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245 results on '"Abhyankar, Avinash"'

1. Coding and noncoding variants in EBF3 are involved in HADDS and simplex autism

Author

Padhi, Evin M, Hayeck, Tristan J, Cheng, Zhang, Chatterjee, Sumantra, Mannion, Brandon J, Byrska-Bishop, Marta, Willems, Marjolaine, Pinson, Lucile, Redon, Sylvia, Benech, Caroline, Uguen, Kevin, Audebert-Bellanger, Séverine, Le Marechal, Cédric, Férec, Claude, Efthymiou, Stephanie, Rahman, Fatima, Maqbool, Shazia, Maroofian, Reza, Houlden, Henry, Musunuri, Rajeeva, Narzisi, Giuseppe, Abhyankar, Avinash, Hunter, Riana D, Akiyama, Jennifer, Fries, Lauren E, Ng, Jeffrey K, Mehinovic, Elvisa, Stong, Nick, Allen, Andrew S, Dickel, Diane E, Bernier, Raphael A, Gorkin, David U, Pennacchio, Len A, Zody, Michael C, and Turner, Tychele N

Subjects
Biological Sciences, Genetics, Neurosciences, Brain Disorders, Pediatric, Mental Health, Intellectual and Developmental Disabilities (IDD), Biotechnology, Autism, Behavioral and Social Science, Human Genome, 1.1 Normal biological development and functioning, 2.1 Biological and endogenous factors, Neurological, Autistic Disorder, Enhancer Elements, Genetic, Exome, Female, Gene Regulatory Networks, Genetic Predisposition to Disease, Humans, Male, Muscle Hypotonia, Mutation, Neurodevelopmental Disorders, Neurons, Transcription Factors, Neurodevelopmental disorder, Enhancer, Gene regulatory network, EBF3, hs737, Genome, Variant, De novo, Genetics & Heredity, Biochemistry and cell biology
Abstract

BackgroundPrevious research in autism and other neurodevelopmental disorders (NDDs) has indicated an important contribution of protein-coding (coding) de novo variants (DNVs) within specific genes. The role of de novo noncoding variation has been observable as a general increase in genetic burden but has yet to be resolved to individual functional elements. In this study, we assessed whole-genome sequencing data in 2671 families with autism (discovery cohort of 516 families, replication cohort of 2155 families). We focused on DNVs in enhancers with characterized in vivo activity in the brain and identified an excess of DNVs in an enhancer named hs737.ResultsWe adapted the fitDNM statistical model to work in noncoding regions and tested enhancers for excess of DNVs in families with autism. We found only one enhancer (hs737) with nominal significance in the discovery (p = 0.0172), replication (p = 2.5 × 10-3), and combined dataset (p = 1.1 × 10-4). Each individual with a DNV in hs737 had shared phenotypes including being male, intact cognitive function, and hypotonia or motor delay. Our in vitro assessment of the DNVs showed they all reduce enhancer activity in a neuronal cell line. By epigenomic analyses, we found that hs737 is brain-specific and targets the transcription factor gene EBF3 in human fetal brain. EBF3 is genome-wide significant for coding DNVs in NDDs (missense p = 8.12 × 10-35, loss-of-function p = 2.26 × 10-13) and is widely expressed in the body. Through characterization of promoters bound by EBF3 in neuronal cells, we saw enrichment for binding to NDD genes (p = 7.43 × 10-6, OR = 1.87) involved in gene regulation. Individuals with coding DNVs have greater phenotypic severity (hypotonia, ataxia, and delayed development syndrome [HADDS]) in comparison to individuals with noncoding DNVs that have autism and hypotonia.ConclusionsIn this study, we identify DNVs in the hs737 enhancer in individuals with autism. Through multiple approaches, we find hs737 targets the gene EBF3 that is genome-wide significant in NDDs. By assessment of noncoding variation and the genes they affect, we are beginning to understand their impact on gene regulatory networks in NDDs.

Published
2021

2. Molecular diagnostic yield of genome sequencing versus targeted gene panel testing in racially and ethnically diverse pediatric patients

Author

Abul-Husn, Noura S., Marathe, Priya N., Kelly, Nicole R., Bonini, Katherine E., Sebastin, Monisha, Odgis, Jacqueline A., Abhyankar, Avinash, Brown, Kaitlyn, Di Biase, Miranda, Gallagher, Katie M., Guha, Saurav, Ioele, Nicolette, Okur, Volkan, Ramos, Michelle A., Rodriguez, Jessica E., Rehman, Atteeq U., Thomas-Wilson, Amanda, Edelmann, Lisa, Zinberg, Randi E., Diaz, George A., Greally, John M., Jobanputra, Vaidehi, Suckiel, Sabrina A., Horowitz, Carol R., Wasserstein, Melissa P., Kenny, Eimear E., and Gelb, Bruce D.

Published
2023
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3. Implementation and Feasibility of Clinical Genome Sequencing Embedded Into the Outpatient Nephrology Care for Patients With Proteinuric Kidney Disease

Author

Marasa, Maddalena, Ahram, Dina F., Rehman, Atteeq U., Mitrotti, Adele, Abhyankar, Avinash, Jain, Namrata G., Weng, Patricia L., Piva, Stacy E., Fernandez, Hilda E., Uy, Natalie S., Chatterjee, Debanjana, Kil, Byum H., Nestor, Jordan G., Felice, Vanessa, Robinson, Dino, Whyte, Dilys, Gharavi, Ali G., Appel, Gerald B., Radhakrishnan, Jai, Santoriello, Dominick, Bomback, Andrew, Lin, Fangming, D’Agati, Vivette D., Jobanputra, Vaidehi, and Sanna-Cherchi, Simone

Published
2023
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4. De Novo Mutation in an Enhancer of EBF3 in simplex autism

Author

Padhi, Evin M, Hayeck, Tristan J, Mannion, Brandon, Chatterjee, Sumantra, Byrska-Bishop, Marta, Musunuri, Rajeeva, Narzisi, Giuseppe, Abhyankar, Avinash, Cheng, Zhang, Hunter, Riana D, Akiyama, Jennifer, Fries, Lauren E, Ng, Jeffrey, Stong, Nick, Allen, Andrew S, Dickel, Diane E, Bernier, Raphael A, Gorkin, David U, Pennacchio, Len A, Zody, Michael C, and Turner, Tychele N

Abstract

AbstractPrevious research in autism and other neurodevelopmental disorders (NDDs) has indicated an important contribution of de novo protein-coding variants within specific genes. The role of de novo noncoding variation has been observable as a general increase in genetic burden but has yet to be resolved to individual functional elements. In this study, we assessed whole-genome sequencing data in 2,671 families with autism, with a specific focus on de novo variation in enhancers with previously characterized in vivo activity. We identified three independent de novo mutations limited to individuals with autism in the enhancer hs737. These mutations result in similar phenotypic characteristics, affect enhancer activity in vitro, and preferentially occur in AAT motifs in the enhancer with predicted disruptions of transcription factor binding. We also find that hs737 is enriched for copy number variation in individuals with NDDs, is dosage sensitive in the human population, is brain-specific, and targets the NDD gene EBF3 that is genome-wide significant for protein coding de novo variants, demonstrating the importance of understanding all forms of variation in the genome.One Sentence SummaryWhole-genome sequencing in thousands of families reveals variants relevant to simplex autism in a brain enhancer of the well-established neurodevelopmental disorder gene EBF3.

Published
2020

5. De novo mutations across 1,465 diverse genomes reveal mutational insights and reductions in the Amish founder population

Author

Kessler, Michael D, Loesch, Douglas P, Perry, James A, Heard-Costa, Nancy L, Taliun, Daniel, Cade, Brian E, Wang, Heming, Daya, Michelle, Ziniti, John, Datta, Soma, Celedón, Juan C, Soto-Quiros, Manuel E, Avila, Lydiana, Weiss, Scott T, Barnes, Kathleen, Redline, Susan S, Vasan, Ramachandran S, Johnson, Andrew D, Mathias, Rasika A, Hernandez, Ryan, Wilson, James G, Nickerson, Deborah A, Abecasis, Goncalo, Browning, Sharon R, Zöllner, Sebastian, O’Connell, Jeffrey R, Mitchell, Braxton D, Lung, and Blood Institute Trans-Omics for Precision Medicine Consortium National Heart, Group, TOPMed Population Genetics Working, O’Connor, Timothy D, Aalbers, Sanne, Abdalla, Moustafa, Abdul-Rahman, Omar, Abecasis, Gonçalo, Abhyankar, Avinash, Adrianto, Indra, Aguet, Francois, Akers, Rachel, Al-Tobasei, Rafet, Albert, Christine, Aldred, Micheala, Almasy, Laura, Almeida, Marcio, Alonso, Alvaro, Ament, Seth, Ampleford, Elizabeth, An, Ping, Anderson, Christopher D, Andersson, Charlotte, Anugu, Pramod, Appelbaum, Elizabeth, Ardlie, Kristin, Arking, Dan, Armasu, Sebastian M, Arnett, Donna K, Arruda, Heather, Arvanitis, Marios, Ashley-Koch, Allison, Ashrani, Aneel, Aslibekyan, Stella, Assimes, Tim, Atkinson, Elizabeth, Auer, Paul, Austin, Thomas R, Avery, Christy, Avila-Pacheco, Julian, Avillach, Paul, Aviv, Abraham, Avramopoulos, Dimitrios, Ballantyne, Christie, Balte, Pallavi, Bamshad, Michael, Bancks, Mike, Barnard, John, Barr, R Graham, Barron-Casella, Emily, Bartz, Traci, Barwick, Lucas, Basu, Saonli, Battle, Alexis, Baumann, Michael, Beame, David, Beaty, Terri, Beck, Gerald, Becker, Lewis, Becker, Diane, Beer, Rebecca, Begum, Ferdouse, Beiser, Alexa, Beitelshees, Amber, Benjamin, Emelia, Benos, Takis, Berk-Rauch, Hanna, Besich, Zachary M, Bezerra, Marcos, Bhatt, Surya, Bi, Wenjian, Bick, Alexander, and Bielak, Larry

