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JOURNAL ARTICLE
Lynda M McSorley, Mehala Tharmabala, Fathiya Al Rahbi, Fergus Keane, Denis Evoy, James G Geraghty, Jane Rothwell, Damian P McCartan, Megan Greally, Miriam O'Connor, Deirdre O'Mahony, Maccon Keane, Michael John Kennedy, Seamus O'Reilly, Steve J Millen, John P Crown, Catherine M Kelly, Ruth S Prichard, Cecily M Quinn, Janice M Walshe
Background: This study, using real-world data, assesses the impact of RS testing on treatment pathways and the associated economic consequences of such testing. This paper pertains to lobular breast cancer. Methods: A retrospective, observational study was undertaken between 2011 and 2019 on a cross-section of hormone receptor-positive (HR+), HER2-negative, lymph node-negative, early-stage breast cancer patients. All patients had ILC and had RS testing in Ireland. The patient population is representative of the national population...
March 1, 2024: Current Oncology
#2
REVIEW
Kristen M Wigby, Deanna Brockman, Gregory Costain, Caitlin Hale, Stacie L Taylor, John Belmont, David Bick, David Dimmock, Susan Fernbach, John Greally, Vaidehi Jobanputra, Shashikant Kulkarni, Elizabeth Spiteri, Ryan J Taft
Early use of genome sequencing (GS) in the diagnostic odyssey can reduce suffering and improve care, but questions remain about which patient populations are most amenable to GS as a first-line diagnostic test. To address this, the Medical Genome Initiative conducted a literature review to identify appropriate clinical indications for GS. Studies published from January 2011 to August 2022 that reported on the diagnostic yield (DY) or clinical utility of GS were included. An exploratory meta-analysis using a random effects model evaluated DY based on cohort size and diagnosed cases per cohort...
February 26, 2024: NPJ Genomic Medicine
#3
Theresa A Grebe, George Khushf, John M Greally, Patrick Turley, Nastaran Foyouzi, Sara Rabin-Havt, Benjamin E Berkman, Kathleen Pope, Matteo Vatta, Shagun Kaur
No abstract text is available yet for this article.
February 6, 2024: Genetics in Medicine: Official Journal of the American College of Medical Genetics
#4
JOURNAL ARTICLE
Elina Jerschow, Robert Dubin, Chien-Chang Chen, Alex iAkushev, Esha Sehanobish, Mohammad Asad, Sergio E Chiarella, Steven A Porcelli, John Greally
BACKGROUND: Previous studies have determined that up to 6% of patients with aspirin-exacerbated respiratory disease (AERD) have family history of AERD, indicating a possible link with genetic polymorphisms. However, whole exome sequencing (WES) studies of such associations are currently lacking. OBJECTIVES: We sought to examine whether WES can identify pathogenic variants associated with AERD. METHODS: Diagnoses of AERD were confirmed in patients with nasal polyps and asthma...
May 2024: J Allergy Clin Immunol Glob
#5
Devin Rocks, Eric Purisic, Eduardo F Gallo, John M Greally, Masako Suzuki, Marija Kundakovic
Sex differences are found in brain structure and function across species, and across brain disorders in humans 1-3 . The major source of brain sex differences is differential secretion of steroid hormones from the gonads across the lifespan 4 . Specifically, ovarian hormones oestrogens and progesterone are known to dynamically change structure and function of the adult female brain, having a major impact on psychiatric risk 5-7 . However, due to limited molecular studies in female rodents 8 , very little is still known about molecular drivers of female-specific brain and behavioural plasticity...
December 21, 2023: bioRxiv
#6
JOURNAL ARTICLE
Caner Saygin, Pu Zhang, Jacob Stauber, Ibrahim Aldoss, Adam S Sperling, Lachelle D Weeks, Marlise R Luskin, Todd C Knepper, Pankhuri Wanjari, Peng Wang, Angela M Lager, Carrie Fitzpatrick, Jeremy P Segal, Mehdi Gharghabi, Sandeep Gurbuxani, Girish Venkataraman, Jason X Cheng, Bart J Eisfelder, Oliver Bohorquez, Anand A Patel, Sheethal Umesh Nagalakshmi, Savita Jayaram, Olatoyosi M Odenike, Richard A Larson, Lucy A Godley, Daniel A Arber, Christopher J Gibson, Nikhil C Munshi, Guido Marcucci, Benjamin L Ebert, John M Greally, Ulrich Steidl, Rosa Lapalombella, Bijal D Shah, Wendy Stock
Myeloid neoplasms arise from pre-existing clonal hematopoiesis (CH), however the role of CH in pathogenesis of ALL is unknown. We found that 18% of adult ALL cases harbored TP53, and 16% had myeloid CH-associated gene mutations. ALL with myeloid mutations (MyM) had distinct genetic and clinical characteristics, associated with inferior survival. By using single cell proteogenomic analysis, we demonstrated that myeloid mutations were present years before the diagnosis of ALL, and a subset of these clones expanded over time to manifest as dominant clones in ALL...
