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2023-2024 publications

CGEn-Toronto

Combining Off-flow, a Nextflow-coded program, and whole genome sequencing reveals unintended genetic variation in CRISPR/Cas-edited iPSCs, Shum C, Han SY, Thiruvahindrapuram B, Wang Z, de Rijke J, et al., Computational and Structural Biotechnology Journal, 2024, 23: 638-647, DOI: 10.1016/j.csbj.2023.12.036. PMID: 38283851

Statistical Learning of Large-Scale Genetic Data: How to Run a Genome-Wide Association Study of Gene-Expression Data Using the 1000 Genomes Project Data, Sugolov A, Emmenegger E, Paterson AD, Sun L, et al., Stat Biosci, 2024, 16(1): 250-264, DOI: 10.1007/s12561-023-09375-9, PMID: 38495080.

Polygenic risk for triglyceride levels in the presence of a high impact rare variant, Ying S, Heung T, Thiruvahindrapuram B, Engchuan W, Yin Y, et al., BMC Med Genomics, 2023, 16(1): 281, DOI: 10.1186/s12920-023-01717-2, PMID: 37940981

Genome screening, reporting, and genetic counseling for healthy populations, Casalino S, Frangione E, Chung M, MacDonald G, Chowdhary S, et al., Human Genetics, 2023, 142: 181-192, DOI: 10.1007/s00439-022-02480-7, PMID: 36331656

Genome-wide enhancer-associated tandem repeats are expanded in cardiomyopathy, Mitina A, Khan M, Lesurf R, Yin Y, Engchuan W, et al., EBioMedicine, 2024, 101: 105027, DOI: 10.1016/j.ebiom.2024.105027, PMID: 38418263

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, et al., HGG Adv, 2022, 4(1): 100156, DOI: 10.1016/j.xhgg.2022.100156, PMID: 36386424

Germline TP53 mutations undergo copy number gain years prior to tumor diagnosis, Light N, Layeghifard M, Attery A, Subasri V, Zatzman M, et al., Nat Commun, 2023, 14(1): 77, DOI: 10.1038/s41467-022-35727-y, PMID: 36604421

Decreased left heart flow in fetal lambs causes left heart hypoplasia and pro-fibrotic tissue remodeling, Reuter MS, Sokolowski DJ, Diaz-Mejia JJ, Keunen J, de Vrijer B, et al., Commun Biol, 2023, 6(1): 770, DOI: 10.1038/s42003-023-05132-2, PMID: 37481629

A second update on mapping the human genetic architecture of COVID-19, COVID-19 Host Genetics Initiative, Nature, 2023, 621(7977): E7-E26, DOI: 10.1038/s41586-023-06355-3, PMID: 36604421

Schizophrenia-associated somatic copy-number variants from 12,834 cases reveal recurrent NRXN1 and ABCB11 disruptions, Maury EA, Sherman MA, Genovese G, Gilgenast TG, Kamath T, et al., Cell Genom, 2023, 3(8): 100356, DOI: 10.1016/j.xgen.2023.100356, PMID: 37601975

Gene copy number variation and pediatric mental health/neurodevelopment in a general population. Zarrei M, Burton CL, Engchuan W, Higginbotham EJ, Wei J, et al., Hum Mol Genet, 2023, 32(15): 2411-2421, DOI: 10.1093/hmg/ddad074, PMID: 37154571

Three generation families: Analysis of de novo variants in autism. Costa CIS, da Silva Campos G, da Silva Montenegro EM, Wang JYT, Scliar M, et al., Eur J Hum Genet, 2023, 31(9): 1017-1022, DOI: 10.1038/s41431-023-01398-6, PMID: 37280359

Genomic architecture of autism spectrum disorder in Qatar: The BARAKA-Qatar Study. Abdi M, Aliyev E, Trost B, Kohailan M, Aamer W, et al., Genome Med, 2023, 15(1): 81, DOI: 10.1186/s13073-023-01228-w, PMID: 37805537

Disruption of DDX53 coding sequence has limited impact on iPSC-derived human NGN2 neurons. Faheem M, Deneault E, Alexandrova R, Rodrigues DC, Pellecchia G, et al., BMC Med Genomics, 2023, 16(1): 5, DOI: 10.1186/s12920-022-01425-3, PMID: 36635662

HostSeq: a Canadian whole genome sequencing and clinical data resource. Yoo S, Garg E, Elliott LT, Hung RJ, Halevy AR, et al., BMC Genom Data, 2023, 24(1): 26, DOI: 10.1186/s12863-023-01128-3, PMID: 37131148

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, et al., Mol Psychiatry, 2023, 28(1): 475-482, DOI: 10.1038/s41380-022-01857-4, PMID: 36380236

A New Sturgeon Herpesvirus from Juvenile Lake Sturgeon Acipenser fulvescens Displaying Epithelial Skin Lesions. Clouthier S, Tomczyk M, Schroeder T, Klassen C, Dufresne A, et al., Pathogens, 2023, 12(9): 1115, DOI: 10.3390/pathogens12091115, PMID: 37764923

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, et al., Hum Genet, 2023, 142(2): 201-216, DOI: 10.1007/s00439-022-02494-1, PMID: 36376761

Characterization of pharmacogenomic variants in a Brazilian admixed cohort of elderly individuals based on whole-genome sequencing data. Bertholim-Nasciben L, Scliar MO, Debortoli G, Thiruvahindrapuram B, Scherer SW, et al., Front Pharmacol, 2023, 14: 1178715, DOI: 10.3389/fphar.2023.1178715, PMID: 37234706

The clinical utility of integrative genomics in childhood cancer extends beyond targetable mutations. Villani A, Davidson S, Kanwar N, Lo WW, Li Y, et al., Nat Cancer, 2023, 4(2): 203-221, DOI: 10.1038/s43018-022-00474-y, PMID: 36585449

The Phenotypic variability of 16p11.2 distal BP2-BP3 deletion in a transgenerational family and in neurodevelopmentally ascertained samples. Woodbury-Smith M, D’Abate L, Stavropoulos DJ, Howe J, Drmic I, et al., J Med Genet, 2023, 60(12): 1153-1160, DOI: 10.1136/jmg-2022-108818, PMID: 37290907

SHP2 Inhibition with TNO155 Increases Efficacy and Overcomes Resistance of ALK Inhibitors in Neuroblastoma. Valencia-Sama I, Kee L, Christopher G, Ohh M, Layeghifard M, et al., Cancer Res Commun, 2023, 3(12): 2608-2622, DOI: 10.1158/2767-9764.CRC-23-0234, PMID: 38032104

The BRD4-NUT Fusion Alone Drives Malignant Transformation of NUT Carcinoma. Durall RT, Huang J, Wojenski L, Huang Y, Gokhale PC, et al., Cancer Res, 2023, 83(23): 3846-3860, DOI: 10.1158/0008-5472.CAN-23-2545, PMID: 37819236

Genomic Microsatellite Signatures Identify Germline Mismatch Repair Deficiency and Risk of Cancer Onset. Chung J, Negm L, Bianchi V, Stengs L, Das A, et al., J Clin Oncol, 2023, 41(4): 766-777, DOI: 10.1200/JCO.21.02873, PMID: 36240479

Myeloproliferative Neoplasm Driven by ETV6-ABL1 in an Adolescent with Recent History of Burkitt Leukemia. Renzi S, Algawahmed F, Davidson S, Langenberg KPS, Fuligni F, et al., Curr Oncol, 2023, 30(7): 5946-5952, DOI: 10.3390/curroncol30070444, PMID: 37503586

