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Article ; Online: Bovine neonate is deficient in innate immunity at birth.

Kaushik, Azad K / Kandavel, Harish / Nalpathamkalam, Thomas / Pasman, Yfke

2021 Volume 133, Page(s) 101–109

Abstract: With an objective to understand acquisition of innate immunity in bovine neonates, we analyzed perinatal expression of cytokine, adhesion molecule and complement component genes involved in innate and adaptive immune functions. Statistically robust ... ...

Abstract	With an objective to understand acquisition of innate immunity in bovine neonates, we analyzed perinatal expression of cytokine, adhesion molecule and complement component genes involved in innate and adaptive immune functions. Statistically robust transcriptomic analysis of 27 cytokines showed low IL1B, IL2 and IL7 but high IL23, TGFB1 and TGFB2 expression in bovine neonates post-birth. Unlike mice and humans, no T
MeSH term(s)	Adaptive Immunity/genetics ; Adaptive Immunity/immunology ; Animals ; Animals, Newborn/immunology ; Cattle ; Complement System Proteins/biosynthesis ; Complement System Proteins/genetics ; Cytokines/biosynthesis ; Cytokines/genetics ; Female ; Gene Expression Profiling ; Immunity, Innate/genetics ; Immunity, Innate/immunology ; Phagocytosis/immunology ; Platelet Aggregation/immunology ; T-Lymphocytes, Regulatory/cytology ; T-Lymphocytes, Regulatory/immunology ; Th17 Cells/cytology ; Th17 Cells/immunology ; Th2 Cells/cytology ; Th2 Cells/immunology
Chemical Substances	Cytokines ; Complement System Proteins (9007-36-7)
Language	English
Publishing date	2021-02-25
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	424427-8
ISSN	1872-9142 ; 0161-5890
ISSN (online)	1872-9142
ISSN	0161-5890
DOI	10.1016/j.molimm.2021.02.005
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Article: A New Sturgeon Herpesvirus from Juvenile Lake Sturgeon

Clouthier, Sharon / Tomczyk, Marek / Schroeder, Tamara / Klassen, Cheryl / Dufresne, André / Emmenegger, Eveline / Nalpathamkalam, Thomas / Wang, Zhuozhi / Thiruvahindrapuram, Bhooma

Pathogens (Basel, Switzerland)

2023 Volume 12, Issue 9

Abstract: Herpesvirus infections of sturgeon pose a potential threat to sturgeon culture efforts worldwide. A new epitheliotropic herpesvirus named Acipenser herpesvirus 3 (AciHV-3) was detected in hatchery-reared Lake ... ...

Abstract	Herpesvirus infections of sturgeon pose a potential threat to sturgeon culture efforts worldwide. A new epitheliotropic herpesvirus named Acipenser herpesvirus 3 (AciHV-3) was detected in hatchery-reared Lake Sturgeon
Language	English
Publishing date	2023-08-31
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2695572-6
ISSN	2076-0817
ISSN	2076-0817
DOI	10.3390/pathogens12091115
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Article ; Online: Estimating the proportion of nonsense variants undergoing the newly described phenomenon of manufactured splice rescue.

Haque, Bushra / Cheerie, David / Birkadze, Saba / Xu, Alice Linyan / Nalpathamkalam, Thomas / Thiruvahindrapuram, Bhooma / Walker, Susan / Costain, Gregory

European journal of human genetics : EJHG

2023 Volume 32, Issue 2, Page(s) 238–242

Abstract: A recent report described a nonsense variant simultaneously creating a donor splice site, resulting in a truncated but functional protein. To explore the generalizability of this unique mechanism, we annotated >115,000 nonsense variants using SpliceAI. ... ...