Subjects
Biological Sciences, Genetics, Human Genome, Good Health and Well Being, Adult, Amish, Cohort Studies, DNA Mutational Analysis, Female, Genetics, Population, Genome, Human, Heterozygote, Humans, Male, Mutation, Pedigree, Whole Genome Sequencing, Young Adult, National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Population Genetics Working Group, de novo mutations, diversity, mutation rate, recombination
Abstract

De novo mutations (DNMs), or mutations that appear in an individual despite not being seen in their parents, are an important source of genetic variation whose impact is relevant to studies of human evolution, genetics, and disease. Utilizing high-coverage whole-genome sequencing data as part of the Trans-Omics for Precision Medicine (TOPMed) Program, we called 93,325 single-nucleotide DNMs across 1,465 trios from an array of diverse human populations, and used them to directly estimate and analyze DNM counts, rates, and spectra. We find a significant positive correlation between local recombination rate and local DNM rate, and that DNM rate explains a substantial portion (8.98 to 34.92%, depending on the model) of the genome-wide variation in population-level genetic variation from 41K unrelated TOPMed samples. Genome-wide heterozygosity does correlate with DNM rate, but only explains

Published
2020

6. Genome-wide Analyses Identify KIF5A as a Novel ALS Gene.

Author

Nicolas, Aude, Kenna, Kevin P, Renton, Alan E, Ticozzi, Nicola, Faghri, Faraz, Chia, Ruth, Dominov, Janice A, Kenna, Brendan J, Nalls, Mike A, Keagle, Pamela, Rivera, Alberto M, van Rheenen, Wouter, Murphy, Natalie A, van Vugt, Joke JFA, Geiger, Joshua T, Van der Spek, Rick A, Pliner, Hannah A, Shankaracharya, Smith, Bradley N, Marangi, Giuseppe, Topp, Simon D, Abramzon, Yevgeniya, Gkazi, Athina Soragia, Eicher, John D, Kenna, Aoife, ITALSGEN Consortium, Mora, Gabriele, Calvo, Andrea, Mazzini, Letizia, Riva, Nilo, Mandrioli, Jessica, Caponnetto, Claudia, Battistini, Stefania, Volanti, Paolo, La Bella, Vincenzo, Conforti, Francesca L, Borghero, Giuseppe, Messina, Sonia, Simone, Isabella L, Trojsi, Francesca, Salvi, Fabrizio, Logullo, Francesco O, D'Alfonso, Sandra, Corrado, Lucia, Capasso, Margherita, Ferrucci, Luigi, Genomic Translation for ALS Care (GTAC) Consortium, Moreno, Cristiane de Araujo Martins, Kamalakaran, Sitharthan, Goldstein, David B, ALS Sequencing Consortium, Gitler, Aaron D, Harris, Tim, Myers, Richard M, NYGC ALS Consortium, Phatnani, Hemali, Musunuri, Rajeeva Lochan, Evani, Uday Shankar, Abhyankar, Avinash, Zody, Michael C, Answer ALS Foundation, Kaye, Julia, Finkbeiner, Steven, Wyman, Stacia K, LeNail, Alex, Lima, Leandro, Fraenkel, Ernest, Svendsen, Clive N, Thompson, Leslie M, Van Eyk, Jennifer E, Berry, James D, Miller, Timothy M, Kolb, Stephen J, Cudkowicz, Merit, Baxi, Emily, Clinical Research in ALS and Related Disorders for Therapeutic Development (CReATe) Consortium, Benatar, Michael, Taylor, J Paul, Rampersaud, Evadnie, Wu, Gang, Wuu, Joanne, SLAGEN Consortium, Lauria, Giuseppe, Verde, Federico, Fogh, Isabella, Tiloca, Cinzia, Comi, Giacomo P, Sorarù, Gianni, Cereda, Cristina, French ALS Consortium, Corcia, Philippe, Laaksovirta, Hannu, Myllykangas, Liisa, Jansson, Lilja, Valori, Miko, Ealing, John, Hamdalla, Hisham, Rollinson, Sara, Pickering-Brown, Stuart, and Orrell, Richard W

Subjects
ITALSGEN Consortium, Genomic Translation for ALS Care (GTAC) Consortium, ALS Sequencing Consortium, NYGC ALS Consortium, Answer ALS Foundation, Clinical Research in ALS and Related Disorders for Therapeutic Development (CReATe) Consortium, SLAGEN Consortium, French ALS Consortium, Project MinE ALS Sequencing Consortium, Humans, Amyotrophic Lateral Sclerosis, Cohort Studies, Amino Acid Sequence, Adult, Aged, Aged, 80 and over, Middle Aged, Female, Male, Genome-Wide Association Study, Young Adult, Loss of Function Mutation, Kinesins, ALS, GWAS, KIF5A, WES, WGS, axonal transport, cargo, Brain Disorders, Genetics, Human Genome, Rare Diseases, Neurosciences, Neurodegenerative, Aetiology, 2.1 Biological and endogenous factors, Neurological, Psychology, Cognitive Sciences, Neurology & Neurosurgery
Abstract

To identify novel genes associated with ALS, we undertook two lines of investigation. We carried out a genome-wide association study comparing 20,806 ALS cases and 59,804 controls. Independently, we performed a rare variant burden analysis comparing 1,138 index familial ALS cases and 19,494 controls. Through both approaches, we identified kinesin family member 5A (KIF5A) as a novel gene associated with ALS. Interestingly, mutations predominantly in the N-terminal motor domain of KIF5A are causative for two neurodegenerative diseases: hereditary spastic paraplegia (SPG10) and Charcot-Marie-Tooth type 2 (CMT2). In contrast, ALS-associated mutations are primarily located at the C-terminal cargo-binding tail domain and patients harboring loss-of-function mutations displayed an extended survival relative to typical ALS cases. Taken together, these results broaden the phenotype spectrum resulting from mutations in KIF5A and strengthen the role of cytoskeletal defects in the pathogenesis of ALS.

Published
2018

8. 86 Genome sequencing as a first-tier prenatal diagnostic test: Is it time to change?

Author

Jobanputra, Vaidehi, primary, Giordano, Jessica L., additional, Pervola, Josie, additional, Okur, Volkan, additional, Thomas-Wilson, Amanda, additional, Guha, Saurav, additional, Rehman, Atteeq U., additional, Wilson, Ashley, additional, Tinfow, Alexandra, additional, Galloway, Stephanie, additional, Abhyankar, Avinash, additional, Felice, Vanessa, additional, Esteves, Cecilia, additional, Hegedus, Endre, additional, Phadke, Shruti, additional, Srinivasa, Sowmya Thirumalai, additional, Khan, Shahid Y., additional, Nava, Caroline, additional, Yan, Qi, additional, Levy, Brynn, additional, and Wapner, Ronald J., additional

Published
2024
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9. Correction to: The NYCKidSeq project: study protocol for a randomized controlled trial incorporating genomics into the clinical care of diverse New York City children

Author

Odgis, Jacqueline A., Gallagher, Katie M., Suckiel, Sabrina A., Donohue, Katherine E., Ramos, Michelle A., Kelly, Nicole R., Bertier, Gabrielle, Blackburn, Christina, Brown, Kaitlyn, Fielding, Lena, Lopez, Jessenia, Aguiniga, Karla Lopez, Maria, Estefany, Rodriguez, Jessica E., Sebastin, Monisha, Teitelman, Nehama, Watnick, Dana, Yelton, Nicole M., Abhyankar, Avinash, Abul-Husn, Noura S., Baum, Aaron, Bauman, Laurie J., Beal, Jules C., Bloom, Toby, Cunningham-Rundles, Charlotte, Diaz, George A., Dolan, Siobhan, Ferket, Bart S., Jobanputra, Vaidehi, Kovatch, Patricia, McDonald, Thomas V., McGoldrick, Patricia E., Rhodes, Rosamond, Rinke, Michael L., Robinson, Mimsie, Rubinstein, Arye, Shulman, Lisa H., Stolte, Christian, Wolf, Steven M., Yozawitz, Elissa, Zinberg, Randi E., Greally, John M., Gelb, Bruce D., Horowitz, Carol R., Wasserstein, Melissa P., and Kenny, Eimear E.

