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Berkalieva A, Kelly NR, Fisher A, Hohmann SF, Abul-Husn NS, Greally JM, Horowitz CR, Wasserstein MP, Kenny EE, Gelb BD, Ferket BS. Physician and informal care use explained by the Pediatric Quality of Life Inventory (PedsQL) in children with suspected genetic disorders. Qual Life Res 2024:10.1007/s11136-024-03677-1. [PMID: 38743313 DOI: 10.1007/s11136-024-03677-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/01/2024] [Indexed: 05/16/2024]
Abstract
PURPOSE To examine associations between Pediatric Quality of Life Inventory (PedsQL) 4.0 Generic Core Scales and PedsQL Infant Scales with formal health care resource utilization (HCRU) and informal caregiver burden. METHODS We studied a pediatric cohort of 837 patients (median age: 8.4 years) with suspected genetic disorders enrolled January 2019 through July 2021 in the NYCKidSeq program for diagnostic sequencing. Using linked ~ nine-month longitudinal survey and physician claims data collected through May 2022, we modeled the association between baseline PedsQL scores and post-baseline HCRU (median follow-up: 21.1 months) and informal care. We also assessed the longitudinal change in PedsQL scores with physician services using linear mixed-effects models. RESULTS Lower PedsQL total and physical health scores were independently associated with increases in 18-month physician services, encounters, and weekly informal care. Comparing low vs. median total scores, increases were 10.6 services (95% CI: 1.0-24.6), 3.3 encounters (95% CI: 0.5-6.8), and $668 (95% CI: $350-965), respectively. For the psychosocial domain, higher scores were associated with decreased informal care. Based on adjusted linear mixed-effects modeling, every additional ten physician services was associated with diminished improvement in longitudinal PedsQL total score trajectories by 1.1 point (95% confidence interval: 0.6-1.6) on average. Similar trends were observed in the physical and psychosocial domains. CONCLUSION PedsQL scores were independently associated with higher utilization of physician services and informal care. Moreover, longitudinal trajectories of PedsQL scores became less favorable with increased physician services. Adding PedsQL survey instruments to conventional measures for improved risk stratification should be evaluated in further research.
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Affiliation(s)
- Asem Berkalieva
- Institute for Healthcare Delivery Science, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1077, New York, NY, 10029-6574, USA
| | - Nicole R Kelly
- Division of Pediatric Genetic Medicine, Department of Pediatrics, Children's Hospital at Montefiore/Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Ashley Fisher
- Center for Advanced Analytics, Vizient, Chicago, IL, USA
| | | | - Noura S Abul-Husn
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- 23andMe Inc, Sunnyvale, CA, USA
- Division for Genomic Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John M Greally
- Division of Genomics, Department of Genetics, Children's Hospital at Montefiore/Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Carol R Horowitz
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of General Internal Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melissa P Wasserstein
- Division of Pediatric Genetic Medicine, Department of Pediatrics, Children's Hospital at Montefiore/Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Eimear E Kenny
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division for Genomic Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bruce D Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bart S Ferket
- Institute for Healthcare Delivery Science, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1077, New York, NY, 10029-6574, USA.
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2
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Rosean S, Sosa EA, O'Shea D, Raj SM, Seoighe C, Greally JM. Regulatory landscape enrichment analysis (RLEA): a computational toolkit for non-coding variant enrichment and cell type prioritization. BMC Bioinformatics 2024; 25:179. [PMID: 38714913 PMCID: PMC11075237 DOI: 10.1186/s12859-024-05794-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/22/2024] [Indexed: 05/12/2024] Open
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/gaiaAssociation . 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.
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Affiliation(s)
- Samuel Rosean
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Eric A Sosa
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Dónal O'Shea
- School of Mathematics, Statistics & Applied Mathematics, National University of Ireland Galway, Galway, H91 TK33, Ireland
| | - Srilakshmi M Raj
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Cathal Seoighe
- School of Mathematics, Statistics & Applied Mathematics, National University of Ireland Galway, Galway, H91 TK33, Ireland
| | - John M Greally
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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3
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Saygin C, Zhang P, Stauber J, Aldoss I, Sperling AS, Weeks LD, Luskin MR, Knepper TC, Wanjari P, Wang P, Lager AM, Fitzpatrick C, Segal JP, Gharghabi M, Gurbuxani S, Venkataraman G, Cheng JX, Eisfelder BJ, Bohorquez O, Patel AA, Umesh Nagalakshmi S, Jayaram S, Odenike OM, Larson RA, Godley LA, Arber DA, Gibson CJ, Munshi NC, Marcucci G, Ebert BL, Greally JM, Steidl U, Lapalombella R, Shah BD, Stock W. Acute Lymphoblastic Leukemia with Myeloid Mutations Is a High-Risk Disease Associated with Clonal Hematopoiesis. Blood Cancer Discov 2024; 5:164-179. [PMID: 38150184 PMCID: PMC11061587 DOI: 10.1158/2643-3230.bcd-23-0106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 10/05/2023] [Accepted: 12/19/2023] [Indexed: 12/28/2023] Open
Abstract
Myeloid neoplasms arise from preexisting clonal hematopoiesis (CH); however, the role of CH in the pathogenesis of acute lymphoblastic leukemia (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. Single-cell RNA sequencing revealed upregulation of genes associated with cell survival and resistance to apoptosis in B-ALL with MyM, which responds better to newer immunotherapeutic approaches. These findings define ALL with MyM as a high-risk disease that can arise from antecedent CH and offer new mechanistic insights to develop better therapeutic and preventative strategies. SIGNIFICANCE CH is a precursor lesion for lymphoblastic leukemogenesis. ALL with MyM has distinct genetic and clinical characteristics, associated with adverse survival outcomes after chemotherapy. CH can precede ALL years before diagnosis, and ALL with MyM is enriched with activated T cells that respond to immunotherapies such as blinatumomab. See related commentary by Iacobucci, p. 142.