December 27, 2023: Blood cancer discovery
#7
JOURNAL ARTICLE
Sabrina A Suckiel, Nicole R Kelly, Jacqueline A Odgis, Katie M Gallagher, Monisha Sebastin, Katherine E Bonini, Priya N Marathe, Kaitlyn Brown, Miranda Di Biase, Michelle A Ramos, Jessica E Rodriguez, Laura Scarimbolo, Beverly J Insel, Kathleen D M Ferar, Randi E Zinberg, George A Diaz, John M Greally, Noura S Abul-Husn, Laurie J Bauman, Bruce D Gelb, Carol R Horowitz, Melissa P Wasserstein, Eimear E Kenny
Digital solutions are needed to support rapid increases in the application of genetic/genomic tests (GTs) in diverse clinical settings and patient populations. We developed GUÍA, a bilingual digital application that facilitates disclosure of GT results. The NYCKidSeq randomized controlled trial enrolled diverse children with neurologic, cardiac, and immunologic conditions who underwent GTs. The trial evaluated GUÍA's impact on understanding the GT results by randomizing families to results disclosure genetic counseling with GUÍA (intervention) or standard of care (SOC)...
December 7, 2023: American Journal of Human Genetics
#8
JOURNAL ARTICLE
Dong Li, Qin Wang, Allan Bayat, Mark R Battig, Yijing Zhou, Daniëlle Gm Bosch, Gijs van Haaften, Leslie Granger, Andrea K Petersen, Luis A Pérez-Jurado, Gemma Aznar-Laín, Anushree Aneja, Miroslava Hancarova, Sarka Bendova, Martin Schwarz, Radka Kremlikova Pourova, Zdenek Sedlacek, Beth A Keena, Michael E March, Cuiping Hou, Nora O'Connor, Elizabeth J Bhoj, Margaret H Harr, Gabrielle Lemire, Kym M Boycott, Meghan Towne, Megan Li, Mark Tarnopolsky, Lauren Brady, Michael J Parker, Hanna Faghfoury, Lea Kristin Parsley, Emanuele Agolini, Maria Lisa Dentici, Antonio Novelli, Meredith Wright, Rachel Palmquist, Khanh Lai, Marcello Scala, Pasquale Striano, Michele Iacomino, Federico Zara, Annina Cooper, Timothy J Maarup, Melissa Byler, Robert Roger Lebel, Tugce B Balci, Raymond Louie, Michael Lyons, Jessica Douglas, Catherine Nowak, Alexandra Afenjar, Juliane Hoyer, Boris Keren, Saskia M Maas, Mahdi M Motazacker, Julian A Martinez-Agosto, Ahna M Rabani, Elizabeth M McCormick, Marni J Falk, Sarah M Ruggiero, Ingo Helbig, Rikke S Møller, Lino Tessarollo, Francesco Tomassoni Ardori, Mary Ellen Palko, Tzung-Chien Hsieh, Peter M Krawitz, Mythily Ganapathi, Bruce D Gelb, Vaidehi Jobanputra, Ashley Wilson, John Greally, Sébastien Jacquemont, Khadijé Jizi, Ange-Line Bruel, Chloé Quelin, Vinod K Misra, Erika Chick, Corrado Romano, Donatella Greco, Alessia Arena, Manuela Morleo, Vincenzo Nigro, Rie Seyama, Yuri Uchiyama, Naomichi Matsumoto, Ryoji Taira, Katsuya Tashiro, Yasunari Sakai, Gökhan Yigit, Bernd Wollnik, Michael Wagner, Barbara Kutsche, Anna Ce Hurst, Michelle L Thompson, Ryan Schmidt, Linda Randolph, Rebecca C Spillmann, Vandana Shashi, Edward J Higginbotham, Dawn Cordeiro, Amanda Carnevale, Gregory Costain, Tayyaba Khan, Benoît Funalot, Frederic Tran Mau-Them, Luis Fernandez Garcia Moya, Sixto García-Miñaúr, Matthew Osmond, Lauren Chad, Nada Quercia, Diana Carrasco, Chumei Li, Amarilis Sanchez-Valle, Meghan Kelley, Mathilde Nizon, Brynjar O Jensson, Patrick Sulem, Kari Stefansson, Svetlana Gorokhova, Tiffany Busa, Marlène Rio, Hamza Hadj Habdallah, Marion Lesieur-Sebellin, Jeanne Amiel, Véronique Pingault, Sandra Mercier, Marie Vincent, Christophe Philippe, Clemence Fatus-Fauconnier, Kathryn Friend, Rebecca K Halligan, Sunita Biswas, Jane Rosser, Cheryl Shoubridge, Mark Corbett, Christopher Barnett, Jozef Gecz, Kathleen Leppig, Anne Slavotinek, Carlo Marcelis, Rolph Pfundt, Bert Ba de Vries, Marjon A van Slegtenhorst, Alice S Brooks, Benjamin Cogne, Thomas Rambaud, Zeynep Tümer, Elaine H Zackai, Naiara Akizu, Yuanquan Song, Hakon Hakonarson