Published
2021
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10. A Dominant Mutation in Human RAD51 Reveals Its Function in DNA Interstrand Crosslink Repair Independent of Homologous Recombination

Author

Wang, Anderson T, Kim, Taeho, Wagner, John E, Conti, Brooke A, Lach, Francis P, Huang, Athena L, Molina, Henrik, Sanborn, Erica M, Zierhut, Heather, Cornes, Belinda K, Abhyankar, Avinash, Sougnez, Carrie, Gabriel, Stacey B, Auerbach, Arleen D, Kowalczykowski, Stephen C, and Smogorzewska, Agata

Subjects
Biological Sciences, Genetics, Hematology, Generic health relevance, Cell Survival, Cross-Linking Reagents, DNA, DNA Helicases, DNA Repair, Exodeoxyribonucleases, Fanconi Anemia, Female, Genomic Instability, HEK293 Cells, Heterozygote, Humans, Infant, Mutation, Rad51 Recombinase, RecQ Helicases, Replication Protein A, Werner Syndrome Helicase, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

Repair of DNA interstrand crosslinks requires action of multiple DNA repair pathways, including homologous recombination. Here, we report a de novo heterozygous T131P mutation in RAD51/FANCR, the key recombinase essential for homologous recombination, in a patient with Fanconi anemia-like phenotype. In vitro, RAD51-T131P displays DNA-independent ATPase activity, no DNA pairing capacity, and a co-dominant-negative effect on RAD51 recombinase function. However, the patient cells are homologous recombination proficient due to the low ratio of mutant to wild-type RAD51 in cells. Instead, patient cells are sensitive to crosslinking agents and display hyperphosphorylation of Replication Protein A due to increased activity of DNA2 and WRN at the DNA interstrand crosslinks. Thus, proper RAD51 function is important during DNA interstrand crosslink repair outside of homologous recombination. Our study provides a molecular basis for how RAD51 and its associated factors may operate in a homologous recombination-independent manner to maintain genomic integrity.

Published
2015

11. Implementation of Rapid Genome Sequencing for Critically Ill Infants With Complex Congenital Heart Disease

Author

Hays, Thomas, primary, Hernan, Rebecca, additional, Disco, Michele, additional, Griffin, Emily L., additional, Goldshtrom, Nimrod, additional, Vargas, Diana, additional, Krishnamurthy, Ganga, additional, Bomback, Miles, additional, Rehman, Atteeq U., additional, Wilson, Amanda T., additional, Guha, Saurav, additional, Phadke, Shruti, additional, Okur, Volkan, additional, Robinson, Dino, additional, Felice, Vanessa, additional, Abhyankar, Avinash, additional, Jobanputra, Vaidehi, additional, and Chung, Wendy K., additional

Published
2023
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12. Genome-wide Analyses Identify KIF5A as a Novel ALS Gene

Author

Logullo, Francesco O., Simone, Isabella, Logroscino, Giancarlo, Salvi, Fabrizio, Bartolomei, Ilaria, Borghero, Giuseppe, Murru, Maria Rita, Costantino, Emanuela, Pani, Carla, Puddu, Roberta, Caredda, Carla, Piras, Valeria, Tranquilli, Stefania, Cuccu, Stefania, Corongiu, Daniela, Melis, Maurizio, Milia, Antonio, Marrosu, Francesco, Marrosu, Maria Giovanna, Floris, Gianluca, Cannas, Antonino, Capasso, Margherita, Caponnetto, Claudia, Mancardi, Gianluigi, Origone, Paola, Mandich, Paola, Conforti, Francesca L., Cavallaro, Sebastiano, Mora, Gabriele, Marinou, Kalliopi, Sideri, Riccardo, Penco, Silvana, Mosca, Lorena, Lunetta, Christian, Pinter, Giuseppe Lauria, Corbo, Massimo, Riva, Nilo, Carrera, Paola, Volanti, Paolo, Mandrioli, Jessica, Fini, Nicola, Fasano, Antonio, Tremolizzo, Lucio, Arosio, Alessandro, Ferrarese, Carlo, Trojsi, Francesca, Tedeschi, Gioacchino, Monsurrò, Maria Rosaria, Piccirillo, Giovanni, Femiano, Cinzia, Ticca, Anna, Ortu, Enzo, La Bella, Vincenzo, Spataro, Rossella, Colletti, Tiziana, Sabatelli, Mario, Zollino, Marcella, Conte, Amelia, Luigetti, Marco, Lattante, Serena, Marangi, Giuseppe, Santarelli, Marialuisa, Petrucci, Antonio, Pugliatti, Maura, Pirisi, Angelo, Parish, Leslie D., Occhineri, Patrizia, Giannini, Fabio, Battistini, Stefania, Ricci, Claudia, Benigni, Michele, Cau, Tea B., Loi, Daniela, Calvo, Andrea, Moglia, Cristina, Brunetti, Maura, Barberis, Marco, Restagno, Gabriella, Casale, Federico, Marrali, Giuseppe, Fuda, Giuseppe, Ossola, Irene, Cammarosano, Stefania, Canosa, Antonio, Ilardi, Antonio, Manera, Umberto, Grassano, Maurizio, Tanel, Raffaella, Pisano, Fabrizio, Harms, Matthew B., Goldstein, David B., Shneider, Neil A., Goutman, Stephen, Simmons, Zachary, Miller, Timothy M., Chandran, Siddharthan, Pal, Suvankar, Manousakis, Georgios, Appel, Stanley H., Simpson, Ericka, Wang, Leo, Baloh, Robert H., Gibson, Summer, Bedlack, Richard, Lacomis, David, Sareen, Dhruv, Sherman, Alexander, Bruijn, Lucie, Penny, Michelle, Allen, Andrew S., Appel, Stanley, Bedlack, Richard S., Boone, Braden E., Brown, Robert, Carulli, John P., Chesi, Alessandra, Chung, Wendy K., Cirulli, Elizabeth T., Cooper, Gregory M., Couthouis, Julien, Day-Williams, Aaron G., Dion, Patrick A., Gitler, Aaron D., Glass, Jonathan D., Han, Yujun, Harris, Tim, Hayes, Sebastian D., Jones, Angela L., Keebler, Jonathan, Krueger, Brian J., Lasseigne, Brittany N., Levy, Shawn E., Lu, Yi-Fan, Maniatis, Tom, McKenna-Yasek, Diane, Myers, Richard M., Petrovski, Slavé, Pulst, Stefan M., Raphael, Alya R., Ravits, John M., Ren, Zhong, Rouleau, Guy A., Sapp, Peter C., Sims, Katherine B., Staropoli, John F., Waite, Lindsay L., Wang, Quanli, Wimbish, Jack R., Xin, Winnie W., Phatnani, Hemali, Kwan, Justin, Broach, James R., Arcila-Londono, Ximena, Lee, Edward B., Van Deerlin, Vivianna M., Fraenkel, Ernest, Ostrow, Lyle W., Baas, Frank, Zaitlen, Noah, Berry, James D., Malaspina, Andrea, Fratta, Pietro, Cox, Gregory A., Thompson, Leslie M., Finkbeiner, Steve, Dardiotis, Efthimios, Hornstein, Eran, MacGowan, Daniel J., Heiman-Patterson, Terry, Hammell, Molly G., Patsopoulos, Nikolaos A., Dubnau, Joshua, Nath, Avindra, Kaye, Julia, Finkbeiner, Steven, Wyman, Stacia, LeNail, Alexander, Lima, Leandro, Rothstein, Jeffrey D., Svendsen, Clive N., Van Eyk, Jenny, Maragakis, Nicholas J., Kolb, Stephen J., Cudkowicz, Merit, Baxi, Emily, Benatar, Michael, Taylor, J. Paul, Wu, Gang, Rampersaud, Evadnie, Wuu, Joanne, Rademakers, Rosa, Züchner, Stephan, Schule, Rebecca, McCauley, Jacob, Hussain, Sumaira, Cooley, Anne, Wallace, Marielle, Clayman, Christine, Barohn, Richard, Statland, Jeffrey, Ravits, John, Swenson, Andrea, Jackson, Carlayne, Trivedi, Jaya, Khan, Shaida, Katz, Jonathan, Jenkins, Liberty, Burns, Ted, Gwathmey, Kelly, Caress, James, McMillan, Corey, Elman, Lauren, Pioro, Erik, Heckmann, Jeannine, So, Yuen, Walk, David, Maiser, Samuel, Zhang, Jinghui, Silani, Vincenzo, Ticozzi, Nicola, Gellera, Cinzia, Ratti, Antonia, Taroni, Franco, Lauria, Giuseppe, Verde, Federico, Fogh, Isabella, Tiloca, Cinzia, Comi, Giacomo P., Sorarù, Gianni, Cereda, Cristina, D’Alfonso, Sandra, Corrado, Lucia, De Marchi, Fabiola, Corti, Stefania, Ceroni, Mauro, Mazzini, Letizia, Siciliano, Gabriele, Filosto, Massimiliano, Inghilleri, Maurizio, Peverelli, Silvia, Colombrita, Claudia, Poletti, Barbara, Maderna, Luca, Del Bo, Roberto, Gagliardi, Stella, Querin, Giorgia, Bertolin, Cinzia, Pensato, Viviana, Castellotti, Barbara, Camu, William, Mouzat, Kevin, Lumbroso, Serge, Corcia, Philippe, Meininger, Vincent, Besson, Gérard, Lagrange, Emmeline, Clavelou, Pierre, Guy, Nathalie, Couratier, Philippe, Vourch, Patrick, Danel, Véronique, Bernard, Emilien, Lemasson, Gwendal, Al Kheifat, Ahmad, Al-Chalabi, Ammar, Andersen, Peter, Basak, A. Nazli, Blair, Ian P., Chio, Adriano, Cooper-Knock, Jonathan, de Carvalho, Mamede, Dekker, Annelot, Drory, Vivian, Redondo, Alberto Garcia, Gotkine, Marc, Hardiman, Orla, Hide, Winston, Iacoangeli, Alfredo, Glass, Jonathan, Kenna, Kevin, Kiernan, Matthew, Kooyman, Maarten, Landers, John, McLaughlin, Russell, Middelkoop, Bas, Mill, Jonathan, Neto, Miguel Mitne, Moisse, Mattieu, Pardina, Jesus Mora, Morrison, Karen, Newhouse, Stephen, Pinto, Susana, Pulit, Sara, Robberecht, Wim, Shatunov, Aleksey, Shaw, Pamela, Shaw, Chris, Sproviero, William, Tazelaar, Gijs, van Damme, Philip, van den Berg, Leonard, van der Spek, Rick, van Eijk, Kristel, van Es, Michael, van Rheenen, Wouter, van Vugt, Joke, Veldink, Jan, Weber, Markus, Williams, Kelly L., Zatz, Mayana, Bauer, Denis C., Twine, Natalie A., Nicolas, Aude, Kenna, Kevin P., Renton, Alan E., Faghri, Faraz, Chia, Ruth, Dominov, Janice A., Kenna, Brendan J., Nalls, Mike A., Keagle, Pamela, Rivera, Alberto M., Murphy, Natalie A., van Vugt, Joke J.F.A., Geiger, Joshua T., Van der Spek, Rick A., Pliner, Hannah A., Shankaracharya, Smith, Bradley N., Topp, Simon D., Abramzon, Yevgeniya, Gkazi, Athina Soragia, Eicher, John D., Kenna, Aoife, Messina, Sonia, Simone, Isabella L., Ferrucci, Luigi, Moreno, Cristiane de Araujo Martins, Kamalakaran, Sitharthan, Musunuri, Rajeeva Lochan, Evani, Uday Shankar, Abhyankar, Avinash, Zody, Michael C., Wyman, Stacia K., LeNail, Alex, Van Eyk, Jennifer E., Laaksovirta, Hannu, Myllykangas, Liisa, Jansson, Lilja, Valori, Miko, Ealing, John, Hamdalla, Hisham, Rollinson, Sara, Pickering-Brown, Stuart, Orrell, Richard W., Sidle, Katie C., Hardy, John, Singleton, Andrew B., Johnson, Janel O., Arepalli, Sampath, Polak, Meraida, Asress, Seneshaw, Al-Sarraj, Safa, King, Andrew, Troakes, Claire, Vance, Caroline, de Belleroche, Jacqueline, ten Asbroek, Anneloor L.M.A., Muñoz-Blanco, José Luis, Hernandez, Dena G., Ding, Jinhui, Gibbs, J. Raphael, Scholz, Sonja W., Floeter, Mary Kay, Campbell, Roy H., Landi, Francesco, Bowser, Robert, MacGowan, Daniel J.L., Kirby, Janine, Pioro, Erik P., Pamphlett, Roger, Broach, James, Gerhard, Glenn, Dunckley, Travis L., Brady, Christopher B., Kowall, Neil W., Troncoso, Juan C., Le Ber, Isabelle, Heiman-Patterson, Terry D., Kamel, Freya, Van Den Bosch, Ludo, Strom, Tim M., Meitinger, Thomas, Van Eijk, Kristel R., Moisse, Matthieu, McLaughlin, Russell L., Van Es, Michael A., Boylan, Kevin B., Van Blitterswijk, Marka, Morrison, Karen E., Mora, Jesús S., Drory, Vivian E., Shaw, Pamela J., Turner, Martin R., Talbot, Kevin, Fifita, Jennifer A., Nicholson, Garth A., Esteban-Pérez, Jesús, García-Redondo, Alberto, Rogaeva, Ekaterina, Zinman, Lorne, Cooper-Knock, Johnathan, Brice, Alexis, Goutman, Stephen A., Feldman, Eva L., Gibson, Summer B., Van Damme, Philip, Ludolph, Albert C., Andersen, Peter M., Weishaupt, Jochen H., Trojanowski, John Q., Brown, Robert H., Jr., van den Berg, Leonard H., Veldink, Jan H., Stone, David J., Tienari, Pentti, Chiò, Adriano, Shaw, Christopher E., Traynor, Bryan J., and Landers, John E.