Spontaneous expression of the CIC::DUX4 fusion oncoprotein from a conditional allele potently drives sarcoma formation in genetically engineered mice, Hendrickson PG, Oristian KM, Browne MR, Luo L, Ma Y, et al., Oncogene, 2024, 43(16): 1223-1230, DOI: 10.1038/s41388-024-02984-8, PMID: 38413794

BARD1 germline variants induce haploinsufficiency and DNA repair defects in neuroblastoma, Randall MP, Egolf LE, Vaksman Z, Samanta M, Tsang M, et al., J Natl Cancer Inst, 2024, 116(1): 138-148, DOI: 10.1093/jnci/djad182, PMID: 37688570

Increased burden of rare protein-truncating variants in constrained, brain-specific and synaptic genes in extremely impulsively violent males with antisocial personality disorder, Mušálková D, Přistoupilová A, Jedličková I, Hartmannová H, Trešlová H, et al., Genes Brain Behav, 2024, 23(1): e12882, DOI: 10.1111/gbb.12882, PMID: 38359179

The development of the pediatric stroke neuroimaging platform (PEDSNIP), Domi T, Robertson A, Lee W, Wintle RF, Stence N, et al., Neuroimage Clin, 2023, 39: 103438, DOI: 10.1016/j.nicl.2023.103438, PMID: 37354865

Survival-based CRISPR genetic screens across a panel of permissive cell lines identify common and cell-specific SARS-CoV-2 host factors, Chan K, Granda Farias A, Lee H, Guvenc F, Mero P, et al., Heliyon, 2023, 9(1): e12744, DOI: 10.1016/j.heliyon.2022.e12744, PMID: 36597481

Comprehensive whole-genome sequence analyses provide insights into the genomic architecture of cerebral palsy, Fehlings DL, Zarrei M, Engchuan W, Sondheimer N, Thiruvahindrapuram B, et al., Nat Genet, 2024, 56(4): 585-594, DOI: 10.1038/s41588-024-01686-x, PMID: 38553553

Clinical actionability of genetic findings in cerebral palsy, Lewis SA, Chopra M, Cohen JS, Bain J, Aravamuthan B, et al., medRxiv [Preprint], 2023, DOI: 10.1101/2023.09.08.23295195, PMID: 37745357

Genetic variants in DDX53 contribute to Autism Spectrum Disorder associated with the Xp22.11 locus, Scala M, Bradley CA, Howe JL, Trost B, Salazar NB, et al., medRxiv [Preprint], 2023, DOI: 10.1101/2023.12.21.23300383, PMID: 38234782

ArHsp90 is important in stress tolerance and embryo development of the brine shrimp, Artemia franciscana, Fatani A, Wu X, Gbotsyo Y, MacRae TH, Song X, et al., Cell Stress Chaperones, 2024, 29(2): 285-299, DOI: 10.1016/j.cstres.2024.02.004, PMID: 38428516

Using whole genome sequence findings to assess gene-disease causality in cardiomyopathy and arrhythmia patients, Krishnan AR, Schwartz ML, Somerville C, Ding Q, Kim RH, et al., Future Cardiol, 2023, 19(12): 583-592, DOI: 10.2217/fca-2023-0082, PMID: 37830358

Identification of a novel NFKB2 mutation in a patient presenting with autoimmune cytopenia and generalized granulomatous lymphadenopathy, Al Ghamdi A, Sham M, Abrego Fuentes L, Vong L, LymphoSign Journal, 2023, 10(1): 7-14, DOI: 10.14785/lymphosign-2023-0001

Large, Nested Variant of Urothelial Carcinoma Is Enriched with Activating Mutations in Fibroblast Growth Factor Receptor-3 among Other Targetable Mutations, Gamallat Y, Afsharpad M, El Hallani S, Maher CA, Alimohamed N, et al., Cancers (Basel), 2023, 15(12): 3167, DOI: 10.3390/cancers15123167, PMID: 37370778

Glucocorticoid exposure modifies the miRNA profile of sperm in the guinea pig: Implications for intergenerational transmission, Casciaro C, Hamada H, Kostaki A, Matthews SG, FASEB J, 2023, 37(4): e22879, DOI: 10.1096/fj.202201784R, PMID: 36928999

Reprogramming of Acute Myeloid Leukemia Patients Cells: Harboring Cancer Mutations Requires Targeting of AML Hierarchy, Golubeva D, Porras DP, Doyle M, Reid JC, Tanasijevic B, et al., Stem Cells Transl Med, 2023, 12(6): 334-354, DOI: 10.1093/stcltm/szad022, PMID: 37226319

The development and characterization of a CRISPR/Cas9-mediated PD-1 functional knockout rat as a tool to study idiosyncratic drug reactions, Cho T, Wierk A, Gertsenstein M, Rodgers CE, Uetrecht J, et al., Toxicol Sci, 2024, 198(2): 233-245, DOI: 10.1093/toxsci/kfae003, PMID: 38230816

A homozygous stop codon in HORMAD2 in a patient with recurrent digynic triploid miscarriage, Liang M, Suresh B, Bareke E, Choufani S, Jagadeesh S, et al., Mol Genet Genomic Med, 2024, 12(2): e2402, DOI: 10.1002/mgg3.2402, PMID: 38400599

Missense variant in SRCAP with distinct DNA methylation signature associated with non-FLHS SRCAP-related neurodevelopmental disorder, White-Brown A, Choufani S, Care4Rare Canada Consortium, Weksberg R, Dyment D, Am J Med Genet A, 2023, 191(10): 2640-2646, DOI: 10.1002/ajmg.a.63329, PMID: 37340855

Overexpression of FRA1 (FOSL1) Leads to Global Transcriptional Perturbations, Reduced Cellular Adhesion and Altered Cell Cycle Progression, Al-Khayyat W, Pirkkanen J, Dougherty J, Laframboise T, Dickinson N, et al., Cells, 2023, 12(19): 2344, DOI: 10.3390/cells12192344, PMID: 37830558

Identification of novel compound heterozygous LRBA mutations associated with recurrent hemophagocytic lymphohistiocytosis and CNS manifestations, Sham M, Merico D, Pereira M, Roifman CM, Roifman M, LymphoSign Journal, 2023, 10(1): 20-26, DOI: 10.14785/lymphosign-2023-0004

Palmitate alters miR-2137 and miR-503-5p to induce orexigenic Npy in hypothalamic neuronal cell models: Rescue by oleate and docosahexaenoic acid, McIlwraith EK, Belsham DD, J Neuroendocrinol, 2023, 35(5): e13271, DOI: 10.1111/jne.13271, PMID: 37208960

Nectary development in Cleome violacea, Carey S, Zenchyzen B, Deneka AJ, Hall JC, Front Plant Sci, 2023, 13: 1085900, DOI: 10.3389/fpls.2022.1085900, PMID: 36844906

Genomic divergence and introgression between cryptic species of a widespread North American songbird, Askelson KK, Spellman GM, Irwin D, Mol Ecol, 2023, 32(24): 6839-6853, DOI: 10.1111/mec.17169, PMID: 37916530

Active microbiota persist in dry permafrost and active layer from Elephant Head, Antarctica, Wood C, Bruinink A, Trembath-Reichert E, Wilhelm MB, Vidal C, et al., ISME Commun, 2024, 4(1): ycad002, DOI: 10.1093/ismeco/ycad002, PMID: 38304082

