المؤلفون: Samuel Rosean, Eric A. Sosa, Dónal O’Shea, Srilakshmi M. Raj, Cathal Seoighe, John M. Greally

المصدر: BMC Bioinformatics, Vol 25, Iss 1, Pp 1-18 (2024)

مصطلحات موضوعية: Cell-type prioritization, Non-coding enrichment, Chromatin architecture, GWAS, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

الوصف: Abstract Background As genomic studies continue to implicate non-coding sequences in disease, testing the roles of these variants requires insights into the cell type(s) in which they are likely to be mediating their effects. Prior methods for associating non-coding variants with cell types have involved approaches using linkage disequilibrium or ontological associations, incurring significant processing requirements. GaiaAssociation is a freely available, open-source software that enables thousands of genomic loci implicated in a phenotype to be tested for enrichment at regulatory loci of multiple cell types in minutes, permitting insights into the cell type(s) mediating the studied phenotype. Results In this work, we present Regulatory Landscape Enrichment Analysis (RLEA) by GaiaAssociation and demonstrate its capability to test the enrichment of 12,133 variants across the cis-regulatory regions of 44 cell types. This analysis was completed in 134.0 ± 2.3 s, highlighting the efficient processing provided by GaiaAssociation. The intuitive interface requires only four inputs, offers a collection of customizable functions, and visualizes variant enrichment in cell-type regulatory regions through a heatmap matrix. GaiaAssociation is available on PyPi for download as a command line tool or Python package and the source code can also be installed from GitHub at https://github.com/GreallyLab/gaiaAssociationTest . Conclusions GaiaAssociation is a novel package that provides an intuitive and efficient resource to understand the enrichment of non-coding variants across the cis-regulatory regions of different cells, empowering studies seeking to identify disease-mediating cell types.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/1471-2105Test

الوصول الحر: https://doaj.org/article/4060e01f1a0740f48e1cf9011cdeebb1Test

المؤلفون: 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

المصدر: Epigenetics & Chromatin, Vol 16, Iss 1, Pp 1-13 (2023)

مصطلحات موضوعية: Single-cell, Open-chromatin regions, Multiplexing, Assay for transposase-accessible chromatin (ATAC), Genetics, QH426-470

الوصف: Abstract 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. We developed a simple nucleus hashing method using oligonucleotide-conjugated antibodies recognizing nuclear pore complex proteins, NuHash, to perform snATAC-seq library preparations by multiplexing. Results We performed multiplexing snATAC-seq analyses on a mixture of human and mouse cell samples (two samples, 2-plex, and four samples, 4-plex) using NuHash. The analyses on nuclei with at least 10,000 read counts showed that the demultiplexing accuracy of NuHash was high, and only ten out of 9144 nuclei (2-plex) and 150 of 12,208 nuclei (4-plex) had discordant classifications between NuHash demultiplexing and discrimination using reference genome alignments. The differential open chromatin region (OCR) analysis between female and male samples revealed that male-specific OCRs were enriched in chromosome Y (four out of nine). We also found that five female-specific OCRs (20 OCRs) were on chromosome X. A comparative analysis between snATAC-seq and deeply sequenced bulk ATAC-seq on the same samples revealed that the bulk ATAC-seq signal intensity was positively correlated with the number of cell clusters detected in snATAC-seq. Moreover, when we categorized snATAC-seq peaks based on the number of cell clusters in which the peak was present, we observed different distributions over different genomic features between the groups. This result suggests that the peak intensities of bulk ATAC-seq can be used to identify different types of functional loci. Conclusions Our multiplexing method using oligo-conjugated anti-nuclear pore complex proteins, NuHash, permits high-accuracy demultiplexing of samples. The NuHash protocol is straightforward, works on frozen samples, and requires no modifications for snATAC-seq library preparation.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/1756-8935Test

الوصول الحر: https://doaj.org/article/f1b57dbd9eda4373b99c5082f8dfd9c5Test

المؤلفون: 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

المصدر: Pilot and Feasibility Studies, Vol 9, Iss 1, Pp 1-13 (2023)