Published
2018
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13. Ribosomal Protein SA Haploinsufficiency in Humans with Isolated Congenital Asplenia

Author

Bolze, Alexandre, Mahlaoui, Nizar, Byun, Minji, Turner, Bridget, Trede, Nikolaus, Ellis, Steven R, Abhyankar, Avinash, Itan, Yuval, Patin, Etienne, Brebner, Samuel, Sackstein, Paul, Puel, Anne, Picard, Capucine, Abel, Laurent, Quintana-Murci, Lluis, Faust, Saul N, Williams, Anthony P, Baretto, Richard, Duddridge, Michael, Kini, Usha, Pollard, Andrew J, Gaud, Catherine, Frange, Pierre, Orbach, Daniel, Emile, Jean-Francois, Stephan, Jean-Louis, Sorensen, Ricardo, Plebani, Alessandro, Hammarstrom, Lennart, Conley, Mary Ellen, Selleri, Licia, and Casanova, Jean-Laurent

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Clinical Research, Congenital Structural Anomalies, Pediatric, DNA Mutational Analysis, Genetic Loci, Haploinsufficiency, Heterotaxy Syndrome, Humans, Mutation, Pedigree, Penetrance, Receptors, Laminin, Ribosomal Proteins, Spleen, General Science & Technology
Abstract

Isolated congenital asplenia (ICA) is characterized by the absence of a spleen at birth in individuals with no other developmental defects. The patients are prone to life-threatening bacterial infections. The unbiased analysis of exomes revealed heterozygous mutations in RPSA in 18 patients from eight kindreds, corresponding to more than half the patients and over one-third of the kindreds studied. The clinical penetrance in these kindreds is complete. Expression studies indicated that the mutations carried by the patients-a nonsense mutation, a frameshift duplication, and five different missense mutations-cause autosomal dominant ICA by haploinsufficiency. RPSA encodes ribosomal protein SA, a component of the small subunit of the ribosome. This discovery establishes an essential role for RPSA in human spleen development.

Published
2013

14. P780: Improving peripartum health is an unappreciated advantage of prenatal genome sequencing

Author

Giordano, Jessica, Pervola, Josie, Wilson, Ashley, Rehman, Atteeq, Thomas-Wilson, Amanda, Guha, Saurav, Okur, Volkan, Tinfow, Alexandra, Galloway, Stephanie, Perrin, Hannah, Esteves, Cecilia, Brace, Poppy, Baptiste, Caitlin, Srinivasa, Sowmya Thirumalai, Khan, Shahid, Elder, Bruce, Hegedus, Endre, Felice, Vanessa, Phadke, Shruti, Abhyankar, Avinash, Jobanputra, Vaidehi, and Wapner, Ronald

Published
2024
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15. O44: Genome sequencing as a first-tier prenatal diagnostic test

Author

Jobanputra, Vaidehi, Giordano, Jessica, Pervola, Josie, Wilson, Ashley, Guha, Saurav, Thomas-Wilson, Amanda, Rehman, Atteeq, Okur, Volkan, Han, Ted, Esteves, Cecilia, Tinfow, Alexandra, Galloway, Stephanie, Srinivasa, Sowmya T., Khan, Shahid, Brace, Poppy, Nava, Caroline, Perrin, Hannah, Elder, Bruce, Hegedus, Endre, Felice, Vanessa, Phadke, Shruti, Abhyankar, Avinash, and Wapner, Ronald

Published
2024
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16. P589: Diagnostic yield of digital gene panel from genome sequencing in common multifactorial endocrine and metabolic disorders

Author

Okur, Volkan, Srinivasa, Sowmya Thirumalai, Halstrom, Amanda, Falcone, John, Rehman, Atteeq, Thomas-Wilson, Amanda, Guha, Saurav, Phadke, Shruti, Abhyankar, Avinash, Wilson, Ashley, Nava, Caroline, Khan, Shahid, Hurd, Maurice, Stewart, Sarah, Claudio, Katerine, Jablonski, Anne, Manohar, Jyothi, Kumar, Sonal, Yeung, Michele, Dakin, Gregory, Bellorin-Marin, Omar, Afaneh, Cheguevara, Hudgins, Lisa, Pena, Jessica, Wei, Esther, Gingras, Laura, King, Alexandra, Tung, Judy, Chen, Shuibing, Smith, Ryan, MacDonald, Theresa, Ritter, Megan, Alonso, Lauro, Elemento, Olivier, Udler, Miriam, Goncalves, Marcus, and Jobanputra, Vaidehi

Published
2024
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18. Molecular diagnostic yield of genome sequencing versus targeted gene panel testing in racially and ethnically diverse pediatric patients

