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Items: 1 to 50 of 142

1.

Customized MethylC-Capture Sequencing to Evaluate Variation in the Human Sperm DNA Methylome Representative of Altered Folate Metabolism.

Chan D, Shao X, Dumargne MC, Aarabi M, Simon MM, Kwan T, Bailey JL, Robaire B, Kimmins S, San Gabriel MC, Zini A, Librach C, Moskovtsev S, Grundberg E, Bourque G, Pastinen T, Trasler JM.

Environ Health Perspect. 2019 Aug;127(8):87002. doi: 10.1289/EHP4812. Epub 2019 Aug 8.

2.

Computational Analysis of HLA-presentation of Non-synonymous Recipient Mismatches Indicates Effect on the Risk of Chronic Graft-vs.-Host Disease After Allogeneic HSCT.

Ritari J, Hyvärinen K, Koskela S, Niittyvuopio R, Nihtinen A, Salmenniemi U, Putkonen M, Volin L, Kwan T, Pastinen T, Itälä-Remes M, Partanen J.

Front Immunol. 2019 Jul 16;10:1625. doi: 10.3389/fimmu.2019.01625. eCollection 2019.

3.

Rheumatoid arthritis-relevant DNA methylation changes identified in ACPA-positive asymptomatic individuals using methylome capture sequencing.

Shao X, Hudson M, Colmegna I, Greenwood CMT, Fritzler MJ, Awadalla P, Pastinen T, Bernatsky S.

Clin Epigenetics. 2019 Jul 31;11(1):110. doi: 10.1186/s13148-019-0699-9.

4.

Integrative analysis of vascular endothelial cell genomic features identifies AIDA as a coronary artery disease candidate gene.

Lalonde S, Codina-Fauteux VA, de Bellefon SM, Leblanc F, Beaudoin M, Simon MM, Dali R, Kwan T, Lo KS, Pastinen T, Lettre G.

Genome Biol. 2019 Jul 8;20(1):133. doi: 10.1186/s13059-019-1749-5.

5.

Publisher Correction: Multiancestry genome-wide association study of 520,000 subjects identifies 32 loci associated with stroke and stroke subtypes.

Malik R, Chauhan G, Traylor M, Sargurupremraj M, Okada Y, Mishra A, Rutten-Jacobs L, Giese AK, van der Laan SW, Gretarsdottir S, Anderson CD, Chong M, Adams HHH, Ago T, Almgren P, Amouyel P, Ay H, Bartz TM, Benavente OR, Bevan S, Boncoraglio GB, Brown RD Jr, Butterworth AS, Carrera C, Carty CL, Chasman DI, Chen WM, Cole JW, Correa A, Cotlarciuc I, Cruchaga C, Danesh J, de Bakker PIW, DeStefano AL, den Hoed M, Duan Q, Engelter ST, Falcone GJ, Gottesman RF, Grewal RP, Gudnason V, Gustafsson S, Haessler J, Harris TB, Hassan A, Havulinna AS, Heckbert SR, Holliday EG, Howard G, Hsu FC, Hyacinth HI, Ikram MA, Ingelsson E, Irvin MR, Jian X, Jiménez-Conde J, Johnson JA, Jukema JW, Kanai M, Keene KL, Kissela BM, Kleindorfer DO, Kooperberg C, Kubo M, Lange LA, Langefeld CD, Langenberg C, Launer LJ, Lee JM, Lemmens R, Leys D, Lewis CM, Lin WY, Lindgren AG, Lorentzen E, Magnusson PK, Maguire J, Manichaikul A, McArdle PF, Meschia JF, Mitchell BD, Mosley TH, Nalls MA, Ninomiya T, O'Donnell MJ, Psaty BM, Pulit SL, Rannikmäe K, Reiner AP, Rexrode KM, Rice K, Rich SS, Ridker PM, Rost NS, Rothwell PM, Rotter JI, Rundek T, Sacco RL, Sakaue S, Sale MM, Salomaa V, Sapkota BR, Schmidt R, Schmidt CO, Schminke U, Sharma P, Slowik A, Sudlow CLM, Tanislav C, Tatlisumak T, Taylor KD, Thijs VNS, Thorleifsson G, Thorsteinsdottir U, Tiedt S, Trompet S, Tzourio C, van Duijn CM, Walters M, Wareham NJ, Wassertheil-Smoller S, Wilson JG, Wiggins KL, Yang Q, Yusuf S; AFGen Consortium; Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium; International Genomics of Blood Pressure (iGEN-BP) Consortium; INVENT Consortium; STARNET, Bis JC, Pastinen T, Ruusalepp A, Schadt EE, Koplev S, Björkegren JLM, Codoni V, Civelek M, Smith NL, Trégouët DA, Christophersen IE, Roselli C, Lubitz SA, Ellinor PT, Tai ES, Kooner JS, Kato N, He J, van der Harst P, Elliott P, Chambers JC, Takeuchi F, Johnson AD; BioBank Japan Cooperative Hospital Group; COMPASS Consortium; EPIC-CVD Consortium; EPIC-InterAct Consortium; International Stroke Genetics Consortium (ISGC); METASTROKE Consortium; Neurology Working Group of the CHARGE Consortium; NINDS Stroke Genetics Network (SiGN); UK Young Lacunar DNA Study; MEGASTROKE Consortium, Sanghera DK, Melander O, Jern C, Strbian D, Fernandez-Cadenas I, Longstreth WT Jr, Rolfs A, Hata J, Woo D, Rosand J, Pare G, Hopewell JC, Saleheen D, Stefansson K, Worrall BB, Kittner SJ, Seshadri S, Fornage M, Markus HS, Howson JMM, Kamatani Y, Debette S, Dichgans M.

