Publications

Articles

Applications Technologiques

Séquençage de génome entier (génome entier, re-séquençage, séquençage de novo)

  • Pavy, N., Lamothe, M., Pelgas, B., Gagnon, F., Birol, I., Bohlmann, J., … Bousquet, J. (2017). A high resolution reference genetic map positioning 8.8K genes for the conifer white spruce: Structural genomics implications and correspondence with physical distance. The Plant Journal: For Cell and Molecular Biology. https://doi.org/10.1111/tpj.13478
  • Low-Kam, C., Rhainds, D., Lo, K. S., Provost, S., Mongrain, I., Dubois, A., … Lettre, G. (2016). Whole-genome sequencing in French Canadians from Quebec. Human Genetics, 135(11), 1213-1221. https://doi.org/10.1007/s00439-016-1702-6
  • Charron G, Marsit S, Hénault M, Martin H, Landry CR. Spontaneous whole-genome duplication restores fertility in interspecific hybrids. Nat Commun. 2019;10(1):4126. Published 2019 Sep 11. https://www.nature.com/articles/s41467-019-12041-8
  • Hagen IJ, Lien S, Billing AM, et al. A genome-wide linkage map for the house sparrow (Passer domesticus) provides insights into the evolutionary history of the avian genome. Mol Ecol Resour. 2020;20(2):544-559. https://onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.13134
  • Hübner S, Bercovich N, Todesco M, et al. Sunflower pan-genome analysis shows that hybridization altered gene content and disease resistance. Nat Plants. 2019;5(1):54-62. https://www.nature.com/articles/s41477-018-0329-0 

Analyse d’ARN (scRNA Seq, RNA Seq, biopuces)

  • Lopez, J. P., Fiori, L. M., Cruceanu, C., Lin, R., Labonte, B., Cates, H. M., … Turecki, G. (2017). MicroRNAs 146a/b-5 and 425-3p and 24-3p are markers of antidepressant response and regulate MAPK/Wnt-system genes. Nature Communications, 8, 15497. https://doi.org/10.1038/ncomms15497
  • Khater, F., Lajoie, M., Langlois, S., Healy, J., Cellot, S., Richer, C., … Sinnett, D. (2017). KMT2E-ASNS: a novel relapse-specific fusion gene in early T-cell precursor acute lymphoblastic leukemia. Blood, blood-2016-10-744219.https://doi.org/10.1182/blood-2016-10-744219
  • Liu, Y., Zhou, J., & White, K. P. (2014). RNA-seq differential expression studies: more sequence or more replication? Bioinformatics, 30(3), 301-304.https://doi.org/10.1093/bioinformatics/btt68
  • Couturier CP, Ayyadhury S, Le PU, et al. Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy. Nat Commun. 2020;11(1):3406. Published 2020 Jul 8. https://www.nature.com/articles/s41467-020-17186-5
  • Xue Y, Zhu X, Meehan B, et al. SMARCB1 loss induces druggable cyclin D1 deficiency via upregulation of MIR17HG in atypical teratoid rhabdoid tumors [published online ahead of print, 2020 Jun 19]. J Pathol. 2020;10.1002/path.5493. https://onlinelibrary.wiley.com/doi/10.1002/path.5493

Séquençage ciblé (Exome Seq, captures d’ADN/ARN, amplicons)