Author

Abul-Husn, Noura S, primary, Marathe, Priya N, additional, Kelly, Nicole R, additional, Bonini, Katherine E, additional, Sebastin, Monisha, additional, Odgis, Jacqueline A, additional, Abhyankar, Avinash, additional, Brown, Kaitlyn, additional, Di Base, Miranda, additional, Gallagher, Katie M, additional, Guha, Saurav, additional, Ioele, Nicolette, additional, Okur, Volkan, additional, Ramos, Michelle A, additional, Rodriguez, Jessica E, additional, Rehman, Atteeq U, additional, Thomas-Wilson, Amanda, additional, Edelmann, Lisa, additional, Zinberg, Randi E, additional, Diaz, George A, additional, Greally, John M, additional, Jobanputra, Vaidehi, additional, Suckiel, Sabrina A, additional, Horowitz, Carol R, additional, Wassersteiin, Melissa P, additional, Kenny, Eimear E, additional, and Gelb, Bruce D, additional

Published
2023
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20. Implementation of Rapid Genome Sequencing for Infants with Congenital Heart Disease

Author

Hays, Thomas, primary, Hernan, Rebecca, additional, Disco, Michele, additional, Griffin, Emily, additional, Goldshtrom, Nimrod, additional, Vargas, Diana, additional, Krishnamurthy, Ganga, additional, Rehman, Atteeq U., additional, Wilson, Amanda T., additional, Guha, Saurav, additional, Phadke, Shruti, additional, Okur, Volkan, additional, Robinson, Dino, additional, Felice, Vanessa, additional, Abhyankar, Avinash, additional, Jobanputra, Vaidehi, additional, and Chung, Wendy K., additional

Published
2022
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21. Identification of copy number variants with genome sequencing: Clinical experiences from the NYCKidSeq program.

Author

Bonini, Katherine E., Thomas‐Wilson, Amanda, Marathe, Priya N., Sebastin, Monisha, Odgis, Jacqueline A., Di Biase, Miranda, Kelly, Nicole R., Ramos, Michelle A., Insel, Beverly J., Scarimbolo, Laura, Rehman, Atteeq U., Guha, Saurav, Okur, Volkan, Abhyankar, Avinash, Phadke, Shruti, Nava, Caroline, Gallagher, Katie M., Elkhoury, Lama, Edelmann, Lisa, and Zinberg, Randi E.

Subjects
NUCLEOTIDE sequencing, GENETIC testing, IDENTIFICATION, DNA copy number variations, PHENOTYPES
Abstract

Copy number variations (CNVs) play a significant role in human disease. While chromosomal microarray has traditionally been the first‐tier test for CNV detection, use of genome sequencing (GS) is increasing. We report the frequency of CNVs detected with GS in a diverse pediatric cohort from the NYCKidSeq program and highlight specific examples of its clinical impact. A total of 1052 children (0–21 years) with neurodevelopmental, cardiac, and/or immunodeficiency phenotypes received GS. Phenotype‐driven analysis was used, resulting in 183 (17.4%) participants with a diagnostic result. CNVs accounted for 20.2% of participants with a diagnostic result (37/183) and ranged from 0.5 kb to 16 Mb. Of participants with a diagnostic result (n = 183) and phenotypes in more than one category, 5/17 (29.4%) were solved by a CNV finding, suggesting a high prevalence of diagnostic CNVs in participants with complex phenotypes. Thirteen participants with a diagnostic CNV (35.1%) had previously uninformative genetic testing, of which nine included a chromosomal microarray. This study demonstrates the benefits of GS for reliable detection of CNVs in a pediatric cohort with variable phenotypes. [ABSTRACT FROM AUTHOR]

Published
2023
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23. Mycobacterial Disease and Impaired IFN-γ Immunity in Humans with Inherited ISG15 Deficiency

Author

Bogunovic, Dusan, Byun, Minji, Durfee, Larissa A., Abhyankar, Avinash, Sanal, Ozden, Mansouri, Davood, Salem, Sandra, Radovanovic, Irena, Grant, Audrey V., Adimi, Parisa, Mansouri, Nahal, Okada, Satoshi, Bryant, Vanessa L., Kong, Xiao-Fei, Kreins, Alexandra, Velez, Marcela Moncada, Boisson, Bertrand, Khalilzadeh, Soheila, Ozcelik, Ugur, Darazam, Ilad Alavi, Schoggins, John W., Rice, Charles M., Al-Muhsen, Saleh, Behr, Marcel, Vogt, Guillaume, Puel, Anne, Bustamante, Jacinta, Gros, Philippe, Huibregtse, Jon M., Abel, Laurent, Boisson-Dupuis, Stéphanie, and Casanova, Jean-Laurent

Published
2012
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24. eP067: Diagnostic yield of genome sequencing versus targeted gene panel testing in diverse pediatric patients in the NYCKidSeq study

Author

Abul-Husn, Noura, primary, Kelly, Nicole, additional, Rodriguez, Jessica, additional, Abhyankar, Avinash, additional, Donohue, Katherine, additional, Brown, Kaitlyn, additional, DiBiase, Miranda, additional, Gallagher, Katie, additional, Guha, Saurav, additional, Ioele, Nicolette, additional, Marathe, Priya, additional, Odgis, Jacqueline, additional, Okur, Volkan, additional, Ramos, Michelle, additional, Rehman, Atteeq, additional, Sebastin, Monisha, additional, Thomas-Wilson, Amanda, additional, Zinberg, Randi, additional, Diaz, George, additional, Suckiel, Sabrina, additional, Greally, John, additional, Jobanputra, Vaidehi, additional, Horowitz, Carol, additional, Wasserstein, Melissa, additional, Kenny, Eimear, additional, and Gelb, Bruce, additional

Published
2022
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25. OP035: Rapid Whole Genome Sequencing (rWGS) in the cardiac NICU

Author

Guha, Saurav, primary, Thomas-Wilson, Amanda, additional, Rahman, Atteeq, additional, Abhyankar, Avinash, additional, Poisner, Hannah, additional, Wilson, Ashley, additional, Hernan, Rebecca, additional, Griffin, Emily, additional, Chung, Wendy, additional, and Jobanputra, Vaidehi, additional

Published
2022
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26. Association of Mitochondrial DNA Copy Number With Brain MRI Markers and Cognitive Function

Author

Zhang, Yuankai, Liu, Xue, Wiggins, Kerri L., Kurniansyah, Nuzulul, Guo, Xiuqing, Rodrigue, Amanda L., Zhao, Wei, Yanek, Lisa R., Ratliff, Scott M., Pitsillides, Achilleas, Aguirre Patiño, Juan Sebastian, Sofer, Tamar, Arking, Dan E., Austin, Thomas R., Beiser, Alexa S., Blangero, John, Boerwinkle, Eric, Bressler, Jan, Curran, Joanne E., Hou, Lifang, Hughes, Timothy M., Kardia, Sharon L.R., Launer, Lenore J., Levy, Daniel, Mosley, Thomas H., Nasrallah, Ilya M., Rich, Stephen S., Rotter, Jerome I., Seshadri, Sudha, Tarraf, Wassim, González, Kevin A., Ramachandran, Vasan, Yaffe, Kristine, Nyquist, Paul A., Psaty, Bruce M., DeCarli, Charles S., Smith, Jennifer A., Glahn, David C., González, Hector M., Bis, Joshua C., Fornage, Myriam, Heckbert, Susan R., Fitzpatrick, Annette L., Liu, Chunyu, Satizabal, Claudia L., Aguilera, Norma, Ament, Seth, Ammous, Farah, Arnett, Donna K, Becker, Diane, Bis, Joshua, Blue, Elizabeth, Boerwinkle, Eric, Breaux, Camille, Bressler, Jan, Chaar, Dima, MHI, Clarkson-Townsend, Danielle, Cooper, Brigidann, Coresh, Josef, Correa, Adolfo, DeStefano, Anita, Ding, Jingzhong, Fardo, David, Fitzpatrick, Annette, Fornage, Myriam, French, Jennifer, Glahn, David, Gonzalez, Hector, Granot-Hershkovitz, Einat, Hanly, Patrick, Hayden, Kathleen, Heckbert, Susan, Heemann, Scott, Horvath, Steve, Hoth, Karin, Hughes, Timothy, Jaiswal, Sidd, Jian, Xueqiu, Katsumata, Yuriko, Kho, Minjung, Kooperberg, Charles, Launer, Lenore, Lin, Honghuang, Litkowski, Elizabeth, Longstreth, Will, Martin, Alexandra, Mayeux, Richard, Mikulla, Julie, Miller, Amy, Misra, Biswapriya, Mosley, Thomas, Nyquist, Paul, O'Connell, Jeff, Olivier, Michael, Peloso, Gina, Perry, James, Psaty, Bruce, Purcell, Shaun, Raffield, Laura, Ranaweera, Yugandi, Reiner, Alex, Rotter, Jerome, Sargurupremraj, Muralidharan, Sarnowski, Chloé, Satizabal, Claudia, Schellenberg, Gerard, Schoenbein, Bonnie L, Seshadri, Sudha, Shade, Lincoln, Short, Meghan I, Simino, Jeannette, Smith, Jennifer, Smith, Mallorie, Smoller, Sylvia, Snively, Beverly, Soemedi, Rachel, Sokolow, Sophie, Thorington, Daune, Thornton, Timothy A., Yanek, Lisa, Yang, Qiong, Yu, Miao, Zare, Habil, Zhao, Wei, Abecasis, Goncalo, Abhyankar, Avinash, Aldred, Micheala, Arking, Dan, Ashley-Koch, Allison, Aviv, Abraham, Barnes, Kathleen, Barron-Casella, Emily, Battle, Stephanie, Blackwell, Thomas, Burkardt, Deepika, Castellani, Christina A, Comhair, Suzy, Cooper, Brigidann, Correa, Adolfo, Crockett, Phyllis, de Andrade, Mariza, DeMeo, Dawn, DePaoli, Maria Rizzo, Ding, Jun, Dobski, Christine, Erzurum, Serpil, Farha, Samar, Fetterman, Jessica, Floyd, Caitlin, Fu, Mao, Gist, Amber, Granot-Hershkovitz, Einat, Gu, C. Charles, Heemann, Scott, Hernandez, Ryan, Hong, Yun Soo, Hsu, Yi-Hsiang, Justice, Anne, Lange, Leslie, Levy, Dan, Lin, Honghuang, Liu, Chunyu, Longchamps, Ryan, Ma, Jiantao, Manson, JoAnn, Markus, Tammy, McDonald, Merry-Lynn, McGarvey, Stephen, Mikulla, Julie, Montgomery, Courtney, Musunuri, Rajeeva Lochan, O'Connell, Jeff, Oppong, Richard, Pankratz, Nathan, Qian, Yong, Rotter, Jerome, Shaw, Jessica R, Smith, Albert Vernon, Sofer, Tamar, Streeten, Elizabeth, Tang, Weihong, Taylor, Kent D., Telen, Marilyn, Thompson, Shelby, Thorington, Daune, Tiwari, Hemant, Walsh, Ann, Wan, Emily, Wang, Cuicui, Wang, Heming, Wang, Penglong, Weir, Bruce, Williams, L. Keoki, Wilson, James, Xiao, Shujie, Xu, Weiling, Yang, Yu-Chung, and Zhao, Wei