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Affiliation(s)
- Caner Saygin
- Section of Hematology/Oncology, University of Chicago, Chicago, Illinois
| | - Pu Zhang
- Division of Hematology, The Ohio State University, Columbus, Ohio
| | - Jacob Stauber
- Albert Einstein College of Medicine–Montefiore Health System, New York, New York
| | - Ibrahim Aldoss
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope, Duarte, California
| | - Adam S. Sperling
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Division of Hematology, Brigham and Women's Hospital, Boston, Massachusetts
| | | | | | | | - Pankhuri Wanjari
- Department of Pathology, University of Chicago, Chicago, Illinois
| | - Peng Wang
- Department of Pathology, University of Chicago, Chicago, Illinois
| | - Angela M. Lager
- Department of Pathology, University of Chicago, Chicago, Illinois
| | | | - Jeremy P. Segal
- Department of Pathology, University of Chicago, Chicago, Illinois
| | - Mehdi Gharghabi
- Division of Hematology, The Ohio State University, Columbus, Ohio
| | | | | | - Jason X. Cheng
- Department of Pathology, University of Chicago, Chicago, Illinois
| | - Bart J. Eisfelder
- Section of Hematology/Oncology, University of Chicago, Chicago, Illinois
| | - Oliver Bohorquez
- Albert Einstein College of Medicine–Montefiore Health System, New York, New York
| | - Anand A. Patel
- Section of Hematology/Oncology, University of Chicago, Chicago, Illinois
| | | | | | | | - Richard A. Larson
- Section of Hematology/Oncology, University of Chicago, Chicago, Illinois
| | - Lucy A. Godley
- Section of Hematology/Oncology, University of Chicago, Chicago, Illinois
| | - Daniel A. Arber
- Department of Pathology, University of Chicago, Chicago, Illinois
| | | | | | - Guido Marcucci
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope, Duarte, California
| | | | - John M. Greally
- Albert Einstein College of Medicine–Montefiore Health System, New York, New York
| | - Ulrich Steidl
- Albert Einstein College of Medicine–Montefiore Health System, New York, New York
| | | | | | - Wendy Stock
- Section of Hematology/Oncology, University of Chicago, Chicago, Illinois
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4
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Grebe TA, Khushf G, Greally JM, Turley P, Foyouzi N, Rabin-Havt S, Berkman BE, Pope K, Vatta M, Kaur S. Clinical utility of polygenic risk scores for embryo selection: A points to consider statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2024; 26:101052. [PMID: 38393332 DOI: 10.1016/j.gim.2023.101052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 02/25/2024] Open
Affiliation(s)
- Theresa A Grebe
- Phoenix Children's, Phoenix, AZ; Department of Child Health, University of Arizona College of Medicine-Phoenix, Phoenix, AZ
| | - George Khushf
- Department of Philosophy, University of South Carolina, Columbia, SC
| | - John M Greally
- Departments of Genetics and Pediatrics, Albert Einstein College of Medicine, Bronx, NY
| | - Patrick Turley
- Center for Economic and Social Research, University of Southern California, Los Angeles, CA; Department of Economics, University of Southern California, Los Angeles, CA
| | | | - Sara Rabin-Havt
- Department of OB/GYN, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY
| | - Benjamin E Berkman
- Department of Bioethics, National Institutes of Health; National Human Genome Research Institute, Bethesda, MD
| | - Kathleen Pope
- Department of Pediatrics, Nemours Children's Hospital, Orlando, FL; University of South Florida College of Public Health, Tampa, FL
| | | | - Shagun Kaur
- Phoenix Children's, Phoenix, AZ; Department of Child Health, University of Arizona College of Medicine-Phoenix, Phoenix, AZ
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5
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Berkalieva A, Kelly NR, Fisher A, Hohmann SF, Sebastin M, Di Biase M, Bonini KE, Marathe P, Odgis JA, Suckiel SA, Ramos MA, Rhodes R, Abul-Husn NS, Greally JM, Horowitz CR, Wasserstein MP, Kenny EE, Gelb BD, Ferket BS. Physician services and costs after disclosure of diagnostic sequencing results in the NYCKidSeq program. Genet Med 2024; 26:101011. [PMID: 37897232 PMCID: PMC10842442 DOI: 10.1016/j.gim.2023.101011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 10/19/2023] [Accepted: 10/22/2023] [Indexed: 10/29/2023] Open
Abstract
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 to 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. RESULTS We included data on 857 patients (median age: 9.6 years) with a median follow-up of 17.3 months after disclosure of diagnostic sequencing results. The likelihood of having ≥1 recommendation for specialist consultation in 155 patients with positive findings was high (72%) vs 23% in 443 patients with uncertain findings and 21% in 259 patients with negative findings (P < .001). Follow-through consultation occurred in 30%. Increases in 18-month physician services and costs following a positive finding diminished after multivariable adjustment. Also, no significant differences between those with uncertain and negative findings were demonstrated. CONCLUSION Our study did not provide evidence for significant increases in downstream physician services and costs after returning positive or uncertain diagnostic sequencing findings. More large-scale longitudinal studies are needed to confirm these findings.
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Affiliation(s)
- Asem Berkalieva
- Institute for Healthcare Delivery Science, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Nicole R Kelly
- Division of Pediatric Genetic Medicine, Department of Pediatrics, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | | | | | - Monisha Sebastin
- Division of Pediatric Genetic Medicine, Department of Pediatrics, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Miranda Di Biase
- Division of Pediatric Genetic Medicine, Department of Pediatrics, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Katherine E Bonini
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Priya Marathe
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jacqueline A Odgis
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Sabrina A Suckiel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Michelle A Ramos
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Rosamond Rhodes
- Department of Education, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Noura S Abul-Husn
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY; 23andMe Inc, Sunnyvale, CA
| | - John M Greally
- Division of Genomics, Department of Genetics, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Carol R Horowitz
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY; Division of General Internal Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Melissa P Wasserstein
- Division of Pediatric Genetic Medicine, Department of Pediatrics, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Eimear E Kenny
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY; Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY; Division for Genomic Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Bruce D Gelb
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Bart S Ferket
- Institute for Healthcare Delivery Science, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY.
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6
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Rocks D, Purisic E, Gallo EF, Greally JM, Suzuki M, Kundakovic M. Egr1 is a sex-specific regulator of neuronal chromatin, synaptic plasticity, and behaviour. bioRxiv 2023:2023.12.20.572697. [PMID: 38187614 PMCID: PMC10769422 DOI: 10.1101/2023.12.20.572697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Sex differences are found in brain structure and function across species, and across brain disorders in humans1-3. The major source of brain sex differences is differential secretion of steroid hormones from the gonads across the lifespan4. 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 risk5-7. However, due to limited molecular studies in female rodents8, very little is still known about molecular drivers of female-specific brain and behavioural plasticity. Here we show that overexpressing Egr1, a candidate oestrous cycle-dependent transcription factor9, induces sex-specific changes in ventral hippocampal neuronal chromatin, gene expression, and synaptic plasticity, along with hippocampus-dependent behaviours. Importantly, Egr1 overexpression mimics the high-oestrogenic phase of the oestrous cycle, and affects behaviours in ovarian hormone-depleted females but not in males. We demonstrate that Egr1 opens neuronal chromatin directly across the sexes, although with limited genomic overlap. Our study not only reveals the first sex-specific chromatin regulator in the brain, but also provides functional evidence that this sex-specific gene regulation drives neuronal gene expression, synaptic plasticity, and anxiety- and depression-related behaviour. Our study exemplifies an innovative sex-based approach to studying neuronal gene regulation1 in order to understand sex-specific synaptic and behavioural plasticity and inform novel brain disease treatments.
