Browsing by Author "Lupski, James R."

Now showing 1 - 4 of 4
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    Inverted triplications formed by iterative template switches generate structural variant diversity at genomic disorder loci
    (Elsevier, 2024) Grochowski, Christopher M.; Bengtsson, Jesse D.; Du, Haowei; Gandhi, Mira; Lun, Ming Yin; Mehaffey, Michele G.; Park, KyungHee; Höps, Wolfram; Benito, Eva; Hasenfeld, Patrick; Korbel, Jan O.; Mahmoud, Medhat; Paulin, Luis F.; Jhangiani, Shalini N.; Hwang, James Paul; Bhamidipati, Sravya V.; Muzny, Donna M.; Fatih, Jawid M.; Gibbs, Richard A.; Pendleton, Matthew; Harrington, Eoghan; Juul, Sissel; Lindstrand, Anna; Sedlazeck, Fritz J.; Pehlivan, Davut; Lupski, James R.; Carvalho, Claudia M. B.
    The duplication-triplication/inverted-duplication (DUP-TRP/INV-DUP) structure is a complex genomic rearrangement (CGR). Although it has been identified as an important pathogenic DNA mutation signature in genomic disorders and cancer genomes, its architecture remains unresolved. Here, we studied the genomic architecture of DUP-TRP/INV-DUP by investigating the DNA of 24 patients identified by array comparative genomic hybridization (aCGH) on whom we found evidence for the existence of 4 out of 4 predicted structural variant (SV) haplotypes. Using a combination of short-read genome sequencing (GS), long-read GS, optical genome mapping, and single-cell DNA template strand sequencing (strand-seq), the haplotype structure was resolved in 18 samples. The point of template switching in 4 samples was shown to be a segment of ∼2.2–5.5 kb of 100% nucleotide similarity within inverted repeat pairs. These data provide experimental evidence that inverted low-copy repeats act as recombinant substrates. This type of CGR can result in multiple conformers generating diverse SV haplotypes in susceptible dosage-sensitive loci.
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    A novel disorder involving dyshematopoiesis, inflammation, and HLH due to aberrant CDC42 function
    (Rockefeller University Press, 2019) Lam, Michael T.; Coppola, Simona; Krumbach, Oliver H.F.; Prencipe, Giusi; Insalaco, Antonella; Cifaldi, Cristina; Brigida, Immacolata; Zara, Erika; Scala, Serena; Di Cesare, Silvia; Martinelli, Simone; Di Rocco, Martina; Pascarella, Antonia; Niceta, Marcello; Pantaleoni, Francesca; Ciolfi, Andrea; Netter, Petra; Carisey, Alexandre F.; Diehl, Michael; Akbarzadeh, Mohammad; Conti, Francesca; Merli, Pietro; Pastore, Anna; Levi Mortera, Stefano; Camerini, Serena; Farina, Luciapia; Buchholzer, Marcel; Pannone, Luca; Cao, Tram N.; Coban-Akdemir, Zeynep H.; Jhangiani, Shalini N.; Muzny, Donna M.; Gibbs, Richard A.; Basso-Ricci, Luca; Chiriaco, Maria; Dvorsky, Radovan; Putignani, Lorenza; Carsetti, Rita; Janning, Petra; Stray-Pedersen, Asbjorg; Erichsen, Hans Christian; Horne, AnnaCarin; Bryceson, Yenan T.; Torralba-Raga, Lamberto; Ramme, Kim; Rosti, Vittorio; Bracaglia, Claudia; Messia, Virginia; Palma, Paolo; Finocchi, Andrea; Locatelli, Franco; Chinn, Ivan K.; Lupski, James R.; Mace, Emily M.; Cancrini, Caterina; Aiuti, Alessandro; Ahmadian, Mohammad R.; Orange, Jordan S.; De Benedetti, Fabrizio; Tartaglia, Marco; Bioengineering
    Hemophagocytic lymphohistiocytosis (HLH) is characterized by immune dysregulation due to inadequate restraint of overactivated immune cells and is associated with a variable clinical spectrum having overlap with more common pathophysiologies. HLH is difficult to diagnose and can be part of inflammatory syndromes. Here, we identify a novel hematological/autoinflammatory condition (NOCARH syndrome) in four unrelated patients with superimposable features, including neonatal-onset cytopenia with dyshematopoiesis, autoinflammation, rash, and HLH. Patients shared the same de novo CDC42 mutation (Chr1:22417990C>T, p.R186C) and altered hematopoietic compartment, immune dysregulation, and inflammation. CDC42 mutations had been associated with syndromic neurodevelopmental disorders. In vitro and in vivo assays documented unique effects of p.R186C on CDC42 localization and function, correlating with the distinctiveness of the trait. Emapalumab was critical to the survival of one patient, who underwent successful bone marrow transplantation. Early recognition of the disorder and establishment of treatment followed by bone marrow transplant are important to survival.