Pre-mRNA splicing is a highly coordinated process. While its dysregulation has been linked to neurological deficits, our understanding of the underlying molecular and cellular mechanisms remains limited. We implicated pathogenic variants in U2AF2 and PRPF19, encoding spliceosome subunits in neurodevelopmental disorders (NDDs), by identifying 46 unrelated individuals with 23 de novo U2AF2 missense variants (including 7 recurrent variants in 30 individuals) and 6 individuals with de novo PRPF19 variants. Eight U2AF2 variants dysregulated splicing of a model substrate...
January 2, 2024: Journal of Clinical Investigation
#9
Eric A Sosa, Samuel Rosean, Dónal O'Shea, Srilakshmi M Raj, Cathal Seoighe, John M Greally
MOTIVATION: To understand whether sets of genomic loci are enriched at the regulatory loci of one or more cell types, we developed the gaiaAssociation package to perform Regulatory Landscape Enrichment Analysis (RLEA). RLEA is a novel analytical process that tests for enrichment of sets of loci in cell type-specific open chromatin regions (OCRs) in the genome. RESULTS: We demonstrate that the application of RLEA to genome-wide association study (GWAS) data reveals cell types likely to be mediating the phenotype studied, and clusters OCRs based on their shared regulatory profiles...
October 16, 2023: bioRxiv
#10
JOURNAL ARTICLE
Asem Berkalieva, Nicole R Kelly, Ashley Fisher, Samuel F Hohmann, Monisha Sebastin, Miranda Di Biase, Katherine E Bonini, Priya Marathe, Jacqueline A Odgis, Sabrina A Suckiel, Michelle A Ramos, Rosamond Rhodes, Noura S Abul-Husn, John M Greally, Carol R Horowitz, Melissa P Wasserstein, Eimear E Kenny, Bruce D Gelb, Bart S Ferket
PURPOSE: To better understand the effects of returning diagnostic sequencing results on clinical actions and economic outcomes for pediatric patients with suspected genetic disorders. METHODS: Longitudinal physician claims data after diagnostic sequencing were obtained for patients aged 0-21 years with neurologic, cardiac, and immunologic disorders with suspected genetic etiology. We assessed specialist consultation rates prompted by primary diagnostic results, as well as marginal effects on overall 18-month physician services and costs...
October 25, 2023: Genetics in Medicine: Official Journal of the American College of Medical Genetics
#11
JOURNAL ARTICLE
Shudan Wang, Anna Broder, Daming Shao, Vartika Kesarwani, Brianna Boderman, Jennifer Aguilan, Simone Sidoli, Masako Suzuki, John M Greally, Yvonne M Saenger, Brad H Rovin, J Michelle Kahlenberg
BACKGROUND: Intrarenal complement activation has been implicated in the pathogenesis of tubulointerstitial fibrosis in lupus nephritis (LN) based on prior animal studies. The assembly of the membrane attack complex (MAC) by complement C5b to C9 on the cell membrane leads to cytotoxic pores and cell lysis, while CD59 inhibits MAC formation by preventing C9 from joining the complex. We hypothesize that complement activation and imbalance between complement activation and inhibition, as defined by increased production of individual complement components and uncontrolled MAC activation relative to CD59 inhibition, are associated with interstitial fibrosis and tubular atrophy (IFTA) in LN and correlate with the key mediators of kidney fibrosis- transforming growth factor receptors beta (TGFRβ), platelet-derived growth factor beta (PDGFβ) and platelet-derived growth factor receptor beta (PDGFRβ)...