Abstract	A recent report described a nonsense variant simultaneously creating a donor splice site, resulting in a truncated but functional protein. To explore the generalizability of this unique mechanism, we annotated >115,000 nonsense variants using SpliceAI. Between 0.61% (donor gain delta score >0.8, for high precision) and 2.57% (>0.2, for high sensitivity) of nonsense variants were predicted to create new donor splice sites at or upstream of the stop codon. These variants were less likely than other nonsense variants in the same genes to be classified as pathogenic/likely pathogenic in ClinVar (p < 0.001). Up to 1 in 175 nonsense variants were predicted to result in small in-frame deletions and loss-of-function evasion through this "manufactured splice rescue" mechanism. We urge caution when interpreting nonsense variants where manufactured splice rescue is a strong possibility and correlation with phenotype is challenging, as will often be the case with secondary findings and newborn genomic screening programs.
MeSH term(s)	Infant, Newborn ; Humans ; Codon, Nonsense ; Codon, Terminator ; Genomics ; Phenotype ; RNA Splice Sites/genetics
Chemical Substances	Codon, Nonsense ; Codon, Terminator ; RNA Splice Sites
Language	English
Publishing date	2023-11-27
Publishing country	England
Document type	Journal Article
ZDB-ID	1141470-4
ISSN	1476-5438 ; 1018-4813
ISSN (online)	1476-5438
ISSN	1018-4813
DOI	10.1038/s41431-023-01495-6
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Article ; Online: Using Next-Generation Sequencing Transcriptomics To Determine Markers of Post-traumatic Symptoms: Preliminary Findings from a Post-deployment Cohort of Soldiers.

Boscarino, Cathy / Nalpathamkalam, Thomas / Pellecchia, Giovanna / Li, Weili / Thiruvahindrapuram, Bhooma / Merico, Daniele

G3 (Bethesda, Md.)

2019 Volume 9, Issue 2, Page(s) 463–471

Abstract: Post-traumatic stress disorder is a concerning psychobehavioral disorder thought to emerge from the complex interaction between genetic and environmental factors. For soldiers exposed to combat, the risk of developing this disorder is twofold and ... ...

Abstract	Post-traumatic stress disorder is a concerning psychobehavioral disorder thought to emerge from the complex interaction between genetic and environmental factors. For soldiers exposed to combat, the risk of developing this disorder is twofold and diagnosis is often late, when much sequela has set in. To be able to identify and diagnose in advance those at "risk" of developing post-traumatic stress disorder, would greatly taper the gap between late sequelae and treatment. Therefore, this study sought to determine whether the transcriptome can be used to track the development of post-traumatic stress disorder in this unique and susceptible cohort of individuals. Gene expression levels in peripheral blood samples from 85 Canadian infantry soldiers (n = 58 participants negative for symptoms of post-traumatic stress disorder and n = 27 participants with symptoms of post-traumatic stress disorder) following return from deployment to Afghanistan were determined using RNA sequencing technology. Count-based gene expression quantification, normalization and differential analysis (with thorough correction for confounders) revealed genes associated to PTSD;
MeSH term(s)	Adult ; Biomarkers/blood ; Gene Expression Profiling/methods ; Humans ; LDL-Receptor Related Proteins/genetics ; LDL-Receptor Related Proteins/metabolism ; Male ; Membrane Proteins/genetics ; Membrane Proteins/metabolism ; Military Personnel ; RNA, Messenger/blood ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Stress Disorders, Post-Traumatic/blood ; Stress Disorders, Post-Traumatic/genetics ; Transcriptome
Chemical Substances	Biomarkers ; GOLM1 protein, human ; LDL-Receptor Related Proteins ; Membrane Proteins ; RNA, Messenger ; low density lipoprotein receptor-related protein 8
Language	English
Publishing date	2019-02-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	2629978-1
ISSN	2160-1836 ; 2160-1836
ISSN (online)	2160-1836
ISSN	2160-1836
DOI	10.1534/g3.118.200516
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Article ; Online: Genome-wide enhancer-associated tandem repeats are expanded in cardiomyopathy.