Published
2023
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27. Immunodeficiency, autoinflammation and amylopectinosis in humans with inherited HOIL-1 and LUBAC deficiency

Author

Boisson, Bertrand, Laplantine, Emmanuel, Prando, Carolina, Giliani, Silvia, Israelsson, Elisabeth, Xu, Zhaohui, Abhyankar, Avinash, Israël, Laura, Trevejo-Nunez, Giraldina, Bogunovic, Dusan, Cepika, Alma-Martina, MacDuff, Donna, Chrabieh, Maya, Hubeau, Marjorie, Bajolle, Fanny, Debré, Marianne, Mazzolari, Evelina, Vairo, Donatella, Agou, Fabrice, Virgin, Herbert W, Bossuyt, Xavier, Rambaud, Caroline, Facchetti, Fabio, Bonnet, Damien, Quartier, Pierre, Fournet, Jean-Christophe, Pascual, Virginia, Chaussabel, Damien, Notarangelo, Luigi D, Puel, Anne, Israël, Alain, Casanova, Jean-Laurent, and Picard, Capucine

Published
2012
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28. Additional file 2 of Coding and noncoding variants in EBF3 are involved in HADDS and simplex autism

Author

Padhi, Evin M., Hayeck, Tristan J., Cheng, Zhang, Chatterjee, Sumantra, Mannion, Brandon J., Byrska-Bishop, Marta, Willems, Marjolaine, Pinson, Lucile, Redon, Sylvia, Benech, Caroline, Uguen, Kevin, Audebert-Bellanger, Séverine, Le Marechal, Cédric, Férec, Claude, Efthymiou, Stephanie, Rahman, Fatima, Maqbool, Shazia, Maroofian, Reza, Houlden, Henry, Musunuri, Rajeeva, Narzisi, Giuseppe, Abhyankar, Avinash, Hunter, Riana D., Akiyama, Jennifer, Fries, Lauren E., Ng, Jeffrey K., Mehinovic, Elvisa, Stong, Nick, Allen, Andrew S., Dickel, Diane E., Bernier, Raphael A., Gorkin, David U., Pennacchio, Len A., Zody, Michael C., and Turner, Tychele N.

Abstract

Additional file 2: Fig S1. Polygenic risk scores (PRS) for the three individuals with hs737 mutations. Fig. S2. Zoom in on the hs737 enhancer with annotations from other datasets. The enhancer is in a PsychEncode fetal enhancer, contains central nervous system DNaseI hypersensitive sites, contains conserved transcription factor binding sites, and is highly conserved across the vertebrate lineage. Also shown are the locations of the hs737 de novo mutations identified in individuals with autism. Fig S3. String-db network analysis, predicts interactions between EBF3 and SPAST, CSNK2A1, HNRNPU, CHD7, KDM6A, KDM6B. Table S2. fitDNM results for de novo mutations in VISTA enhancers driving brain expression. Table S3. Other de novo SNVs/indels seen in individuals with hs737 enhancer mutations. Table S4. Other copy number variation in individuals with hs737 de novo mutations. Table S5. Statistical significance calculations for the luciferase assays. Table S6. Expression of transcription factors potentially binding at variant locations in the hs737 enhancers.

Published
2021
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29. Additional file 1 of The NYCKidSeq project: study protocol for a randomized controlled trial incorporating genomics into the clinical care of diverse New York City children

Author

Odgis, Jacqueline A., Gallagher, Katie M., Suckiel, Sabrina A., Donohue, Katherine E., Ramos, Michelle A., Kelly, Nicole R., Bertier, Gabrielle, Blackburn, Christina, Brown, Kaitlyn, Fielding, Lena, Jessenia Lopez, Aguiniga, Karla Lopez, Estefany Maria, Rodriguez, Jessica E., Sebastin, Monisha, Nehama Teitelman, Watnick, Dana, Yelton, Nicole M., Abhyankar, Avinash, Abul-Husn, Noura S., Baum, Aaron, Bauman, Laurie J., Beal, Jules C., Bloom, Toby, Cunningham-Rundles, Charlotte, Diaz, George A., Dolan, Siobhan, Ferket, Bart S., Vaidehi Jobanputra, Kovatch, Patricia, McDonald, Thomas V., McGoldrick, Patricia E., Rhodes, Rosamond, Rinke, Michael L., Mimsie Robinson, Rubinstein, Arye, Shulman, Lisa H., Stolte, Christian, Wolf, Steven M., Yozawitz, Elissa, Zinberg, Randi E., Greally, John M., Gelb, Bruce D., Horowitz, Carol R., Wasserstein, Melissa P., and Kenny, Eimear E.

Abstract

Additional file 1. SPIRIT checklist.

Published
2021
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30. Impaired intrinsic immunity to HSV-1 in human iPSC-derived TLR3-deficient CNS cells

Author

Lafaille, Fabien G., Pessach, Itai M., Zhang, Shen-Ying, Ciancanelli, Michael J., Herman, Melina, Abhyankar, Avinash, Ying, Shui-Wang, Keros, Sotirios, Goldstein, Peter A., Mostoslavsky, Gustavo, Ordovas-Montanes, Jose, Jouanguy, Emmanuelle, Plancoulaine, Sabine, Tu, Edmund, Elkabetz, Yechiel, Muhsen, Saleh Al-, Tardieu, Marc, Schlaeger, Thorsten M., Daley, George Q., Abel, Laurent, Casanova, Jean-Laurent, Studer, Lorenz, and Notarangelo, Luigi D.

Subjects
Neurons -- Physiological aspects -- Health aspects -- Research, Virulence (Microbiology) -- Research -- Physiological aspects -- Health aspects, Stem cells -- Physiological aspects -- Health aspects -- Research, Herpes simplex virus -- Physiological aspects -- Health aspects -- Research, Toll-like receptors -- Physiological aspects -- Health aspects -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

In the course of primary infection with herpes simplex virus 1 (HSV-1), children with inborn errors of toll-like receptor 3 (TLR3) immunity are prone to HSV-1 encephalitis (HSE) (1-3). We tested the hypothesis that the pathogenesis of HSE involves non-haematopoietic CNS-resident cells. We derived induced pluripotent stem cells (iPSCs) from the dermal fibroblasts of TLR3- and UNC-93B-deficient patients and from controls. These iPSCs were differentiated into highly purified populations of neural stem cells (NSCs), neurons, astrocytes and oligodendrocytes. The induction of interferon-β (IFN-β) and/or IFN-λ1 in response to stimulation by the dsRNA analogue polyinosinic:polycytidylic acid (poly(I:C)) was dependent on TLR3 and UNC-93B in all cells tested. However, the induction of IFN-β and IFN-λ1 in response to HSV-1 infection was impaired selectively in UNC-93B-deficient neurons and oligodendrocytes. These cells were also much more susceptible to HSV-1 infection than control cells, whereas UNC-93B-deficient NSCs and astrocytes were not. TLR3-deficient neurons were also found to be susceptible to HSV-1 infection. The rescue of UNC-93B- and TLR3deficient cells with the corresponding wild-type allele showed that the genetic defect was the cause of the poly(I:C) and HSV-1 phenotypes. The viral infection phenotype was rescued further by treatment with exogenous IFN-a or IFN-β (IFN-α/β) but not IFN-λ1. Thus, impaired TLR3- and UNC-93B-dependent IFN-α/β intrinsic immunity to HSV-1 in the CNS, in neurons and oligodendrocytes in particular, may underlie the pathogenesis of HSE in children with TLR3-pathway deficiencies., Childhood HSE is a rare, life-threatening, central nervous system (CNS)-restricted complication of primary infection with HSV-1, an almost ubiquitous virus that is typically innocuous4. Children with HSE are not unusually [...]