Increased sensitivity to chemically induced colitis in mice harboring a DNA-binding deficient aryl hydrocarbon receptor, Alvik K, Shao P, Hutin D, Baglole C, Grant DM, Matthews J, Toxicol Sci, 2023, 191(2): 321-331, DOI: 10.1093/toxsci/kfac132, PMID: 36519841

ANKRD11 pathogenic variants and 16q24.3 microdeletions share an altered DNA methylation signature in patients with KBG syndrome, Awamleh Z, Choufani S, Cytrynbaum C, Alkuraya FS, Scherer S, et al., Hum Mol Genet, 2023, 32(9): 1429-1438, DOI: 10.1093/hmg/ddac289, PMID: 36440975

The human Stat1 gain-of-function T385M mutation causes expansion of activated T-follicular helper/T-helper 1-like CD4 T cells and sex-biased autoimmunity in specific pathogen-free mice, Scott O, Visuvanathan S, Reddy E, Mahamed D, Gu B, et al., Front Immunol, 2023, 14: 1183273, DOI: 10.3389/fimmu.2023.1183273, PMID: 37275873

Surface material of acoustic transmitters influences the inflammatory response of rainbow trout (Oncorhynchus mykiss) during long-term implantation, Heath G, Semple SL, Rodríguez-Ramos T, Hardy S, Harrison P, et al., Vet Immunol Immunopathol, 2023, 264: 110660, DOI: 10.1016/j.vetimm.2023.110660, PMID: 37820428

Polygenic risk scores analyses of psychiatric and metabolic traits with antipsychotic-induced weight gain in schizophrenia: an exploratory study, Yoshida K, Marshe VS, Elsheikh SSM, Maciukiewicz M, Tiwari AK, et al., Pharmacogenomics J, 2023, 23(5): 119-126, DOI: 10.1038/s41397-023-00305-y, PMID: 37106021

Effects of temperature on food intake and the expression of appetite regulators in three Characidae fish: The black-skirted tetra (Gymnocorymbus ternetzi), neon tetra (Paracheirodon innesi), and Mexican cavefish (Astyanax mexicanus), Kuhn J, Azari S, Volkoff H, Comp Biochem Physiol A Mol Integr Physiol, 2023, 275: 111333, DOI: 10.1016/j.cbpa.2022.111333, PMID: 36244591

LncRNAs exhibit subtype-specific expression, survival associations, and cancer-promoting effects in breast cancer, Wasson MC, Venkatesh J, Cahill HF, McLean ME, Dean CA, et al., Gene, 2024, DOI: 10.1016/j.gene.2024.148165, PMID: 38219875

EZH2 and matrix co-regulate phenotype and KCNB2 expression in bladder smooth muscle cells, Yadav P, Ahmed T, Park S, Sidler M, Schröder A, et al., Am J Clin Exp Urol, 2023, 11(4): 293-303, DOI: 10.1093/ajceu/kfad002, PMID: 37645613

Reduced kinase function in two ultra-rare TNNI3K variants in families with congenital junctional ectopic tachycardia, Pham C, Koopmann TT, Vinocur JM, Blom NA, Silbiger VN, et al., Clin Genet, 2024, 106(1): 37-46, DOI: 10.1111/cge.14504, PMID: 38424693

Diploid and triploid Chinook salmon (Oncorhynchus tshawytscha) have altered microRNA responses in immune tissues after infection with Vibrio anguillarum, Cadonic IG, Heath JW, Dixon B, Craig PM, Comp Biochem Physiol Part D Genomics Proteomics, 2023, 48: 101121, DOI: 10.1016/j.cbd.2023.101121, PMID: 37634278

Genomic heterozygosity is associated with a lower risk of osteoarthritis, Gill R, Liu M, Sun G, Furey A, Spector T, et al., BMC Genomics, 2024, 25(1): 85, DOI: 10.1186/s12864-024-10015-9, PMID: 38245676

FBXW7-loss Sensitizes Cells to ATR Inhibition Through Induced Mitotic Catastrophe, O’Brien S, Ubhi T, Wolf L, Gandhi K, Lin S, et al., Cancer Res Commun, 2023, 3(12): 2596-2607, DOI: 10.1158/2767-9764.CRC-23-0306, PMID: 38032106

Folate receptor targeted nanoparticles containing niraparib and doxorubicin as a potential candidate for the treatment of high grade serous ovarian cancer, Wang L, Evans JC, Ahmed L, Allen C, Sci Rep, 2023, 13(1): 3226, DOI: 10.1038/s41598-023-28424-3, PMID: 36828860

Multiplatform molecular profiling uncovers two subgroups of malignant peripheral nerve sheath tumors with distinct therapeutic vulnerabilities, Suppiah S, Mansouri S, Mamatjan Y, Liu JC, Bhunia M, et al., Nat Commun, 2023, 14(1): 2696, DOI: 10.1038/s41467-023-38432-6, PMID: 37164978

Peripheral blood DNA methylation and neuroanatomical responses to HDACi treatment that rescues neurological deficits in a Kabuki syndrome mouse model, Goodman SJ, Romeo Luperchio T, Ellegood J, Chater-Diehl E, Lerch JP, et al., Clin Epigenetics, 2023, 15(1): 172, DOI: 10.1186/s13148-023-01582-x, PMID: 37884963

Genomic population structure and inbreeding history of Lake Superior caribou, Puckett EE, Johnson AJ, Robinson Z, Deacy WT, Fish NA, et al., Ecol Evol, 2023, 13(10): e10278, DOI: 10.1002/ece3.10278

High-throughput phenotyping of infection by diverse microsporidia species reveals a wild C. elegans strain with opposing resistance and susceptibility traits, Mok C, Xiao MA, Wan YC, Zhao W, Ahmed SM, et al., PLoS Pathog, 2023, 19(3): e1011225, DOI: 10.1371/journal.ppat.1011225, PMID: 36893187

A systematic evaluation of normalization methods and probe replicability using infinium EPIC methylation data, Welsh H, Batalha CMPF, Li W, Mpye KL, Souza-Pinto NC, Naslavsky MS, Parra EJ, Clin Epigenetics, 2023, 15(1): 41, DOI: 10.1186/s13148-023-01459-z, PMID: 36906598

Developmental and genetic basis of the androgynophore in Gynandropsis gynandra, Zenchyzen B, Carey S, Antochi-Crihan G, Hall JC, Am J Bot, 2023, 110(7): e16193, DOI: 10.1002/ajb2.16193, PMID: 37210747

Complex Autism Spectrum Disorder in a Patient with a Novel De Novo Heterozygous MYT1L Variant, Yip S, Calli K, Qiao Y, Trost B, Scherer SW, et al., Genes (Basel), 2023, 14(12): 2122, DOI: 10.3390/genes14122122, PMID: 38136944

CRISPR-resolved virus-host interactions in a municipal landfill include non-specific viruses, hyper-targeted viral populations, and interviral conflicts, George NA, Hug LA, Sci Rep, 2023, 13(1): 5611, DOI: 10.1038/s41598-023-32078-6, PMID: 37019939

Taxonomy and nomenclature of Oophila amblystomatis (Chlorophyceae, Chlamydomonadales), Bishop CD, Garbary DJ, J Phycol, 2024, 60(2): 380-386, DOI: 10.1111/jpy.13430, PMID: 38224483

