CGEn-Supported Published Papers

HostSeq: a Canadian whole genome sequencing and clinical data resource. Yoo S, Garg E, Elliott LT, Hung RJ, Halevy AR, Brooks JD, Bull SB, Gagnon F, Greenwood C, Lawless JF, et al. BMC Genom Data. 2023 May 2;24(1):26. doi: 10.1186/s12863-023-01128-3. PMID: 37131148

A second update on mapping the human genetic architecture of COVID-19. COVID-19 Host Genetics Initiative. Nature. 2023 Sep;621(7977):E7-E26. doi: 10.1038/s41586-023-06355-3. Epub 2023 Sep 6. PMID: 37674002

Liu Y, Lv Y, Zarrei M, Dong R, Yang X, Higginbotham EJ, Li Y, Zhao D, Song F, Yang Y, et al. (2022). Chromosomal microarray analysis of 410 Han Chinese patients with autism spectrum disorder or unexplained intellectual disability and developmental delay. NPJ Genomic Medicine 7,1. [PMID: 35022430].  (WS:0; GS:0)

Woodbury-Smith M, Lamoureux S, Begum G, Nassir N, Akter H, O’Rielly DD, Rahman P, Wintle RF, Scherer SW and Uddin M. (2022). Mutational landscape of autism spectrum disorder brain tissue. Genes (Basel) 13, 207. [PMID: 35205252]. (WS:N/A; GS:0)

Lesurf R, Said A, Akinrinade O, Breckpot J, Delfosse K, Liu T, Yao R, Persad G, McKenna F, Noche RR, et al.; Genomics England Research Consortium. (2022). Whole genome sequencing delineates regulatory, copy number, and cryptic splice variants in early onset cardiomyopathy. NPJ Genomic Medicine 7, 18. [PMID: 35288587]. (WS:0; GS:0)

Reuter MS, Zech M, Hempel M, Altmüller J, Heung T, Pölsler L, Santer R, Thiele H, Trost B, Kubisch C,  et al. (2022). Biallelic PAN2 variants in individuals with a syndromic neurodevelopmental disorder and multiple congenital anomalies. European Journal of Human Genetics [Epub ahead of print Mar 18]. [PMID: 35304602]. (WS:0; GS:0)

Mojarad BA, Engchuan W, Trost B, Backstrom I, Yin Y, Thiruvahindrapuram B, Pallotto L, Mitina A, Khan M, Pellecchia G, et al. (2022). Genome-wide tandem repeat expansions contribute to schizophrenia risk. Molecular Psychiatry [Epub ahead of print May 12]. [PMID: 35546631] (WS:0; GS:1)

Lok S, Lau TNH, Trost B, Tong AHY, Wintle RF, Engstrom MD, Stacy E, Waits LP, Scrafford M and *Scherer SW. (2022). Chromosomal-Level Reference Genome Assembly of the North American Wolverine (Gulo gulo luscus): A Resource for Conservation Genomics. G3 (Bethesda) [Epub ahead of print Jun 8]. [PMID: 35674384] (WS:NA; GS:0)

Maihofer AX, Engchuan W, Huguet G, Klein M, MacDonald JR, Shanta O, Thiruvahindrapuram B, Jean-Louis M, Saci Z, Jacquemont S, et al. (2022). Rare copy number variation in posttraumatic stress disorder. Molecular Psychiatry [Epub ahead of print Sep 21]. [PMID: 36131047] (WS:NA; GS:0)

Chan AJS, Engchuan W, Reuter MS, Wang Z, Thiruvahindrapuram B, Trost B, Nalpathamkalam T, Negrijn C, Lamoureux S, Pellecchia G, et al. (2022). Genome-wide rare variant score associates with morphological subtypes of autism spectrum disorder. Nature Communications 13, 6463. [PMID: 36309498] (WS:NA; GS:1)

Gong J, He G, Wang C, Bartlett C, Panjwani N, Mastromatteo S, Lin F, Keenan K, Avolio J, Halevy A, Shaw M, et al. (2022). Genetic evidence supports the development of SLC26A9 targeting therapies for the treatment of lung disease. NPJ Genom Med, Apr 8;7(1):28. doi: 10.1038/s41525-022-00299-9.