Nat Genet. 2019 Jul;51(7):1192-1193. doi: 10.1038/s41588-019-0449-0.

6.

Points-to-consider on the return of results in epigenetic research.

Dyke SOM, Saulnier KM, Dupras C, Webster AP, Maschke K, Rothstein M, Siebert R, Walter J, Beck S, Pastinen T, Joly Y.

Genome Med. 2019 May 23;11(1):31. doi: 10.1186/s13073-019-0646-6.

7.

Correction to: Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome.

Cheung WA, Shao X, Morin A, Siroux V, Kwan T, Ge B, Aïssi D, Chen L, Vasquez L, Allum F, Guénard F, Bouzigon E, Simon MM, Boulier E, Redensek A, Watt S, Datta A, Clarke L, Flicek P, Mead D, Paul DS, Beck S, Bourque G, Lathrop M, Tchernof A, Vohl MC, Demenais F, Pin I, Downes K, Stunnenberg HG, Soranzo N, Pastinen T, Grundberg E.

Genome Biol. 2019 May 7;20(1):89. doi: 10.1186/s13059-019-1702-7.

8.

H3K27M induces defective chromatin spread of PRC2-mediated repressive H3K27me2/me3 and is essential for glioma tumorigenesis.

Harutyunyan AS, Krug B, Chen H, Papillon-Cavanagh S, Zeinieh M, De Jay N, Deshmukh S, Chen CCL, Belle J, Mikael LG, Marchione DM, Li R, Nikbakht H, Hu B, Cagnone G, Cheung WA, Mohammadnia A, Bechet D, Faury D, McConechy MK, Pathania M, Jain SU, Ellezam B, Weil AG, Montpetit A, Salomoni P, Pastinen T, Lu C, Lewis PW, Garcia BA, Kleinman CL, Jabado N, Majewski J.

Nat Commun. 2019 Mar 19;10(1):1262. doi: 10.1038/s41467-019-09140-x.

9.

Dissecting features of epigenetic variants underlying cardiometabolic risk using full-resolution epigenome profiling in regulatory elements.

Allum F, Hedman ÅK, Shao X, Cheung WA, Vijay J, Guénard F, Kwan T, Simon MM, Ge B, Moura C, Boulier E, Rönnblom L, Bernatsky S, Lathrop M, McCarthy MI, Deloukas P, Tchernof A, Pastinen T, Vohl MC, Grundberg E.

Nat Commun. 2019 Mar 14;10(1):1209. doi: 10.1038/s41467-019-09184-z.

10.

Very long intergenic non-coding RNA transcripts and expression profiles are associated to specific childhood acute lymphoblastic leukemia subtypes.

Caron M, St-Onge P, Drouin S, Richer C, Sontag T, Busche S, Bourque G, Pastinen T, Sinnett D.

PLoS One. 2018 Nov 15;13(11):e0207250. doi: 10.1371/journal.pone.0207250. eCollection 2018.

11.

Promoter capture Hi-C-based identification of recurrent noncoding mutations in colorectal cancer.

Orlando G, Law PJ, Cornish AJ, Dobbins SE, Chubb D, Broderick P, Litchfield K, Hariri F, Pastinen T, Osborne CS, Taipale J, Houlston RS.

Nat Genet. 2018 Oct;50(10):1375-1380. doi: 10.1038/s41588-018-0211-z. Epub 2018 Sep 17.

12.

Exploring rare and low-frequency variants in the Saguenay-Lac-Saint-Jean population identified genes associated with asthma and allergy traits.

Morin A, Madore AM, Kwan T, Ban M, Partanen J, Rönnblom L, Syvänen AC, Sawcer S, Stunnenberg H, Lathrop M, Pastinen T, Laprise C.

Eur J Hum Genet. 2019 Jan;27(1):90-101. doi: 10.1038/s41431-018-0266-4. Epub 2018 Sep 11.

13.

Genome-wide association study implicates immune dysfunction in the development of Hodgkin lymphoma.

Sud A, Thomsen H, Orlando G, Försti A, Law PJ, Broderick P, Cooke R, Hariri F, Pastinen T, Easton DF, Pharoah PDP, Dunning AM, Peto J, Canzian F, Eeles R, Kote-Jarai Z, Muir K, Pashayan N, Campa D; PRACTICAL Consortium, Hoffmann P, Nöthen MM, Jöckel KH, von Strandmann EP, Swerdlow AJ, Engert A, Orr N, Hemminki K, Houlston RS.