Optimization of differential filtration-based mitochondrial isolation for mitochondrial transplant to cerebral organoids, Bodenstein DF, Powlowski P, Zachos KA, El Soufi El Sabbagh D, Jeong H, et al., Stem Cell Res Ther, 2023, 14(1): 202, DOI: 10.1186/s13287-023-03436-y, PMID: 37580812

The impact of elevated sulfur and nitrogen levels on cadmium tolerance in Euglena species, Kennedy V, Kaszecki E, Donaldson ME, Saville BJ, Sci Rep, 2024, 14(1): 11734, DOI: 10.1038/s41598-024-61964-w, PMID: 38777815

Investigating nitrogen movement in North Pacific spiny dogfish (Squalus acanthias suckleyi), with focus on UT, Rhp2, and Rhbg mRNA abundance, Hoogenboom JL, Anderson WG, J Comp Physiol B, 2023, 193(4): 439-451, DOI: 10.1007/s00360-023-01487-4, PMID: 37162540

Multimodal CRISPR perturbations of GWAS loci associated with coronary artery disease in vascular endothelial cells, Wünnemann F, Fotsing Tadjo T, Beaudoin M, Lalonde S, Lo KS, et al., PLoS Genet, 2023, 19(3): e1010680, DOI: 10.1371/journal.pgen.1010680, PMID: 36928188

Estimating the proportion of nonsense variants undergoing the newly described phenomenon of manufactured splice rescue, Haque B, Cheerie D, Birkadze S, Xu AL, Nalpathamkalam T, et al., Eur J Hum Genet, 2024, 32(2): 238-242, DOI: 10.1038/s41431-023-01495-6, PMID: 38012313

Palmitate alters miRNA content of small extracellular vesicles secreted from NPY/AgRP-expressing hypothalamic neurons, McIlwraith EK, Belsham DD, Brain Res, 2023, 1810: 148367, DOI: 10.1016/j.brainres.2023.148367, PMID: 37054963

Combined anti-S1 and anti-S2 antibodies from hybrid immunity elicit potent cross-variant ADCC against SARS-CoV-2, Grant MD, Bentley K, Fielding CA, Hatfield KM, Ings DP, et al., JCI Insight, 2023, 8(15): e170681, DOI: 10.1172/jci.insight.170681, PMID: 37338994

Combined Immunotherapy Improves Outcome for Replication-Repair-Deficient (RRD) High-Grade Glioma Failing Anti-PD-1 Monotherapy: A Report from the International RRD Consortium, Das A, Fernandez NR, Levine A, Bianchi V, Stengs L, et al., Cancer Discov, 2024, 14(2): 258-273, DOI: 10.1158/2159-8290.CD-23-0559, PMID: 37823831

A new blood DNA methylation signature for Koolen-de Vries syndrome: Classification of missense KANSL1 variants and comparison to fibroblast cells, Awamleh Z, Choufani S, Wu W, Rots D, Dingemans AJM, et al., Eur J Hum Genet, 2024, 32(3): 324-332, DOI: 10.1038/s41431-024-01538-6, PMID: 38282074

Linkage of whole genome sequencing and administrative health data in autism: A proof of concept study, Baribeau DA, Arneja J, Wang X, Howe J, McLaughlin JR, et al., Autism Res, 2023, 16(8): 1600-1608, DOI: 10.1002/aur.2999, PMID: 37526168

Longitudinal analysis of the intestinal microbiota among children in rural and urban areas of Pakistan, Veeraraghavan Balaji, Dinh DM, Kane AV, Soofi S, Ahmed I, et al., Nutrients, 2023, 15(5): 1213, DOI: 10.3390/nu15051213, PMID: 36904212

Identification of druggable regulators of cell secretion via a kinome-wide screen and high-throughput immunomagnetic cell sorting, Labib M, Wang Z, Kim Y, Lin S, Abdrabou A, et al., Nat Biomed Eng, 2024, 8(3): 263-277, DOI: 10.1038/s41551-023-01135-w, PMID: 38012306

A cell-based optimized approach for rapid and efficient gene editing of human pluripotent stem cells, Cuevas-Ocaña S, Yang JY, Aushev M, Schlossmacher G, Bear CE, et al., Int J Mol Sci, 2023, 24(12): 10266, DOI: 10.3390/ijms241210266, PMID: 37373413

MATR3 pathogenic variants differentially impair its cryptic splicing repression function, Khan M, Chen XXL, Dias M, Santos JR, Kour S, et al., FEBS Lett, 2024, 598(4): 415-436, DOI: 10.1002/1873-3468.14806, PMID: 38320753

Hedgehog signalling in Foxd1+ embryonic kidney stromal progenitors controls nephron formation via Cxcl12 and Wnt5a, D’Cruz R, Kim YK, Mulder J, Ibeh N, Jiang N, et al., J Pathol, 2023, 261(4): 385-400, DOI: 10.1002/path.6195, PMID: 37772431

Structural and functional insights into the delivery of a bacterial Rhs pore-forming toxin to the membrane, González-Magaña A, Tascón I, Altuna-Alvarez J, Queralt-Martín M, Colautti J, et al., Nat Commun, 2023, 14(1): 7808, DOI: 10.1038/s41467-023-43585-5, PMID: 38016939

Rare de novo gain-of-function missense variants in DOT1L are associated with developmental delay and congenital anomalies, Nil Z, Deshwar AR, Huang Y, Barish S, Zhang X, et al., Am J Hum Genet, 2023, 110(11): 1919-1937, DOI: 10.1016/j.ajhg.2023.09.009, PMID: 37827158

Glycoside hydrolase processing of the Pel polysaccharide alters biofilm biomechanics and Pseudomonas aeruginosavirulence, Razvi E, Whitfield GB, Reichhardt C, Dreifus JE, Willis AR, et al., NPJ Biofilms Microbiomes, 2023, 9(1): 7, DOI: 10.1038/s41522-023-00375-7, PMID: 36732330

Angiopoietin-1 derived peptide hydrogel promotes molecular hallmarks of regeneration and wound healing in dermal fibroblasts, Vizely K, Wagner KT, Mandla S, Gustafson D, Fish JE, Radisic M, iScience, 2023, 26(2): 105984, DOI: 10.1016/j.isci.2023.105984, PMID: 36818306

Loss of Mtm1 causes cholestatic liver disease in a model of X-linked myotubular myopathy, Karolczak S, Deshwar AR, Aristegui E, Kamath BM, Lawlor MW, et al., J Clin Invest, 2023, 133(18): e166275, DOI: 10.1172/JCI166275, PMID: 37490339

Transcriptomic classes of BCR-ABL1 lymphoblastic leukemia, Kim JC, Chan-Seng-Yue M, Ge S, Zeng AGX, Ng K, et al., Nat Genet, 2023, 55(7): 1186-1197, DOI: 10.1038/s41588-023-01429-4, PMID: 37337105

High genetic load without purging in caribou, a diverse species at risk, Taylor RS, Manseau M, Keobouasone S, Liu P, Mastromonaco G, et al., Curr Biol, 2024, 34(6): 1234-1246.e7, DOI: 10.1016/j.cub.2024.02.002, PMID: 38417444

Conserved transcriptional programming across sex and species after peripheral nerve injury predicts treatments for neuropathic pain, Ghazisaeidi S, Muley MM, Tu Y, Finn DP, Kolahdouzan M, et al., Br J Pharmacol, 2023, 180(21): 2822-2836, DOI: 10.1111/bph.16168, PMID: 37336547