September 27, 2023: Seminars in Arthritis and Rheumatism
#12
JOURNAL ARTICLE
Devin Rocks, Ivana Jaric, Fabio Bellia, Heining Cham, John M Greally, Masako Suzuki, Marija Kundakovic
Early-life stress and ovarian hormones contribute to increased female vulnerability to cocaine addiction. Here, we reveal molecular substrates in the reward area, the nucleus accumbens, through which these female-specific factors affect immediate and conditioning responses to cocaine. We find shared involvement of X chromosome inactivation-related and estrogen signaling-related gene regulation in enhanced conditioning responses following early-life stress and during the low-estrogenic state in females. Low-estrogenic females respond to acute cocaine by opening neuronal chromatin enriched for the sites of ΔFosB, a transcription factor implicated in chronic cocaine response and addiction...
September 29, 2023: Cell Reports
#13
Koki Ueda, Shu Shien Chin, Noriko Sato, Miyu Nishikawa, Kaori Yasuda, Naoyuki Miyasaka, Betelehem Solomon Bera, Laurent Chorro, Reanna Doña-Termine, Wade R Koba, David Reynolds, Ulrich G Steidl, Gregoire Lauvau, John M Greally, Masako Suzuki
Vitamin D deficiency is a common deficiency worldwide, particularly among women of reproductive age. During pregnancy, it increases the risk of immune-related diseases in offspring later in life. However, exactly how the body remembers exposure to an adverse environment during development is poorly understood. Herein, we explore the effects of prenatal vitamin D deficiency on immune cell proportions in offspring using vitamin D deficient mice established by dietary manipulation. We show that prenatal vitamin D deficiency alters immune cell proportions in offspring by changing the transcriptional properties of genes downstream of vitamin D receptor signaling in hematopoietic stem and progenitor cells of both the fetus and adults...
September 13, 2023: bioRxiv
#14
Sabrina A Suckiel, Nicole R Kelly, Jacqueline A Odgis, Katie M Gallagher, Monisha Sebastin, Katherine E Bonini, Priya N Marathe, Kaitlyn Brown, Miranda Di Biase, Michelle A Ramos, Jessica E Rodriguez, Laura Scarimbolo, Beverly J Insel, Kathleen D M Ferar, Randi E Zinberg, George A Diaz, John M Greally, Noura S Abul-Husn, Laurie J Bauman, Bruce D Gelb, Carol R Horowitz, Melissa P Wasserstein, Eimear E Kenny
BACKGROUND: Digital solutions are needed to support rapid increases in the application of genetic and genomic tests (GT) in diverse clinical settings and patient populations. We developed GUÍA, a bi-lingual web-based platform that facilitates disclosure of GT results. The NYCKidSeq randomized controlled trial evaluated GUÍA's impact on understanding of GT results. METHODS: NYCKidSeq enrolled diverse children with neurologic, cardiac, and immunologic conditions who underwent GT...
July 7, 2023: medRxiv
#15
JOURNAL ARTICLE
Katherine E Bonini, Amanda Thomas-Wilson, Priya N Marathe, Monisha Sebastin, Jacqueline A Odgis, Miranda Di Biase, Nicole R Kelly, Michelle A Ramos, Beverly J Insel, Laura Scarimbolo, Atteeq U Rehman, Saurav Guha, Volkan Okur, Avinash Abhyankar, Shruti Phadke, Caroline Nava, Katie M Gallagher, Lama Elkhoury, Lisa Edelmann, Randi E Zinberg, Noura S Abul-Husn, George A Diaz, John M Greally, Sabrina A Suckiel, Carol R Horowitz, Eimear E Kenny, Melissa Wasserstein, Bruce D Gelb, Vaidehi Jobanputra
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...
June 19, 2023: Clinical Genetics
#16
JOURNAL ARTICLE
Noura S Abul-Husn, Priya N Marathe, Nicole R Kelly, Katherine E Bonini, Monisha Sebastin, Jacqueline A Odgis, Avinash Abhyankar, Kaitlyn Brown, Miranda Di Biase, Katie M Gallagher, Saurav Guha, Nicolette Ioele, Volkan Okur, Michelle A Ramos, Jessica E Rodriguez, Atteeq U Rehman, Amanda Thomas-Wilson, Lisa Edelmann, Randi E Zinberg, George A Diaz, John M Greally, Vaidehi Jobanputra, Sabrina A Suckiel, Carol R Horowitz, Melissa P Wasserstein, Eimear E Kenny, Bruce D Gelb
PURPOSE: Adoption of genome sequencing (GS) as a first-line test requires evaluation of its diagnostic yield. We evaluated the GS and targeted gene panel (TGP) testing in diverse pediatric patients (probands) with suspected genetic conditions. METHODS: Probands with neurologic, cardiac, or immunologic conditions were offered GS and TGP testing. Diagnostic yield was compared using a fully paired study design. RESULTS: 645 probands (median age 9 years) underwent genetic testing, and 113 (17...
