Publications

Selected CGEn Supported Publications (CGEn-linked authors in bold )

 
  • Akbari V, Garant JM, O’Neill K, Pandoh P, Moore R, Marra MA, Hirst M, Jones SJM (2021). Megabase-scale methylation phasing using nanopore long reads and NanoMethPhase. Genome Biol. 22(1):68.
  • Baskurt Z, et al. (incl. Mastromatteo S, Wintle RF, Scherer SW, Strug LJ) (2020). VikNGS: a C++ variant integration kit for next generation sequencing association analysis. Bioinformatics 36(4):1283-1285.
  • Bayega A, et al. (incl. Djambazian H, Dewar K, Ragoussis J) (2020). De novo assembly of the olive fruit fly (Bactrocera oleae) genome with linked-reads and long-read technologies minimizes gaps and provides exceptional Y chromosome assembly. BMC Genomics 21(1):259.
  • Bourgey M, et al. (incl. Dali R, Eveleigh R, Letourneau L, Michaud M, Caron M, Lefebvre F, Leveque G, Mercier E, Bujold D, Marquis P, Shao X, Henrion E, Gonzalez E, Quirion PO, Bourque G) (2019). GenPipes: an open-source framework for distributed and scalable genomic analyses. Gigascience 2019 Jun 1;8(6):giz037.
  • Corbett RD, Eveleigh R, Whitney J, Barai N, Bourgey M, Chuah E, Johnson J, Moore RA, Moradin N, Mungall KL, Pereira S, Reuter MS, Thiruvahindrapuram B, Wintle RF, Ragoussis J, Strug LJ, Herbrick JA, Aziz N, JonesSJM, Lathrop M, Scherer SW, Staffa A, Mungall AJ (2020). A distributed whole genome sequencing benchmark study. Front Genet. 11:612515.
  • Costain G, Cohn RD, Scherer SW, Marshall CR (2021). Genome sequencing as a diagnostic test. CMAJ193(42):E1626-E1629.
  • Costain G, et al. (incl. Walker S, Reuter MS, Thiruvahindrapuram B, Trost B, Sung WWL, Yuen RKC, Stavropoulos DJ, Scherer SW, Marshall CR) (2020). Genome sequencing as a diagnostic test in children with unexplained medical complexity. JAMA Netw Open 3(9):e2018109.
  • Farouni R, et al. (incl. Ragoussis J) (2020). Model-based analysis of sample index hopping reveals its widespread artifacts in multiplexed single-cell RNA-sequencing. Nat Commun. 11(1):2704
  • Ferchaud A-L, et al. (incl. Ragoussis J, Djambazian H, Bérubé P) (2021). Chromosome-level assembly reveals a putative Y-autosomal fusion in the sex determination system of the Greenland Halibut (Reinhardtius hippoglossoides). G3(Bethesda), in press.
  • Gong J, et al. (incl. Mastromatteo S, Baskurt Z, Strug L) (2019). Genetic association and transcriptome integration identify contributing genes and tissues at cystic fibrosis modifier loci. PLoS Genet. 15(2):e1008007.
  • Groza C, Kwan T, Soranzo N, Pastinen T, Bourque G (2020). Personalized and graph genomes reveal missing signal in epigenomic data. Genome Biol. 21(1):124.
  • Hildebrandt MR, et al. (incl. Reuter MS, Scherer SW) (2019). Precision health resource of control iPSC lines for versatile multilineage differentiation. Stem Cell Reports. 13(6):1126-1141.
  • Kwan HH, Culibrk L, Taylor GA, Leelakumari S, Tan R, Jackman SD, Tse K, MacLeod T, Cheng D, Chuah E, Kirk H, Pandoh P, Carlsen R, Zhao Y, Mungall AJ, Moore R, Birol I, Marra MA, Rosen DAS, Haulena M, Jones SJM (2019). The genome of the Steller Sea Lion (Eumetopias jubatus). Genes (Basel) 10(7):486.
  • Laks E, et al. (incl. Ma Y, Coope RJN, Corbett R, Pleasance S, Moore R, Mungall AJ, Marra MA) (2019). Clonal decomposition and DNA replication states defined by scaled single-cell genome sequencing. Cell. 179(5):1207-1221.e22
  • Lin YC, et al. (incl. Paterson AD, Strug LJ) (2020). Statistical power in COVID-19 case-control host genomic study design. Genome Med. 12(1):115.