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Affiliation(s)
- Devin Rocks
- Department of Biological Sciences, Fordham University, Bronx, NY, USA
| | - Eric Purisic
- Department of Biological Sciences, Fordham University, Bronx, NY, USA
| | - Eduardo F. Gallo
- Department of Biological Sciences, Fordham University, Bronx, NY, USA
| | - John M. Greally
- Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Masako Suzuki
- Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Nutrition, Texas A&M University, College Station, TX, USA
| | - Marija Kundakovic
- Department of Biological Sciences, Fordham University, Bronx, NY, USA
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7
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Suckiel SA, Kelly NR, Odgis JA, Gallagher KM, Sebastin M, Bonini KE, Marathe PN, Brown K, Di Biase M, Ramos MA, Rodriguez JE, Scarimbolo L, Insel BJ, Ferar KDM, Zinberg RE, Diaz GA, Greally JM, Abul-Husn NS, Bauman LJ, Gelb BD, Horowitz CR, Wasserstein MP, Kenny EE. The NYCKidSeq randomized controlled trial: Impact of GUÍA digitally enhanced genetic results disclosure in diverse families. Am J Hum Genet 2023; 110:2029-2041. [PMID: 38006881 PMCID: PMC10716481 DOI: 10.1016/j.ajhg.2023.10.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/27/2023] Open
Abstract
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). Parents/legal guardians (participants) completed surveys at baseline, post-results disclosure, and 6 months later. Survey measures assessed the primary study outcomes of participants' perceived understanding of and confidence in explaining their child's GT results and the secondary outcome of objective understanding. The analysis included 551 diverse participants, 270 in the GUÍA arm and 281 in SOC. Participants in the GUÍA arm had significantly higher perceived understanding post-results (OR = 2.8, CI[1.004, 7.617], p = 0.049) and maintained higher objective understanding over time (OR = 1.1, CI[1.004, 1.127], p = 0.038) compared to SOC. There was no impact on perceived confidence. Hispanic/Latino(a) individuals in the GUÍA arm maintained higher perceived understanding (OR = 3.9, CI[1.603, 9.254], p = 0.003), confidence (OR = 2.7, CI[1.021, 7.277], p = 0.046), and objective understanding (OR = 1.1, CI[1.009, 1.212], p = 0.032) compared to SOC. This trial demonstrates that GUÍA positively impacts understanding of GT results in diverse parents of children with suspected genetic conditions and builds a case for utilizing GUÍA to deliver complex results. Continued development and evaluation of digital applications in diverse populations are critical for equitably scaling GT offerings in specialty clinics.
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Affiliation(s)
- Sabrina A Suckiel
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Nicole R Kelly
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY 10467, USA
| | - Jacqueline A Odgis
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Katie M Gallagher
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY 10467, USA
| | - Monisha Sebastin
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY 10467, USA
| | - Katherine E Bonini
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Priya N Marathe
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kaitlyn Brown
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY 10467, USA
| | - Miranda Di Biase
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY 10467, USA
| | - Michelle A Ramos
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jessica E Rodriguez
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Laura Scarimbolo
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Beverly J Insel
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kathleen D M Ferar
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Randi E Zinberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - George A Diaz
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - John M Greally
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY 10467, USA
| | - Noura S Abul-Husn
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Laurie J Bauman
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY 10467, USA; Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY 10467, USA
| | - Bruce D Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carol R Horowitz
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Melissa P Wasserstein
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY 10467, USA
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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8
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Wang S, Broder A, Shao D, Kesarwani V, Boderman B, Aguilan J, Sidoli S, Suzuki M, Greally JM, Saenger YM, Rovin BH, Michelle Kahlenberg J. Urine Proteomics Link Complement Activation with Interstitial Fibrosis/Tubular Atrophy in Lupus Nephritis Patients. Semin Arthritis Rheum 2023; 63:152263. [PMID: 37802003 PMCID: PMC10783434 DOI: 10.1016/j.semarthrit.2023.152263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 08/14/2023] [Accepted: 08/27/2023] [Indexed: 10/08/2023]
Abstract
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). METHODS We included urine samples from 46 adults and pediatric biopsy-proven lupus nephritis patients who underwent clinically indicated kidney biopsies between 2010 and 2019. We compared individual urinary complement components and the urinary C9-to-CD59 ratio between LN patients with moderate/severe IFTA and none/mild IFTA. IFTA was defined as none/mild (<25% of interstitium affected) versus moderate/severe (≥ 25% of interstitium affected). Proteomics analysis was performed using mass spectrometry (Orbitrap Fusion Lumos, Thermo Scientific) and processed by the Proteome Discoverer. Urinary complement proteins enriched in LN patients with moderate/severe IFTA were correlated with serum creatinine, TGFβR1, TGFβR2, PDGFβ, and PDGFRβ. RESULTS Of the 46 LN patients included in the study, 41 (89.1%) were women, 20 (43.5%) self-identified as Hispanic or Latino, and 26 (56.5%) self-identified as Black or African American. Ten of the 46 (21.7%) LN patients had moderate/severe IFTA on kidney biopsy. LN patients with moderate/severe IFTA had an increased urinary C9-to-CD59 ratio [median 0.91 (0.83-1.05) vs 0.81 (0.76-0.91), p=0.01]. Urinary C3 and CFI levels in LN patients with moderate/severe IFTA were higher compared to those with none/mild IFTA [C3 median (IQR) 24.4(23.5-25.5) vs. 20.2 (18.5-22.2), p= 0.02], [CFI medium (IQR) 28.8 (21.8-30.6) vs. 20.4 (18.5-22.9), p=0.01]. Complement C9, CD59, C3 and CFI correlated with TGFβR1, PDGFβ, and PDGFRβ, while C9, CD59 and C3 correlated with TGFβR2. CONCLUSION This study is one of the first to compare the urinary complement profile in LN patients with moderate/severe IFTA and none/mild IFTA in human tissues. This study identified C3, CFI, and C9-to-CD59 ratio as potential markers of tubulointerstitial fibrosis in LN.