Blood. 2018 Nov 8;132(19):2040-2052. doi: 10.1182/blood-2018-06-855296. Epub 2018 Sep 7.

14.

A hidden markov model for identifying differentially methylated sites in bisulfite sequencing data.

Shokoohi F, Stephens DA, Bourque G, Pastinen T, Greenwood CMT, Labbe A.

Biometrics. 2019 Mar;75(1):210-221. doi: 10.1111/biom.12965. Epub 2018 Oct 9.

PMID:
30168593
15.

Genomic prediction of relapse in recipients of allogeneic haematopoietic stem cell transplantation.

Ritari J, Hyvärinen K, Koskela S, Itälä-Remes M, Niittyvuopio R, Nihtinen A, Salmenniemi U, Putkonen M, Volin L, Kwan T, Pastinen T, Partanen J.

Leukemia. 2019 Jan;33(1):240-248. doi: 10.1038/s41375-018-0229-3. Epub 2018 Aug 8.

16.

Hidden genomic MHC disparity between HLA-matched sibling pairs in hematopoietic stem cell transplantation.

Koskela S, Ritari J, Hyvärinen K, Kwan T, Niittyvuopio R, Itälä-Remes M, Pastinen T, Partanen J.

Sci Rep. 2018 Mar 29;8(1):5396. doi: 10.1038/s41598-018-23682-y.

17.

Multiancestry genome-wide association study of 520,000 subjects identifies 32 loci associated with stroke and stroke subtypes.

Malik R, Chauhan G, Traylor M, Sargurupremraj M, Okada Y, Mishra A, Rutten-Jacobs L, Giese AK, van der Laan SW, Gretarsdottir S, Anderson CD, Chong M, Adams HHH, Ago T, Almgren P, Amouyel P, Ay H, Bartz TM, Benavente OR, Bevan S, Boncoraglio GB, Brown RD Jr, Butterworth AS, Carrera C, Carty CL, Chasman DI, Chen WM, Cole JW, Correa A, Cotlarciuc I, Cruchaga C, Danesh J, de Bakker PIW, DeStefano AL, den Hoed M, Duan Q, Engelter ST, Falcone GJ, Gottesman RF, Grewal RP, Gudnason V, Gustafsson S, Haessler J, Harris TB, Hassan A, Havulinna AS, Heckbert SR, Holliday EG, Howard G, Hsu FC, Hyacinth HI, Ikram MA, Ingelsson E, Irvin MR, Jian X, Jiménez-Conde J, Johnson JA, Jukema JW, Kanai M, Keene KL, Kissela BM, Kleindorfer DO, Kooperberg C, Kubo M, Lange LA, Langefeld CD, Langenberg C, Launer LJ, Lee JM, Lemmens R, Leys D, Lewis CM, Lin WY, Lindgren AG, Lorentzen E, Magnusson PK, Maguire J, Manichaikul A, McArdle PF, Meschia JF, Mitchell BD, Mosley TH, Nalls MA, Ninomiya T, O'Donnell MJ, Psaty BM, Pulit SL, Rannikmäe K, Reiner AP, Rexrode KM, Rice K, Rich SS, Ridker PM, Rost NS, Rothwell PM, Rotter JI, Rundek T, Sacco RL, Sakaue S, Sale MM, Salomaa V, Sapkota BR, Schmidt R, Schmidt CO, Schminke U, Sharma P, Slowik A, Sudlow CLM, Tanislav C, Tatlisumak T, Taylor KD, Thijs VNS, Thorleifsson G, Thorsteinsdottir U, Tiedt S, Trompet S, Tzourio C, van Duijn CM, Walters M, Wareham NJ, Wassertheil-Smoller S, Wilson JG, Wiggins KL, Yang Q, Yusuf S; AFGen Consortium; Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium; International Genomics of Blood Pressure (iGEN-BP) Consortium; INVENT Consortium; STARNET, Bis JC, Pastinen T, Ruusalepp A, Schadt EE, Koplev S, Björkegren JLM, Codoni V, Civelek M, Smith NL, Trégouët DA, Christophersen IE, Roselli C, Lubitz SA, Ellinor PT, Tai ES, Kooner JS, Kato N, He J, van der Harst P, Elliott P, Chambers JC, Takeuchi F, Johnson AD; BioBank Japan Cooperative Hospital Group; COMPASS Consortium; EPIC-CVD Consortium; EPIC-InterAct Consortium; International Stroke Genetics Consortium (ISGC); METASTROKE Consortium; Neurology Working Group of the CHARGE Consortium; NINDS Stroke Genetics Network (SiGN); UK Young Lacunar DNA Study; MEGASTROKE Consortium, Sanghera DK, Melander O, Jern C, Strbian D, Fernandez-Cadenas I, Longstreth WT Jr, Rolfs A, Hata J, Woo D, Rosand J, Pare G, Hopewell JC, Saleheen D, Stefansson K, Worrall BB, Kittner SJ, Seshadri S, Fornage M, Markus HS, Howson JMM, Kamatani Y, Debette S, Dichgans M.

