Use the keywords feature with a free QxMD account.
Use Read by QxMD to access full text via your institution or open access sources.
Read also provides personalized recommendations to keep you up to date in your field.
Existing User
Sign InNew to Read
Sign Up#21
JOURNAL ARTICLE
Kevin M Bowling, Michelle L Thompson, Melissa A Kelly, Sarah Scollon, Anne M Slavotinek, Bradford C Powell, Brian M Kirmse, Laura G Hendon, Kyle B Brothers, Bruce R Korf, Gregory M Cooper, John M Greally, Anna C E Hurst
BACKGROUND: The uptake of exome/genome sequencing has introduced unexpected testing results (incidental findings) that have become a major challenge for both testing laboratories and providers. While the American College of Medical Genetics and Genomics has outlined guidelines for laboratory management of clinically actionable secondary findings, debate remains as to whether incidental findings should be returned to patients, especially those representing pediatric populations. METHODS: The Sequencing Analysis and Diagnostic Yield working group in the Clinical Sequencing Evidence-Generating Research Consortium has collected a cohort of pediatric patients found to harbor a genomic sequencing-identified non-ACMG-recommended incidental finding...
November 21, 2022: Genome Medicine
#22
JOURNAL ARTICLE
Netha Ulahannan, Ronald Cutler, Reanna Doña-Termine, Claudia A Simões-Pires, N Ari Wijetunga, Matthew McKnight Croken, Andrew D Johnston, Yu Kong, Shahina B Maqbool, Masako Suzuki, John M Greally
To gain insights into the molecular interactions of an intracellular pathogen and its host cell, we studied the gene expression and chromatin states of human fibroblasts infected with the Apicomplexan parasite Toxoplasma gondii. We show a striking activation of host cell genes that regulate a number of cellular processes, some of which are protective of the host cell, others likely to be advantageous to the pathogen. The simultaneous capture of host and parasite genomic information allowed us to gain insights into the regulation of the T...
2022: PloS One
#23
JOURNAL ARTICLE
Patricia A Shi, Larry L Luchsinger, John M Greally, Colleen S Delaney
PURPOSE OF REVIEW: The purpose of this review is to primarily discuss the unwarranted decline in the use of umbilical cord blood (UCB) as a source of donor hematopoietic stem cells (HSC) for hematopoietic cell transplantation (HCT) and the resulting important implications in addressing healthcare inequities, and secondly to highlight the incredible potential of UCB and related birthing tissues for the development of a broad range of therapies to treat human disease including but not limited to oncology, neurologic, cardiac, orthopedic and immunologic conditions...
August 30, 2022: Current Opinion in Hematology
#24
JOURNAL ARTICLE
Stacey R McGee, Shivakumar Rajamanickam, Sandeep Adhikari, Oluwatosin C Falayi, Theresa A Wilson, Brian J Shayota, Jessica A Cooley Coleman, Cindy Skinner, Raymond C Caylor, Roger E Stevenson, Caio Robledo D' Angioli Costa Quaio, Berenice Cunha Wilke, Jennifer M Bain, Kwame Anyane-Yeboa, Kaitlyn Brown, John M Greally, Emilia K Bijlsma, Claudia A L Ruivenkamp, Keren Politi, Lydia A Arbogast, Michael W Collard, Jodi I Huggenvik, Sarah H Elsea, Philip J Jensik
De novo deleterious and heritable biallelic mutations in the DNA binding domain (DBD) of the transcription factor deformed epidermal autoregulatory factor 1 (DEAF1) result in a phenotypic spectrum of disorders termed DEAF1-associated neurodevelopmental disorders (DAND). RNA-sequencing using hippocampal RNA from mice with conditional deletion of Deaf1 in the central nervous system indicate that loss of Deaf1 activity results in the altered expression of genes involved in neuronal function, dendritic spine maintenance, development, and activity, with reduced dendritic spines in hippocampal regions...
August 18, 2022: Human Molecular Genetics
#25
JOURNAL ARTICLE
Parvathi A Myer, Hyunjin Kim, Anna M Blümel, Ellen Finnegan, Alexander Kel, Taylor V Thompson, John M Greally, Jochen Hm Prehn, Darran P O'Connor, Richard A Friedman, Aris Floratos, Sudipto Das
Background and Aims: Individuals of African (AFR) ancestry have a higher incidence of colorectal cancer (CRC) than those of European (EUR) ancestry and exhibit significant health disparities. Previous studies have noted differences in the tumor microenvironment between AFR and EUR patients with CRC. However, the molecular regulatory processes that underpin these immune differences remain largely unknown. Methods: Multiomics analysis was carried out for 55 AFR and 456 EUR patients with microsatellite-stable CRC using The Cancer Genome Atlas...