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Affiliation(s)
- Shudan Wang
- Division of Rheumatology, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA.
| | - Anna Broder
- Division of Rheumatology, Hackensack University Medical Center, Hackensack, NJ, USA
| | - Daming Shao
- Department of Medicine, Jacobi Medical Center, Bronx, NY, USA
| | - Vartika Kesarwani
- Department of Medicine, University of Wisconsin Hospital and Clinics, WI, USA
| | - Brianna Boderman
- Department of Medicine, University of Connecticut School of Medicine, CT, USA
| | - Jennifer Aguilan
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Masako Suzuki
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY USA
| | - John M Greally
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY USA
| | - Yvonne M Saenger
- Department of Oncology and Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, NY USA
| | - Brad H Rovin
- Division of Nephrology, Ohio State University Wexner Medical Center, Columbus, Ohio, USA
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9
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Rocks D, Jaric I, Bellia F, Cham H, Greally JM, Suzuki M, Kundakovic M. Early-life stress and ovarian hormones alter transcriptional regulation in the nucleus accumbens resulting in sex-specific responses to cocaine. Cell Rep 2023; 42:113187. [PMID: 37777968 PMCID: PMC10753961 DOI: 10.1016/j.celrep.2023.113187] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/29/2023] [Accepted: 09/12/2023] [Indexed: 10/03/2023] Open
Abstract
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.
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Affiliation(s)
- Devin Rocks
- Department of Biological Sciences, Fordham University, Bronx, NY, USA
| | - Ivana Jaric
- Department of Biological Sciences, Fordham University, Bronx, NY, USA
| | - Fabio Bellia
- Department of Biological Sciences, Fordham University, Bronx, NY, USA
| | - Heining Cham
- Department of Psychology, Fordham University, Bronx, NY, USA
| | - John M Greally
- Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Masako Suzuki
- Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA; Department of Nutrition, Texas A&M University, College Station, TX, USA
| | - Marija Kundakovic
- Department of Biological Sciences, Fordham University, Bronx, NY, USA.
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10
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Sosa EA, Rosean S, O’Shea D, Raj SM, Seoighe C, Greally JM. Regulatory Landscape Enrichment Analysis (RLEA) using gaiaAssociation. bioRxiv 2023:2023.10.11.561933. [PMID: 37905111 PMCID: PMC10614734 DOI: 10.1101/2023.10.11.561933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
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. GaiaAssociation is Python code that is freely available for use in functional genomics studies. Availability and Implementation Gaia Association is available on PyPi (https://pypi.org/project/gaiaAssociation/0.6.0/#description) for pip download and use on the command line or as an inline Python package. Gaia Association can also be installed from GitHub at https://github.com/GreallyLab/gaiaAssociation.
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Affiliation(s)
- Eric A. Sosa
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Samuel Rosean
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Dónal O’Shea
- School of Mathematics, Statistics & Applied Mathematics, National University of Ireland Galway, Galway, H91 TK33, Ireland
| | - Srilakshmi M. Raj
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Cathal Seoighe
- School of Mathematics, Statistics & Applied Mathematics, National University of Ireland Galway, Galway, H91 TK33, Ireland
| | - John M. Greally
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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11
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Ueda K, Chin SS, Sato N, Nishikawa M, Yasuda K, Miyasaka N, Bera BS, Chorro L, Doña-Termine R, Koba WR, Reynolds D, Steidl UG, Lauvau G, Greally JM, Suzuki M. Prenatal vitamin D deficiency alters immune cell proportions of young adult offspring through alteration of long-term stem cell fates. bioRxiv 2023:2023.09.11.557255. [PMID: 37745570 PMCID: PMC10515841 DOI: 10.1101/2023.09.11.557255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
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. Further investigations of the associations between maternal vitamin D levels and cord blood immune cell profiles from 75 healthy pregnant women and their term babies also confirm that maternal vitamin D levels significantly affect immune cell proportions in the babies. Thus, lack of prenatal vitamin D, particularly at the time of hematopoietic stem cell migration from the liver to the bone marrow, has long-lasting effects on immune cell proportions. This highlights the importance of providing vitamin D supplementation at specific stages of pregnancy.
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Affiliation(s)
- Koki Ueda
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY, 10461, USA
- Department of Blood Transfusion and Transplantation Immunology, Fukushima Medical University, 1 Hikarigaoka, Fukushima, Fukushima, 960-1295, Japan
| | - Shu Shien Chin
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY, 10461, USA
| | - Noriko Sato
- Department of Food and Nutrition, Faculty of Human Sciences and Design, Japan Women’s University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo 112-8681, Japan
| | - Miyu Nishikawa
- Department of Biotechnology, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Kaori Yasuda
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Naoyuki Miyasaka
- Graduate School of Medical and Dental Sciences, Medical and Dental Sciences, Systemic Organ Regulation, Comprehensive Reproductive Medicine, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo
| | - Betelehem Solomon Bera
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY, 10461, USA
| | - Laurent Chorro
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY, 10461, USA
| | - Reanna Doña-Termine
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY, 10461, USA
| | - Wade R Koba
- Department of Radiology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY, 10461, USA
| | - David Reynolds
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY, 10461, USA
| | - Ulrich G. Steidl
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY, 10461, USA
- Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA
- Department of Oncology, Albert Einstein College of Medicine – Montefiore Medical Center, 1300 Morris Park Ave, Bronx, NY 10461, USA
- Montefiore-Einstein Cancer Center, Albert Einstein College of Medicine – Montefiore Medical Center, 1300 Morris Park Ave, Bronx, NY 10461, USA
| | - Gregoire Lauvau
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY, 10461, USA
| | - John M. Greally
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY, 10461, USA
- Department of Pediatrics, Albert Einstein College of Medicine – Montefiore Medical Center, 1300 Morris Park Ave, Bronx, NY 10461, USA
| | - Masako Suzuki
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY, 10461, USA
- Department of Nutrition, Texas A&M University, 2253 TAMU, College Station, TX, 77840, USA
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12
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Abul-Husn NS, Marathe PN, Kelly NR, Bonini KE, Sebastin M, Odgis JA, Abhyankar A, Brown K, Di Biase M, Gallagher KM, Guha S, Ioele N, Okur V, Ramos MA, Rodriguez JE, Rehman AU, Thomas-Wilson A, Edelmann L, Zinberg RE, Diaz GA, Greally JM, Jobanputra V, Suckiel SA, Horowitz CR, Wasserstein MP, Kenny EE, Gelb BD. Molecular diagnostic yield of genome sequencing versus targeted gene panel testing in racially and ethnically diverse pediatric patients. Genet Med 2023; 25:100880. [PMID: 37158195 PMCID: PMC10789486 DOI: 10.1016/j.gim.2023.100880] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 04/27/2023] [Accepted: 04/30/2023] [Indexed: 05/10/2023] Open
Abstract
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 A total of 645 probands (median age 9 years) underwent genetic testing, and 113 (17.5%) received a molecular diagnosis. Among 642 probands with both GS and TGP testing, GS yielded 106 (16.5%) and TGPs yielded 52 (8.1%) diagnoses (P < .001). Yield was greater for GS vs TGPs in Hispanic/Latino(a) (17.2% vs 9.5%, P < .001) and White/European American (19.8% vs 7.9%, P < .001) but not in Black/African American (11.5% vs 7.7%, P = .22) population groups by self-report. A higher rate of inconclusive results was seen in the Black/African American (63.8%) vs White/European American (47.6%; P = .01) population group. Most causal copy number variants (17 of 19) and mosaic variants (6 of 8) were detected only by GS. CONCLUSION GS may yield up to twice as many diagnoses in pediatric patients compared with TGP testing but not yet across all population groups.