Published
2012
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31. Human RHOH deficiency causes T cell defects and susceptibility to EV-HPV infections

Author

Crequer, Amandine, Troeger, Anja, Patin, Etienne, Ma, Cindy S., Picard, Capucine, Pedergnana, Vincent, Fieschi, Claire, Lim, Annick, Abhyankar, Avinash, Gineau, Laure, Mueller-Fleckenstein, Ingrid, Schmidt, Monika, Taieb, Alain, Krueger, James, Abel, Laurent, Tangye, Stuart G., Orth, Gerard, Williams, David A., Casanova, Jean-Laurent, and Jouanguy, Emmanuelle

Subjects
T cells -- Genetic aspects, Skin diseases -- Diagnosis -- Care and treatment, Papillomavirus infections -- Diagnosis -- Care and treatment, Health care industry
Abstract

Epidermodysplasia verruciformis (EV) is a rare genetic disorder characterized by increased susceptibility to specific human papillomaviruses, the betapapillomaviruses. These EV-HPVs cause warts and increase the risk of skin carcinomas in otherwise healthy individuals. Inactivating mutations in epidermodysplasia verruciformis 1 (EVER1) or EVER2 have been identified in most, but not all, patients with autosomal recessive EV. We found that 2 young adult siblings presenting with T cell deficiency and various infectious diseases, including persistent EV-HPV infections, were homozygous for a mutation creating a stop codon in the ras homolog gene family member H (RHOH) gene. RHOH encodes an atypical Rho GTPase expressed predominantly in hematopoietic cells. Patients' circulating T cells contained predominantly effector memory T cells, which displayed impaired TCR signaling. Additionally, very few circulating T cells expressed the β7 integrin subunit, which homes T cells to specific tissues. Similarly, Rhoh-null mice exhibited a severe overall T cell defect and abnormally small numbers of circulating β7-positive cells. Expression of the WT, but not of the mutated RHOH, allele in Rhoh-/- hematopoietic stem cells corrected the T cell lymphopenia in mice after bone marrow transplantation. We conclude that RHOH deficiency leads to T cell defects and persistent EV-HPV infections, suggesting that T cells play a role in the pathogenesis of chronic EV-HPV infections., Introduction Epidermodysplasia verruciformis (EV) is a rare, lifelong disorder characterized by disseminated and persistent flat warts or pityriasis versicolor-like (PV-like) lesions due to an abnormal and selective susceptibility to a [...]

Published
2012
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32. A novel mutation in the POLE2 gene causing combined immunodeficiency

Author

Frugoni, Francesco, Dobbs, Kerry, Felgentreff, Kerstin, Aldhekri, Hasan, Al Saud, Bandar K., Arnaout, Rand, Ali, Afshan Ashraf, Abhyankar, Avinash, Alroqi, Fayhan, Giliani, Silvia, Ojeda, Mayra Martinez, Tsitsikov, Erdyni, Pai, Sung-Yun, Casanova, Jean Laurent, Notarangelo, Luigi D., and Manis, John P.

Published
2016
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33. Whole-exome-sequencing-based discovery of human FADD deficiency

Author

Bolze, Alexandre, Byun, Minji, McDonald, David, Morgan, Neil V., Abhyankar, Avinash, Premkumar, Lakshmannane, Puel, Anne, Bacon, Chris M., Rieux-Laucat, Frederic, Ki Pang, Britland, Alison, Abel, Laurent, Cant, Andrew, Maher, Eamonn R., Riedl, Stefan J., Hambleton, Sophie, and Casanova, Jean-Laurent

Subjects
Gene mutations -- Analysis, Autoimmune diseases -- Genetic aspects, Autoimmune diseases -- Research, Biological sciences
Abstract

A combination of genome-wide linkage and whole-exome sequencing was used to identify a homozygous missense mutation in FADD, encoding the Fas-associated death domain protein (FADD) which cause dominantly inherited autoimmune lymphoproliferative syndrome (ALPS) in the patients. The results provide insight into the key role of FADD in Fas-dependent and Fas-independent signaling pathways in humans and genetic basis of the complex clinical disorder and some of the key mechanisms underlying its pathogenesis.

Published
2010

34. A Homozygous PDE6D Mutation in Joubert Syndrome Impairs Targeting of Farnesylated INPP5E Protein to the Primary Cilium

Author

Thomas, Sophie, Wright, Kevin J., Le Corre, Stéphanie, Micalizzi, Alessia, Romani, Marta, Abhyankar, Avinash, Saada, Julien, Perrault, Isabelle, Amiel, Jeanne, Litzler, Julie, Filhol, Emilie, Elkhartoufi, Nadia, Kwong, Mandy, Casanova, Jean-Laurent, Boddaert, Nathalie, Baehr, Wolfgang, Lyonnet, Stanislas, Munnich, Arnold, Burglen, Lydie, Chassaing, Nicolas, Encha-Ravazi, Ferechté, Vekemans, Michel, Gleeson, Joseph G., Valente, Enza Maria, Jackson, Peter K., Drummond, Iain A., Saunier, Sophie, and Attié-Bitach, Tania

Published
2014
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35. Novel microdeletions in the SOX5 gene in two patients with Lamb-Shaffer syndrome phenotype in the NYCKidSeq Study

Author

Guha, Saurav, primary, Donohue, Katherine, additional, Brown, Kaitlyn, additional, Thomas-Wilson, Amanda, additional, Rahman, Atteeq, additional, Abhyankar, Avinash, additional, Poisner, Hannah, additional, Wilson, Ashley, additional, Horowitz, Carol, additional, Kenny, Eimear, additional, Greally, John, additional, Gelb, Bruce, additional, Diaz, George, additional, Wasserstein, Melissa, additional, and Jobanputra, Vaidehi, additional

Published
2021
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36. De Novo Mutation in an Enhancer of EBF3 in simplex autism

Author

Padhi, Evin, Padhi, Evin, Hayeck, Tristan, Mannion, Brandon, Chatterjee, Sumantra, Byrska-Bishop, Marta, Musunuri, Rajeeva, Narzisi, Giuseppe, Abhyankar, Avinash, Cheng, Zhang, Hunter, Riana, Akiyama, Jennifer, Fries, Lauren, Ng, Jeffrey, Stong, Nick, Allen, Andrew, Dickel, Diane, Bernier, Raphael, Gorkin, David, Pennacchio, Len, Zody, Michael, Turner, Tychele, Padhi, Evin, Padhi, Evin, Hayeck, Tristan, Mannion, Brandon, Chatterjee, Sumantra, Byrska-Bishop, Marta, Musunuri, Rajeeva, Narzisi, Giuseppe, Abhyankar, Avinash, Cheng, Zhang, Hunter, Riana, Akiyama, Jennifer, Fries, Lauren, Ng, Jeffrey, Stong, Nick, Allen, Andrew, Dickel, Diane, Bernier, Raphael, Gorkin, David, Pennacchio, Len, Zody, Michael, and Turner, Tychele

Abstract

Previous research in autism and other neurodevelopmental disorders (NDDs) has indicated an important contribution of de novo protein-coding variants within specific genes. The role of de novo noncoding variation has been observable as a general increase in genetic burden but has yet to be resolved to individual functional elements. In this study, we assessed whole-genome sequencing data in 2,671 families with autism, with a specific focus on de novo variation in enhancers with previously characterized in vivo activity. We identified three independent de novo mutations limited to individuals with autism in the enhancer hs737. These mutations result in similar phenotypic characteristics, affect enhancer activity in vitro , and preferentially occur in AAT motifs in the enhancer with predicted disruptions of transcription factor binding. We also find that hs737 is enriched for copy number variation in individuals with NDDs, is dosage sensitive in the human population, is brain-specific, and targets the NDD gene EBF3 that is genome-wide significant for protein coding de novo variants, demonstrating the importance of understanding all forms of variation in the genome. One Sentence Summary Whole-genome sequencing in thousands of families reveals variants relevant to simplex autism in a brain enhancer of the well-established neurodevelopmental disorder gene EBF3 .