Nat Genet. 2018 Apr;50(4):524-537. doi: 10.1038/s41588-018-0058-3. Epub 2018 Mar 12. Erratum in: Nat Genet. 2019 Jul;51(7):1192-1193.

18.

Publisher Correction: A PRDX1 mutant allele causes a MMACHC secondary epimutation in cblC patients.

Guéant JL, Chéry C, Oussalah A, Nadaf J, Coelho D, Josse T, Flayac J, Robert A, Koscinski I, Gastin I, Filhine-Tresarrieu P, Pupavac M, Brebner A, Watkins D, Pastinen T, Montpetit A, Hariri F, Tregouët D, Raby BA, Chung WK, Morange PE, Froese DS, Baumgartner MR, Benoist JF, Ficicioglu C, Marchand V, Motorin Y, Bonnemains C, Feillet F, Majewski J, Rosenblatt DS.

Nat Commun. 2018 Feb 2;9(1):554. doi: 10.1038/s41467-018-03054-w.

19.

Pioneer factor Pax7 deploys a stable enhancer repertoire for specification of cell fate.

Mayran A, Khetchoumian K, Hariri F, Pastinen T, Gauthier Y, Balsalobre A, Drouin J.

Nat Genet. 2018 Feb;50(2):259-269. doi: 10.1038/s41588-017-0035-2. Epub 2018 Jan 22.

PMID:
29358650
20.

Accuracy of Programs for the Determination of Human Leukocyte Antigen Alleles from Next-Generation Sequencing Data.

Larjo A, Eveleigh R, Kilpeläinen E, Kwan T, Pastinen T, Koskela S, Partanen J.

Front Immunol. 2017 Dec 13;8:1815. doi: 10.3389/fimmu.2017.01815. eCollection 2017.

21.

APRDX1 mutant allele causes a MMACHC secondary epimutation in cblC patients.

Guéant JL, Chéry C, Oussalah A, Nadaf J, Coelho D, Josse T, Flayac J, Robert A, Koscinski I, Gastin I, Filhine-Tresarrieu P, Pupavac M, Brebner A, Watkins D, Pastinen T, Montpetit A, Hariri F, Tregouët D, Raby BA, Chung WK, Morange PE, Froese DS, Baumgartner MR, Benoist JF, Ficicioglu C, Marchand V, Motorin Y, Bonnemains C, Feillet F, Majewski J, Rosenblatt DS.

Nat Commun. 2018 Jan 4;9(1):67. doi: 10.1038/s41467-017-02306-5. Erratum in: Nat Commun. 2018 Feb 2;9(1):554.

22.

Genetic Predisposition to Multiple Myeloma at 5q15 Is Mediated by an ELL2 Enhancer Polymorphism.

Li N, Johnson DC, Weinhold N, Kimber S, Dobbins SE, Mitchell JS, Kinnersley B, Sud A, Law PJ, Orlando G, Scales M, Wardell CP, Försti A, Hoang PH, Went M, Holroyd A, Hariri F, Pastinen T, Meissner T, Goldschmidt H, Hemminki K, Morgan GJ, Kaiser M, Houlston RS.

Cell Rep. 2017 Sep 12;20(11):2556-2564. doi: 10.1016/j.celrep.2017.08.062.

23.

Pitx1 directly modulates the core limb development program to implement hindlimb identity.

Nemec S, Luxey M, Jain D, Huang Sung A, Pastinen T, Drouin J.

Development. 2017 Sep 15;144(18):3325-3335. doi: 10.1242/dev.154864. Epub 2017 Aug 14.

24.

Mutations in THAP11 cause an inborn error of cobalamin metabolism and developmental abnormalities.

Quintana AM, Yu HC, Brebner A, Pupavac M, Geiger EA, Watson A, Castro VL, Cheung W, Chen SH, Watkins D, Pastinen T, Skovby F, Appel B, Rosenblatt DS, Shaikh TH.

Hum Mol Genet. 2017 Aug 1;26(15):2838-2849. doi: 10.1093/hmg/ddx157.

25.

Novel insights into systemic autoimmune rheumatic diseases using shared molecular signatures and an integrative analysis.

Hudson M, Bernatsky S, Colmegna I, Lora M, Pastinen T, Klein Oros K, Greenwood CMT.

Epigenetics. 2017 Jun 3;12(6):433-440. doi: 10.1080/15592294.2017.1303581. Epub 2017 Apr 7.

26.

Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome.

Cheung WA, Shao X, Morin A, Siroux V, Kwan T, Ge B, Aïssi D, Chen L, Vasquez L, Allum F, Guénard F, Bouzigon E, Simon MM, Boulier E, Redensek A, Watt S, Datta A, Clarke L, Flicek P, Mead D, Paul DS, Beck S, Bourque G, Lathrop M, Tchernof A, Vohl MC, Demenais F, Pin I, Downes K, Stunnenberg HG, Soranzo N, Pastinen T, Grundberg E.