مصطلحات موضوعية: Whole genome sequencing, Genomic sequencing, Telehealth, Telegenetics, Genetic counseling, Clinical utility, Medicine (General), R5-920

الوصف: Abstract 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. Methods We aim to enroll 496 participants between 0 and 21 years old to receive clinical genome sequencing. These individuals have a neurologic, cardiovascular, and/or immunologic disease. Participants will be English- or Spanish-speaking and predominantly from underrepresented groups who receive care in the New York metropolitan area. Prior to enrollment, participants will be randomized to either genetic counseling via videoconferencing with screen-sharing or genetic counseling via videoconferencing without screen-sharing. Using surveys administered at baseline, results disclosure, and 6-months post-results disclosure, we will evaluate the impact of the use of screen-sharing on participant understanding, satisfaction, and uptake of medical recommendations, as well as the psychological and socioeconomic implications of obtaining genome sequencing. Clinical utility, cost, and diagnostic yield of genome sequencing will also be assessed. Discussion The TeleKidSeq pilot study will contribute to innovations in communicating genomic test results to diverse populations through telehealth technology. In conjunction with NYCKidSeq, this work will inform best practices for the implementation of genomic medicine in diverse, English- and Spanish-speaking populations.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/2055-5784Test

الوصول الحر: https://doaj.org/article/7f48af20b3204a4caf929dd7fb55d159Test

المؤلفون: Devin Rocks, Ivana Jaric, Fabio Bellia, Heining Cham, John M. Greally, Masako Suzuki, Marija Kundakovic

المصدر: Cell Reports, Vol 42, Iss 10, Pp 113187- (2023)

مصطلحات موضوعية: CP: Neuroscience, Biology (General), QH301-705.5

الوصف: Summary: 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. Conversely, high-estrogenic females respond to cocaine by preferential chromatin closing, providing a mechanism for limiting cocaine-driven chromatin and synaptic plasticity. We find that physiological estrogen withdrawal, early-life stress, and absence of one X chromosome all nullify the protective effect of a high-estrogenic state on cocaine conditioning in females. Our findings offer a molecular framework to enable understanding of sex-specific neuronal mechanisms underlying cocaine use disorder.

وصف الملف: electronic resource

العلاقة: http://www.sciencedirect.com/science/article/pii/S2211124723011993Test; https://doaj.org/toc/2211-1247Test

الوصول الحر: https://doaj.org/article/b6e296708a1a4b089f80e461674c8161Test

المؤلفون: 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

المصدر: Genome Medicine, Vol 14, Iss 1, Pp 1-17 (2022)

مصطلحات موضوعية: Incidental findings, Genomics, Genetic testing, Pediatrics, Disease severity, Personal utility, Medicine, Genetics, QH426-470

الوصف: Abstract 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. The incidental variants were not thought to be associated with the indication for testing and were disclosed to patients and families. Results In total, 23 "non-ACMG-recommended incidental findings were identified in 21 pediatric patients included in the study. These findings span four different research studies/laboratories and demonstrate differences in incidental finding return rate across study sites. We summarize specific cases to highlight core considerations that surround identification and return of incidental findings (uncertainty of disease onset, disease severity, age of onset, clinical actionability, and personal utility), and suggest that interpretation of incidental findings in pediatric patients can be difficult given evolving phenotypes. Furthermore, return of incidental findings can benefit patients and providers, but do present challenges. Conclusions While there may be considerable benefit to return of incidental genetic findings, these findings can be burdensome to providers and present risk to patients. It is important that laboratories conducting genomic testing establish internal guidelines in anticipation of detection. Moreover, cross-laboratory guidelines may aid in reducing the potential for policy heterogeneity across laboratories as it relates to incidental finding detection and return. However, future discussion is required to determine whether cohesive guidelines or policy statements are warranted.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/1756-994XTest