  • Morin, A., Kwan, T., Ge, B., Letourneau, L., Ban, M., Tandre, K., … Pastinen, T. (2016). Immunoseq: the identification of functionally relevant variants through targeted capture and sequencing of active regulatory regions in human immune cells. BMC Medical Genomics, 9(1), 59. https://doi.org/10.1186/s12920-016-0220-7
  • Carrot-Zhang, J., & Majewski, J. (2016). LoLoPicker: Detecting Low Allelic-Fraction Variants in Low-Quality Cancer Samples from Whole-exome Sequencing Data. bioRxiv, 43612. https://doi.org/10.1101/043612
  • Ejaz, R., Qin, W., Huang, L., Blaser, S., Tetreault, M., Hartley, T., … Carter, M. T. (2016). Lateral meningocele (Lehman) syndrome: A child with a novel NOTCH3 mutation. American Journal of Medical Genetics. Part A, 170A(4), 1070-5.https://doi.org/10.1002/ajmg.a.37541
  • Choquet, K., Tétreault, M., Yang, S., La Piana, R., Dicaire, M.-J., Vanstone, M. R., … Brais, B. (2016). SPG7 mutations explain a significant proportion of French Canadian spastic ataxia cases. European Journal of Human Genetics : EJHG, 24(7), 1016-21. https://doi.org/10.1038/ejhg.2015.240
  • Nicolas, G., Wallon, D., Charbonnier, C., Quenez, O., Rousseau, S., Richard, A.-C., … Hannequin, D. (2016). Screening of dementia genes by whole-exome sequencing in early-onset Alzheimer disease: input and lessons. European Journal of Human Genetics, 24(5), 710-716. https://doi.org/10.1038/ejhg.2015.173
  • de Kock, L., Wang, Y. C., Revil, T., Badescu, D., Rivera, B., Sabbaghian, N., … Foulkes, W. D. (2016). High-sensitivity sequencing reveals multi-organ somatic mosaicism causing DICER1 syndrome. Journal of Medical Genetics, 53(1), 43-52.https://doi.org/10.1136/jmedgenet-2015-103428
  • Nikbakht, H., Panditharatna, E., Mikael, L. G., Li, R., Gayden, T., Osmond, M., … Nazarian, J. (2016). Spatial and temporal homogeneity of driver mutations in diffuse intrinsic pontine glioma. Nature Communications, 7, 11185.https://doi.org/10.1038/ncomms11185
  • Rivera, B., Gayden, T., Carrot-Zhang, J., Nadaf, J., Boshari, T., Faury, D., … Majewski, J. (2016). Germline and somatic FGFR1 abnormalities in dysembryoplastic neuroepithelial tumors. Acta Neuropathologica, 131(6), 847-863. https://doi.org/10.1007/s00401-016-1549-x
  • Armour, C. M., Smith, A., Hartley, T., Chardon, J. W., Sawyer, S., Schwartzentruber, J., … Boycott, K. M. (2016). Syndrome disintegration: Exome sequencing reveals that Fitzsimmons syndrome is a co-occurrence of multiple events. American Journal of Medical Genetics Part A, 170(7), 1820-1825.https://doi.org/10.1002/ajmg.a.37684
  • McCluggage WG, Chong AL, de Kock L, Foulkes WD. Somatic tumour testing establishes that bilateral DICER1-associated ovarian Sertoli-Leydig cell tumours represent independent primary neoplasms [published online ahead of print, 2020 Apr 24]. Histopathology. 2020;10.https://onlinelibrary.wiley.com/doi/abs/10.1111/his.14123

Séquençage PacBio

  • Xiong, J., Déraspe, M., Iqbal, N., Ma, J., Jamieson, F. B., Wasserscheid, J., … Roy, P. H. (2016). Genome and Plasmid Analysis of blaIMP-4-Carrying Citrobacter freundii B38. Antimicrobial Agents and Chemotherapy, 60(11), 6719-6725. https://doi.org/10.1128/AAC.00588-16
  • Ricker, N., Shen, S. Y., Goordial, J., Jin, S., & Fulthorpe, R. R. (2016). PacBio SMRT assembly of a complex multi-replicon genome reveals chlorocatechol degradative operon in a region of genome plasticity. Gene, 586(2), 239-247. https://doi.org/10.1016/j.gene.2016.04.018
  • Bromfield ESP, Cloutier S, Nguyen HDT. Description and complete genome sequence of Bradyrhizobium amphicarpaeae sp. nov., harbouring photosystem and nitrogen-fixation genes. Int J Syst Evol Microbiol. 2019;69(9):2841-2848. https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.003569

Épigénétique (Methyl Seq, biopuces)

