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2. Expanding the genetics and phenotypes of ocular congenital cranial dysinnervation disorders

Author

Abarca-Barriga, Hugo, Al-Haddad, Christiane, Berman, Jeffrey L., Bothun, Erick D., Capasso, Jenina, Chacon-Camacho, Oscar Francisco, Chang, Lan, Christiansen, Stephen P., Ciccarelli, Maria Laura, Cordonnier, Monique, Cox, Gerald F., Curry, Cynthia J., Dagi, Linda R., Lee Dahm, Thomas, David, Karen L., Davitt, Bradley V., De Berardinis, Teresa, Demer, Joseph L., Désir, Julie, D’Esposito, Fabiana, Drack, Arlene V., Eggenberger, Eric, Elder, James E., Elliott, Alexandra T., Epley, K. David, Feldman, Hagit Baris, Ferreira, Carlos R., Flaherty, Maree P., Fulton, Anne B., Gerth-Kahlert, Christina, Gottlob, Irene, Grill, Stephen, Halliday, Dorothy J., Hanisch, Frank, Hay, Eleanor, Heidary, Gena, Holder, Christopher, Horton, Jonathan C., Iannaccone, Alessandro, Isenberg, Sherwin J., Johnston, Suzanne C., Kahana, Alon, Katowitz, James A., Kazlas, Melanie, Kerr, Natalie C., Kimonis, Virginia, Ko, Melissa W., Koc, Feray, Larsen, Dorte Ancher, Lay-Son, Guillermo, Ledoux, Danielle M., Levin, Alex V., Levy, Richard L., Lyons, Christopher J., Mackey, David A., Magli, Adriano, Mantagos, Iason S., Marti, Candice, Maystadt, Isabelle, McKenzie, Fiona, Menezes, Manoj P., Mikail, Claudia N., Miller, David T., Miller, Kathryn Bisceglia, Mills, Monte D., Miyana, Kaori, Moller, H.U., Mullineaux, Lisa, Nishimura, Julie K., Noble, A. Gwendolyn, Pandey, Pramod Kumar, Pavone, Piero, Penzien, Johann, Petersen, Robert, Phalen, James A., Poduri, Annapurna, Polo, Claudia R., Prasov, Lev, Ramos, Feliciano J., Ramos-Caceres, Maria, Robb, Richard M., Rossillion, Béatrice, Sahin, Mustafa, Singer, Harvey S., Smith, Lois E.H., Sorkin, Jeffrey A., Soul, Janet S., Staffieri, Sandra E., Stalker, Heather J., Stasheff, Steven F., Strassberg, Sonya, Strominger, Mitchell B., Taranath, Deepa Ajay, Thomas, Ioan Talfryn, Traboulsi, Elias I., Ugrin, Maria Cristina, VanderVeen, Deborah K., Vincent, Andrea L., Vogel G, Marlene C., Wabbels, Bettina, Wong, Agnes M.F., Woods, C. Geoffrey, Wu, Carolyn, Yang, Edward, Yeung, Alison, Young, Terri L., Zenteno, Juan C., Zubcov-Iwantscheff, Alexandra A., Zwaan, Johan, Jurgens, Julie A., Barry, Brenda J., Chan, Wai-Man, MacKinnon, Sarah, Whitman, Mary C., Matos Ruiz, Paola M., Pratt, Brandon M., England, Eleina M., Pais, Lynn, Lemire, Gabrielle, Groopman, Emily, Glaze, Carmen, Russell, Kathryn A., Singer-Berk, Moriel, Di Gioia, Silvio Alessandro, Lee, Arthur S., Andrews, Caroline, Shaaban, Sherin, Wirth, Megan M., Bekele, Sarah, Toffoloni, Melissa, Bradford, Victoria R., Foster, Emma E., Berube, Lindsay, Rivera-Quiles, Cristina, Mensching, Fiona M., Sanchis-Juan, Alba, Fu, Jack M., Wong, Isaac, Zhao, Xuefang, Wilson, Michael W., Weisburd, Ben, Lek, Monkol, Brand, Harrison, Talkowski, Michael E., MacArthur, Daniel G., O’Donnell-Luria, Anne, Robson, Caroline D., Hunter, David G., and Engle, Elizabeth C.

Published
2024
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3. Development of a cyclic ion mobility spectrometry‐mass spectrometry‐based collision cross‐section database of permethylated human milk oligosaccharides.