الوصول الحر: https://doaj.org/article/e4cc7a2958a74910939d83b6cfc1eb15Test

المؤلفون: Jamie M. Ellingford, Joo Wook Ahn, Richard D. Bagnall, Diana Baralle, Stephanie Barton, Chris Campbell, Kate Downes, Sian Ellard, Celia Duff-Farrier, David R. FitzPatrick, John M. Greally, Jodie Ingles, Neesha Krishnan, Jenny Lord, Hilary C. Martin, William G. Newman, Anne O’Donnell-Luria, Simon C. Ramsden, Heidi L. Rehm, Ebony Richardson, Moriel Singer-Berk, Jenny C. Taylor, Maggie Williams, Jordan C. Wood, Caroline F. Wright, Steven M. Harrison, Nicola Whiffin

المصدر: Genome Medicine, Vol 14, Iss 1, Pp 1-19 (2022)

مصطلحات موضوعية: Variant interpretation, Non-coding variation, Gene regulation, Medicine, Genetics, QH426-470

الوصف: Abstract Background The majority of clinical genetic testing focuses almost exclusively on regions of the genome that directly encode proteins. The important role of variants in non-coding regions in penetrant disease is, however, increasingly being demonstrated, and the use of whole genome sequencing in clinical diagnostic settings is rising across a large range of genetic disorders. Despite this, there is no existing guidance on how current guidelines designed primarily for variants in protein-coding regions should be adapted for variants identified in other genomic contexts. Methods We convened a panel of nine clinical and research scientists with wide-ranging expertise in clinical variant interpretation, with specific experience in variants within non-coding regions. This panel discussed and refined an initial draft of the guidelines which were then extensively tested and reviewed by external groups. Results We discuss considerations specifically for variants in non-coding regions of the genome. We outline how to define candidate regulatory elements, highlight examples of mechanisms through which non-coding region variants can lead to penetrant monogenic disease, and outline how existing guidelines can be adapted for the interpretation of these variants. Conclusions These recommendations aim to increase the number and range of non-coding region variants that can be clinically interpreted, which, together with a compatible phenotype, can lead to new diagnoses and catalyse the discovery of novel disease mechanisms.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/1756-994XTest

الوصول الحر: https://doaj.org/article/592317068741464ab4f2701a8ccc78e4Test

المؤلفون: Devin Rocks, Ivana Jaric, Lydia Tesfa, John M. Greally, Masako Suzuki, Marija Kundakovic

المصدر: Epigenetics, Vol 17, Iss 2, Pp 202-219 (2022)

مصطلحات موضوعية: chromatin accessibility, epigenomics, atac-seq, cell type-specific, mouse brain, human brain, freezing method, neuron, facs, Genetics, QH426-470

الوصف: 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. Here we tested three protocols for neuronal chromatin accessibility analysis, including a varying brain tissue freezing method followed by fluorescence-activated nuclei sorting (FANS) and ATAC-seq. Our study shows that the cryopreservation method impacts the number of open chromatin regions identified from frozen brain tissue using ATAC-seq. However, we show that all protocols generate consistent and robust data and enable the identification of functional regulatory elements in neuronal cells. Our study implies that the broad biological interpretation of chromatin accessibility data is not significantly affected by the freezing condition. We also reveal additional challenges of doing chromatin analysis on post-mortem human brain tissue. Overall, ATAC-seq coupled with FANS is a powerful method to capture cell-type-specific chromatin accessibility information in mouse and human brain. Our study provides alternative brain preservation methods that generate high-quality ATAC-seq data while fitting in different study designs, and further encourages the use of this method to uncover the role of epigenetic (dys)regulation in the brain.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/1559-2294Test; https://doaj.org/toc/1559-2308Test

الوصول الحر: https://doaj.org/article/c75be0690e9a4720b34f4ad8e2b307b0Test

المؤلفون: Julia J. Wattacheril, Srilakshmi Raj, David A. Knowles, John M. Greally

المصدر: PLoS Genetics, Vol 19, Iss 1 (2023)

مصطلحات موضوعية: Genetics, QH426-470

الوصف: 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. With the understanding that the interpretation of these associations is more complex than originally recognised, this model may be oversimplistic; therefore, adopting novel perspectives and experimental approaches when examining how environmental exposures are linked to phenotypes may prove worthwhile. In this review, we have chosen to use the example of nonalcoholic fatty liver disease (NAFLD), a common, complex human disease with strong environmental and genetic influences. We describe how epigenomic approaches combined with emerging functional genetic and single-cell genomic techniques are poised to generate new insights into the pathogenesis of environmentally influenced human disease phenotypes exemplified by NAFLD.