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Affiliation(s)
- Noura S Abul-Husn
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY; 23andMe, Inc., Sunnyvale, CA
| | - Priya N Marathe
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Nicole R Kelly
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Katherine E Bonini
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Monisha Sebastin
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Jacqueline A Odgis
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Kaitlyn Brown
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY; Illumina Incorporated, San Diego, CA
| | - Miranda Di Biase
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Katie M Gallagher
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY; Invitae Corporation, San Francisco, CA
| | - Saurav Guha
- Molecular Diagnostics, New York Genome Center, New York, NY
| | - Nicolette Ioele
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY; Memorial Sloan Kettering Cancer Center, New York, NY
| | - Volkan Okur
- Molecular Diagnostics, New York Genome Center, New York, NY
| | - Michelle A Ramos
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY; Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jessica E Rodriguez
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | | | | | - Randi E Zinberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - George A Diaz
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY; iECURE Incorporated, Philadelphia, PA
| | - John M Greally
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Vaidehi Jobanputra
- Molecular Diagnostics, New York Genome Center, New York, NY; Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Sabrina A Suckiel
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Carol R Horowitz
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY; Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Melissa P Wasserstein
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY.
| | - Bruce D Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY.
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13
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Bonini KE, Thomas-Wilson A, Marathe PN, Sebastin M, Odgis JA, Biase MD, Kelly NR, Ramos MA, Insel BJ, Scarimbolo L, Rehman AU, Guha S, Okur V, Abhyankar A, Phadke S, Nava C, Gallagher KM, Elkhoury L, Edelmann L, Zinberg RE, Abul-Husn NS, Diaz GA, Greally JM, Suckiel SA, Horowitz CR, Kenny EE, Wasserstein M, Gelb BD, Jobanputra V. Identification of copy number variants with genome sequencing: Clinical experiences from the NYCKidSeq program. Clin Genet 2023; 104:210-225. [PMID: 37334874 PMCID: PMC10505482 DOI: 10.1111/cge.14365] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/28/2023] [Accepted: 05/15/2023] [Indexed: 06/21/2023]
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.
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Affiliation(s)
- Katherine E. Bonini
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Priya N. Marathe
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Monisha Sebastin
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Jacqueline A. Odgis
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Miranda Di Biase
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Nicole R. Kelly
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Michelle A. Ramos
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Beverly J. Insel
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Laura Scarimbolo
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Saurav Guha
- Molecular Diagnostics, New York Genome Center, New York, NY
| | - Volkan Okur
- Molecular Diagnostics, New York Genome Center, New York, NY
| | | | - Shruti Phadke
- Molecular Diagnostics, New York Genome Center, New York, NY
| | - Caroline Nava
- Molecular Diagnostics, New York Genome Center, New York, NY
| | - Katie M. Gallagher
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | | | | | - Randi E. Zinberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Noura S. Abul-Husn
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - George A. Diaz
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
| | - John M. Greally
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Sabrina A. Suckiel
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Carol R. Horowitz
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Eimear E. Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Melissa Wasserstein
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Bruce D. Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Vaidehi Jobanputra
- Molecular Diagnostics, New York Genome Center, New York, NY
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY
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14
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Suckiel SA, Kelly NR, Odgis JA, Gallagher KM, Sebastin M, Bonini KE, Marathe PN, Brown K, Di Biase M, Ramos MA, Rodriguez JE, Scarimbolo L, Insel BJ, Ferar KD, Zinberg RE, Diaz GA, Greally JM, Abul-Husn NS, Bauman LJ, Gelb BD, Horowitz CR, Wasserstein MP, Kenny EE. The NYCKidSeq randomized controlled trial: Impact of GUÍA digitally enhanced genetic counseling in racially and ethnically diverse families. medRxiv 2023:2023.07.05.23292193. [PMID: 37461450 PMCID: PMC10350148 DOI: 10.1101/2023.07.05.23292193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
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. Families were randomized to genetic counseling with GUÍA (intervention) or standard of care (SOC) genetic counseling for results disclosure. Parents/legal guardians (participants) completed surveys at baseline, post-results disclosure, and 6-months later. Survey measures assessed the primary study outcomes of perceived understanding of and confidence in explaining their child's GT results and the secondary outcome of objective understanding. We used regression models to evaluate the association between the intervention and the study outcomes. Results The analysis included 551 participants, 270 in the GUÍA arm and 281 in SOC. Participants' mean age was 41.1 years and 88.6% were mothers. Most participants were Hispanic/Latino(a) (46.3%), White/European American (24.5%), or Black/African American (15.8%). Participants in the GUÍA arm had significantly higher perceived understanding post-results (OR=2.8, CI[1.004,7.617], P=0.049) and maintained higher objective understanding over time (OR=1.1, CI[1.004, 1.127], P=0.038) compared to those in the SOC arm. There was no impact on perceived confidence. Hispanic/Latino(a) individuals in the GUÍA arm maintained higher perceived understanding (OR=3.9, CI[1.6, 9.3], P=0.003), confidence (OR=2.7, CI[1.021, 7.277], P=0.046), and objective understanding (OR=1.1, CI[1.009, 1.212], P=0.032) compared to SOC . Conclusions This trial demonstrates that GUÍA positively impacts understanding of GT results in diverse parents of children with suspected genetic conditions. These findings build a case for utilizing GUÍA to deliver complex and often ambiguous genetic results. Continued development and evaluation of digital applications in diverse populations are critical for equitably scaling GT offerings in specialty clinics. Trial Registration Clinicaltrials.gov identifier NCT03738098.