Mitina, Aleksandra / Khan, Mahreen / Lesurf, Robert / Yin, Yue / Engchuan, Worrawat / Hamdan, Omar / Pellecchia, Giovanna / Trost, Brett / Backstrom, Ian / Guo, Keyi / Pallotto, Linda M / Lam Doong, Phoenix Hoi / Wang, Zhuozhi / Nalpathamkalam, Thomas / Thiruvahindrapuram, Bhooma / Papaz, Tanya / Pearson, Christopher E / Ragoussis, Jiannis / Subbarao, Padmaja /

Azad, Meghan B / Turvey, Stuart E / Mandhane, Piushkumar / Moraes, Theo J / Simons, Elinor / Scherer, Stephen W / Lougheed, Jane / Mondal, Tapas / Smythe, John / Altamirano-Diaz, Luis / Oechslin, Erwin / Mital, Seema / Yuen, Ryan K C

EBioMedicine

2024 Volume 101, Page(s) 105027

Abstract: Background: Cardiomyopathy is a clinically and genetically heterogeneous heart condition that can lead to heart failure and sudden cardiac death in childhood. While it has a strong genetic basis, the genetic aetiology for over 50% of cardiomyopathy ... ...

Abstract	Background: Cardiomyopathy is a clinically and genetically heterogeneous heart condition that can lead to heart failure and sudden cardiac death in childhood. While it has a strong genetic basis, the genetic aetiology for over 50% of cardiomyopathy cases remains unknown. Methods: In this study, we analyse the characteristics of tandem repeats from genome sequence data of unrelated individuals diagnosed with cardiomyopathy from Canada and the United Kingdom (n = 1216) and compare them to those found in the general population. We perform burden analysis to identify genomic and epigenomic features that are impacted by rare tandem repeat expansions (TREs), and enrichment analysis to identify functional pathways that are involved in the TRE-associated genes in cardiomyopathy. We use Oxford Nanopore targeted long-read sequencing to validate repeat size and methylation status of one of the most recurrent TREs. We also compare the TRE-associated genes to those that are dysregulated in the heart tissues of individuals with cardiomyopathy. Findings: We demonstrate that tandem repeats that are rarely expanded in the general population are predominantly expanded in cardiomyopathy. We find that rare TREs are disproportionately present in constrained genes near transcriptional start sites, have high GC content, and frequently overlap active enhancer H3K27ac marks, where expansion-related DNA methylation may reduce gene expression. We demonstrate the gene silencing effect of expanded CGG tandem repeats in DIP2B through promoter hypermethylation. We show that the enhancer-associated loci are found in genes that are highly expressed in human cardiomyocytes and are differentially expressed in the left ventricle of the heart in individuals with cardiomyopathy. Interpretation: Our findings highlight the underrecognized contribution of rare tandem repeat expansions to the risk of cardiomyopathy and suggest that rare TREs contribute to ∼4% of cardiomyopathy risk. Funding: Government of Ontario (RKCY), The Canadian Institutes of Health Research PJT 175329 (RKCY), The Azrieli Foundation (RKCY), SickKids Catalyst Scholar in Genetics (RKCY), The University of Toronto McLaughlin Centre (RKCY, SM), Ted Rogers Centre for Heart Research (SM), Data Sciences Institute at the University of Toronto (SM), The Canadian Institutes of Health Research PJT 175034 (SM), The Canadian Institutes of Health Research ENP 161429 under the frame of ERA PerMed (SM, RL), Heart and Stroke Foundation of Ontario & Robert M Freedom Chair in Cardiovascular Science (SM), Bitove Family Professorship of Adult Congenital Heart Disease (EO), Canada Foundation for Innovation (SWS, JR), Canada Research Chair (PS), Genome Canada (PS, JR), The Canadian Institutes of Health Research (PS).
MeSH term(s)	Humans ; Adult ; Heart Defects, Congenital/genetics ; Tandem Repeat Sequences/genetics ; DNA Methylation ; Cardiomyopathies/genetics ; Ontario ; Nerve Tissue Proteins/genetics
Chemical Substances	DIP2B protein, human ; Nerve Tissue Proteins
Language	English
Publishing date	2024-02-27
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2851331-9
ISSN	2352-3964
ISSN (online)	2352-3964
DOI	10.1016/j.ebiom.2024.105027
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Article: Genetic Analysis Workshop 18 single-nucleotide variant prioritization based on protein impact, sequence conservation, and gene annotation.