Jegathisawaran J, Tsiplova K, Hayeems RZ, Marshall CR, Stavropoulos DJ, Pereira SL, Thiruvahindrapuram B, Liston E, Reuter MS, et al. (2022). Trio genome sequencing for developmental delay and pediatric heart conditions: A comparative microcost analysis. Genet Med. May;24(5):1027-1036. doi: 10.1016/j.gim.2022.01.020. Epub 2022 Feb 24.

Trost B, Thiruvahindrapuram B, Chan AJS, Engchuan W, Higginbotham EJ, Howe JL, Loureiro LO, Reuter MS, Roshandel D, Whitney J, et al.  (2022). Genomic architecture of autism spectrum disorder from comprehensive whole-genome sequence annotation. Cell. Nov 10;185(23):4409-4427.

Disruption of DDX53 coding sequence has limited impact on iPSC-derived human NGN2 neurons. Faheem M, Deneault E, Alexandrova R, Rodrigues DC, Pellecchia G, Shum C, Zarrei M, Piekna A, Wei W, Howe JL, et al. BMC Med Genomics. 2023 Jan 12;16(1):5. doi: 10.1186/s12920-022-01425-3.PMID: 36635662

High-quality read-based phasing of cystic fibrosis cohort informs genetic understanding of disease modification. Mastromatteo S, Chen A, Gong J, Lin F, Thiruvahindrapuram B, Sung WWL, Whitney J, Wang Z, Patel RV, et al. HGG Adv. 2022 Oct 20;4(1):100156. doi: 10.1016/j.xhgg.2022.100156. eCollection 2023 Jan 12.PMID: 36386424

Rare tandem repeat expansions associate with genes involved in synaptic and neuronal signaling functions in schizophrenia. Wen J, Trost B, Engchuan W, Halvorsen M, Pallotto LM, Mitina A, Ancalade N, Farrell M, Backstrom I, et al. Mol Psychiatry. 2023 Jan;28(1):475-482. doi: 10.1038/s41380-022-01857-4. Epub 2022 Nov 16.PMID: 36380236

SCIP: software for efficient clinical interpretation of copy number variants detected by whole-genome sequencing. Ding Q, Somerville C, Manshaei R, Trost B, Reuter MS, Kalbfleisch K, Stanley K, Okello JBA, Hosseini SM, Liston E, et al. Hum Genet. 2023 Feb;142(2):201-216. doi: 10.1007/s00439-022-02494-1. Epub 2022 Nov 14.PMID: 36376761

Pharmacogenetic profiling via genome sequencing in children with medical complexity. Pan A, Scodellaro S, Khan T, Ushcatz I, Wu W, Curtis M, Cohen E, Cohn RD, Hayeems RZ, Meyn MS, et al. Pediatr Res. 2023 Mar;93(4):905-910. doi: 10.1038/s41390-022-02313-3. Epub 2022 Sep 27.PMID: 36167815

Gene copy number variation and pediatric mental health/neurodevelopment in a general population. Zarrei M, Burton CL, Engchuan W, Higginbotham EJ, Wei J, Shaikh S, Roslin NM, MacDonald JR, Pellecchia G, Nalpathamkalam T, Lamoureux S, et al. Hum Mol Genet. 2023 Jul 20;32(15):2411-2421. doi: 10.1093/hmg/ddad074. PMID: 37154571

Decreased left heart flow in fetal lambs causes left heart hypoplasia and pro-fibrotic tissue remodeling. Reuter MS, Sokolowski DJ, Javier Diaz-Mejia J, Keunen J, de Vrijer B, Chan C, Wang L, Ryan G, Chiasson DA, Ketela T, et al. 2023 Jul 22;6(1):770. doi: 10.1038/s42003-023-05132-2.PMID: 37481629