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Affiliation(s)
- Sabrina A. Suckiel
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Nicole R. Kelly
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Jacqueline A. Odgis
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Katie M. Gallagher
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Monisha Sebastin
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Katherine E. Bonini
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Priya N. Marathe
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Kaitlyn Brown
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Miranda Di Biase
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Michelle A. Ramos
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jessica E. Rodriguez
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Laura Scarimbolo
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Beverly J. Insel
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Kathleen D.M. Ferar
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Randi E. Zinberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, NY
| | - George A. Diaz
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York
| | - John M. Greally
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Noura S. Abul-Husn
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Laurie J. Bauman
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY
| | - Bruce D. Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Carol R. Horowitz
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Melissa P. Wasserstein
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Eimear E. Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
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15
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Bera BS, Thompson TV, Sosa E, Nomaru H, Reynolds D, Dubin RA, Maqbool SB, Zheng D, Morrow BE, Greally JM, Suzuki M. An optimized approach for multiplexing single-nuclear ATAC-seq using oligonucleotide-conjugated antibodies. Epigenetics Chromatin 2023; 16:14. [PMID: 37118773 PMCID: PMC10142415 DOI: 10.1186/s13072-023-00486-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 04/13/2023] [Indexed: 04/30/2023] Open
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.
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Affiliation(s)
- Betelehem Solomon Bera
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Center for Genetic Medicine, Children's National Medical Center, Washington, DC, USA
| | - Taylor V Thompson
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Eric Sosa
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Hiroko Nomaru
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Thinkcyte Inc., Tokyo, Japan
| | - David Reynolds
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Robert A Dubin
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Shahina B Maqbool
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Departments of Neurology and Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Bernice E Morrow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - John M Greally
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Masako Suzuki
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
- Department of Nutrition, Texas A&M University, College Station, TX, USA.
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16
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Sebastin M, Odgis JA, Suckiel SA, Bonini KE, Di Biase M, Brown K, Marathe P, Kelly NR, Ramos MA, Rodriguez JE, Aguiñiga KL, Lopez J, Maria E, Rodriguez MA, Yelton NM, Cunningham-Rundles C, Gallagher K, McDonald TV, McGoldrick PE, Robinson M, Rubinstein A, Shulman LH, Wolf SM, Yozawitz E, Zinberg RE, Abul-Husn NS, Bauman LJ, Diaz GA, Ferket BS, Greally JM, Jobanputra V, Gelb BD, Horowitz CR, Kenny EE, Wasserstein MP. The TeleKidSeq pilot study: incorporating telehealth into clinical care of children from diverse backgrounds undergoing whole genome sequencing. Pilot Feasibility Stud 2023; 9:47. [PMID: 36949526 PMCID: PMC10031704 DOI: 10.1186/s40814-023-01259-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 02/02/2023] [Indexed: 03/24/2023] Open
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.
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Affiliation(s)
- Monisha Sebastin
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, 3411 Wayne Ave, 9th Floor, Bronx, NY, 10467, USA
| | - Jacqueline A Odgis
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sabrina A Suckiel
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Katherine E Bonini
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Miranda Di Biase
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, 3411 Wayne Ave, 9th Floor, Bronx, NY, 10467, USA
| | - Kaitlyn Brown
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, 3411 Wayne Ave, 9th Floor, Bronx, NY, 10467, USA
| | - Priya Marathe
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nicole R Kelly
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, 3411 Wayne Ave, 9th Floor, Bronx, NY, 10467, USA
| | - Michelle A Ramos
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jessica E Rodriguez
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Karla López Aguiñiga
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jessenia Lopez
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, 3411 Wayne Ave, 9th Floor, Bronx, NY, 10467, USA
| | - Estefany Maria
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, 3411 Wayne Ave, 9th Floor, Bronx, NY, 10467, USA
| | - Michelle A Rodriguez
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nicole M Yelton
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Charlotte Cunningham-Rundles
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Katie Gallagher
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, 3411 Wayne Ave, 9th Floor, Bronx, NY, 10467, USA
| | - Thomas V McDonald
- Department of Medicine (Cardiology), Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Patricia E McGoldrick
- Department of Pediatrics, Division of Child Neurology, New York Medical College, Valhalla, NY, USA
- Pediatric Neurology, Boston Children's Health Physicians/Maria Fareri Children's Hospital, Hawthorne, NY, USA
| | | | - Arye Rubinstein
- Department of Allergy and Immunology, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Lisa H Shulman
- Department of Pediatrics, Division of Developmental Medicine, Rose F. Kennedy Children's Evaluation & Rehabilitation Center at Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Steven M Wolf
- Department of Pediatrics, Division of Child Neurology, New York Medical College, Valhalla, NY, USA
- Pediatric Neurology, Boston Children's Health Physicians/Maria Fareri Children's Hospital, Hawthorne, NY, USA
| | - Elissa Yozawitz
- Isabelle Rapin Division of Child Neurology of the Saul R Korey Department of Neurology at Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Pediatrics, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Randi E Zinberg
- Department of Genetics and Genomic Sciences , Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Noura S Abul-Husn
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences , Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laurie J Bauman
- Department of Pediatrics, Division of Ambulatory Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - George A Diaz
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences , Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bart S Ferket
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John M Greally
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, 3411 Wayne Ave, 9th Floor, Bronx, NY, 10467, USA
| | - Vaidehi Jobanputra
- Molecular Diagnostics, New York Genome Center, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Bruce D Gelb
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences , Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carol R Horowitz
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eimear E Kenny
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences , Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melissa P Wasserstein
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, 3411 Wayne Ave, 9th Floor, Bronx, NY, 10467, USA.
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17
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Abul-Husn NS, Marathe PN, Kelly NR, Bonini KE, Sebastin M, Odgis JA, Abhyankar A, Brown K, Di Biase M, Gallagher KM, Guha S, Ioele N, Okur V, Ramos MA, Rodriguez JE, Rehman AU, Thomas-Wilson A, Edelmann L, Zinberg RE, Diaz GA, Greally JM, Jobanputra V, Suckiel SA, Horowitz CR, Wasserstein MP, Kenny EE, Gelb BD. Molecular diagnostic yield of genome sequencing versus targeted gene panel testing in racially and ethnically diverse pediatric patients. medRxiv 2023:2023.03.18.23286992. [PMID: 36993157 PMCID: PMC10055570 DOI: 10.1101/2023.03.18.23286992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
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 (17.5%) received a molecular diagnosis. Among 642 probands with both GS and TGP testing, GS yielded 106 (16.5%) and TGPs yielded 52 (8.1%) diagnoses ( P < .001). Yield was greater for GS vs . TGPs in Hispanic/Latino(a) (17.2% vs . 9.5%, P < .001) and White/European American (19.8% vs . 7.9%, P < .001), but not in Black/African American (11.5% vs . 7.7%, P = .22) population groups by self-report. A higher rate of inconclusive results was seen in the Black/African American (63.8%) vs . White/European American (47.6%; P = .01) population group. Most causal copy number variants (17 of 19) and mosaic variants (6 of 8) were detected only by GS. Conclusion GS may yield up to twice as many diagnoses in pediatric patients compared to TGP testing, but not yet across all population groups.
