Browsing by Author "O'Donnell-Luria, Anne"

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    Heterozygous loss-of-function SMC3 variants are associated with variable and incompletely penetrant growth and developmental features
    (medRxiv, 2023-09-28) Ansari, Morad; Faour, Kamli N. W.; Shimamura, Akiko; Grimes, Graeme; Kao, Emeline M.; Denhoff, Erica R.; Blatnik, Ana; Ben-Isvy, Daniel; Wang, Lily; Helm, Benjamin M.; Firth, Helen; Breman, Amy M.; Bijlsma, Emilia K.; Iwata-Otsubo, Aiko; de Ravel, Thomy J. L.; Fusaro, Vincent; Fryer, Alan; Nykamp, Keith; Stühn, Lara G.; Haack, Tobias B.; Korenke, G. Christoph; Constantinou, Panayiotis; Bujakowska, Kinga M.; Low, Karen J.; Place, Emily; Humberson, Jennifer; Napier, Melanie P.; Hoffman, Jessica; Juusola, Jane; Deardorff, Matthew A.; Shao, Wanqing; Rockowitz, Shira; Krantz, Ian; Kaur, Maninder; Raible, Sarah; Kliesch, Sabine; Singer-Berk, Moriel; Groopman, Emily; DiTroia, Stephanie; Ballal, Sonia; Srivastava, Siddharth; Rothfelder, Kathrin; Biskup, Saskia; Rzasa, Jessica; Kerkhof, Jennifer; McConkey, Haley; O'Donnell-Luria, Anne; Sadikovic, Bekim; Hilton, Sarah; Banka, Siddharth; Tüttelmann, Frank; Conrad, Donald; Talkowski, Michael E.; FitzPatrick, David R.; Boone, Philip M.; Medical and Molecular Genetics, School of Medicine
    Heterozygous missense variants and in-frame indels in SMC3 are a cause of Cornelia de Lange syndrome (CdLS), marked by intellectual disability, growth deficiency, and dysmorphism, via an apparent dominant-negative mechanism. However, the spectrum of manifestations associated with SMC3 loss-of-function variants has not been reported, leading to hypotheses of alternative phenotypes or even developmental lethality. We used matchmaking servers, patient registries, and other resources to identify individuals with heterozygous, predicted loss-of-function (pLoF) variants in SMC3, and analyzed population databases to characterize mutational intolerance in this gene. Here, we show that SMC3 behaves as an archetypal haploinsufficient gene: it is highly constrained against pLoF variants, strongly depleted for missense variants, and pLoF variants are associated with a range of developmental phenotypes. Among 13 individuals with SMC3 pLoF variants, phenotypes were variable but coalesced on low growth parameters, developmental delay/intellectual disability, and dysmorphism reminiscent of atypical CdLS. Comparisons to individuals with SMC3 missense/in-frame indel variants demonstrated a milder presentation in pLoF carriers. Furthermore, several individuals harboring pLoF variants in SMC3 were nonpenetrant for growth, developmental, and/or dysmorphic features, some instead having intriguing symptomatologies with rational biological links to SMC3 including bone marrow failure, acute myeloid leukemia, and Coats retinal vasculopathy. Analyses of transcriptomic and epigenetic data suggest that SMC3 pLoF variants reduce SMC3 expression but do not result in a blood DNA methylation signature clustering with that of CdLS, and that the global transcriptional signature of SMC3 loss is model-dependent. Our finding of substantial population-scale LoF intolerance in concert with variable penetrance in subjects with SMC3 pLoF variants expands the scope of cohesinopathies, informs on their allelic architecture, and suggests the existence of additional clearly LoF-constrained genes whose disease links will be confirmed only by multi-layered genomic data paired with careful phenotyping.