Author

Habibi, Sanaz C., Bradford, Victoria R., Baird, Sophie C., Lucas, Shadrack Wilson, Chouinard, Christopher D., and Nagy, Gabe

Subjects
*LIQUID chromatography-mass spectrometry, *ION mobility, *MASS spectrometry, *BREAST milk, *IONIC mobility, *ION mobility spectroscopy
Abstract

Human milk oligosaccharides (HMOs) are an important class of biomolecules responsible for the healthy development of the brain‐gut axis of infants. Unfortunately, their accurate characterization is largely precluded due to a variety of reasons – there are over 200 possible HMO structures whereas only 10s of these are available as authentic analytical standards. Furthermore, their isomeric heterogeneity stemming from their many possible glycosidic linkage positions and corresponding α/β anomericities further complicates their analyses. While liquid chromatography coupled to tandem mass spectrometry remains the gold standard for HMO analyses, it often times cannot resolve all possible isomeric species and thus warrants the development of other orthogonal approaches. High‐resolution ion mobility spectrometry coupled to mass spectrometry has emerged as a rapid alternative to condensed‐phase separations but largely has remained limited to qualitative information related to the resolution of isomers. In this work, we have assessed the use of permethylation to improve both the resolution and sensitivity of HMO analyses with cyclic ion mobility separations coupled with mass spectrometry. In addition to this, we have developed the first‐ever high‐resolution collision cross‐section database for permethylated HMOs using our previously established calibration protocol. We envision that this internal reference database generated from high‐resolution cyclic ion mobility spectrometry‐mass spectrometry will greatly aid in the accurate characterization of HMOs and provide a valuable, orthogonal, approach to existing liquid chromatography–tandem mass spectrometry‐based methods. [ABSTRACT FROM AUTHOR]

Published
2024
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4. A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders

Author

Lee, Arthur S, primary, Ayers, Lauren J, additional, Kosicki, Michael, additional, Chan, Wai-Man, additional, Fozo, Lydia N, additional, Pratt, Brandon M, additional, Collins, Thomas E, additional, Zhao, Boxun, additional, Rose, Matthew F, additional, Sanchis-Juan, Alba, additional, Fu, Jack M, additional, Wong, Isaac, additional, Zhao, Xuefang, additional, Tenney, Alan P, additional, Lee, Cassia, additional, Laricchia, Kristen M, additional, Barry, Brenda J, additional, Bradford, Victoria R, additional, Lek, Monkol, additional, MacArthur, Daniel G, additional, Lee, Eunjung Alice, additional, Talkowski, Michael E, additional, Brand, Harrison, additional, Pennacchio, Len A, additional, and Engle, Elizabeth C, additional

Published
2023
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5. Hemodynamic and anatomic changes after fetal aortic valvuloplasty are associated with procedural success and postnatal biventricular circulation

Author

Bradford, Victoria R., primary, Tworetzky, Wayne, additional, Callahan, Ryan, additional, Wilkins‐Haug, Louise E., additional, Benson, Carol B., additional, Porras, Diego, additional, Guseh, Stephanie H., additional, Lu, Minmin, additional, Sleeper, Lynn A., additional, Gellis, Laura, additional, and Friedman, Kevin G., additional

Published
2022
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7. Coagulation profiles and viscoelastic testing in multisystem inflammatory syndrome in children

Author

Ankola, Ashish A., primary, Bradford, Victoria R., additional, Newburger, Jane W., additional, Emani, Sirisha, additional, Dionne, Audrey, additional, Friedman, Kevin, additional, Son, Mary Beth, additional, Henderson, Lauren A., additional, Lee, Pui Y., additional, Hellinger, Amy, additional, Hawkins, Beth, additional, Ventresco, Courtney, additional, Esteso, Paul, additional, and VanderPluym, Christina J., additional

Published
2021
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8. Expanding the genetics and phenotypes of ocular congenital cranial dysinnervation disorders