GWAS of biological aging to find longevity genes in schizophrenia, Qian J, Fischer C, Burhan A, Mak M, Gerretsen P, et al., Eur Arch Psychiatry Clin Neurosci, 2024, 274(5): 1025-1036, DOI: 10.1007/s00406-023-01622-w, PMID: 37420032

Buffering of transcription rate by mRNA half-life is a conserved feature of Rett syndrome models, Rodrigues DC, Mufteev M, Yuki KE, Narula A, Wei W, et al., Nat Commun, 2023, 14(1): 1896, DOI: 10.1038/s41467-023-37339-6, PMID: 37019888

Genomic and phenotypic evolution of nematode-infecting microsporidia, Wadi L, El Jarkass HT, Tran TD, Islah N, Luallen RJ, Reinke AW, PLoS Pathog, 2023, 19(7): e1011510, DOI: 10.1371/journal.ppat.1011510, PMID: 37471459

Prevention of early-onset cardiomyopathy in Dmd exon 52-54 deletion mice by CRISPR-Cas9-mediated exon skipping, Rok M, Wong TWY, Maino E, Ahmed A, Yang G, et al., Mol Ther Methods Clin Dev, 2023, 30: 246-258, DOI: 10.1016/j.omtm.2023.07.004, PMID: 37545481

Arabidopsis Calmodulin-like Proteins CML13 and CML14 Interact with Calmodulin-Binding Transcriptional Activators and Function in Salinity Stress Response, Hau B, Symonds K, Teresinski H, Janssen A, Duff L, et al., Plant Cell Physiol, 2024, 65(2): 282-300, DOI: 10.1093/pcp/pcad152, PMID: 38036467

The P-body protein 4E-T represses translation to regulate the balance between cell genesis and the establishment of the postnatal neural stem cell (NSC) pool, Kolaj A, Zahr SK, Wang BS, Krawec T, Kazan H, et al., Cell Rep, 2023, 42(3): 112242, DOI: 10.1016/j.celrep.2023.112242, PMID: 36924490

Membrane contact site detection (MCS-DETECT) reveals dual control of rough mitochondria-ER contacts, Cardoen B, Vandevoorde KR, Gao G, Ortiz-Silva M, Alan P, et al., J Cell Biol, 2024, 223(1): e202206109, DOI: 10.1083/jcb.202206109, PMID: 37948126

Genomic analyses in Cornelia de Lange Syndrome and related diagnoses: Novel candidate genes, genotype-phenotype correlations and common mechanisms, Kaur M, Blair J, Devkota B, Fortunato S, Clark D, et al., Am J Med Genet A, 2023, 191(8): 2113-2131, DOI: 10.1002/ajmg.a.63247, PMID: 37377026

Dominant negative variants in IKZF2 cause ICHAD syndrome, characterized by immunodysregulation, craniofacial anomalies, hearing impairment, athelia, and developmental delay, Mohajeri A, Vaseghi-Shanjani M, Rosenfeld JA, Yang GX, Lu H, et al., J Med Genet, 2023, 60(11): 1092-1104, DOI: 10.1136/jmg-2022-109127, PMID: 37316189

Multiple germline events contribute to cancer development in patients with Li-Fraumeni syndrome, Subasri V, Light N, Kanwar N, Brzezinski J, Luo P, et al., Cancer Res Commun, 2023, 3(5): 738-754, DOI: 10.1158/2767-9764.CRC-22-0402, PMID: 37377903

Construction of copy number variation landscape and characterization of associated genes in a Bangladeshi cohort of neurodevelopmental disorders, Akter H, Rahman MM, Sarker S, Basiruzzaman M, Islam MM, et al., Front Genet, 2023, 14: 955631, DOI: 10.3389/fgene.2023.955631, PMID: 36959829

Early postnatal defects in neurogenesis in the 3xTg mouse model of Alzheimer’s disease, Liu Y, Bilen M, McNicoll MM, Harris RA, Fong BC, et al., Cell Death Dis, 2023, 14(2): 138, DOI: 10.1038/s41419-023-05650-1, PMID: 36801910

Mapping the conformational landscape of the stimulatory heterotrimeric G protein, Huang SK, Picard LP, Rahmatullah RSM, et al., Nat Struct Mol Biol, 2023, 30: 502–511, DOI: 10.1038/s41594-023-00957-1

CD142 identifies neoplastic desmoid tumor cells, uncovering interactions between neoplastic and stromal cells that drive proliferation, Al-Jazrawe M, Xu S, Poon R, Wei Q, Przybyl J, et al., Cancer Res Commun, 2023, 3(4): 697-708, DOI: 10.1158/2767-9764.CRC-22-0403, PMID: 37377751

Boring Bivalves: Using molecular phylogenetics to resolve species identities in Botula (Mytilidae), Hayes SK, Rawlings TA, Bieler R, American Malacological Bulletin, 2023, 40(1): 1-17, DOI: 10.4003/006.040.0102

Directed differentiation of human hindbrain neuroepithelial stem cells recapitulates cerebellar granule neurogenesis, Dave BM, Chen X, McCready F, Charton CS, Morley RM, et al., Development, 2023, 150(13): dev201534, DOI: 10.1242/dev.201534, PMID: 37381820

Dynamic change in genome-wide methylation in response to increased suicidal ideation in schizophrenia spectrum disorders, Al-Chalabi N, Qian J, Gerretsen P, Chaudhary Z, Fischer C, et al., J Neural Transm (Vienna), 2023, 130(10): 1303-1313, DOI: 10.1007/s00702-023-02661-2, PMID: 37584690

Analysis of prognostic germline polymorphisms in patients with advanced hepatocellular carcinoma, Herman M, Lok BH, Gallinger S, Dawson L, Kim R, et al., Transl Gastroenterol Hepatol, 2023, 8: 32, DOI: 10.21037/tgh-23-22, PMID: 38021355

Small molecule inhibition of an exopolysaccharide modification enzyme is a viable strategy to block Pseudomonas aeruginosa Pel biofilm formation, Razvi E, DiFrancesco BR, Wasney GA, Morrison ZA, Tam J, et al., Microbiol Spectr, 2023, 11(3): e0029623, DOI: 10.1128/spectrum.00296-23, PMID: 37098898

Trio-whole exome and whole genome sequencing in fetal central nervous system anomalies, Gershon A, Anandampillai T, Arshad M, Martin N, Stavropoulos J, Noor A, Genetics in Medicine Open, 2024, Volume 2, Article 101677, DOI: 10.1016/j.gimo.2024.101677

Droplet-based proteomics reveals CD36 as a marker for progenitors in mammary basal epithelium, Waas M, Khoo A, Tharmapalan P, McCloskey CW, Govindarajan M, et al., Cell Rep Methods, 2024, 4(4): 100741, DOI: 10.1016/j.crmeth.2024.100741, PMID: 38569541

Anoxygenic phototroph of the Chloroflexota uses a type I reaction centre, Tsuji JM, Shaw NA, Nagashima S, Venkiteswaran JJ, Schiff SL, et al., Nature, 2024, 627(8005): 915-922, DOI: 10.1038/s41586-024-07180-y, PMID: 38480893