  • Chen, G. G., Gross, J. A., Lutz, P.-E., Vaillancourt, K., Maussion, G., Bramoulle, A., … Ernst, C. (2017). Medium throughput bisulfite sequencing for accurate detection of 5-methylcytosine and 5-hydroxymethylcytosine. BMC Genomics, 18(1), 96. https://doi.org/10.1186/s12864-017-3489-9
  • Chen, L., Ge, B., Casale, F. P., Vasquez, L., Kwan, T., Garrido-Martín, D., … Soranzo, N. (2016). Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells. Cell, 167(5), 1398-1414.e24.https://doi.org/10.1016/j.cell.2016.10.026
  • Ho, V., Ashbury, J. E., Taylor, S., Vanner, S., & King, W. D. (2016). Quantification of gene-specific methylation of DNMT3B and MTHFR using sequenom EpiTYPER®. Data in Brief, 6, 39-46. https://doi.org/10.1016/j.dib.2015.11.039
  • Sarnowski, C., Laprise, C., Malerba, G., Moffatt, M. F., Dizier, M.-H., Morin, A., … Bouzigon, E. (2016). DNA methylation within melatonin receptor 1A (MTNR1A) mediates paternally transmitted genetic variant effect on asthma plus rhinitis.Journal of Allergy and Clinical Immunology, 138(3), 748-753. https://doi.org/10.1016/j.jaci.2015.12.1341 https://doi.org/10.1111/tpj.13478
  • Allum, F., Shao, X., Guénard, F., Simon, M.-M., Busche, S., Caron, M., … Grundberg, E. (2015). Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants. Nature Communications, 6, 7211. https://doi.org/10.1038/ncomms8211
  • Busche, S., Shao, X., Caron, M., Kwan, T., Allum, F., Cheung, W. A., … Grundberg, E. (2015). Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation. Genome Biology, 16(1), 290. https://doi.org/10.1186/s13059-015-0856-1
  • El-Zein M, Cheishvili D, Gotlieb W, et al. Genome-wide DNA methylation profiling identifies two novel genes in cervical neoplasia [published online ahead of print, 2020 Jan 25]. Int J Cancer. 2020;10.1002/ijc.32880. https://onlinelibrary.wiley.com/doi/full/10.1002/ijc.32880
  • Lu T, Klein KO, Colmegna I, Lora M, Greenwood CMT, Hudson M. Whole-genome bisulfite sequencing in systemic sclerosis provides novel targets to understand disease pathogenesis. BMC Med Genomics. 2019;12(1):144. Published 2019 Oct 24. https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s12920-019-0602-8
  • Barría A, Christensen KA, Yoshida G, et al. Whole Genome Linkage Disequilibrium and Effective Population Size in a Coho Salmon (Oncorhynchus kisutch) Breeding Population Using a High-Density SNP Array. Front Genet. 2019;10:498. Published 2019 May 22. https://www.frontiersin.org/articles/396472

Génotypage (biopuces, iPLEX Gold, TaqMan)

  • Pavy, N., Gagnon, F., Deschênes, A., Boyle, B., Beaulieu, J., & Bousquet, J. (2016). Development of highly reliable in silico SNP resource and genotyping assay from exome capture and sequencing: an example from black spruce ( Picea mariana ). Molecular Ecology Resources, 16(2), 588-598.https://doi.org/10.1111/1755-0998.12468
  • Gagné V, Aubry-Morin A, Plesa M, et al. Genes identified through genome-wide association studies of osteonecrosis in childhood acute lymphoblastic leukemia patients. Pharmacogenomics. 2019;20(17):1189-1197. https://www.futuremedicine.com/doi/10.2217/pgs-2019-0087

ChIP Seq

  • Hocking, T. D., Goerner-Potvin, P., Morin, A., Shao, X., Pastinen, T., & Bourque, G. (2016). Optimizing ChIP-seq peak detectors using visual labels and supervised machine learning. Bioinformatics (Oxford, England), 33(4), 491-499.https://doi.org/10.1093/bioinformatics/btw672
  • Furey, T. S. (2012). ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. Nature Reviews Genetics, 13(12), 840-852. https://doi.org/10.1038/nrg3306
  • Kidder, B. L., Hu, G., & Zhao, K. (2011). ChIP-Seq: technical considerations for obtaining high-quality data. Nature Immunology, 12(10), 918-922.https://doi.org/10.1038/ni.2117
  • Behl S, Hamel N, de Ladurantaye M, et al. Founder BRCA1/BRCA2/PALB2 pathogenic variants in French-Canadian breast cancer cases and controls. Sci Rep. 2020;10(1):6491. Published 2020 Apr 16. https://www.nature.com/articles/s41598-020-63100-w

Métagénomiques et métabarcoding

RETOUR AU SOMMAIRE

Articles

Secteurs d’activités

Bio-informatique

  • Hocking, T. D., Goerner-Potvin, P., Morin, A., Shao, X., Pastinen, T., & Bourque, G. (2016). Optimizing ChIP-seq peak detectors using visual labels and supervised machine learning. Bioinformatics (Oxford, England), 33(4), 491-499.https://doi.org/10.1093/bioinformatics/btw672
  • Carrot-Zhang, J., & Majewski, J. (2016). LoLoPicker: Detecting Low Allelic-Fraction Variants in Low-Quality Cancer Samples from Whole-exome Sequencing Data. bioRxiv, 43612. https://doi.org/10.1101/043612