Author

Jurgens, Julie A., Barry, Brenda J., Chan, Wai-Man, MacKinnon, Sarah, Whitman, Mary C., Matos Ruiz, Paola M., Pratt, Brandon M., England, Eleina M., Pais, Lynn, Lemire, Gabrielle, Groopman, Emily, Glaze, Carmen, Russell, Kathryn A., Singer-Berk, Moriel, Di Gioia, Silvio Alessandro, Lee, Arthur S., Andrews, Caroline, Shaaban, Sherin, Wirth, Megan M., Bekele, Sarah, Toffoloni, Melissa, Bradford, Victoria R., Foster, Emma E., Berube, Lindsay, Rivera-Quiles, Cristina, Mensching, Fiona M., Sanchis-Juan, Alba, Fu, Jack M., Wong, Isaac, Zhao, Xuefang, Wilson, Michael W., Weisburd, Ben, Lek, Monkol, Abarca-Barriga, Hugo, Al-Haddad, Christiane, Berman, Jeffrey L., Bothun, Erick D., Capasso, Jenina, Chacon-Camacho, Oscar Francisco, Chang, Lan, Christiansen, Stephen P., Ciccarelli, Maria Laura, Cordonnier, Monique, Cox, Gerald F., Curry, Cynthia J., Dagi, Linda R., Lee Dahm, Thomas, David, Karen L., Davitt, Bradley V., De Berardinis, Teresa, Demer, Joseph L., Désir, Julie, D’Esposito, Fabiana, Drack, Arlene V., Eggenberger, Eric, Elder, James E., Elliott, Alexandra T., Epley, K. David, Feldman, Hagit Baris, Ferreira, Carlos R., Flaherty, Maree P., Fulton, Anne B., Gerth-Kahlert, Christina, Gottlob, Irene, Grill, Stephen, Halliday, Dorothy J., Hanisch, Frank, Hay, Eleanor, Heidary, Gena, Holder, Christopher, Horton, Jonathan C., Iannaccone, Alessandro, Isenberg, Sherwin J., Johnston, Suzanne C., Kahana, Alon, Katowitz, James A., Kazlas, Melanie, Kerr, Natalie C., Kimonis, Virginia, Ko, Melissa W., Koc, Feray, Larsen, Dorte Ancher, Lay-Son, Guillermo, Ledoux, Danielle M., Levin, Alex V., Levy, Richard L., Lyons, Christopher J., Mackey, David A., Magli, Adriano, Mantagos, Iason S., Marti, Candice, Maystadt, Isabelle, McKenzie, Fiona, Menezes, Manoj P., Mikail, Claudia N., Miller, David T., Miller, Kathryn Bisceglia, Mills, Monte D., Miyana, Kaori, Moller, H.U., Mullineaux, Lisa, Nishimura, Julie K., Noble, A. Gwendolyn, Pandey, Pramod Kumar, Pavone, Piero, Penzien, Johann, Petersen, Robert, Phalen, James A., Poduri, Annapurna, Polo, Claudia R., Prasov, Lev, Ramos, Feliciano J., Ramos-Caceres, Maria, Robb, Richard M., Rossillion, Béatrice, Sahin, Mustafa, Singer, Harvey S., Smith, Lois E.H., Sorkin, Jeffrey A., Soul, Janet S., Staffieri, Sandra E., Stalker, Heather J., Stasheff, Steven F., Strassberg, Sonya, Strominger, Mitchell B., Taranath, Deepa Ajay, Thomas, Ioan Talfryn, Traboulsi, Elias I., Ugrin, Maria Cristina, VanderVeen, Deborah K., Vincent, Andrea L., Vogel G, Marlene C., Wabbels, Bettina, Wong, Agnes M.F., Woods, C. Geoffrey, Wu, Carolyn, Yang, Edward, Yeung, Alison, Young, Terri L., Zenteno, Juan C., Zubcov-Iwantscheff, Alexandra A., Zwaan, Johan, Brand, Harrison, Talkowski, Michael E., MacArthur, Daniel G., O’Donnell-Luria, Anne, Robson, Caroline D., Hunter, David G., and Engle, Elizabeth C.

Abstract

To identify genetic etiologies and genotype/phenotype associations for unsolved ocular congenital cranial dysinnervation disorders (oCCDDs).

Published
2024
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9. Expanding the genetics and phenotypes of ocular congenital cranial dysinnervation disorders.