Nalpathamkalam, Thomas / Derkach, Andriy / Paterson, Andrew D / Merico, Daniele

BMC proceedings

2014 Volume 8, Issue Suppl 1 Genetic Analysis Workshop 18Vanessa Olmo, Page(s) S11

Abstract: Grouping variants based on gene mapping can augment the power of rare variant association tests. Weighting or sorting variants based on their expected functional impact can provide additional benefit. We defined groups of prioritized variants based on ... ...

Abstract	Grouping variants based on gene mapping can augment the power of rare variant association tests. Weighting or sorting variants based on their expected functional impact can provide additional benefit. We defined groups of prioritized variants based on systematic annotation of Genetic Analysis Workshop 18 (GAW18) single-nucleotide variants; we focused on variants detected by whole genome sequencing, specifically on the high-quality subset presented in the genotype files. First, we divided variants between coding and noncoding. Coding variants are fewer than 1% of the total and are more likely to have a biological effect than noncoding variants. Coding variants were further stratified into protein changing and protein damaging groups based on the effect on protein amino acid sequence. In particular, missense variants predicted to be damaging, splice-site alterations, and stop gains were assigned to the protein damaging category. Impact of noncoding variants is more difficult to predict. We decided to rely uniquely on conservation: we combined (a) the mammalian phastCons Conserved Element and (b) the PhyloP score, which identify conserved intervals and the single-nucleotide position, respectively. This reduced the noncoding variants to a number comparable to coding variants. Finally, using gene structure definition from the widely used RefSeq database, we mapped variants to genes to support association tests that require collapsing rare variants to genes. Companion GAW18 papers used these variant priority groups and gene mapping; one of these paper specifically found evidence of stronger association signal for protein damaging variants.
Language	English
Publishing date	2014-06-17
Publishing country	England
Document type	Journal Article
ZDB-ID	2411867-9
ISSN	1753-6561
ISSN	1753-6561
DOI	10.1186/1753-6561-8-S1-S11
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Article ; Online: MicroRNA Expression during Bovine Oocyte Maturation and Fertilization.

Gilchrist, Graham C / Tscherner, Allison / Nalpathamkalam, Thomas / Merico, Daniele / LaMarre, Jonathan

International journal of molecular sciences

2016 Volume 17, Issue 3, Page(s) 396

Abstract: Successful fertilization and subsequent embryo development rely on complex molecular processes starting with the development of oocyte competence through maturation. MicroRNAs (miRNAs) are small non-coding RNA molecules that function as gene regulators ... ...