Environnement/Écologie

  • Ricker, N., Shen, S. Y., Goordial, J., Jin, S., & Fulthorpe, R. R. (2016). PacBio SMRT assembly of a complex multi-replicon genome reveals chlorocatechol degradative operon in a region of genome plasticity. Gene, 586(2), 239-247.https://doi.org/10.1016/j.gene.2016.04.018
  • Xiong, J., Déraspe, M., Iqbal, N., Ma, J., Jamieson, F. B., Wasserscheid, J., … Roy, P. H. (2016). Genome and Plasmid Analysis of blaIMP-4-Carrying Citrobacter freundii B38. Antimicrobial Agents and Chemotherapy, 60(11), 6719-6725.https://doi.org/10.1128/AAC.00588-16
  • Athey, T. B. T., Teatero, S., Takamatsu, D., Wasserscheid, J., Dewar, K., Gottschalk, M., & Fittipaldi, N. (2016). Population Structure and Antimicrobial Resistance Profiles of Streptococcus suis Serotype 2 Sequence Type 25 Strains. PLOS ONE, 11(3), e0150908. https://doi.org/10.1371/journal.pone.0150908

Foresterie

  • Pavy, N., Lamothe, M., Pelgas, B., Gagnon, F., Birol, I., Bohlmann, J., … Bousquet, J. (2017). A high resolution reference genetic map positioning 8.8K genes for the conifer white spruce: Structural genomics implications and correspondence with physical distance. The Plant Journal : For Cell and Molecular Biology. https://doi.org/10.1111/tpj.13478
  • Pavy, N., Gagnon, F., Deschênes, A., Boyle, B., Beaulieu, J., & Bousquet, J. (2016). Development of highly reliable in silico SNP resource and genotyping assay from exome capture and sequencing: an example from black spruce ( Picea mariana ). Molecular Ecology Resources, 16(2), 588-598.https://doi.org/10.1111/1755-0998.12468

Santé animale

  • Mehner, T., Pohlmann, K., Elkin, C., Monaghan, M. T., Nitz, B., & Freyhof, J. (2010). Genetic population structure of sympatric and allopatric populations of Baltic ciscoes (Coregonus albula complex, Teleostei, Coregonidae). BMC Evolutionary Biology, 10, 85. https://doi.org/10.1186/1471-2148-10-85

 