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18
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Odgis JA, Gallagher KM, Rehman AU, Marathe P, Bonini KE, Sebastin M, Di Biase M, Brown K, Kelly NR, Ramos MA, Thomas-Wilson A, Guha S, Okur V, Ganapathi M, Elkhoury L, Edelmann L, Zinberg RE, Abul-Husn NS, Diaz GA, Greally JM, Suckiel SA, Jobanputra V, Horowitz CR, Kenny EE, Wasserstein MP, Gelb BD. Detection of mosaic variants using genome sequencing in a large pediatric cohort. Am J Med Genet A 2023; 191:699-710. [PMID: 36563179 PMCID: PMC10266700 DOI: 10.1002/ajmg.a.63062] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 11/07/2022] [Accepted: 11/18/2022] [Indexed: 12/24/2022]
Abstract
The increased use of next-generation sequencing has expanded our understanding of the involvement and prevalence of mosaicism in genetic disorders. We describe a total of eleven cases: nine in which mosaic variants detected by genome sequencing (GS) and/or targeted gene panels (TGPs) were considered to be causative for the proband's phenotype, and two of apparent parental mosaicism. Variants were identified in the following genes: PHACTR1, SCN8A, KCNT1, CDKL5, NEXMIF, CUX1, TSC2, GABRB2, and SMARCB1. In addition, we identified one large duplication including three genes, UBE3A, GABRB3, and MAGEL2, and one large deletion including deletion of ARFGAP1, EEF1A2, CHRNA4, and KCNQ2. All patients were enrolled in the NYCKidSeq study, a research program studying the communication of genomic information in clinical care, as well as the clinical utility and diagnostic yield of GS for children with suspected genetic disorders in diverse populations in New York City. We observed variability in the correlation between reported variant allele fraction and the severity of the patient's phenotype, although we were not able to determine the mosaicism percentage in clinically relevant tissue(s). Although our study was not sufficiently powered to assess differences in mosaicism detection between the two testing modalities, we saw a trend toward better detection by GS as compared with TGP testing. This case series supports the importance of mosaicism in childhood-onset genetic conditions and informs guidelines for laboratory and clinical interpretation of mosaic variants detected by GS.
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Affiliation(s)
- Jacqueline A. Odgis
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Katie M. Gallagher
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Atteeq U. Rehman
- Molecular Diagnostics, New York Genome Center, New York, NY, USA
| | - Priya Marathe
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Katherine E. Bonini
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Monisha Sebastin
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Miranda Di Biase
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Kaitlyn Brown
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Nicole R. Kelly
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Michelle A. Ramos
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Saurav Guha
- Molecular Diagnostics, New York Genome Center, New York, NY, USA
| | - Volkan Okur
- Molecular Diagnostics, New York Genome Center, New York, NY, USA
| | | | | | | | - Randi E. Zinberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Noura S. Abul-Husn
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - George A. Diaz
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - John M. Greally
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Sabrina A. Suckiel
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vaidehi Jobanputra
- Molecular Diagnostics, New York Genome Center, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Carol R. Horowitz
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eimear E. Kenny
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melissa P. Wasserstein
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Bruce D. Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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19
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McGee SR, Rajamanickam S, Adhikari S, Falayi OC, Wilson TA, Shayota BJ, Cooley Coleman JA, Skinner C, Caylor RC, Stevenson RE, Quaio CRDAC, Wilke BC, Bain JM, Anyane-Yeboa K, Brown K, Greally JM, Bijlsma EK, Ruivenkamp CAL, Politi K, Arbogast LA, Collard MW, Huggenvik JI, Elsea SH, Jensik PJ. Expansion and mechanistic insights into de novo DEAF1 variants in DEAF1-associated neurodevelopmental disorders. Hum Mol Genet 2023; 32:386-401. [PMID: 35981081 PMCID: PMC10310974 DOI: 10.1093/hmg/ddac200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/11/2022] [Accepted: 08/08/2022] [Indexed: 01/24/2023] Open
Abstract
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. Since DEAF1 is not a dosage-sensitive gene, we assessed the dominant negative activity of previously identified de novo variants and a heritable recessive DEAF1 variant on selected DEAF1-regulated genes in 2 different cell models. While no altered gene expression was observed in cells over-expressing the recessive heritable variant, the gene expression profiles of cells over-expressing de novo variants resulted in similar gene expression changes as observed in CRISPR-Cas9-mediated DEAF1-deleted cells. Altered expression of DEAF1-regulated genes was rescued by exogenous expression of WT-DEAF1 but not by de novo variants in cells lacking endogenous DEAF1. De novo heterozygous variants within the DBD of DEAF1 were identified in 10 individuals with a phenotypic spectrum including autism spectrum disorder, developmental delays, sleep disturbance, high pain tolerance, and mild dysmorphic features. Functional assays demonstrate these variants alter DEAF1 transcriptional activity. Taken together, this study expands the clinical phenotypic spectrum of individuals with DAND, furthers our understanding of potential roles of DEAF1 on neuronal function, and demonstrates dominant negative activity of identified de novo variants.