A New Sturgeon Herpesvirus from Juvenile Lake Sturgeon Acipenser fulvescensDisplaying Epithelial Skin Lesions. Clouthier S, Tomczyk M, Schroeder T, Klassen C, Dufresne A, Emmenegger E, Nalpathamkalam T, Wang Z, Thiruvahindrapuram B. Pathogens. 2023 Aug 31;12(9):1115. doi: 10.3390/pathogens12091115.PMID: 37764923

Three generation families: Analysis of de novo variants in autism. Costa CIS, da Silva Campos G, da Silva Montenegro EM, Wang JYT, Scliar M, Monfardini F, Zachi EC, Lourenço NCV, Chan AJS, et al. Eur J Hum Genet. 2023 Sep;31(9):1017-1022. doi: 10.1038/s41431-023-01398-6. Epub 2023 Jun 6.PMID: 37280359

Andrade AF, Chen CCL, Jabado N. Oncohistones in brain tumors: the soil and seed. Trends Cancer. 2023 May;9(5):444-455. doi: 10.1016/j.trecan.2023.02.003. Epub 2023 Mar 16. PMID: 36933956.

Khazaei S, Chen CCL, Andrade AF, Kabir N, Azarafshar P, Morcos SM, França JA, Lopes M, Lund PJ, Danieau G, et al. Single substitution in H3.3G34 alters DNMT3A recruitment to cause progressive neurodegeneration. Cell. 2023 Mar 16;186(6):1162-1178.e20. doi: 10.1016/j.cell.2023.02.023. PMID: 36931244; PMCID: PMC10112048.

Hamideh D, Das A, Bianchi V, Chung J, Negm L, Levine A, Basbous M, et al; International Replication Repair Deficiency Consortium (IRRDC). Using comprehensive genomic and functional analyses for resolving genotype-phenotype mismatches in children with suspected CMMRD in Lebanon: an IRRDC study. Hum Genet. 2023 Apr;142(4):563-576. doi: 10.1007/s00439-023-02530-8. Epub 2023 Feb 15. PMID: 36790526.

Lazure F, Farouni R, Sahinyan K, Blackburn DM, Hernández-Corchado A, Perron G, Lu T, Osakwe A, Ragoussis J, Crist C, et al. Transcriptional reprogramming of skeletal muscle stem cells by the niche environment. Nat Commun. 2023 Feb 1;14(1):535. doi: 10.1038/s41467-023-36265-x. PMID: 36726011; PMCID: PMC9892560.

Chen Y, Lu T, Pettersson-Kymmer U, Stewart ID, Butler-Laporte G, Nakanishi T, Cerani A, Liang KYH, Yoshiji S, Willett JDS, et al. Genomic atlas of the plasma metabolome prioritizes metabolites implicated in human diseases. Nat Genet. 2023 Jan;55(1):44-53. doi: 10.1038/s41588-022-01270-1. Epub 2023 Jan 12. PMID: 36635386; PMCID: PMC7614162.

Pellerin D, Danzi MC, Wilke C, Renaud M, Fazal S, Dicaire MJ, Scriba CK, Ashton C, Yanick C, Beijer D, et al. Deep Intronic FGF14 GAA Repeat Expansion in Late-Onset Cerebellar Ataxia. N Engl J Med. 2023 Jan 12;388(2):128-141. doi: 10.1056/NEJMoa2207406. Epub 2022 Dec 14. PMID: 36516086; PMCID: PMC10042577.

Jessa S, Mohammadnia A, Harutyunyan AS, Hulswit M, Varadharajan S, Lakkis H, Kabir N, Bashardanesh Z, Hébert S, Faury D, et al. K27M in canonical and noncanonical H3 variants occurs in distinct oligodendroglial cell lineages in brain midline gliomas. Nat Genet. 2022 Dec;54(12):1865-1880. doi: 10.1038/s41588-022-01205-w. Epub 2022 Dec 5. PMID: 36471070; PMCID: PMC9742294.