Author

Jurgens JA, Barry BJ, Chan WM, MacKinnon S, Whitman MC, Matos Ruiz PM, Pratt BM, England EM, Pais L, Lemire G, Groopman E, Glaze C, Russell KA, Singer-Berk M, Di Gioia SA, Lee AS, Andrews C, Shaaban S, Wirth MM, Bekele S, Toffoloni M, Bradford VR, Foster EE, Berube L, Rivera-Quiles C, Mensching FM, Sanchis-Juan A, Fu JM, Wong I, Zhao X, Wilson MW, Weisburd B, Lek M, Brand H, Talkowski ME, MacArthur DG, O'Donnell-Luria A, Robson CD, Hunter DG, and Engle EC

Abstract

Purpose: To identify genetic etiologies and genotype/phenotype associations for unsolved ocular congenital cranial dysinnervation disorders (oCCDDs)., Methods: We coupled phenotyping with exome or genome sequencing of 467 pedigrees with genetically unsolved oCCDDs, integrating analyses of pedigrees, human and animal model phenotypes, and de novo variants to identify rare candidate single nucleotide variants, insertion/deletions, and structural variants disrupting protein-coding regions. Prioritized variants were classified for pathogenicity and evaluated for genotype/phenotype correlations., Results: Analyses elucidated phenotypic subgroups, identified pathogenic/likely pathogenic variant(s) in 43/467 probands (9.2%), and prioritized variants of uncertain significance in 70/467 additional probands (15.0%). These included known and novel variants in established oCCDD genes, genes associated with syndromes that sometimes include oCCDDs (e.g., MYH10, KIF21B, TGFBR2, TUBB6), genes that fit the syndromic component of the phenotype but had no prior oCCDD association (e.g., CDK13, TGFB2 ), genes with no reported association with oCCDDs or the syndromic phenotypes (e.g., TUBA4A, KIF5C, CTNNA1, KLB, FGF21 ), and genes associated with oCCDD phenocopies that had resulted in misdiagnoses., Conclusion: This study suggests that unsolved oCCDDs are clinically and genetically heterogeneous disorders often overlapping other Mendelian conditions and nominates many candidates for future replication and functional studies., Competing Interests: Conflict of interest D.G.M. is a paid adviser to GlaxoSmithKline, Insitro, Variant Bio and Overtone Therapeutics and has received research support from AbbVie, Astellas, Biogen, BioMarin, Eisai, Merck, Microsoft, Pfizer and Sanofi-Genzyme; none of these activities are related to the work presented here. M.E.T. is provided with research reagents and/or resources from Microsoft, Illumina, Pacific Biosciences, and Ionis Pharmaceuticals; none of these are related to the work presented here. A.O’D.L. is on the scientific advisory board for Congenica Inc. S.A.D.G. is an employee and stockholder of Regeneron Pharmaceutical.

Published
2024
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10. A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders.

Author

Lee AS, Ayers LJ, Kosicki M, Chan WM, Fozo LN, Pratt BM, Collins TE, Zhao B, Rose MF, Sanchis-Juan A, Fu JM, Wong I, Zhao X, Tenney AP, Lee C, Laricchia KM, Barry BJ, Bradford VR, Lek M, MacArthur DG, Lee EA, Talkowski ME, Brand H, Pennacchio LA, and Engle EC

Abstract

Unsolved Mendelian cases often lack obvious pathogenic coding variants, suggesting potential non-coding etiologies. Here, we present a single cell multi-omic framework integrating embryonic mouse chromatin accessibility, histone modification, and gene expression assays to discover cranial motor neuron (cMN) cis-regulatory elements and subsequently nominate candidate non-coding variants in the congenital cranial dysinnervation disorders (CCDDs), a set of Mendelian disorders altering cMN development. We generated single cell epigenomic profiles for ~86,000 cMNs and related cell types, identifying ~250,000 accessible regulatory elements with cognate gene predictions for ~145,000 putative enhancers. Seventy-five percent of elements (44 of 59) validated in an in vivo transgenic reporter assay, demonstrating that single cell accessibility is a strong predictor of enhancer activity. Applying our cMN atlas to 899 whole genome sequences from 270 genetically unsolved CCDD pedigrees, we achieved significant reduction in our variant search space and nominated candidate variants predicted to regulate known CCDD disease genes MAFB, PHOX2A, CHN1 , and EBF3 - as well as new candidates in recurrently mutated enhancers through peak- and gene-centric allelic aggregation. This work provides novel non-coding variant discoveries of relevance to CCDDs and a generalizable framework for nominating non-coding variants of potentially high functional impact in other Mendelian disorders.

Published
2023
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