Biallelic EPCAM deletions induce tissue-specific DNA repair deficiency and cancer predisposition, Forster VJ, Aronson M, Zhang C, Chung J, Sudhaman S, et al., NPJ Precis Oncol, 2024, 8(1): 69, DOI: 10.1038/s41698-024-00537-6, PMID: 38467830

Nearshore fish diversity changes with sampling method and human disturbance: Comparing eDNA metabarcoding and seine netting along the Upper St. Lawrence River, Maracle SR, Tournayre O, Windle MJS, Cormier E, Schwartz K, et al., J Great Lakes Res, 2024, 50(3): 102317, DOI: 10.1016/j.jglr.2024.102317

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A syngeneic spontaneous zebrafish model of tp53-deficient, EGFRvIII, and PI3KCAH1047R-driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapse in vivo, Weiss A, D’Amata C, Pearson BJ, Hayes MN, eLife, 2024, DOI: 10.7554/eLife.93077, PMID: 39052000

Transcriptional buffering and 3’UTR lengthening are shaped during human neurodevelopment by shifts in mRNA stability and microRNA load, Mufteev M, Rodrigues DC, Yuki KE, Narula A, Wei W, et al., bioRxiv, 2023, Preprint, DOI: 10.1101/2023.03.01.530249

A reproducible approach for the use of aptamer libraries for the identification of Aptamarkers for brain amyloid deposition based on plasma analysis, Meehan C, Lecocq S, Penner G, bioRxiv, 2023, Preprint, DOI: 10.1101/2023.09.11.557220

Brain development mutations in the β-tubulin TUBB result in defective ciliogenesis, Mollica A, Omer S, Evagelou SL, Naumenko S, Li LY, et al., medRxiv, 2023, Preprint, DOI: 10.1101/2023.05.23.23290232

A flexible transgene integration ‘landing-pad’ toolkit in human induced pluripotent stem cells enables facile cellular engineering, gene zygosity control, and parallel transgene integration, Rosenstein AH, Nguyen M, Al-Attar R, Serra D, Gulati N, et al., bioRxiv, 2023, Preprint, DOI: 10.1101/2023.03.03.531057

Age, sex, and cell type-resolved hypothalamic gene expression across the pubertal transition in mice, Sokolowski DJ, Hou H, Yuki KE, Roy A, Chan C, et al., bioRxiv, 2023, Preprint, DOI: 10.1101/2023.10.12.562121

A Cas9-fusion proximity-based approach generates an Irak1-Mecp2 tandem duplication mouse model for the study of MeCP2 duplication syndrome, Maino E, Scott O, Rizvi SZ, Visuvanathan S, Ben Zablah Y, et al., bioRxiv, 2023, Preprint, DOI: 10.1101/2023.02.07.527511

Generation and characterization of a novel mouse model of Becker Muscular Dystrophy with a deletion of exons 52 to 55, Perillat LOM, Wong TWY, Maino E, Ahmed A, Scott O, et al., bioRxiv, 2023, Preprint, DOI: 10.1101/2023.11.16.567440

A genome wide CRISPR screen reveals that HOXA9 promotes Enzalutamide resistance in prostate cancer, Roes MV, Dick FA, bioRxiv, 2023, Preprint, DOI: 10.1101/2023.12.15.571833

Droplet based low input proteomic platform for rare cell populations, Waas M, Khoo A, Tharmapalan P, McCloskey CW, Govindarajan M, et al., bioRxiv, 2023, Preprint, DOI: 10.1101/2023.09.11.557098

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Single-nucleus profiling identifies accelerated oligodendrocyte precursor cell senescence in a mouse model of Down syndrome, Rusu B, Kukreja B, Wu T, Dan SJ, Feng MY, Kalish BT, eNeuro, 2023, 10(8): ENEURO.0147-23.2023, DOI: 10.1523/ENEURO.0147-23.2023

iPSC-derived healthy human astrocytes selectively load miRNAs targeting neuronal genes into extracellular vesicles, Gordillo-Sampedro S, Antounians L, Wei W, Mufteev M, Lendemeijer B, et al., Mol Cell Neurosci, 2024, Volume 129: 103933, DOI: 10.1016/j.mcn.2024.103933

The unfolded protein response of the endoplasmic reticulum protects Caenorhabditis elegans against DNA damage caused by stalled replication forks, Xu J, Sabatino B, Taubert S, bioRxiv, 2023, Preprint, DOI: 10.1101/2023.02.23.529758

Differential effects of MATR3 variants on its cryptic splicing repression function, Khan M, Chen XXL, Dias M, Santos JR, Kour S, et al., bioRxiv, 2023, Preprint, DOI: 10.1101/2023.12.07.570685

Refining the resolution of the yeast genotype-phenotype map using single-cell RNA-sequencing, N’Guessan A, Tong WY, Heydari H, Nguyen Ba AN, bioRxiv, 2023, Preprint, DOI: 10.1101/2023.10.18.562953

Epigenetic reprogramming of a distal developmental enhancer cluster drives SOX2 overexpression in breast and lung adenocarcinoma, Abatti LE, Lado-Fernández P, Huynh L, Collado M, Hoffman MM, Mitchell JA, Nucleic Acids Res, 2023, 51(19): 10109–10131, DOI: 10.1093/nar/gkad734

Gut environmental factors explain variations in the gut microbiome composition and metabolism within and between healthy adults, Procházková N, Laursen MF, La Barbera G, Tsekitsidi E, Jørgensen MS, et al., bioRxiv, 2024, Preprint, DOI: 10.1101/2024.01.23.574598

MRCK-1 activates non-muscle myosin for outgrowth of a unicellular tube in Caenorhabditis elegans, Popiel EM, Derry WB, bioRxiv, 2024, Preprint, DOI: 10.1101/2024.01.25.577256

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CGEn- Montreal

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Shah SB, Carlson CR, Lai K, Zhong Z, Marsico G, et al., Combinatorial Treatment Rescues Tumour-Microenvironment-Mediated Attenuation of MALT1 Inhibitors in B-Cell Lymphomas. Nat Mater. 2023. 22(4):511-523. DOI: 10.1038/s41563-023-01495-3, PMID: 36928381.

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Davies JR, Hilton LK, Jiang A, Barrans S, Burton C, et al., Comparison of MHG and DZsig Reveals Shared Biology and a Core Overlap Group with Inferior Prognosis in DLBCL. Blood Adv. 2023. 7(20):6156-6162. DOI: 10.1182/bloodadvances.2023010673, PMID: 37595057.

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Rao H, Zhang H, Zou Y, Ma P, Huang T, et al., Analysis of Chromosomal Structural Variations in Patients with Recurrent Spontaneous Abortion Using Optical Genome Mapping. Frontiers in Genetics. 2023. 14:1248755. DOI: 10.3389/fgene.2023.1248755, PMID: 37732322.

Sathiyaseelan P, Chittaranjan S, Kalloger SE, Chan J, Go NE, et al., Loss of ATG4B and ATG4A Results in Two-Stage Cell Cycle Defects in Pancreatic Ductal Adenocarcinoma Cells. Journal of Cell Science. 2023. 136(19):jcs260644. DOI: 10.1242/jcs.260644, PMID: 37701987.

Schaffner SL, Wassouf Z, Hentrich T, Nuesch-Germano M, Kobor MS, Schulze-Hentrich JM, Distinct Impacts of Alpha-Synuclein Overexpression on the Hippocampal Epigenome of Mice in Standard and Enriched Environments. Neurobiology of Disease. 2023. 186:106274. DOI: 10.1016/j.nbd.2023.106274, PMID: 37648037.