May 5, 2023: Genetics in Medicine: Official Journal of the American College of Medical Genetics
#17
JOURNAL ARTICLE
Betelehem Solomon Bera, Taylor V Thompson, Eric Sosa, Hiroko Nomaru, David Reynolds, Robert A Dubin, Shahina B Maqbool, Deyou Zheng, Bernice E Morrow, John M Greally, Masako Suzuki
BACKGROUND: Single-cell technologies to analyze transcription and chromatin structure have been widely used in many research areas to reveal the functions and molecular properties of cells at single-cell resolution. Sample multiplexing techniques are valuable when performing single-cell analysis, reducing technical variation and permitting cost efficiencies. Several commercially available methods have been used in many scRNA-seq studies. On the other hand, while several methods have been published, multiplexing techniques for single nuclear assay for transposase-accessible chromatin (snATAC)-seq assays remain under development...
April 28, 2023: Epigenetics & Chromatin
#18
Noura S Abul-Husn, Priya N Marathe, Nicole R Kelly, Katherine E Bonini, Monisha Sebastin, Jacqueline A Odgis, Avinash Abhyankar, Kaitlyn Brown, Miranda Di Biase, Katie M Gallagher, Saurav Guha, Nicolette Ioele, Volkan Okur, Michelle A Ramos, Jessica E Rodriguez, Atteeq U Rehman, Amanda Thomas-Wilson, Lisa Edelmann, Randi E Zinberg, George A Diaz, John M Greally, Vaidehi Jobanputra, Sabrina A Suckiel, Carol R Horowitz, Melissa P Wasserstein, Eimear E Kenny, Bruce D Gelb
PURPOSE: Adoption of genome sequencing (GS) as a first-line test requires evaluation of its diagnostic yield. We evaluated the GS and targeted gene panel (TGP) testing in diverse pediatric patients (probands) with suspected genetic conditions. METHODS: Probands with neurologic, cardiac, or immunologic conditions were offered GS and TGP testing. Diagnostic yield was compared using a fully paired study design. RESULTS: 645 probands (median age 9 years) underwent genetic testing, and 113 (17...
March 20, 2023: medRxiv
#19
JOURNAL ARTICLE
Monisha Sebastin, Jacqueline A Odgis, Sabrina A Suckiel, Katherine E Bonini, Miranda Di Biase, Kaitlyn Brown, Priya Marathe, Nicole R Kelly, Michelle A Ramos, Jessica E Rodriguez, Karla López Aguiñiga, Jessenia Lopez, Estefany Maria, Michelle A Rodriguez, Nicole M Yelton, Charlotte Cunningham-Rundles, Katie Gallagher, Thomas V McDonald, Patricia E McGoldrick, Mimsie Robinson, Arye Rubinstein, Lisa H Shulman, Steven M Wolf, Elissa Yozawitz, Randi E Zinberg, Noura S Abul-Husn, Laurie J Bauman, George A Diaz, Bart S Ferket, John M Greally, Vaidehi Jobanputra, Bruce D Gelb, Carol R Horowitz, Eimear E Kenny, Melissa P Wasserstein
BACKGROUND: The COVID-19 pandemic forced healthcare institutions and many clinical research programs to adopt telehealth modalities in order to mitigate viral spread. With the expanded use of telehealth, there is the potential to increase access to genomic medicine to medically underserved populations, yet little is known about how best to communicate genomic results via telehealth while also ensuring equitable access. NYCKidSeq, a multi-institutional clinical genomics research program in New York City, launched the TeleKidSeq pilot study to assess alternative forms of genomic communication and telehealth service delivery models with families from medically underserved populations...
March 22, 2023: Pilot and Feasibility Studies
#20
REVIEW
Julia J Wattacheril, Srilakshmi Raj, David A Knowles, John M Greally
It is a generally accepted model that environmental influences can exert their effects, at least in part, by changing the molecular regulators of transcription that are described as epigenetic. As there is biochemical evidence that some epigenetic regulators of transcription can maintain their states long term and through cell division, an epigenetic model encompasses the idea of maintenance of the effect of an exposure long after it is no longer present. The evidence supporting this model is mostly from the observation of alterations of molecular regulators of transcription following exposures...
January 2023: PLoS Genetics
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