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    Sequencing individual genomes with recurrent genomic disorder deletions: an approach to characterize genes for autosomal recessive rare disease traits
    (Springer Nature, 2022) Yuan, Bo; Schulze, Katharina V.; Assia Batzir, Nurit; Sinson, Jefferson; Dai, Hongzheng; Zhu, Wenmiao; Bocanegra, Francia; Fong, Chin-To; Holder, Jimmy; Nguyen, Joanne; Schaaf, Christian P.; Yang, Yaping; Bi, Weimin; Eng, Christine; Shaw, Chad; Lupski, James R.; Liu, Pengfei
    In medical genetics, discovery and characterization of disease trait contributory genes and alleles depends on genetic reasoning, study design, and patient ascertainment; we suggest a segmental haploid genetics approach to enhance gene discovery and molecular diagnostics.
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    A visual and curatorial approach to clinical variant prioritization and disease gene discovery in genome-wide diagnostics
    (BioMed Central, 2016) James, Regis A.; Campbell, Ian M.; Chen, Edward S.; Boone, Philip M.; Rao, Mitchell A.; Bainbridge, Matthew N.; Lupski, James R.; Yang, Yaping; Eng, Christine M.; Posey, Jennifer E.; Shaw, Chad A.
    Background: Genome-wide data are increasingly important in the clinical evaluation of human disease. However, the large number of variants observed in individual patients challenges the efficiency and accuracy of diagnostic review. Recent work has shown that systematic integration of clinical phenotype data with genotype information can improve diagnostic workflows and prioritization of filtered rare variants. We have developed visually interactive, analytically transparent analysis software that leverages existing disease catalogs, such as the Online Mendelian Inheritance in Man database (OMIM) and the Human Phenotype Ontology (HPO), to integrate patient phenotype and variant data into ranked diagnostic alternatives. Methods: Our tool, “OMIM Explorer” (http://www.omimexplorer.com), extends the biomedical application of semantic similarity methods beyond those reported in previous studies. The tool also provides a simple interface for translating free-text clinical notes into HPO terms, enabling clinical providers and geneticists to contribute phenotypes to the diagnostic process. The visual approach uses semantic similarity with multidimensional scaling to collapse high-dimensional phenotype and genotype data from an individual into a graphical format that contextualizes the patient within a low-dimensional disease map. The map proposes a differential diagnosis and algorithmically suggests potential alternatives for phenotype queries—in essence, generating a computationally assisted differential diagnosis informed by the individual’s personal genome. Visual interactivity allows the user to filter and update variant rankings by interacting with intermediate results. The tool also implements an adaptive approach for disease gene discovery based on patient phenotypes. Results: We retrospectively analyzed pilot cohort data from the Baylor Miraca Genetics Laboratory, demonstrating performance of the tool and workflow in the re-analysis of clinical exomes. Our tool assigned to clinically reported variants a median rank of 2, placing causal variants in the top 1 % of filtered candidates across the 47 cohort cases with reported molecular diagnoses of exome variants in OMIM Morbidmap genes. Our tool outperformed Phen-Gen, eXtasy, PhenIX, PHIVE, and hiPHIVE in the prioritization of these clinically reported variants. Conclusions: Our integrative paradigm can improve efficiency and, potentially, the quality of genomic medicine by more effectively utilizing available phenotype information, catalog data, and genomic knowledge.