Genome Biol. 2017 Mar 10;18(1):50. doi: 10.1186/s13059-017-1173-7. Erratum in: Genome Biol. 2019 May 7;20(1):89.

27.

Conserved expression of transposon-derived non-coding transcripts in primate stem cells.

Ramsay L, Marchetto MC, Caron M, Chen SH, Busche S, Kwan T, Pastinen T, Gage FH, Bourque G.

BMC Genomics. 2017 Feb 28;18(1):214. doi: 10.1186/s12864-017-3568-y.

28.

Combining omics data to identify genes associated with allergic rhinitis.

Morin A, Laviolette M, Pastinen T, Boulet LP, Laprise C.

Clin Epigenetics. 2017 Jan 18;9:3. doi: 10.1186/s13148-017-0310-1. eCollection 2017.

29.

Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types.

Ecker S, Chen L, Pancaldi V, Bagger FO, Fernández JM, Carrillo de Santa Pau E, Juan D, Mann AL, Watt S, Casale FP, Sidiropoulos N, Rapin N, Merkel A; BLUEPRINT Consortium, Stunnenberg HG, Stegle O, Frontini M, Downes K, Pastinen T, Kuijpers TW, Rico D, Valencia A, Beck S, Soranzo N, Paul DS.

Genome Biol. 2017 Jan 26;18(1):18. doi: 10.1186/s13059-017-1156-8.

30.

Evolving data access policy: The Canadian context.

Dyke SO, Saulnier KM, Pastinen T, Bourque G, Joly Y.

Facets (Ott). 2016 Sep 15;1(1):138-147.

31.

Increased DNA methylation variability in type 1 diabetes across three immune effector cell types.

Paul DS, Teschendorff AE, Dang MA, Lowe R, Hawa MI, Ecker S, Beyan H, Cunningham S, Fouts AR, Ramelius A, Burden F, Farrow S, Rowlston S, Rehnstrom K, Frontini M, Downes K, Busche S, Cheung WA, Ge B, Simon MM, Bujold D, Kwan T, Bourque G, Datta A, Lowy E, Clarke L, Flicek P, Libertini E, Heath S, Gut M, Gut IG, Ouwehand WH, Pastinen T, Soranzo N, Hofer SE, Karges B, Meissner T, Boehm BO, Cilio C, Elding Larsson H, Lernmark Å, Steck AK, Rakyan VK, Beck S, Leslie RD.

Nat Commun. 2016 Nov 29;7:13555. doi: 10.1038/ncomms13555.

32.

The International Human Epigenome Consortium Data Portal.

Bujold D, Morais DAL, Gauthier C, Côté C, Caron M, Kwan T, Chen KC, Laperle J, Markovits AN, Pastinen T, Caron B, Veilleux A, Jacques PÉ, Bourque G.

Cell Syst. 2016 Nov 23;3(5):496-499.e2. doi: 10.1016/j.cels.2016.10.019. Epub 2016 Nov 15.

33.

The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease.

Astle WJ, Elding H, Jiang T, Allen D, Ruklisa D, Mann AL, Mead D, Bouman H, Riveros-Mckay F, Kostadima MA, Lambourne JJ, Sivapalaratnam S, Downes K, Kundu K, Bomba L, Berentsen K, Bradley JR, Daugherty LC, Delaneau O, Freson K, Garner SF, Grassi L, Guerrero J, Haimel M, Janssen-Megens EM, Kaan A, Kamat M, Kim B, Mandoli A, Marchini J, Martens JHA, Meacham S, Megy K, O'Connell J, Petersen R, Sharifi N, Sheard SM, Staley JR, Tuna S, van der Ent M, Walter K, Wang SY, Wheeler E, Wilder SP, Iotchkova V, Moore C, Sambrook J, Stunnenberg HG, Di Angelantonio E, Kaptoge S, Kuijpers TW, Carrillo-de-Santa-Pau E, Juan D, Rico D, Valencia A, Chen L, Ge B, Vasquez L, Kwan T, Garrido-Martín D, Watt S, Yang Y, Guigo R, Beck S, Paul DS, Pastinen T, Bujold D, Bourque G, Frontini M, Danesh J, Roberts DJ, Ouwehand WH, Butterworth AS, Soranzo N.

Cell. 2016 Nov 17;167(5):1415-1429.e19. doi: 10.1016/j.cell.2016.10.042.

34.

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells.

Chen L, Ge B, Casale FP, Vasquez L, Kwan T, Garrido-Martín D, Watt S, Yan Y, Kundu K, Ecker S, Datta A, Richardson D, Burden F, Mead D, Mann AL, Fernandez JM, Rowlston S, Wilder SP, Farrow S, Shao X, Lambourne JJ, Redensek A, Albers CA, Amstislavskiy V, Ashford S, Berentsen K, Bomba L, Bourque G, Bujold D, Busche S, Caron M, Chen SH, Cheung W, Delaneau O, Dermitzakis ET, Elding H, Colgiu I, Bagger FO, Flicek P, Habibi E, Iotchkova V, Janssen-Megens E, Kim B, Lehrach H, Lowy E, Mandoli A, Matarese F, Maurano MT, Morris JA, Pancaldi V, Pourfarzad F, Rehnstrom K, Rendon A, Risch T, Sharifi N, Simon MM, Sultan M, Valencia A, Walter K, Wang SY, Frontini M, Antonarakis SE, Clarke L, Yaspo ML, Beck S, Guigo R, Rico D, Martens JHA, Ouwehand WH, Kuijpers TW, Paul DS, Stunnenberg HG, Stegle O, Downes K, Pastinen T, Soranzo N.