Published
2020

37. The NYCKidSeq project: study protocol for a randomized controlled trial incorporating genomics into the clinical care of diverse New York City children

Author

Odgis, Jacqueline A., primary, Gallagher, Katie M., additional, Suckiel, Sabrina A., additional, Donohue, Katherine E., additional, Ramos, Michelle A., additional, Kelly, Nicole R., additional, Bertier, Gabrielle, additional, Blackburn, Christina, additional, Brown, Kaitlyn, additional, Fielding, Lena, additional, Lopez, Jessenia, additional, Aguiniga, Karla Lopez, additional, Maria, Estefany, additional, Rodriguez, Jessica E., additional, Sebastin, Monisha, additional, Teitelman, Nehama, additional, Watnick, Dana, additional, Yelton, Nicole M., additional, Abhyankar, Avinash, additional, Abul-Husn, Noura S., additional, Baum, Aaron, additional, Bauman, Laurie J., additional, Beal, Jules C., additional, Bloom, Toby, additional, Cunningham-Rundles, Charlotte, additional, Diaz, George A., additional, Dolan, Siobhan, additional, Ferket, Bart S., additional, Jobanputra, Vaidehi, additional, Kovatch, Patricia, additional, McDonald, Thomas V., additional, McGoldrick, Patricia E., additional, Rhodes, Rosamond, additional, Rinke, Michael L., additional, Robinson, Mimsie, additional, Rubinstein, Arye, additional, Shulman, Lisa H., additional, Stolte, Christian, additional, Wolf, Steven M., additional, Yozawitz, Elissa, additional, Zinberg, Randi E., additional, Greally, John M., additional, Gelb, Bruce D., additional, Horowitz, Carol R., additional, Wasserstein, Melissa P., additional, and Kenny, Eimear E., additional

Published
2021
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39. New and recurrent gain-of-function STAT1 mutations in patients with chronic mucocutaneous candidiasis from Eastern and Central Europe

Author

Soltész, Beáta, Tóth, Beáta, Shabashova, Nadejda, Bondarenko, Anastasia, Okada, Satoshi, Cypowyj, Sophie, Abhyankar, Avinash, Csorba, Gabriella, Taskó, Szilvia, Sarkadi, Adrien Katalin, Méhes, Leonóra, Rozsíval, Pavel, Neumann, David, Chernyshova, Liudmyla, Tulassay, Zsolt, Puel, Anne, Casanova, Jean-Laurent, Sediva, Anna, Litzman, Jiri, and Maródi, László

Published
2013
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40. Haploinsufficiency at the human IFNGR2 locus contributes to mycobacterial disease

Author

Kong, Xiao-Fei, Vogt, Guillaume, Itan, Yuval, Macura-Biegun, Anna, Szaflarska, Anna, Kowalczyk, Danuta, Chapgier, Ariane, Abhyankar, Avinash, Furthner, Dieter, Djambas Khayat, Claudia, Okada, Satoshi, Bryant, Vanessa L., Bogunovic, Dusan, Kreins, Alexandra, Moncada-Vélez, Marcela, Migaud, Mélanie, Al-Ajaji, Sulaiman, Al-Muhsen, Saleh, Holland, Steven M., Abel, Laurent, Picard, Capucine, Chaussabel, Damien, Bustamante, Jacinta, Casanova, Jean-Laurent, and Boisson-Dupuis, Stéphanie

Published
2013
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41. Dominant-negative STAT1 SH2 domain mutations in unrelated patients with mendelian susceptibility to mycobacterial disease

Author

Tsumura, Miyuki, Okada, Satoshi, Sakai, Hidemasa, Yasunaga, Shinʼichiro, Ohtsubo, Motoaki, Murata, Takuji, Obata, Hideto, Yasumi, Takahiro, Kong, Xiao-Fei, Abhyankar, Avinash, Heike, Toshio, Nakahata, Tatsutoshi, Nishikomori, Ryuta, Al-Muhsen, Saleh, Boisson-Dupuis, Stéphanie, Casanova, Jean-Laurent, AlZahrani, Mofareh, Shehri, Mohammed Al, ElGhazali, Geyhad, Takihara, Yoshihiro, and Kobayashi, Masao

Published
2012
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43. The NYCKidSeq project: study protocol for a randomized controlled trial incorporating genomics into the clinical care of diverse New York City children

Author

Odgis, Jacqueline A, primary, Gallagher, Katie M., additional, Suckiel, Sabrina A., additional, Donohue, Katherine E., additional, Ramos, Michelle A., additional, Kelly, Nicole R., additional, Bertier, Gabrielle, additional, Blackburn, Christina, additional, Brown, Kaitlyn, additional, Fielding, Lena, additional, Lopez, Jessenia, additional, Aguiniga, Karla Lopez, additional, Maria, Estefany, additional, Rodriguez, Jessica E., additional, Sebastin, Monisha, additional, Teitelman, Nehama, additional, Watnick, Dana, additional, Yelton, Nicole M., additional, Abhyankar, Avinash, additional, Abul-Husn, Noura S., additional, Baum, Aaron, additional, Bauman, Laurie J., additional, Beal, Jules C., additional, Bloom, Toby, additional, Cunningham-Rundles, Charlotte, additional, Diaz, George A., additional, Dolan, Siobhan, additional, Ferket, Bart S., additional, Jobanputra, Vaidehi, additional, Kovatch, Patricia, additional, McDonald, Thomas V., additional, McGoldrick, Patricia E., additional, Rhodes, Rosamond, additional, Rinke, Michael L., additional, Robinson, Mimsie, additional, Rubinstein, Arye, additional, Shulman, Lisa H., additional, Stolte, Christian, additional, Wolf, Steven M., additional, Yozawitz, Elissa, additional, Zinberg, Randi E., additional, Greally, John M., additional, Gelb, Bruce D., additional, Horowitz, Carol R., additional, Wasserstein, Melissa P., additional, and Kenny, Eimear E., additional

Published
2020
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44. Variant Classification Concordance using the ACMG-AMP Variant Interpretation Guidelines across Nine Genomic Implementation Research Studies

Author

Amendola, Laura M., primary, Muenzen, Kathleen, additional, Biesecker, Leslie G., additional, Bowling, Kevin M., additional, Cooper, Greg M., additional, Dorschner, Michael O., additional, Driscoll, Catherine, additional, Foreman, Ann Katherine M., additional, Golden-Grant, Katie, additional, Greally, John M., additional, Hindorff, Lucia, additional, Kanavy, Dona, additional, Jobanputra, Vaidehi, additional, Johnston, Jennifer J., additional, Kenny, Eimear E., additional, McNulty, Shannon, additional, Murali, Priyanka, additional, Ou, Jeffrey, additional, Powell, Bradford C., additional, Rehm, Heidi L., additional, Rolf, Bradley, additional, Roman, Tamara S., additional, Van Ziffle, Jessica, additional, Guha, Saurav, additional, Abhyankar, Avinash, additional, Crosslin, David, additional, Venner, Eric, additional, Yuan, Bo, additional, Zouk, Hana, additional, and Jarvik, Gail P., additional

Published
2020
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45. The NYCKidSeq project: study protocol for a randomized controlled trial incorporating genomics into the clinical care of diverse New York City children

Author

Odgis, Jacqueline A., primary, Gallagher, Katie M., additional, Suckiel, Sabrina A., additional, Donohue, Katherine E., additional, Ramos, Michelle A., additional, Kelly, Nicole R., additional, Bertier, Gabrielle, additional, Blackburn, Christina, additional, Brown, Kaitlyn, additional, Fielding, Lena, additional, Lopez, Jessenia, additional, Aguiniga, Karla Lopez, additional, Maria, Estefany, additional, Rodriguez, Jessica E., additional, Sebastin, Monisha, additional, Teitelman, Nehama, additional, Watnick, Dana, additional, Yelton, Nicole M., additional, Abhyankar, Avinash, additional, Abul-Husn, Noura S., additional, Baum, Aaron, additional, Bauman, Laurie J., additional, Beal, Jules C., additional, Bloom, Toby, additional, Cunningham-Rundles, Charlotte, additional, Diaz, George A., additional, Dolan, Siobhan, additional, Ferket, Bart S., additional, Jobanputra, Vaidehi, additional, Kovatch, Patricia, additional, McDonald, Thomas V., additional, McGoldrick, Patricia E., additional, Rhodes, Rosamond, additional, Rinke, Michael L., additional, Robinson, Mimsie, additional, Rubinstein, Arye, additional, Shulman, Lisa H., additional, Stolte, Christian, additional, Wolf, Steven M., additional, Yozawitz, Elissa, additional, Zinberg, Randi E., additional, Greally, John M., additional, Gelb, Bruce D., additional, Horowitz, Carol R., additional, Wasserstein, Melissa P., additional, and Kenny, Eimear E., additional

Published
2020
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46. De Novo Mutation in an Enhancer of EBF3 in simplex autism

Author

Padhi, Evin M., primary, Hayeck, Tristan J., additional, Mannion, Brandon, additional, Chatterjee, Sumantra, additional, Byrska-Bishop, Marta, additional, Musunuri, Rajeeva, additional, Narzisi, Giuseppe, additional, Abhyankar, Avinash, additional, Cheng, Zhang, additional, Hunter, Riana D., additional, Akiyama, Jennifer, additional, Fries, Lauren E., additional, Ng, Jeffrey, additional, Stong, Nick, additional, Allen, Andrew S., additional, Dickel, Diane E., additional, Bernier, Raphael A., additional, Gorkin, David U., additional, Pennacchio, Len A., additional, Zody, Michael C., additional, and Turner, Tychele N., additional

Published
2020
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50. CDG: an online server proposing biologically closest disease-causing genes and pathologies and its application to primary immunodeficiency

Author

Requena, David, Maffucci, Patrick, Bigio, Benedetta, Shang, Lei, Abhyankar, Avinash, Boisson, Bertrand, Stenson, Peter D, Cooper, David N, Cunningham-Rundles, Charlotte, Casanova, Jean-Laurent, Abel, Laurent, and Itan, Yuval

Abstract

Summary: In analyses of exome data, candidate gene selection can be challenging in the absence of variants in known disease-causing genes. We calculated the putative biologically closest known disease-causing genes for 13,005 human genes not currently reported to be disease-causing. We used these data to construct the Closest Disease-Causing Genes (CDG) server, which can be used to infer the closest associated disease-causing genes and phenotypes for lists of candidate genes. This resource will be a considerable asset for ascertaining the poten-tial relevance of lists of genes to specific diseases of interest.

Published
2018

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