Santé humaine

  • Lopez, J. P., Fiori, L. M., Cruceanu, C., Lin, R., Labonte, B., Cates, H. M., … Turecki, G. (2017). MicroRNAs 146a/b-5 and 425-3p and 24-3p are markers of antidepressant response and regulate MAPK/Wnt-system genes. Nature Communications, 8, 15497. https://doi.org/10.1038/ncomms15497
  • Khater, F., Lajoie, M., Langlois, S., Healy, J., Cellot, S., Richer, C., … Sinnett, D. (2017). KMT2E-ASNS: a novel relapse-specific fusion gene in early T-cell precursor acute lymphoblastic leukemia. Blood, blood-2016-10-744219.https://doi.org/10.1182/blood-2016-10-744219
  • Chen, L., Ge, B., Casale, F. P., Vasquez, L., Kwan, T., Garrido-Martín, D., … Soranzo, N. (2016). Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells. Cell, 167(5), 1398-1414.e24.https://doi.org/10.1016/j.cell.2016.10.026
  • Morin, A., Kwan, T., Ge, B., Letourneau, L., Ban, M., Tandre, K., … Pastinen, T. (2016). Immunoseq: the identification of functionally relevant variants through targeted capture and sequencing of active regulatory regions in human immune cells. BMC Medical Genomics, 9(1), 59. https://doi.org/10.1186/s12920-016-0220-7
  • Ejaz, R., Qin, W., Huang, L., Blaser, S., Tetreault, M., Hartley, T., … Carter, M. T. (2016). Lateral meningocele (Lehman) syndrome: A child with a novel NOTCH3 mutation. American Journal of Medical Genetics. Part A, 170A(4), 1070-5.https://doi.org/10.1002/ajmg.a.37541
  • Choquet, K., Tétreault, M., Yang, S., La Piana, R., Dicaire, M.-J., Vanstone, M. R., … Brais, B. (2016). SPG7 mutations explain a significant proportion of French Canadian spastic ataxia cases. European Journal of Human Genetics : EJHG, 24(7), 1016-21. https://doi.org/10.1038/ejhg.2015.240
  • Nicolas, G., Wallon, D., Charbonnier, C., Quenez, O., Rousseau, S., Richard, A.-C., … Hannequin, D. (2016). Screening of dementia genes by whole-exome sequencing in early-onset Alzheimer disease: input and lessons. European Journal of Human Genetics, 24(5), 710-716. https://doi.org/10.1038/ejhg.2015.173
  • Morrissy, A. S., Garzia, L., Shih, D. J. H., Zuyderduyn, S., Huang, X., Skowron, P., … Taylor, M. D. (2016). Divergent clonal selection dominates medulloblastoma at recurrence. Nature, 529(7586), 351-357. https://doi.org/10.1038/nature16478
  • Low-Kam, C., Rhainds, D., Lo, K. S., Provost, S., Mongrain, I., Dubois, A., … Lettre, G. (2016). Whole-genome sequencing in French Canadians from Quebec. Human Genetics, 135(11), 1213-1221. https://doi.org/10.1007/s00439-016-1702-6
  • de Kock, L., Wang, Y. C., Revil, T., Badescu, D., Rivera, B., Sabbaghian, N., … Foulkes, W. D. (2016). High-sensitivity sequencing reveals multi-organ somatic mosaicism causing DICER1 syndrome. Journal of Medical Genetics, 53(1), 43-52.https://doi.org/10.1136/jmedgenet-2015-103428
  • Bennett, J. T., Tan, T. Y., Alcantara, D., Tétrault, M., Timms, A. E., Jensen, D., … McDonell, L. M. (2016). Mosaic Activating Mutations in FGFR1 Cause Encephalocraniocutaneous Lipomatosis. The American Journal of Human Genetics, 98(3), 579-587. https://doi.org/10.1016/j.ajhg.2016.02.006
  • Sarnowski, C., Laprise, C., Malerba, G., Moffatt, M. F., Dizier, M.-H., Morin, A., … Bouzigon, E. (2016). DNA methylation within melatonin receptor 1A (MTNR1A) mediates paternally transmitted genetic variant effect on asthma plus rhinitis. Journal of Allergy and Clinical Immunology, 138(3), 748-753.https://doi.org/10.1016/j.jaci.2015.12.1341
  • Petridis, C., Brook, M. N., Shah, V., Kohut, K., Gorman, P., Caneppele, M., … Sawyer, E. J. (2016). Genetic predisposition to ductal carcinoma in situ of the breast. Breast Cancer Research, 18(1), 22. https://doi.org/10.1186/s13058-016-0675-7
  • Nikbakht, H., Panditharatna, E., Mikael, L. G., Li, R., Gayden, T., Osmond, M., … Nazarian, J. (2016). Spatial and temporal homogeneity of driver mutations in diffuse intrinsic pontine glioma. Nature Communications, 7, 11185.https://doi.org/10.1038/ncomms11185
  • Rivera, B., Gayden, T., Carrot-Zhang, J., Nadaf, J., Boshari, T., Faury, D., … Majewski, J. (2016). Germline and somatic FGFR1 abnormalities in dysembryoplastic neuroepithelial tumors. Acta Neuropathologica, 131(6), 847-863. https://doi.org/10.1007/s00401-016-1549-x
  • Le Guennec, K., Nicolas, G., Quenez, O., Charbonnier, C., Wallon, D., Bellenguez, C., … CNR-MAJ collaborators. (2016). ABCA7 rare variants and Alzheimer disease risk. Neurology, 86(23), 2134-2137.https://doi.org/10.1212/WNL.0000000000002627
  • Allum, F., Shao, X., Guénard, F., Simon, M.-M., Busche, S., Caron, M., … Grundberg, E. (2015). Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants. Nature Communications, 6, 7211. https://doi.org/10.1038/ncomms8211
  • Busche, S., Shao, X., Caron, M., Kwan, T., Allum, F., Cheung, W. A., … Grundberg, E. (2015). Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation. Genome Biology, 16(1), 290. https://doi.org/10.1186/s13059-015-0856-1