2022: Gastro Hep Adv
#26
JOURNAL ARTICLE
Kassidy Lundy, John F Greally, Grace Essilfie-Bondzie, Josephine B Olivier, Reanna Doña-Termine, John M Greally, Masako Suzuki
Vitamin D, a fat-soluble vitamin, plays a critical role in calcium homeostasis, the immune system, and normal development. Many epidemiological cohort studies globally have found high prevalence rates of vitamin D deficiency and insufficiency, recognized as an important health issue that needs to be solved. In particular, reproductive age and pregnant women low in vitamin D status may confer risks of diseases like obesity on their offspring. While observational studies have suggested associations between prenatal vitamin D deficiency and metabolic phenotypes in offspring, not yet determined is whether prenatal vitamin D deficiency permanently alters the development of the liver, a major metabolic organ...
2022: Frontiers in Endocrinology
#27
Jonathan Foox, Jessica Nordlund, Claudia Lalancette, Ting Gong, Michelle Lacey, Samantha Lent, Bradley W Langhorst, V K Chaithanya Ponnaluri, Louise Williams, Karthik Ramaswamy Padmanabhan, Raymond Cavalcante, Anders Lundmark, Daniel Butler, Christopher Mozsary, Justin Gurvitch, John M Greally, Masako Suzuki, Mark Menor, Masaki Nasu, Alicia Alonso, Caroline Sheridan, Andreas Scherer, Stephen Bruinsma, Gosia Golda, Agata Muszynska, Paweł P Łabaj, Matthew A Campbell, Frank Wos, Amanda Raine, Ulrika Liljedahl, Tomas Axelsson, Charles Wang, Zhong Chen, Zhaowei Yang, Jing Li, Xiaopeng Yang, Hongwei Wang, Ari Melnick, Shang Guo, Alexander Blume, Vedran Franke, Inmaculada Ibanez de Caceres, Carlos Rodriguez-Antolin, Rocio Rosas, Justin Wade Davis, Jennifer Ishii, Dalila B Megherbi, Wenming Xiao, Will Liao, Joshua Xu, Huixiao Hong, Baitang Ning, Weida Tong, Altuna Akalin, Yunliang Wang, Youping Deng, Christopher E Mason
No abstract text is available yet for this article.
December 23, 2021: Genome Biology
#28
JOURNAL ARTICLE
Jonathan Foox, Jessica Nordlund, Claudia Lalancette, Ting Gong, Michelle Lacey, Samantha Lent, Bradley W Langhorst, V K Chaithanya Ponnaluri, Louise Williams, Karthik Ramaswamy Padmanabhan, Raymond Cavalcante, Anders Lundmark, Daniel Butler, Christopher Mozsary, Justin Gurvitch, John M Greally, Masako Suzuki, Mark Menor, Masaki Nasu, Alicia Alonso, Caroline Sheridan, Andreas Scherer, Stephen Bruinsma, Gosia Golda, Agata Muszynska, Paweł P Łabaj, Matthew A Campbell, Frank Wos, Amanda Raine, Ulrika Liljedahl, Tomas Axelsson, Charles Wang, Zhong Chen, Zhaowei Yang, Jing Li, Xiaopeng Yang, Hongwei Wang, Ari Melnick, Shang Guo, Alexander Blume, Vedran Franke, Inmaculada Ibanez de Caceres, Carlos Rodriguez-Antolin, Rocio Rosas, Justin Wade Davis, Jennifer Ishii, Dalila B Megherbi, Wenming Xiao, Will Liao, Joshua Xu, Huixiao Hong, Baitang Ning, Weida Tong, Altuna Akalin, Yunliang Wang, Youping Deng, Christopher E Mason
BACKGROUND: Cytosine modifications in DNA such as 5-methylcytosine (5mC) underlie a broad range of developmental processes, maintain cellular lineage specification, and can define or stratify types of cancer and other diseases. However, the wide variety of approaches available to interrogate these modifications has created a need for harmonized materials, methods, and rigorous benchmarking to improve genome-wide methylome sequencing applications in clinical and basic research. Here, we present a multi-platform assessment and cross-validated resource for epigenetics research from the FDA's Epigenomics Quality Control Group...