Zenchyzen B, Carey S, Antochi-Crihan G, Hall JC, Developmental and Genetic Basis of the Androgynophore in Gynandropsis Gynandra. Am J Bot. 2023. 110(7):e16193. DOI: 10.1002/ajb2.16193, PMID: 37210747.

Lee E, Lee D, Fan W, Lytle A, Fu Y, et al., ESQmodel: Biologically Informed Evaluation of 2-D Cell Segmentation Quality in Multiplexed Tissue Images. Bioinformatics. 2024. 40(1):btad783. DOI: 10.1093/bioinformatics/btad783, PMID: 38152895.

Cui Y, Yang G, Goodwin D, O’Flanagan C, Sinha A, et al., Expansion Microscopy Using a Single Anchor Molecule for High-Yield Multiplexed Imaging of Proteins and RNAs. PLOS ONE. 2023. 18(9):e0291506. DOI: 10.1371/journal.pone.0291506, PMID: 37729182.

Cannell IG, Sawicka K, Pearsall I, Wild SA, Deighton L, et al., FOXC2 Promotes Vasculogenic Mimicry and Resistance to Anti-Angiogenic Therapy. Cell Reports. 2023. 42(8):112791. DOI: 10.1016/j.celrep.2023.112791, PMID: 37499655.

Zhang H, Delaidelli A, Javed S, Turgu B, Morrison T, et al., A MYCN-Independent Mechanism Mediating Secretome Reprogramming and Metastasis in MYCN-Amplified Neuroblastoma. Science Advances. 2023. 9(34):eadg6693. DOI: 10.1126/sciadv.adg6693, PMID: 37611092.

Nguyen HL, Geukens T, Maetens M, Aparicio S, Bassez A, et al., Obesity-Associated Changes in Molecular Biology of Primary Breast Cancer. Nature Communications. 2023. 14(1):4418. DOI: 10.1038/s41467-023-39996-z, PMID: 37479706.

Salehi S, Dorri F, Chern K, Kabeer F, Rusk N, et al., Cancer Phylogenetic Tree Inference at Scale from 1000s of Single Cell Genomes. Peer Community Journal. 2023. 3:e63. DOI: 10.24072/pcjournal.292.

Ceglia N, Sethna Z, Freeman S, Uhlitz F, Bojilova V, et al., Identification of Transcriptional Programs Using Dense Vector Representations Defined by Mutual Information with GeneVector. Nature Communications. 2023. 14(1):4400. DOI: 10.1038/s41467-023-39985-2, PMID: 37474509.

Lee E, Chern K, Nissen M, Wang X, Huang C, et al., SpatialSort: A Bayesian Model for Clustering and Cell Population Annotation of Spatial Proteomics Data. Bioinformatics. 2023. 39(39 Suppl 1):e131-E139. DOI: 10.1093/bioinformatics/btad242, PMID: 37387130.

CGEn- Vancouver

Titmuss E, Yu IS, Pleasance ED, Williamson LM, Mungall K, et al., Exploration of germline correlates and risk of immune-related adverse events in advanced cancer patients treated with immune checkpoint inhibitors. Curr Oncol. 2024. 31(4):1865-1875 DOI: 10.3390/curroncol31040140. PMID: 38668043.

Warren RL, Abraham R, Calingo M, Garant J-M, Jones SJM, et al., Establishing association between HLA-C*04:01 and severe COVID-19. HLA. 2024. 103(1):e15355. DOI: 10.1111/tan.15355. PMID: 38273454.

Lo T, Coombe L, Gagalova KK, Marr A, Warren RL, et al., Assembly and annotation of the black spruce genome provide insights on spruce phylogeny and evolution of stress response, G3 (Bethesda). 2023. 14(1):jkad247. DOI: 10.1093/g3journal/jkad247. PMID: 37875130.

Elbert A, Dixon K, Shen Y, Hamilton S, Boerkoel CF, et al., Mitofusin 2 Variant Presenting With a Phenotype of Multiple System Atrophy of Cerebellar Subtype. Neurol Genet. 2023. 10(1):e200114. DOI: 10.1212/NXG.0000000000200114, PMID: 38170145.

Omairi HK, Grisdale CJ, Meode M, Bohm AK, Black S, et al., Mitogen-Induced Defective Mitosis Transforms Neural Progenitor Cells. Neuro Oncol. 2023. 25(10):1763-1774. DOI: 10.1093/neuonc/noad082. PMID: 37186014.

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

Romero JM, Titmuss E, Wang Y, Vafiadis J, Pacis A, et al., Chemokine expression predicts T cell-inflammation and improved survival with checkpoint inhibition across solid cancers. NPJ Precis Oncol. 2023. 7(1):73. DOI: 10.1038/s41698-023-00428-2, PMID: 37558751.

Xu J, Pandoh PK, Corbett RD, Smailus D, Bowlby R, et al., A high-throughput pipeline for DNA/RNA/small RNA purification from tissue samples for sequencing. Biotechniques. 2023. 75(2):47-55. DOI: 10.2144/btn-2023-0011, PMID: 37551834.

Chang G, Jones S, Leelakumari S, Ashkani J, Culibrk L, et al., The genome sequence of the Loggerhead sea turtle, Caretta caretta Linnaeus 1758. F1000Res. 2023. 12:336 DOI: 10.12688/f1000research.131283.2, PMID: 37455852.

Li Z, Jiao X, Robertson AG, Di Sante G, Ashton AW, et al., The DACH1 gene is frequently deleted in prostate cancer, restrains prostatic intraepithelial neoplasia, decreases DNA damage repair, and predicts therapy responses. Oncogene. 2023. 42(22):1857-1873. DOI: 10.1038/s41388-023-02668-9, PMID: 37095257.

Nikolic A, Maule F, Bobyn A, Ellestad K, Paik S, et al., macroH2A2 antagonizes epigenetic programs of stemness in glioblastoma. Nat Commun. 2023. 14(1):3062. DOI: 10.1038/s41467-023-30626-2, PMID: 37244935.

Dixon K, Shen Y, O’Neill K, Mungall KL, Chan S, et al., Defining the heterogeneity of unbalanced structural variation underlying breast cancer susceptibility by nanopore genome sequencing. Eur J Hum Genet. 2023. 31(5):602-606. DOI: 10.1038/s41431-023-01284-1, PMID: 36797466.

Yoo S, Garg E, Elliott LT, Hung RJ, Halevy AR, et al., HostSeq: a Canadian whole genome sequencing and clinical data resource. BMC Genom Data. 2023. 24(1):26 DOI: 10.1186/s12863-023-01128-3, PMID: 37131148.

Arora R, Haynes L, Kumar M, McNeil R, Ashkani J, et al., NCBP2 and TFRC are novel prognostic biomarkers in oral squamous cell carcinoma. Cancer Gene Ther. 2023. 30(5):752-765. DOI: 10.1038/s41417-023-00578-8, PMID: 36635327.

Rondeau EB, Christensen KA, Minkley DR, Leong JS, Chan MTT, et al., Population-size history inferences from the coho salmon (Oncorhynchus kisutch) genome. G3 (Bethesda). 2023. 13(4):jkad033. DOI: 10.1093/g3journal/jkad033, PMID: 36759939.

Alduaij W, Collinge B, Ben-Neriah S, Jiang A, Hilton LK, et al., Molecular determinants of clinical outcomes in a real-world diffuse large B-cell lymphoma population. Blood. 2023. 141(20):2493-2507. DOI: 10.1182/blood.2022018248, PMID: 36302166.