Cell. 2016 Nov 17;167(5):1398-1414.e24. doi: 10.1016/j.cell.2016.10.026.

35.

Are Data Sharing and Privacy Protection Mutually Exclusive?

Joly Y, Dyke SOM, Knoppers BM, Pastinen T.

Cell. 2016 Nov 17;167(5):1150-1154. doi: 10.1016/j.cell.2016.11.004.

36.

Optimizing ChIP-seq peak detectors using visual labels and supervised machine learning.

Hocking TD, Goerner-Potvin P, Morin A, Shao X, Pastinen T, Bourque G.

Bioinformatics. 2017 Feb 15;33(4):491-499. doi: 10.1093/bioinformatics/btw672.

37.

Association of breast cancer risk in BRCA1 and BRCA2 mutation carriers with genetic variants showing differential allelic expression: identification of a modifier of breast cancer risk at locus 11q22.3.

Hamdi Y, Soucy P, Kuchenbaeker KB, Pastinen T, Droit A, Lemaçon A, Adlard J, Aittomäki K, Andrulis IL, Arason A, Arnold N, Arun BK, Azzollini J, Bane A, Barjhoux L, Barrowdale D, Benitez J, Berthet P, Blok MJ, Bobolis K, Bonadona V, Bonanni B, Bradbury AR, Brewer C, Buecher B, Buys SS, Caligo MA, Chiquette J, Chung WK, Claes KB, Daly MB, Damiola F, Davidson R, De la Hoya M, De Leeneer K, Diez O, Ding YC, Dolcetti R, Domchek SM, Dorfling CM, Eccles D, Eeles R, Einbeigi Z, Ejlertsen B; EMBRACE, Engel C, Gareth Evans D, Feliubadalo L, Foretova L, Fostira F, Foulkes WD, Fountzilas G, Friedman E, Frost D, Ganschow P, Ganz PA, Garber J, Gayther SA; GEMO Study Collaborators, Gerdes AM, Glendon G, Godwin AK, Goldgar DE, Greene MH, Gronwald J, Hahnen E, Hamann U, Hansen TV, Hart S, Hays JL; HEBON, Hogervorst FB, Hulick PJ, Imyanitov EN, Isaacs C, Izatt L, Jakubowska A, James P, Janavicius R, Jensen UB, John EM, Joseph V, Just W, Kaczmarek K, Karlan BY; KConFab Investigators, Kets CM, Kirk J, Kriege M, Laitman Y, Laurent M, Lazaro C, Leslie G, Lester J, Lesueur F, Liljegren A, Loman N, Loud JT, Manoukian S, Mariani M, Mazoyer S, McGuffog L, Meijers-Heijboer HE, Meindl A, Miller A, Montagna M, Mulligan AM, Nathanson KL, Neuhausen SL, Nevanlinna H, Nussbaum RL, Olah E, Olopade OI, Ong KR, Oosterwijk JC, Osorio A, Papi L, Park SK, Pedersen IS, Peissel B, Segura PP, Peterlongo P, Phelan CM, Radice P, Rantala J, Rappaport-Fuerhauser C, Rennert G, Richardson A, Robson M, Rodriguez GC, Rookus MA, Schmutzler RK, Sevenet N, Shah PD, Singer CF, Slavin TP, Snape K, Sokolowska J, Sønderstrup IM, Southey M, Spurdle AB, Stadler Z, Stoppa-Lyonnet D, Sukiennicki G, Sutter C, Tan Y, Tea MK, Teixeira MR, Teulé A, Teo SH, Terry MB, Thomassen M, Tihomirova L, Tischkowitz M, Tognazzo S, Toland AE, Tung N, van den Ouweland AM, van der Luijt RB, van Engelen K, van Rensburg EJ, Varon-Mateeva R, Wappenschmidt B, Wijnen JT, Rebbeck T, Chenevix-Trench G, Offit K, Couch FJ, Nord S, Easton DF, Antoniou AC, Simard J.

Breast Cancer Res Treat. 2017 Jan;161(1):117-134. doi: 10.1007/s10549-016-4018-2. Epub 2016 Oct 28.

38.

Association of breast cancer risk with genetic variants showing differential allelic expression: Identification of a novel breast cancer susceptibility locus at 4q21.