December 6, 2021: Genome Biology
#29
JOURNAL ARTICLE
Lisa Prior, Richard O'Dwyer, Abdul Rehman Farooq, Megan Greally, Cian Ward, Connor O'Leary, Razia Aslam, Waseem Darwish, Nada Ahmed, Elly Che Othman, Geoffrey Watson, Deirdre Kelly, Jack Gleeson, Lisa Kiely, Anees Hassan, Elaine M Walsh, David O'Reilly, Alfred Jones, Hannah Featherstone, Marvin Lim, Hazel Murray, Bryan T Hennessy, Lillian M Smyth, Gregory Leonard, Liam Grogan, Oscar Breathnach, Paula Calvert, Anne M Horgan, Linda Coate, Emmet J Jordan, Deirdre O'Mahony, Rajnish Gupta, Maccon M Keane, Jennifer Westrup, Karen Duffy, Miriam O'Connor, Patrick G Morris, M John Kennedy, Seamus O'Reilly, John McCaffrey, Catherine M Kelly, Desmond Carney, Giuseppe Gullo, John Crown, Michaela J Higgins, Paul M Walsh, Janice M Walshe
PURPOSE: Pregnancy-associated breast cancer (PABC) is defined as breast cancer diagnosed during the gestational period (gp-PABC) or in the first postpartum year (pp-PABC). Despite its infrequent occurrence, the incidence of PABC appears to be rising due to the increasing propensity for women to delay childbirth. We have established the first retrospective registry study of PABC in Ireland to examine specific clinicopathological characteristics, treatments, and maternal and foetal outcomes...
August 2021: Breast Cancer Research and Treatment
#30
JOURNAL ARTICLE
Nathaniel M Pearson, Christian Stolte, Kevin Shi, Faygel Beren, Noura S Abul-Husn, Gabrielle Bertier, Kaitlyn Brown, George A Diaz, Jacqueline A Odgis, Sabrina A Suckiel, Carol R Horowitz, Melissa Wasserstein, Bruce D Gelb, Eimear E Kenny, Charles Gagnon, Vaidehi Jobanputra, Toby Bloom, John M Greally
PURPOSE: Making a diagnosis from clinical genomic sequencing requires well-structured phenotypic data to guide genotype interpretation. A patient's phenotypic features can be documented using the Human Phenotype Ontology (HPO), generating terms used to prioritize genes potentially causing the patient's disease. We have developed GenomeDiver to provide a user interface for clinicians that allows more effective collaboration with the clinical diagnostic laboratory, with the goal of improving the success of the diagnostic process...
June 10, 2021: Genetics in Medicine: Official Journal of the American College of Medical Genetics
#31
JOURNAL ARTICLE
Masako Suzuki, Tao Wang, Diana Garretto, Carmen R Isasi, Wellington V Cardoso, John M Greally, Loredana Quadro
Background: While the current national prevalence rate of vitamin A deficiency (VAD) is estimated to be less than 1%, it is suggested that it varies between different ethnic groups and races within the U.S. We assessed the prevalence of VAD in pregnant women of different ethnic groups and tested these prevalence rates for associations with the vitamin A-related single nucleotide polymorphism (SNP) allele frequencies in each ethnic group. Methods: We analyzed two independent datasets of serum retinol levels with self-reported ethnicities and the differences of allele frequencies of the SNPs associated with vitamin A metabolism between groups in publicly available datasets...
May 21, 2021: Nutrients
#32
JOURNAL ARTICLE
Devin Rocks, Ivana Jaric, Lydia Tesfa, John M Greally, Masako Suzuki, Marija Kundakovic
The Assay for Transposase Accessible Chromatin by sequencing (ATAC-seq) is becoming popular in the neuroscience field where chromatin regulation is thought to be involved in neurodevelopment, activity-dependent gene regulation, hormonal and environmental responses, and pathophysiology of neuropsychiatric disorders. The advantages of using ATAC-seq include a small amount of material needed, fast protocol, and the ability to capture a range of gene regulatory elements with a single assay. With increasing interest in chromatin research, it is an imperative to have feasible, reliable assays that are compatible with a range of neuroscience study designs...