Abstract	Successful fertilization and subsequent embryo development rely on complex molecular processes starting with the development of oocyte competence through maturation. MicroRNAs (miRNAs) are small non-coding RNA molecules that function as gene regulators in many biological systems, including the oocyte and embryo. In order to further explore the roles of miRNAs in oocyte maturation, we employed small RNA sequencing as a screening tool to identify and characterize miRNA populations present in pools of bovine germinal vesicle (GV) oocytes, metaphase II (MII) oocytes, and presumptive zygotes (PZ). Each stage contained a defined miRNA population, some of which showed stable expression while others showed progressive changes between stages that were subsequently confirmed by quantitative reverse transcription polymerase chain reaction (RT-PCR). Bta-miR-155, bta-miR-222, bta-miR-21, bta-let-7d, bta-let-7i, and bta-miR-190a were among the statistically significant differentially expressed miRNAs (p < 0.05). To determine whether changes in specific primary miRNA (pri-miRNA) transcripts were responsible for the observed miRNA changes, we evaluated pri-miR-155, -222 and let-7d expression. Pri-miR-155 and -222 were not detected in GV oocytes but pri-miR-155 was present in MII oocytes, indicating transcription during maturation. In contrast, levels of pri-let-7d decreased during maturation, suggesting that the observed increase in let-7d expression was likely due to processing of the primary transcript. This study demonstrates that both dynamic and stable populations of miRNAs are present in bovine oocytes and zygotes and extend previous studies supporting the importance of the small RNA landscape in the maturing bovine oocyte and early embryo.
MeSH term(s)	Animals ; Cattle ; Female ; Fertilization ; Gene Expression Regulation, Developmental ; MicroRNAs/genetics ; Oocytes/cytology ; Oocytes/metabolism ; Oogenesis
Chemical Substances	MicroRNAs
Language	English
Publishing date	2016-03-18
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms17030396
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Article ; Online: Clinical Genetic Risk Variants Inform a Functional Protein Interaction Network for Tetralogy of Fallot.

Reuter, Miriam S / Chaturvedi, Rajiv R / Jobling, Rebekah K / Pellecchia, Giovanna / Hamdan, Omar / Sung, Wilson W L / Nalpathamkalam, Thomas / Attaluri, Pratyusha / Silversides, Candice K / Wald, Rachel M / Marshall, Christian R / Williams, Simon G / Keavney, Bernard D / Thiruvahindrapuram, Bhooma / Scherer, Stephen W / Bassett, Anne S

Circulation. Genomic and precision medicine

2021 Volume 14, Issue 4, Page(s) e003410

Abstract: Background: Tetralogy of Fallot (TOF)-the most common cyanotic heart defect in newborns-has evidence of multiple genetic contributing factors. Identifying variants that are clinically relevant is essential to understand patient-specific disease ... ...

Abstract	Background: Tetralogy of Fallot (TOF)-the most common cyanotic heart defect in newborns-has evidence of multiple genetic contributing factors. Identifying variants that are clinically relevant is essential to understand patient-specific disease susceptibility and outcomes and could contribute to delineating pathomechanisms. Methods: Using a clinically driven strategy, we reanalyzed exome sequencing data from 811 probands with TOF, to identify rare loss-of-function and other likely pathogenic variants in genes associated with congenital heart disease. Results: We confirmed a major contribution of likely pathogenic variants in Conclusions: The results are relevant to precision medicine for TOF. They suggest considerable clinical yield from genome-wide sequencing, with further evidence for
MeSH term(s)	Female ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Humans ; Infant, Newborn ; Male ; Protein Interaction Maps ; Tetralogy of Fallot/genetics ; Exome Sequencing
Language	English
Publishing date	2021-07-30
Publishing country	United States
Document type	Clinical Trial ; Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2574-8300
ISSN (online)	2574-8300
DOI	10.1161/CIRCGEN.121.003410
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Article ; Online: Gene copy number variation and pediatric mental health/neurodevelopment in a general population.

Zarrei, Mehdi / Burton, Christie L / Engchuan, Worrawat / Higginbotham, Edward J / Wei, John / Shaikh, Sabah / Roslin, Nicole M / MacDonald, Jeffrey R / Pellecchia, Giovanna / Nalpathamkalam, Thomas / Lamoureux, Sylvia / Manshaei, Roozbeh / Howe, Jennifer / Trost, Brett / Thiruvahindrapuram, Bhooma / Marshall, Christian R / Yuen, Ryan K C / Wintle, Richard F / Strug, Lisa J /

Stavropoulos, Dimitri J / Vorstman, Jacob A S / Arnold, Paul / Merico, Daniele / Woodbury-Smith, Marc / Crosbie, Jennifer / Schachar, Russell J / Scherer, Stephen W

Human molecular genetics

2023 Volume 32, Issue 15, Page(s) 2411–2421

Abstract: We assessed the relationship of gene copy number variation (CNV) in mental health/neurodevelopmental traits and diagnoses, physical health and cognition in a community sample of 7100 unrelated children and youth of European or East Asian ancestry (Spit ... ...