Holstege H, Hulsman M, Charbonnier C, Grenier-Boley B, Quenez O, Grozeva D, van Rooij JGJ, Sims R, Ahmad S, Amin N, et al. Exome sequencing identifies rare damaging variants in ATP8B4 and ABCA1 as risk factors for Alzheimer’s disease. Nat Genet. 2022 Dec;54(12):1786-1794. doi: 10.1038/s41588-022-01208-7. Epub 2022 Nov 21. PMID: 36411364; PMCID: PMC9729101.

Butler-Laporte G, Povysil G, Kosmicki JA, Cirulli ET, Drivas T, Furini S, Saad C, Schmidt A, Olszewski P, Korotko U, et al. Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative. PLoS Genet. 2022 Nov 3;18(11):e1010367. doi: 10.1371/journal.pgen.1010367. PMID: 36327219; PMCID: PMC9632827.

Li Y, Goldberg EM, Chen X, Xu X, McGuire JT, Leuzzi G, Karagiannis D, Tate T, Farhangdoost N, Horth C, Dai E, et al. Histone methylation antagonism drives tumor immune evasion in squamous cell carcinomas. Mol Cell. 2022 Oct 20;82(20):3901-3918.e7. doi: 0.1016/j.molcel.2022.09.007. Epub 2022 Oct 6. PMID: 36206767; PMCID: PMC9588679.

Mishra A, Malik R, Hachiya T, Jürgenson T, Namba S, Posner DC, Kamanu FK, Koido M, Le Grand Q, Shi M, et al. Stroke genetics informs drug discovery and risk prediction across ancestries. Nature. 2022 Nov;611(7934):115-123. doi: 10.1038/s41586-022-05165-3. Epub 2022 Sep 30. Erratum in: Nature. 2022 Dec;612(7938):E7. PMID: 36180795; PMCID: PMC9524349.

Hendrikse LD, Haldipur P, Saulnier O, Millman J, Sjoboen AH, Erickson AW, Ong W, Gordon V, Coudière-Morrison L, Mercier AL, et al. Failure of human rhombic lip differentiation underlies medulloblastoma formation. Nature. 2022 Sep;609(7929):1021-1028. doi: 10.1038/s41586-022-05215-w. Epub 2022 Sep 21. Erratum in: Nature. 2022 Dec;612(7940):E12. PMID: 36131014; PMCID: PMC10026724.

Nada D, Julien C, Papillon-Cavanagh S, Majewski J, Elbakry M, Elremaly W, Samuels ME, Moreau A. Identification of FAT3 as a new candidate gene for adolescent idiopathic scoliosis. Sci Rep. 2022 Jul 19;12(1):12298. doi: 10.1038/s41598-022-16620-6. PMID: 35853984; PMCID: PMC9296578.

Dubois FPB, Shapira O, Greenwald NF, Zack T, Wala J, Tsai JW, Crane A, Baguette A, Hadjadj D, Harutyunyan AS, et al. Structural variants shape driver combinations and outcomes in pediatric high-grade glioma. Nat Cancer. 2022 Aug;3(8):994-1011. doi: 10.1038/s43018-022-00403-z. Epub 2022 Jul 4. PMID: 35788723; PMCID: PMC10365847.

Nagano M, Hu B, Yokobayashi S, Yamamura A, Umemura F, Coradin M, Ohta H, Yabuta Y, Ishikura Y, Okamoto I, et al. Nucleome programming is required for the foundation of totipotency in mammalian germline development. EMBO J. 2022 Jul 4;41(13):e110600. doi: 10.15252/embj.2022110600. Epub 2022 Jun 15. PMID: 35703121; PMCID: PMC9251848.

Fava VM, Bourgey M, Nawarathna PM, Orlova M, Cassart P, Vinh DC, Cheng MP, Bourque G, Schurr E, Langlais D. A systems biology approach identifies candidate drugs to reduce mortality in severely ill patients with COVID-19. Sci Adv. 2022 Jun 3;8(22):eabm2510. doi: 10.1126/sciadv.abm2510. Epub 2022 Jun 1. PMID: 35648852; PMCID: PMC9159580.