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    Heterozygous loss-of-function SMC3 variants are associated with variable growth and developmental features
    (Elsevier, 2024) Ansari, Morad; Faour, Kamli N. W.; Shimamura, Akiko; Grimes, Graeme; Kao, Emeline M.; Denhoff, Erica R.; Blatnik, Ana; Ben-Isvy, Daniel; Wang, Lily; Helm, Benjamin M.; Firth, Helen; Breman, Amy M.; Bijlsma, Emilia K.; Iwata-Otsubo, Aiko; de Ravel, Thomy J. L.; Fusaro, Vincent; Fryer, Alan; Nykamp, Keith; Stühn, Lara G.; Haack, Tobias B.; Korenke, G. Christoph; Constantinou, Panayiotis; Bujakowska, Kinga M.; Low, Karen J.; Place, Emily; Humberson, Jennifer; Napier, Melanie P.; Hoffman, Jessica; Juusola, Jane; Deardorff, Matthew A.; Shao, Wanqing; Rockowitz, Shira; Krantz, Ian; Kaur, Maninder; Raible, Sarah; Dortenzio, Victoria; Kliesch, Sabine; Singer-Berk, Moriel; Groopman, Emily; DiTroia, Stephanie; Ballal, Sonia; Srivastava, Siddharth; Rothfelder, Kathrin; Biskup, Saskia; Rzasa, Jessica; Kerkhof, Jennifer; McConkey, Haley; Sadikovic, Bekim; Hilton, Sarah; Banka, Siddharth; Tüttelmann, Frank; Conrad, Donald F.; O'Donnell-Luria, Anne; Talkowski, Michael E.; FitzPatrick, David R.; Boone, Philip M.; Medical and Molecular Genetics, School of Medicine
    Heterozygous missense variants and in-frame indels in SMC3 are a cause of Cornelia de Lange syndrome (CdLS), marked by intellectual disability, growth deficiency, and dysmorphism, via an apparent dominant-negative mechanism. However, the spectrum of manifestations associated with SMC3 loss-of-function variants has not been reported, leading to hypotheses of alternative phenotypes or even developmental lethality. We used matchmaking servers, patient registries, and other resources to identify individuals with heterozygous, predicted loss-of-function (pLoF) variants in SMC3, and analyzed population databases to characterize mutational intolerance in this gene. Here, we show that SMC3 behaves as an archetypal haploinsufficient gene: it is highly constrained against pLoF variants, strongly depleted for missense variants, and pLoF variants are associated with a range of developmental phenotypes. Among 14 individuals with SMC3 pLoF variants, phenotypes were variable but coalesced on low growth parameters, developmental delay/intellectual disability, and dysmorphism, reminiscent of atypical CdLS. Comparisons to individuals with SMC3 missense/in-frame indel variants demonstrated an overall milder presentation in pLoF carriers. Furthermore, several individuals harboring pLoF variants in SMC3 were nonpenetrant for growth, developmental, and/or dysmorphic features, and some had alternative symptomatologies with rational biological links to SMC3. Analyses of tumor and model system transcriptomic data and epigenetic data in a subset of cases suggest that SMC3 pLoF variants reduce SMC3 expression but do not strongly support clustering with functional genomic signatures of typical CdLS. Our finding of substantial population-scale LoF intolerance in concert with variable growth and developmental features in subjects with SMC3 pLoF variants expands the scope of cohesinopathies, informs on their allelic architecture, and suggests the existence of additional clearly LoF-constrained genes whose disease links will be confirmed only by multilayered genomic data paired with careful phenotyping.
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    Systematic evaluation of genome sequencing for the diagnostic assessment of autism spectrum disorder and fetal structural anomalies
    (Elsevier, 2023) Lowther, Chelsea; Valkanas, Elise; Giordano, Jessica L.; Wang, Harold Z.; Currall, Benjamin B.; O'Keefe, Kathryn; Pierce-Hoffman, Emma; Kurtas, Nehir E.; Whelan, Christopher W.; Hao, Stephanie P.; Weisburd, Ben; Jalili, Vahid; Fu, Jack; Wong, Isaac; Collins, Ryan L.; Zhao, Xuefang; Austin-Tse, Christina A.; Evangelista, Emily; Lemire, Gabrielle; Aggarwal, Vimla S.; Lucente, Diane; Gauthier, Laura D.; Tolonen, Charlotte; Sahakian, Nareh; Stevens, Christine; An, Joon-Yong; Dong, Shan; Norton, Mary E.; MacKenzie, Tippi C.; Devlin, Bernie; Gilmore, Kelly; Powell, Bradford C.; Brandt, Alicia; Vetrini, Francesco; DiVito, Michelle; Sanders, Stephan J.; MacArthur, Daniel G.; Hodge, Jennelle C.; O'Donnell-Luria, Anne; Rehm, Heidi L.; Vora, Neeta L.; Levy, Brynn; Brand, Harrison; Wapner, Ronald J.; Talkowski, Michael E.; Medical and Molecular Genetics, School of Medicine
    Short-read genome sequencing (GS) holds the promise of becoming the primary diagnostic approach for the assessment of autism spectrum disorder (ASD) and fetal structural anomalies (FSAs). However, few studies have comprehensively evaluated its performance against current standard-of-care diagnostic tests: karyotype, chromosomal microarray (CMA), and exome sequencing (ES). To assess the clinical utility of GS, we compared its diagnostic yield against these three tests in 1,612 quartet families including an individual with ASD and in 295 prenatal families. Our GS analytic framework identified a diagnostic variant in 7.8% of ASD probands, almost 2-fold more than CMA (4.3%) and 3-fold more than ES (2.7%). However, when we systematically captured copy-number variants (CNVs) from the exome data, the diagnostic yield of ES (7.4%) was brought much closer to, but did not surpass, GS. Similarly, we estimated that GS could achieve an overall diagnostic yield of 46.1% in unselected FSAs, representing a 17.2% increased yield over karyotype, 14.1% over CMA, and 4.1% over ES with CNV calling or 36.1% increase without CNV discovery. Overall, GS provided an added diagnostic yield of 0.4% and 0.8% beyond the combination of all three standard-of-care tests in ASD and FSAs, respectively. This corresponded to nine GS unique diagnostic variants, including sequence variants in exons not captured by ES, structural variants (SVs) inaccessible to existing standard-of-care tests, and SVs where the resolution of GS changed variant classification. Overall, this large-scale evaluation demonstrated that GS significantly outperforms each individual standard-of-care test while also outperforming the combination of all three tests, thus warranting consideration as the first-tier diagnostic approach for the assessment of ASD and FSAs.