Abstract	We assessed the relationship of gene copy number variation (CNV) in mental health/neurodevelopmental traits and diagnoses, physical health and cognition in a community sample of 7100 unrelated children and youth of European or East Asian ancestry (Spit for Science). Clinically significant or susceptibility CNVs were present in 3.9% of participants and were associated with elevated scores on a continuous measure of attention-deficit/hyperactivity disorder (ADHD) traits (P = 5.0 × 10-3), longer response inhibition (a cognitive deficit found in several mental health and neurodevelopmental disorders; P = 1.0 × 10-2) and increased prevalence of mental health diagnoses (P = 1.9 × 10-6, odds ratio: 3.09), specifically ADHD, autism spectrum disorder anxiety and learning problems/learning disorder (P's < 0.01). There was an increased burden of rare deletions in gene-sets related to brain function or expression in brain associated with more ADHD traits. With the current mental health crisis, our data established a baseline for delineating genetic contributors in pediatric-onset conditions.
MeSH term(s)	Adolescent ; Humans ; Child ; Mental Health ; DNA Copy Number Variations/genetics ; Autism Spectrum Disorder/genetics ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Attention Deficit Disorder with Hyperactivity/epidemiology ; Attention Deficit Disorder with Hyperactivity/genetics ; Gene Dosage
Language	English
Publishing date	2023-10-05
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1108742-0
ISSN	1460-2083 ; 0964-6906
ISSN (online)	1460-2083
ISSN	0964-6906
DOI	10.1093/hmg/ddad074
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Article ; Online: Genome-wide rare variant score associates with morphological subtypes of autism spectrum disorder.

Chan, Ada J S / Engchuan, Worrawat / Reuter, Miriam S / Wang, Zhuozhi / Thiruvahindrapuram, Bhooma / Trost, Brett / Nalpathamkalam, Thomas / Negrijn, Carol / Lamoureux, Sylvia / Pellecchia, Giovanna / Patel, Rohan V / Sung, Wilson W L / MacDonald, Jeffrey R / Howe, Jennifer L / Vorstman, Jacob / Sondheimer, Neal / Takahashi, Nicole / Miles, Judith H / Anagnostou, Evdokia /

Tammimies, Kristiina / Zarrei, Mehdi / Merico, Daniele / Stavropoulos, Dimitri J / Yuen, Ryan K C / Fernandez, Bridget A / Scherer, Stephen W

Nature communications

2022 Volume 13, Issue 1, Page(s) 6463

Abstract: Defining different genetic subtypes of autism spectrum disorder (ASD) can enable the prediction of developmental outcomes. Based on minor physical and major congenital anomalies, we categorize 325 Canadian children with ASD into dysmorphic and ... ...

Abstract	Defining different genetic subtypes of autism spectrum disorder (ASD) can enable the prediction of developmental outcomes. Based on minor physical and major congenital anomalies, we categorize 325 Canadian children with ASD into dysmorphic and nondysmorphic subgroups. We develop a method for calculating a patient-level, genome-wide rare variant score (GRVS) from whole-genome sequencing (WGS) data. GRVS is a sum of the number of variants in morphology-associated coding and non-coding regions, weighted by their effect sizes. Probands with dysmorphic ASD have a significantly higher GRVS compared to those with nondysmorphic ASD (P = 0.03). Using the polygenic transmission disequilibrium test, we observe an over-transmission of ASD-associated common variants in nondysmorphic ASD probands (P = 2.9 × 10
MeSH term(s)	Child ; Humans ; Autism Spectrum Disorder/genetics ; Canada/epidemiology ; Genome ; Multifactorial Inheritance/genetics ; Whole Genome Sequencing ; Genetic Predisposition to Disease
Language	English
Publishing date	2022-10-29
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-34112-z
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