Dreval K, Hilton LK, Cruz M, Shaalan H, Ben-Neriah S, et al., Genetic subdivisions of follicular lymphoma defined by distinct coding and noncoding mutation patterns. Blood. 2023. 142(6):561-573. DOI: 10.1182/blood.2022018719, PMID: 37084389.

Colijn MA, Carrion P, Poirier-Morency G, Rogic S, Torres I, et al., SETD1A variant-associated psychosis: A systematic review of the clinical literature and description of two new cases. 2024. 129:110888. DOI: 10.1016/j.pnpbp.2023.110888, PMID: 37918557.

Küpper JC, Sullivan ES, Coope RJN, Wilson DR, Design of a double acting pneumatic cartilage loading device for magnetic resonance imaging. J Mech Behav Biomed Mater. 2023. 142:105810. DOI: 10.1016/j.jmbbm.2023.105810, PMID: 37028122.

Coope RJ, Pleasance S, Pandoh P, Schlosser C, Corbett RD, et al., Rapid microdissection of tissue sections via laser ablation. J Clin Pathol. 2024. 77(6):430-434. DOI: 10.1136/jcp-2023-209361, PMID: 38429092.

Fedrigo R, Coope R, Cheng JC, English C, Polson L, et al., Towards harmonized 18F-PSMA PET imaging: design and early results from a multi-center, multi-vendor phantom study. J. Nucl. Med. 2024. 64(1):P533. DOI: Not available, PMID: Not available.

Fedrigo R, Coope R, Rahmim A, Bénard F, Uribe CF, Development of the quantitative PET prostate phantom (Q3P) for improved quality assurance of 18F-PSMA PET imaging in metastatic prostate cancer. Med Phys. 2024. 51(6):4311-4323. DOI: 10.1002/mp.16977, PMID: 38348927.

Schrader K, Akbari V, Hanlon V, Leung T, Dixon K, et al., Detection of variant parent-of-origin in diverse hereditary cancer syndromes using only the proband’s blood sample. Genetics in Medicine Open. 2024. 2(1):101563. DOI: doi.org/10.1016/j.gimo.2024.101563, PMID: Not available.

Tolmeijer SH, Boerrigter E, Sumiyoshi T, Kwan EM, Ng S, et al., Early on-treatment changes in circulating tumor DNA fraction and response to enzalutamide or abiraterone in metastatic castration-resistant prostate cancer. Clin Cancer Res. 2023. 29(15):2835-2844. DOI: 10.1158/1078-0432.CCR-22-2998, PMID: 36996325.

Herberts C, Wyatt AW, Nguyen PL, Cheng HH, Genetic and Genomic Testing for Prostate Cancer: Beyond DNA Repair. Am Soc Clin Oncol Educ Book. 2023. 43:e390384. DOI: 10.1200/EDBK_390384, PMID: 37207301.

Tortora D, Roberts ME, Kumar G, Kotapalli SS, Ritch E, et al., A genome-wide CRISPR screen maps endogenous regulators of PPARG gene expression in bladder cancer. iScience. 2023. 26(5):106525. DOI: 10.1016/j.isci.2023.106525, PMID: 37250326.

Lundberg A, Zhang M, Aggarwal R, Li H, Zhang L, et al., The genomic and epigenomic landscape of double-negative metastatic prostate cancer. Cancer Res. 2023. 83(16):2763-2774. DOI: 10.1158/0008-5472.CAN-23-0593, PMID: 37289025.

Helzer KT, Sharifi MN, Sperger JM, Shi Y, Annala M, et al., Fragmentomic analysis of circulating tumor DNA-targeted cancer panels. Ann Oncol. 2023. 34(9):813-825. DOI: 10.1016/j.annonc.2023.06.001, PMID: 37330052.

Sumiyoshi T, Wang X, Warner EW, Sboner A, Annala M, et al., Molecular features of prostate cancer post-neoadjuvant therapy in the Phase 3 CALGB 90203 trial. J Natl Cancer Inst. 2023. 116(1):115-126. DOI: 10.1093/jnci/djad184, PMID: 37676819.

Schostak M, Bradbury A, Briganti A, Gonzalez D, Gomella L, et al., Practical Guidance on Establishing a Molecular Testing Pathway for Alterations in Homologous Recombination Repair Genes in Clinical Practice for Patients with Metastatic Prostate Cancer. Eur Urol Oncol. 2023. 7(3):344-354. DOI: 10.1016/j.euo.2023.08.004, PMID: 37714762.

Rendon RA, Selvarajah S, Wyatt AW, Kolinsky M, Schrader KA, et al., 2023 Canadian Urological Association guideline: Genetic testing in prostate cancer. Can Urol Assoc J. 2023. 17(10):314-325. DOI: 10.5489/cuaj.8588, PMID: 37851913.

Wyatt AW, Rare Genetic Drivers of Lethal Prostate Cancer. JAMA Oncol. 2023. 9(11):1499-1501. DOI: 10.1001/jamaoncol.2023.3352, PMID: 37733349.

Zhao JL, Antonarakis ES, Cheng HH, George DJ, Aggarwal R, et al., Phase 1b study of enzalutamide plus CC-115, a dual mTORC1/2 and DNA-PK inhibitor, in men with metastatic castration-resistant prostate cancer (mCRPC). Br J Cancer. 2023. 130(1):53-62. DOI: 10.1038/s41416-023-02487-5, PMID: 37980367.

Warner EW, Van der Eecken K, Murtha AJ, Kwan EM, Herberts C, et al., Multiregion sampling of de novo metastatic prostate cancer reveals complex polyclonality and augments clinical genotyping. Nat Cancer. 2024. 5(1):114-130. DOI: 10.1038/s43018-023-00692-y, PMID: 38177459.

Fonseca NM, Maurice-Dror C, Herberts C, Tu W, Fan W, et al., Prediction of plasma ctDNA fraction and prognostic implications of liquid biopsy in advanced prostate cancer. Nat Commun. 2024. 15(1):1828. DOI: 10.1038/s41467-024-45475-w, PMID: 38418825.

Steidl C, Kridel R, Binkley M, Morton LM, Chadburn A, The Pathobiology of Select Adolescent Young Adult Lymphomas. EJHaem. 2023. 4(4):892-901. DOI: 10.1002/jha2.785, PMID: 38024596.

Hilton LK, Scott DW, Morin RD, Biological Heterogeneity in Diffuse Large B-Cell Lymphoma. Semin Hematol. 2023. 60(5):267-276. DOI: 10.1053/j.seminhematol.2023.11.006 PMID: 38151380.

Holland LA, Casto-Boggess LD, Gels in Microscale Electrophoresis. Annual Review of Analytical Chemistry. 2023. 16(1):161-179. DOI: 10.1146/annurev-anchem-091522-080207, PMID: 37314879.

2022-2023 publications

HostSeq

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

CGEn-Toronto

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

CGEn-Montreal

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.

CGEn-Vancouver

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

Publications prior to 2022

A Distributed Whole Genome Sequencing Benchmark Study, Richard D Corbett, Robert Eveleigh, Joe Whitney, Namrata Barai, Mathieu Bourgey, Eric Chuah, Joanne Johnson, Richard A Moore, et al. Front Genet. 2020 Dec 1:11:612515. doi: 10.3389