Hamdi Y, Soucy P, Adoue V, Michailidou K, Canisius S, Lemaçon A, Droit A, Andrulis IL, Anton-Culver H, Arndt V, Baynes C, Blomqvist C, Bogdanova NV, Bojesen SE, Bolla MK, Bonanni B, Borresen-Dale AL, Brand JS, Brauch H, Brenner H, Broeks A, Burwinkel B, Chang-Claude J; NBCS Collaborators, Couch FJ, Cox A, Cross SS, Czene K, Darabi H, Dennis J, Devilee P, Dörk T, Dos-Santos-Silva I, Eriksson M, Fasching PA, Figueroa J, Flyger H, García-Closas M, Giles GG, Goldberg MS, González-Neira A, Grenaker-Alnæs G, Guénel P, Haeberle L, Haiman CA, Hamann U, Hallberg E, Hooning MJ, Hopper JL, Jakubowska A, Jones M, Kabisch M, Kataja V, Lambrechts D, Le Marchand L, Lindblom A, Lubinski J, Mannermaa A, Maranian M, Margolin S, Marme F, Milne RL, Neuhausen SL, Nevanlinna H, Neven P, Olswold C, Peto J, Plaseska-Karanfilska D, Pylkäs K, Radice P, Rudolph A, Sawyer EJ, Schmidt MK, Shu XO, Southey MC, Swerdlow A, Tollenaar RA, Tomlinson I, Torres D, Truong T, Vachon C, Van Den Ouweland AM, Wang Q, Winqvist R; kConFab/AOCS Investigators, Zheng W, Benitez J, Chenevix-Trench G, Dunning AM, Pharoah PD, Kristensen V, Hall P, Easton DF, Pastinen T, Nord S, Simard J.

Oncotarget. 2016 Dec 6;7(49):80140-80163. doi: 10.18632/oncotarget.12818.

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Immunoseq: the identification of functionally relevant variants through targeted capture and sequencing of active regulatory regions in human immune cells.

Morin A, Kwan T, Ge B, Letourneau L, Ban M, Tandre K, Caron M, Sandling JK, Carlsson J, Bourque G, Laprise C, Montpetit A, Syvanen AC, Ronnblom L, Sawcer SJ, Lathrop MG, Pastinen T.

BMC Med Genomics. 2016 Sep 13;9(1):59. doi: 10.1186/s12920-016-0220-7.

40.

DNA methylome analysis of acute lymphoblastic leukemia cells reveals stochastic de novo DNA methylation in CpG islands.

Wahlberg P, Lundmark A, Nordlund J, Busche S, Raine A, Tandre K, Rönnblom L, Sinnett D, Forestier E, Pastinen T, Lönnerholm G, Syvänen AC.

Epigenomics. 2016 Oct;8(10):1367-1387. Epub 2016 Aug 23.

41.

Inborn Error of Cobalamin Metabolism Associated with the Intracellular Accumulation of Transcobalamin-Bound Cobalamin and Mutations in ZNF143, Which Codes for a Transcriptional Activator.

Pupavac M, Watkins D, Petrella F, Fahiminiya S, Janer A, Cheung W, Gingras AC, Pastinen T, Muenzer J, Majewski J, Shoubridge EA, Rosenblatt DS.

Hum Mutat. 2016 Sep;37(9):976-82. doi: 10.1002/humu.23037. Epub 2016 Jul 12.

PMID:
27349184
42.

An evaluation of methods correcting for cell-type heterogeneity in DNA methylation studies.

McGregor K, Bernatsky S, Colmegna I, Hudson M, Pastinen T, Labbe A, Greenwood CM.

Genome Biol. 2016 May 3;17:84. doi: 10.1186/s13059-016-0935-y.

43.

Demonstration of Autosomal Monoallelic Expression in Thyroid Tissue Assessed by Whole-Exome and Bulk RNA Sequencing.

Magne F, Ge B, Larrivée-Vanier S, Van Vliet G, Samuels ME, Pastinen T, Deladoëy J.

Thyroid. 2016 Jun;26(6):852-9. doi: 10.1089/thy.2016.0009. Epub 2016 May 18.

PMID:
27125219
44.

DNA methylation within melatonin receptor 1A (MTNR1A) mediates paternally transmitted genetic variant effect on asthma plus rhinitis.

Sarnowski C, Laprise C, Malerba G, Moffatt MF, Dizier MH, Morin A, Vincent QB, Rohde K, Esparza-Gordillo J, Margaritte-Jeannin P, Liang L, Lee YA, Bousquet J, Siroux V, Pignatti PF, Cookson WO, Lathrop M, Pastinen T, Demenais F, Bouzigon E.

J Allergy Clin Immunol. 2016 Sep;138(3):748-753. doi: 10.1016/j.jaci.2015.12.1341. Epub 2016 Mar 30.

PMID:
27038909
45.

Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation.

Busche S, Shao X, Caron M, Kwan T, Allum F, Cheung WA, Ge B, Westfall S, Simon MM; Multiple Tissue Human Expression Resource, Barrett A, Bell JT, McCarthy MI, Deloukas P, Blanchette M, Bourque G, Spector TD, Lathrop M, Pastinen T, Grundberg E.

Genome Biol. 2015 Dec 23;16:290. doi: 10.1186/s13059-015-0856-1.