Golbourn BJ, Halbert ME, Halligan K, Varadharajan S, Krug B, Mbah NE, Kabir N, Stanton AJ, Locke AL, Casillo SM, et al. Loss of MAT2A compromises methionine metabolism and represents a vulnerability in H3K27M mutant glioma by modulating the epigenome. Nat Cancer. 2022 May;3(5):629-648. doi: 10.1038/s43018-022-00348-3. Epub 2022 Apr 14. Erratum in: Nat Cancer. 2022 Jun 23;: PMID: 35422502; PMCID: PMC9551679.

Chen H, Hu B, Horth C, Bareke E, Rosenbaum P, Kwon SY, Sirois J, Weinberg DN, Robison FM, Garcia BA, et al. H3K36 dimethylation shapes the epigenetic interaction landscape by directing repressive chromatin modifications in embryonic stem cells. Genome Res. 2022 May;32(5):825-837. doi: 10.1101/gr.276383.121. Epub 2022 Apr 8. PMID: 35396277; PMCID: PMC9104706.

Moldoveanu D, Ramsay L, Lajoie M, Anderson-Trocme L, Lingrand M, Berry D, Perus LJM, Wei Y, Moraes C, Alkallas R, Rajkumar S, et al. Spatially mapping the immune landscape of melanoma using imaging mass cytometry. Sci Immunol. 2022 Apr;7(70):eabi5072. doi: 10.1126/sciimmunol.abi5072. Epub 2022 Apr 1. PMID: 35363543.

Tsang ES, Csizmok V, Williamson LM, Pleasance E, Topham JT, Karasinska JM, Titmuss E, Schrader I, Yip S, Tessier-Cloutier B, et al. Homologous recombination deficiency signatures in gastrointestinal and thoracic cancers correlate with platinum therapy duration. NPJ Precis Oncol. 2023 Mar 24;7(1):31. doi: 10.1038/s41698-023-00368-x. PMID: 36964191

Rondeau EB, Christensen KA, Minkley DR, Leong JS, Chan MTT, Despins CA, Mueller A, Sakhrani D, Biagi CA, Rougemont Q, et al. Population-size history inferences from the coho salmon (Oncorhynchus kisutch) genome. G3 (Bethesda). 2023 Feb 10:jkad033. Epub ahead of print. PMID: 36759939

Dixon K, Shen Y, O’Neill K, Mungall KL, Chan S, Bilobram S, Zhang W, Bezeau M, Sharma A, Fok A, et al. Defining the heterogeneity of unbalanced structural variation underlying breast cancer susceptibility by nanopore genome sequencing. Eur J Hum Genet. 2023 Feb 16. Epub ahead of print. PMID: 36797466

Akbari V, Hanlon CT, O’Neill K, Lefebvre L, Schrader KA, Lansdorp PM, Jones SJM. Parent-of-origin detection and chromosome-scale haplotyping using long-read DNA methylation sequencing and Strand-seq. Cell Genom. 2022 Dec 21;3(1):100233. PMID: 36777186

Arora R, Haynes L, Kumar M, McNeil R, Ashkani J, Nakoneshny SC, Matthews TW, Chandarana S, Hart RD, Jones SJM, et al. NCBP2 and TFRC are novel prognostic biomarkers in oral squamous cell carcinoma. Cancer Gene Ther. 2023 Jan 12. Epub ahead of print. PMID: 36635327

Rive CM, Yung E, Dreolini L, Brown SD, May CG, Woodsworth DJ, Holt RA. Selective B cell depletion upon intravenous infusion of replication-incompetent anti-CD19 CAR lentivirus. Mol Ther Methods Clin Dev. 2022 May 29;26:4-14. doi: 10.1016/j.omtm.2022.05.006. PMID: 35755944; PMCID: PMC9198363.