2022: Epigenetics: Official Journal of the DNA Methylation Society
#33
Jacqueline A Odgis, Katie M Gallagher, Sabrina A Suckiel, Katherine E Donohue, Michelle A Ramos, Nicole R Kelly, Gabrielle Bertier, Christina Blackburn, Kaitlyn Brown, Lena Fielding, Jessenia Lopez, Karla Lopez Aguiniga, Estefany Maria, Jessica E Rodriguez, Monisha Sebastin, Nehama Teitelman, Dana Watnick, Nicole M Yelton, Avinash Abhyankar, Noura S Abul-Husn, Aaron Baum, Laurie J Bauman, Jules C Beal, Toby Bloom, Charlotte Cunningham-Rundles, George A Diaz, Siobhan Dolan, Bart S Ferket, Vaidehi Jobanputra, Patricia Kovatch, Thomas V McDonald, Patricia E McGoldrick, Rosamond Rhodes, Michael L Rinke, Mimsie Robinson, Arye Rubinstein, Lisa H Shulman, Christian Stolte, Steven M Wolf, Elissa Yozawitz, Randi E Zinberg, John M Greally, Bruce D Gelb, Carol R Horowitz, Melissa P Wasserstein, Eimear E Kenny
No abstract text is available yet for this article.
February 16, 2021: Trials
#34
JOURNAL ARTICLE
Andrew D Johnston, Alali Abdulrazak, Hanae Sato, Shahina B Maqbool, Masako Suzuki, John M Greally, Claudia A Simões-Pires
The CRISPR-Cas9 system can be modified to perform "epigenetic editing" by utilizing the catalytically inactive (dead) Cas9 (dCas9) to recruit regulatory proteins to specific genomic locations. In prior studies, epigenetic editing with multimers of the transactivator VP16 and guide RNAs (gRNAs) was found to cause adverse cellular responses. These side effects may confound studies inducing new cellular properties, especially if the cellular responses are maintained through cell divisions-an epigenetic regulatory property...
June 2020: CRISPR Journal
#35
JOURNAL ARTICLE
Sabrina A Suckiel, Jaqueline A Odgis, Katie M Gallagher, Jessica E Rodriguez, Dana Watnick, Gabrielle Bertier, Monisha Sebastin, Nicole Yelton, Estefany Maria, Jessenia Lopez, Michelle Ramos, Nicole Kelly, Nehama Teitelman, Faygel Beren, Tom Kaszemacher, Kojo Davis, Irma Laguerre, Lynne D Richardson, George A Diaz, Nathaniel M Pearson, Stephen B Ellis, Christian Stolte, Mimsie Robinson, Patricia Kovatch, Carol R Horowitz, Bruce D Gelb, John M Greally, Laurie J Bauman, Randi E Zinberg, Noura S Abul-Husn, Melissa P Wasserstein, Eimear E Kenny
PURPOSE: Use of genomic sequencing is increasing at a pace that requires technological solutions to effectively meet the needs of a growing patient population. We developed GUÍA, a web-based application, to enhance the delivery of genomic results and related clinical information to patients and families. METHODS: GUÍA development occurred in five overlapping phases: formative research, content development, stakeholder/community member input, user interface design, and web application development...
May 2021: Genetics in Medicine: Official Journal of the American College of Medical Genetics
#36
JOURNAL ARTICLE
David O'Reilly, Hailey Carroll, Mairi Lucas, Jane Sui, Maha Al Sendi, David McMahon, Waseem Darwish, Ronan McLaughlin, Mohammed Raza Khan, Hazel O Sullivan, Sonya Chew, Colum Dennehy, Catherine M Kelly, John McCaffrey, Megan Greally, Desmond Carney, Michaela J Higgins
BACKGROUND: The COVID-19 pandemic has resulted in radical changes in the delivery of healthcare worldwide. Our oncology service (at an Irish national cancer centre) rapidly transitioned to the use of telemedicine or virtual clinics (VC) to minimise potential risk of exposure to COVID-19 amongst an immunosuppressed, high-risk population. Our study aimed to evaluate the use of VC in this setting. METHODS: An 18-point questionnaire was designed to investigate the patient experience of VC during the COVID-19 pandemic in Ireland and compliance with guidelines developed in Ireland to conduct VC and the role of VC in the future...