46.

Exome and regulatory element sequencing of neuromyelitis optica patients.

Siuko M, Valori M, Kivelä T, Setälä K, Morin A, Kwan T, Pastinen T, Tienari P.

J Neuroimmunol. 2015 Dec 15;289:139-42. doi: 10.1016/j.jneuroim.2015.11.002. Epub 2015 Nov 3.

PMID:
26616883
47.

funtooNorm: an R package for normalization of DNA methylation data when there are multiple cell or tissue types.

Oros Klein K, Grinek S, Bernatsky S, Bouchard L, Ciampi A, Colmegna I, Fortin JP, Gao L, Hivert MF, Hudson M, Kobor MS, Labbe A, MacIsaac JL, Meaney MJ, Morin AM, O'Donnell KJ, Pastinen T, Van Ijzendoorn MH, Voisin G, Greenwood CM.

Bioinformatics. 2016 Feb 15;32(4):593-5. doi: 10.1093/bioinformatics/btv615. Epub 2015 Oct 24.

48.

Bacterial infection remodels the DNA methylation landscape of human dendritic cells.

Pacis A, Tailleux L, Morin AM, Lambourne J, MacIsaac JL, Yotova V, Dumaine A, Danckaert A, Luca F, Grenier JC, Hansen KD, Gicquel B, Yu M, Pai A, He C, Tung J, Pastinen T, Kobor MS, Pique-Regi R, Gilad Y, Barreiro LB.

Genome Res. 2015 Dec;25(12):1801-11. doi: 10.1101/gr.192005.115. Epub 2015 Sep 21.

49.

Whole-genome sequencing identifies EN1 as a determinant of bone density and fracture.

Zheng HF, Forgetta V, Hsu YH, Estrada K, Rosello-Diez A, Leo PJ, Dahia CL, Park-Min KH, Tobias JH, Kooperberg C, Kleinman A, Styrkarsdottir U, Liu CT, Uggla C, Evans DS, Nielson CM, Walter K, Pettersson-Kymmer U, McCarthy S, Eriksson J, Kwan T, Jhamai M, Trajanoska K, Memari Y, Min J, Huang J, Danecek P, Wilmot B, Li R, Chou WC, Mokry LE, Moayyeri A, Claussnitzer M, Cheng CH, Cheung W, Medina-Gómez C, Ge B, Chen SH, Choi K, Oei L, Fraser J, Kraaij R, Hibbs MA, Gregson CL, Paquette D, Hofman A, Wibom C, Tranah GJ, Marshall M, Gardiner BB, Cremin K, Auer P, Hsu L, Ring S, Tung JY, Thorleifsson G, Enneman AW, van Schoor NM, de Groot LC, van der Velde N, Melin B, Kemp JP, Christiansen C, Sayers A, Zhou Y, Calderari S, van Rooij J, Carlson C, Peters U, Berlivet S, Dostie J, Uitterlinden AG, Williams SR, Farber C, Grinberg D, LaCroix AZ, Haessler J, Chasman DI, Giulianini F, Rose LM, Ridker PM, Eisman JA, Nguyen TV, Center JR, Nogues X, Garcia-Giralt N, Launer LL, Gudnason V, Mellström D, Vandenput L, Amin N, van Duijn CM, Karlsson MK, Ljunggren Ö, Svensson O, Hallmans G, Rousseau F, Giroux S, Bussière J, Arp PP, Koromani F, Prince RL, Lewis JR, Langdahl BL, Hermann AP, Jensen JE, Kaptoge S, Khaw KT, Reeve J, Formosa MM, Xuereb-Anastasi A, Åkesson K, McGuigan FE, Garg G, Olmos JM, Zarrabeitia MT, Riancho JA, Ralston SH, Alonso N, Jiang X, Goltzman D, Pastinen T, Grundberg E, Gauguier D, Orwoll ES, Karasik D, Davey-Smith G; AOGC Consortium, Smith AV, Siggeirsdottir K, Harris TB, Zillikens MC, van Meurs JB, Thorsteinsdottir U, Maurano MT, Timpson NJ, Soranzo N, Durbin R, Wilson SG, Ntzani EE, Brown MA, Stefansson K, Hinds DA, Spector T, Cupples LA, Ohlsson C, Greenwood CM; UK10K Consortium, Jackson RD, Rowe DW, Loomis CA, Evans DM, Ackert-Bicknell CL, Joyner AL, Duncan EL, Kiel DP, Rivadeneira F, Richards JB.

Nature. 2015 Oct 1;526(7571):112-7. doi: 10.1038/nature14878. Epub 2015 Sep 14.

50.

High-dose folic acid supplementation alters the human sperm methylome and is influenced by the MTHFR C677T polymorphism.

Aarabi M, San Gabriel MC, Chan D, Behan NA, Caron M, Pastinen T, Bourque G, MacFarlane AJ, Zini A, Trasler J.

Hum Mol Genet. 2015 Nov 15;24(22):6301-13. doi: 10.1093/hmg/ddv338. Epub 2015 Aug 24.

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