  • Maitra M, et al. (incl. Wang YC, Ragoussis J) (2021). Extraction of nuclei from archived postmortem tissues for single-nucleus sequencing applications.Nat Protoc. 16(6):2788-2801.
  • Marshall CR, et al. (incl. Stavropoulos DJ) (2020). Best practices for the analytical validation of clinical whole-genome sequencing intended for the diagnosis of germline disease. NPJ Genom Med 5:47.
  • Nagy C, et al. (incl. Wang YC, Ragoussis J) (2020).Single-nucleus transcriptomics of the prefrontal cortex in major depressive disorder implicates oligodendrocyte precursor cells and excitatory neurons.Nat Neurosci.  23(6):771-781.
  • Pleasance E, et al. (incl. Titmuss E, Williamson L, Kwan H, Culibrk L, Zhao EY, Fan K, Bowlby R, Jones MR, Shen Y, Grewal JK, Ashkani J, Wee K, Grisdale CJ, Thibodeau ML, Bozoky Z, Majounie E, Vira T, Shenwai R, Mungall KL, Chuah E, Davies A, Warren M, Reisle C, Bonakdar M, Taylor GA, Csizmok V, Chan SK, Zong Z,Bilobram S, Muhammadzadeh A, D’Souza D, Corbett RD, MacMillan D, Carreira M, Choo C, Bleile D, Sadeghi S, Zhang W, Wong T, Cheng D, Brown SD, Holt RA, Moore RA, Mungall AJ, Zhao Y, Nelson J, Fok A, Ma Y, Jones SJM, Marra MA) (2020). Pan-cancer analysis of patient tumors reveals interactions between therapy and genomic landscapes. Nat Cancer 1:452–468.
  • Povysil G, et al. (incl. Eveleigh RJ, Bourgey M, Aziz N, Jones SJ, Scherer SW, Strug LJ, Lepage P, Ragoussis J, Bourque G) (2021). Rare loss-of-function variants in type I IFN immunity genes are not associated with severe COVID-19. J Clin Invest. 131(14):e147834.
  • Reuter MS, et al. (incl. Pereira SL, Raajkumar A, Thiruvahindrapuram B, Scherer SW). (2020). The Cardiac Genome Clinic: implementing genome sequencing in pediatric heart disease. Genet Med. 22(6):1015-1024.
  • Suzuki H, et al. (incl. Jabado N, Ragoussis J, Marra MA, Taylor MD) (2019). Recurrent noncoding U1 snRNA mutations drive cryptic splicing in SHH medulloblastoma. Nature. 574(7780):707-711.
  • Tremblay K, et al. (incl. Auld D) (2021). The Biobanque Québécoise de la COVID-19 (BQC19)-A cohort to prospectively study the clinical and biological determinants of COVID-19 clinical trajectories. PLoS One. 16(5):e0245031
  • Trost B, et al. (incl. Engchuan W, Nguyen CM, Thiruvahindrapuram B, Hamdan O, Pellecchia G, Howe JL, Whitney J, Hoang N, Scherer SW, Yuen RKC) (2020). Genome-wide detection of tandem DNA repeats that are expanded in autism. Nature 586(7827):80-86.
  • Trost B, Walker S, Haider SA, Sung WWL, Pereira S, Phillips CL, Higginbotham EJ, Strug LJ, Nguyen C, Raajkumar A, Szego MJ, Marshall CR, Scherer SW (2019). Impact of DNA source on genetic variant detection from genome sequencing data. J Med Genet. 56(12):809-817.
  • Vladoiu MC et al. (incl. Marra MA, Jabado N, Taylor MD) (2019). Childhood cerebellar tumours mirror conserved fetal transcriptional programs. Nature. 572(7767):67-73
  • Zarrei M, et al. (incl. Engchuan W, Higginbotham EJ, MacDonald JR, Trost B, Chan AJS, Walker S, Lamoureux S, Kellam B, Paton T, Faheem M, Miron K, Lu C, Wang T, Samler K, Wang X, Pellecchia G, Wei J, Patel RV, Thiruvahindrapuram B, Howe JL, Yuen RKC, Buchanan JA, Marshall CR, Wintle RF, Scherer SW) (2019). A large data resource of genomic copy number variation across neurodevelopmental disorders. NPJ Genom Med. 4:26.