وصف الملف: electronic resource

العلاقة: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9851565/?tool=EBITest; https://doaj.org/toc/1553-7390Test; https://doaj.org/toc/1553-7404Test

الوصول الحر: https://doaj.org/article/e13f4d0d12af433398bb454f2a643598Test

المؤلفون: 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

المصدر: Gastro Hep Advances, Vol 1, Iss 3, Pp 328-341 (2022)

مصطلحات موضوعية: Health Disparities, Colorectal Cancer, Genomic Profiling, African Americans., Diseases of the digestive system. Gastroenterology, RC799-869

الوصف: 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. We evaluated the tumor microenvironment by using gene expression and methylation data, transcription factor, and master transcriptional regulator analysis to identify the cell signaling pathways mediating the observed phenotypic differences. Results: We demonstrate that downregulated genes in AFR patients with CRC showed enrichment for canonical pathways, including chemokine signaling. Moreover, evaluation of the tumor microenvironment showed that cytotoxic lymphocytes and neutrophil cell populations are significantly decreased in AFR compared with EUR patients, suggesting AFR patients have an attenuated immune response. We further demonstrate that molecules called “master transcriptional regulators” (MTRs) play a critical role in regulating the expression of genes impacting key immune processes through an intricate signal transduction network mediated by disease-associated transcription factors (TFs). Furthermore, a core set of these MTRs and TFs showed a positive correlation with levels of cytotoxic lymphocytes and neutrophils across both AFR and EUR patients with CRC, thus suggesting their role in driving the immune infiltrate differences between the two ancestral groups. Conclusion: Our study provides an insight into the intricate regulatory landscape of MTRs and TFs that orchestrate the differences in the tumor microenvironment between patients with CRC of AFR and EUR ancestry.

وصف الملف: electronic resource

العلاقة: http://www.sciencedirect.com/science/article/pii/S2772572322000115Test; https://doaj.org/toc/2772-5723Test

الوصول الحر: https://doaj.org/article/18a7ea9fffb34eac8439f8f87e7ef340Test

المؤلفون: 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

المصدر: Genome Biology, Vol 22, Iss 1, Pp 1-30 (2021)

مصطلحات موضوعية: Biology (General), QH301-705.5, Genetics, QH426-470

الوصف: Abstract 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. Results Each sample is processed in multiple replicates by three whole-genome bisulfite sequencing (WGBS) protocols (TruSeq DNA methylation, Accel-NGS MethylSeq, and SPLAT), oxidative bisulfite sequencing (TrueMethyl), enzymatic deamination method (EMSeq), targeted methylation sequencing (Illumina Methyl Capture EPIC), single-molecule long-read nanopore sequencing from Oxford Nanopore Technologies, and 850k Illumina methylation arrays. After rigorous quality assessment and comparison to Illumina EPIC methylation microarrays and testing on a range of algorithms (Bismark, BitmapperBS, bwa-meth, and BitMapperBS), we find overall high concordance between assays, but also differences in efficiency of read mapping, CpG capture, coverage, and platform performance, and variable performance across 26 microarray normalization algorithms. Conclusions The data provided herein can guide the use of these DNA reference materials in epigenomics research, as well as provide best practices for experimental design in future studies. By leveraging seven human cell lines that are designated as publicly available reference materials, these data can be used as a baseline to advance epigenomics research.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/1474-760XTest

الوصول الحر: https://doaj.org/article/8a322eba1d2e4d2ca87ac4166dc473a4Test