Akbari V, Garant JM, O’Neill K, Pandoh P, Moore R, Marra MA, Hirst M, Jones SJM. Genome-wide detection of imprinted differentially methylated regions using nanopore sequencing. Elife. 2022 Jul 5;11:e77898. PMID: 35787786

Gagalova KK, Warren RL, Coombe L, Wong J, Nip KM, Yuen MMS, Whitehill JGA, Celedon JM, Ritland C, Taylor GA, et al. Spruce giga-genomes: structurally similar yet distinctive with differentially expanding gene families and rapidly evolving genes. Plant J. 2022 Sep;111(5):1469-1485. PMID: 35789009

Coope RJN, Matic N, Pandoh PK, Corbett RD, Smailus DE, Pleasance S, Lowe CF, Ritchie G, Chorlton SD, Young M, et al. Automated Library Construction and Analysis for High-Throughput Nanopore Sequencing of SARS-CoV-2. J Appl Lab Med. 2022 Sep 1;7(5):1025-1036. PMID: 35723286

Yu IS, Wee K, Williamson L, Titmuss E, An J, Naderi-Azad S, Metcalf C, Yip S, Horst B, Jones SJM, et al. Exceptional response to combination ipilimumab and nivolumab in metastatic uveal melanoma: Insights from genomic analysis. Melanoma Res. 2022 Aug 1;32(4):278-285. PMID: 35726793

Pleasance E, Bohm A, Williamson LM, Nelson JMT, Shen Y, Bonakdar M, Titmuss E, Csizmok V, Wee K, Hosseinzadeh S, et al. Whole-genome and transcriptome analysis enhances precision cancer treatment options. Ann Oncol. 2022 Sep;33(9):939-949. PMID: 35691590

Lavoie JM, Csizmok V, Williamson LM, Culibrk L, Wang G, Marra MA, Laskin J, Jones SJM, Renouf DJ, Kollmannsberger CK. Whole-genome and transcriptome analysis of advanced adrenocortical cancer highlights multiple alterations affecting epigenome and DNA repair pathways. Cold Spring Harb Mol Case Stud. 2022 Apr 28;8(3):a006148. PMID: 35483882

Dodani DD, Nguyen MH, Morin RD, Marra MA, Corbett RD. Combinatorial and Machine Learning Approaches for Improved Somatic Variant Calling From Formalin-Fixed Paraffin-Embedded Genome Sequence Data. Front Genet. 2022 Apr 27;13:834764. doi: 10.3389/fgene.2022.834764. PMID: 35571031; PMCID: PMC9092826.

Stubbins RJ, Platzbecker U, Karsan A. Inflammation and myeloid malignancy: quenching the flame. Blood. 2022 Sept 8; 140(10):1067-1074. PMID: 35468199.

Cheng X, Liu Y, Wang J, Chen Y, Robertson AG, Zhang X, Jones SJM, Taubert S. cSurvival: a web resource for biomarker interactions in cancer outcomes and in cell lines. Brief Bioinform. 2022 Apr 2:bbac090. PMID: 35368077

Titmuss E, Milne K, Jones MR, Ng T, Topham JT, Brown SD, Schaeffer DF, Kalloger S, Wilson D, Corbett RD, et al. Immune Activation following Irbesartan Treatment in a Colorectal Cancer Patient: A Case Study. Int J Mol Sci. 2023 Mar 20;24(6):5869. PMID: 36982943

Thomas N, Dreval K, Gerhard DS, Hilton LK, Abramson JS, Ambinder RF, Barta S, Bartlett NL, Bethony J, Bhatia K, et al. Genetic subgroups inform on pathobiology in adult and pediatric Burkitt lymphoma. Blood. 2023 Feb 23;141(8):904-916. doi: 10.1182/blood.2022016534.

Topham JT, Tsang ES, Karasinska JM, Metcalfe A, Ali H, Kalloger SE, Csizmok V, Williamson LM, Titmuss E, Nielsen K, et al. Integrative analysis of KRAS wildtype metastatic pancreatic ductal adenocarcinoma reveals mutation and expression-based similarities to cholangiocarcinoma. Nat Commun. 2022 Oct 8;13(1):5941. PMID: 36209277