, Andrade DM, Engelsen BA, Crespel A, Lindenau M, Lohmann E, Saletti V, Massano J, Privitera M, Espay AJ, Kauffmann B, Duchowny M, Møller RS, Straussberg R, Afawi Z, Ben-Zeev B, Samocha KE, Daly MJ, Petrou S, Lerche H, Palotie A, Lehesjoki AE
A recurrent de novo mutation in KCNC1 causes progressive myoclonus epilepsy.
Nat Genet. 2014;:ePub - PMID: 25401298
De Rubeis S, He X, Goldberg AP, Poultney CS, Samocha K, Ercument Cicek A, Kou Y, Liu L, Fromer M, Walker S, Singh T, Klei L, Kosmicki J, Fu SC, Aleksic B, Biscaldi M, Bolton PF, Brownfeld JM, Cai J, Campbell NG, Carracedo A, Chahrour MH, Chiocchetti AG, Coon H, Crawford EL, Crooks L, Curran SR, Dawson G, Duketis E, Fernandez BA, Gallagher L, Geller E, Guter SJ, Sean Hill R, Ionita-Laza I, Jimenez Gonzalez P, Kilpinen H, Klauck SM, Kolevzon A, Lee I, Lei J, Lehtimäki T, Lin CF, Ma'ayan A, Marshall CR, McInnes AL, Neale B, Owen MJ, Ozaki N, Parellada M, Parr JR, Purcell S, Puura K, Rajagopalan D, Rehnström K, Reichenberg A, Sabo A, Sachse M, Sanders SJ, Schafer C, Schulte-Rüther M, Skuse D, Stevens C, Szatmari P, Tammimies K, Valladares O, Voran A, Wang LS, Weiss LA, Jeremy Willsey A, Yu TW, Yuen RK, , , , , Cook EH, Freitag CM, Gill M, Hultman CM, Lehner T, Palotie A, Schellenberg GD, Sklar P, State MW, Sutcliffe JS, Walsh CA, Scherer SW, Zwick ME, Barrett JC, Cutler DJ, Roeder K, Devlin B, Daly MJ, Buxbaum JD
Synaptic, transcriptional and chromatin genes disrupted in autism.
Nature. 2014;:ePub - PMID: 25363760
Robinson EB, Samocha KE, Kosmicki JA, McGrath L, Neale BM, Perlis RH, Daly MJ
Autism spectrum disorder severity reflects the average contribution of de novo and familial influences.
Proc Natl Acad Sci U S A. 2014;:ePub - PMID: 25288738
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
Zuk O, Schaffner SF, Samocha K, Do R, Hechter E, Kathiresan S, Daly MJ, Neale BM, Sunyaev SR, Lander ES
Searching for missing heritability: Designing rare variant association studies.
Proc Natl Acad Sci U S A. 2014;111(4):E455-64 - PMID: 24443550 - PMCID: PMC3910587
Liu L, Sabo A, Neale BM, Nagaswamy U, Stevens C, Lim E, Bodea CA, Muzny D, Reid JG, Banks E, Coon H, Depristo M, Dinh H, Fennel T, Flannick J, Gabriel S, Garimella K, Gross S, Hawes A, Lewis L, Makarov V, Maguire J, Newsham I, Poplin R, Ripke S, Shakir K, Samocha KE, Wu Y, Boerwinkle E, Buxbaum JD, Cook EH, Devlin B, Schellenberg GD, Sutcliffe JS, Daly MJ, Gibbs RA, Roeder K
Analysis of rare, exonic variation amongst subjects with autism spectrum disorders and population controls.
PLoS Genet. 2013;9(4):e1003443 - PMID: 23593035 - PMCID: PMC3623759
Neale BM, Kou Y, Liu L, Ma'ayan A, Samocha KE, Sabo A, Lin CF, Stevens C, Wang LS, Makarov V, Polak P, Yoon S, Maguire J, Crawford EL, Campbell NG, Geller ET, Valladares O, Schafer C, Liu H, Zhao T, Cai G, Lihm J, Dannenfelser R, Jabado O, Peralta Z, Nagaswamy U, Muzny D, Reid JG, Newsham I, Wu Y, Lewis L, Han Y, Voight BF, Lim E, Rossin E, Kirby A, Flannick J, Fromer M, Shakir K, Fennell T, Garimella K, Banks E, Poplin R, Gabriel S, DePristo M, Wimbish JR, Boone BE, Levy SE, Betancur C, Sunyaev S, Boerwinkle E, Buxbaum JD, Cook EH, Devlin B, Gibbs RA, Roeder K, Schellenberg GD, Sutcliffe JS, Daly MJ
Patterns and rates of exonic de novo mutations in autism spectrum disorders.
Nature. 2012;485(7397):242-5 - PMID: 22495311 - PMCID: PMC3613847
Samocha KE, Lim JE, Cheng R, Sokoloff G, Palmer AA
Fine mapping of QTL for prepulse inhibition in LG/J and SM/J mice using F(2) and advanced intercross lines.
Genes Brain Behav. 2010;9(7):759-67 - PMID: 20597988 - PMCID: PMC3749925
Cheng R, Lim JE, Samocha KE, Sokoloff G, Abney M, Skol AD, Palmer AA
Genome-wide association studies and the problem of relatedness among advanced intercross lines and other highly recombinant populations.
Genetics. 2010;185(3):1033-44 - PMID: 20439773 - PMCID: PMC2907190
Norgard EA, Jarvis JP, Roseman CC, Maxwell TJ, Kenney-Hunt JP, Samocha KE, Pletscher LS, Wang B, Fawcett GL, Leatherwood CJ, Wolf JB, Cheverud JM
Replication of long-bone length QTL in the F9-F10 LG,SM advanced intercross.
Mamm Genome. 2009;20(4):224-35 - PMID: 19306044 - PMCID: PMC2736561