January 15, 2021: Irish Journal of Medical Science
#37
JOURNAL ARTICLE
Jacqueline A Odgis, Katie M Gallagher, Sabrina A Suckiel, Katherine E Donohue, Michelle A Ramos, Nicole R Kelly, Gabrielle Bertier, Christina Blackburn, Kaitlyn Brown, Lena Fielding, Jessenia Lopez, Karla Lopez Aguiniga, Estefany Maria, Jessica E Rodriguez, Monisha Sebastin, Nehama Teitelman, Dana Watnick, Nicole M Yelton, Avinash Abhyankar, Noura S Abul-Husn, Aaron Baum, Laurie J Bauman, Jules C Beal, Toby Bloom, Charlotte Cunningham-Rundles, George A Diaz, Siobhan Dolan, Bart S Ferket, Vaidehi Jobanputra, Patricia Kovatch, Thomas V McDonald, Patricia E McGoldrick, Rosamond Rhodes, Michael L Rinke, Mimsie Robinson, Arye Rubinstein, Lisa H Shulman, Christian Stolte, Steven M Wolf, Elissa Yozawitz, Randi E Zinberg, John M Greally, Bruce D Gelb, Carol R Horowitz, Melissa P Wasserstein, Eimear E Kenny
BACKGROUND: Increasingly, genomics is informing clinical practice, but challenges remain for medical professionals lacking genetics expertise, and in access to and clinical utility of genomic testing for minority and underrepresented populations. The latter is a particularly pernicious problem due to the historical lack of inclusion of racially and ethnically diverse populations in genomic research and genomic medicine. A further challenge is the rapidly changing landscape of genetic tests and considerations of cost, interpretation, and diagnostic yield for emerging modalities like whole-genome sequencing...
January 14, 2021: Trials
#38
JOURNAL ARTICLE
Laurence de Torrenté, Samuel Zimmerman, Masako Suzuki, Maximilian Christopeit, John M Greally, Jessica C Mar
BACKGROUND: In genomics, we often assume that continuous data, such as gene expression, follow a specific kind of distribution. However we rarely stop to question the validity of this assumption, or consider how broadly applicable it may be to all genes that are in the transcriptome. Our study investigated the prevalence of a range of gene expression distributions in three different tumor types from the Cancer Genome Atlas (TCGA). RESULTS: Surprisingly, the expression of less than 50% of all genes was Normally-distributed, with other distributions including Gamma, Bimodal, Cauchy, and Lognormal also represented...
December 28, 2020: BMC Bioinformatics
#39
JOURNAL ARTICLE
Laura M Amendola, Kathleen Muenzen, Leslie G Biesecker, Kevin M Bowling, Greg M Cooper, Michael O Dorschner, Catherine Driscoll, Ann Katherine M Foreman, Katie Golden-Grant, John M Greally, Lucia Hindorff, Dona Kanavy, Vaidehi Jobanputra, Jennifer J Johnston, Eimear E Kenny, Shannon McNulty, Priyanka Murali, Jeffrey Ou, Bradford C Powell, Heidi L Rehm, Bradley Rolf, Tamara S Roman, Jessica Van Ziffle, Saurav Guha, Avinash Abhyankar, David Crosslin, Eric Venner, Bo Yuan, Hana Zouk, Gail P Jarvik
Harmonization of variant pathogenicity classification across laboratories is important for advancing clinical genomics. The two CLIA-accredited Electronic Medical Record and Genomics Network sequencing centers and the six CLIA-accredited laboratories and one research laboratory performing genome or exome sequencing in the Clinical Sequencing Evidence-Generating Research Consortium collaborated to explore current sources of discordance in classification. Eight laboratories each submitted 20 classified variants in the ACMG secondary finding v...
October 15, 2020: American Journal of Human Genetics
#40
JOURNAL ARTICLE
Daniel G Piqué, John M Greally, Jessica C Mar
BACKGROUND: Endometrial cancer (EC) is the most common gynecologic cancer in women, and the incidence of EC has increased by about 1% per year in the U. S over the last 10 years. Although 5-year survival rates for early-stage EC are around 80%, certain subtypes of EC that lose nuclear hormone receptor (NHR) expression are associated with poor survival rates. For example, estrogen receptor (ER)-negative EC typically harbors a worse prognosis compared to ER-positive EC. The molecular basis for the loss of NHR expression in endometrial tumors and its contribution to poor survival is largely unknown...
September 7, 2020: BMC Cancer
Make the most of Read.
Download the mobile app.
Download the mobile app.
Fetching more papers... 