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Affiliation(s)
- Stacey R McGee
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, IL USA
| | - Shivakumar Rajamanickam
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, IL USA
| | - Sandeep Adhikari
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, IL USA
| | | | - Theresa A Wilson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, USA
| | - Brian J Shayota
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, USA
- Department of Pediatrics, Division of Genetics, University of Utah, Salt Lake City, UT
| | | | | | | | | | - Caio Robledo D' Angioli Costa Quaio
- Instituto da Criança (Children’s Hospital), Hospital das Clínicas (HCFMUSP), Faculdade de Medicina (FMUSP), Universidade de São Paulo, São Paulo, SP, Brazil
- Laboratório Clínico, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | | | - Jennifer M Bain
- Department of Neurology, Division of Child Neurology, Columbia University Irving Medical Center, New York, USA
| | - Kwame Anyane-Yeboa
- Department of Pediatrics, Division of Clinical Genetics, Columbia University Irving Medical Center, New York, USA
| | - Kaitlyn Brown
- Departments of Pediatrics and Genetics, Albert Einstein College of Medicine, Bronx, NY USA
| | - John M Greally
- Departments of Pediatrics and Genetics, Albert Einstein College of Medicine, Bronx, NY USA
- Departments of Genetics, Albert Einstein College of Medicine, Bronx, NY USA
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Centre, PO box 9600, 2300 RC, Leiden, The Netherlands
| | - Claudia A L Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Centre, PO box 9600, 2300 RC, Leiden, The Netherlands
| | | | - Lydia A Arbogast
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, IL USA
| | - Michael W Collard
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, IL USA
| | - Jodi I Huggenvik
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, IL USA
| | - Sarah H Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, USA
| | - Philip J Jensik
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, IL USA
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20
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Wattacheril JJ, Raj S, Knowles DA, Greally JM. Using epigenomics to understand cellular responses to environmental influences in diseases. PLoS Genet 2023; 19:e1010567. [PMID: 36656803 PMCID: PMC9851565 DOI: 10.1371/journal.pgen.1010567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
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.
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Affiliation(s)
- Julia J. Wattacheril
- Department of Medicine, Center for Liver Disease and Transplantation, Columbia University Irving Medical Center, New York Presbyterian Hospital, New York, New York, United States of America
| | - Srilakshmi Raj
- Division of Genomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - David A. Knowles
- New York Genome Center, New York, New York, United States of America
- Department of Computer Science, Columbia University, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
| | - John M. Greally
- Division of Genomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
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21
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Bowling KM, Thompson ML, Kelly MA, Scollon S, Slavotinek AM, Powell BC, Kirmse BM, Hendon LG, Brothers KB, Korf BR, Cooper GM, Greally JM, Hurst ACE. Return of non-ACMG recommended incidental genetic findings to pediatric patients: considerations and opportunities from experiences in genomic sequencing. Genome Med 2022; 14:131. [PMID: 36414972 PMCID: PMC9682742 DOI: 10.1186/s13073-022-01139-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 11/10/2022] [Indexed: 11/23/2022] Open
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.
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Affiliation(s)
- Kevin M Bowling
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | | | - Melissa A Kelly
- HudsonAlpha Clinical Services Lab, LLC, HudsonAlpha Institute for Biotechnology, Huntsville, USA
| | - Sarah Scollon
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Anne M Slavotinek
- Department of Pediatrics, University of California, San Francisco, CA, 94158, USA
| | - Bradford C Powell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Brian M Kirmse
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Laura G Hendon
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Kyle B Brothers
- Norton Children's Research Institute Affiliated with UofL School of Medicine, Louisville, KY, 40202, USA
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 25294, USA
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - John M Greally
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Anna C E Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 25294, USA.
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22
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Shi PA, Luchsinger LL, Greally JM, Delaney CS. Umbilical cord blood: an undervalued and underutilized resource in allogeneic hematopoietic stem cell transplant and novel cell therapy applications. Curr Opin Hematol 2022; 29:317-326. [PMID: 36066376 PMCID: PMC9547826 DOI: 10.1097/moh.0000000000000732] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
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. RECENT FINDINGS When current best practices are followed, unrelated donor umbilical cord blood transplant (CBT) can provide superior quality of life-related survival compared to other allogeneic HSC donor sources (sibling, matched or mismatched unrelated, and haploidentical) through decreased risks of relapse and chronic graft vs. host disease. Current best practices include improved UCB donor selection criteria with consideration of higher resolution human leukocyte antigen (HLA) typing and CD34+ cell dose, availability of newer myeloablative but reduced toxicity conditioning regimens, and rigorous supportive care in the early posttransplant period with monitoring for known complications, especially related to viral and other infections that may require intervention. Emerging best practice may include the use of ex vivo expanded single-unit CBT rather than double-unit CBT (dCBT) or 'haplo-cord' transplant, and the incorporation of posttransplant cyclophosphamide as with haploidentical transplant and/or incorporation of novel posttransplant therapies to reduce the risk of relapse, such as NK cell adoptive transfer. Novel, non-HCT uses of UCB and birthing tissue include the production of UCB-derived immune effector cell therapies such as unmodified NK cells, chimeric antigen receptor-natural killer cells and immune T-cell populations, the isolation of mesenchymal stem cells for immune modulatory treatments and derivation of induced pluripotent stem cells haplobanks for regenerative medicine development and population studies to facilitate exploration of drug development through functional genomics. SUMMARY The potential of allogeneic UCB for HCT and novel cell-based therapies is undervalued and underutilized. The inventory of high-quality UCB units available from public cord blood banks (CBB) should be expanding rather than contracting in order to address ongoing healthcare inequities and to maintain a valuable source of cellular starting material for cell and gene therapies and regenerative medicine approaches. The expertise in Good Manufacturing Practice-grade manufacturing provided by CBB should be supported to effectively partner with groups developing UCB for novel cell-based therapies.
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Affiliation(s)
- Patricia A. Shi
- Lindsley F. Kimball Research Institute, New York Blood Center, New York City, NY 10065
| | - Larry L. Luchsinger
- Lindsley F. Kimball Research Institute, New York Blood Center, New York City, NY 10065
| | - John M. Greally
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Colleen S. Delaney
- Division of Hematology-Oncology, Seattle Children’s Hospital, Seattle WA; and Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195
- Deverra Therapeutics, Inc., Seattle, WA 98102
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23
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Ulahannan N, Cutler R, Doña-Termine R, Simões-Pires CA, Wijetunga NA, Croken MM, Johnston AD, Kong Y, Maqbool SB, Suzuki M, Greally JM. Genomic insights into host and parasite interactions during intracellular infection by Toxoplasma gondii. PLoS One 2022; 17:e0275226. [PMID: 36178892 PMCID: PMC9524707 DOI: 10.1371/journal.pone.0275226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 08/02/2022] [Indexed: 11/18/2022] Open
Abstract
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. gondii genome. We show how chromatin accessibility and transcriptional profiling together permit novel annotation of the parasite's genome, including more accurate mapping of known genes and the identification of new genes and cis-regulatory elements. Motif analysis reveals not only the known T. gondii AP2 transcription factor-binding site but also a previously-undiscovered candidate TATA box-containing motif at one-quarter of promoters. By inferring the transcription factor and upstream cell signaling responses involved in the host cell, we can use genomic information to gain insights into T. gondii's perturbation of host cell physiology. Our resulting model builds on previously-described human host cell signalling responses to T. gondii infection, linked to induction of specific transcription factors, some of which appear to be solely protective of the host cell, others of which appear to be co-opted by the pathogen to enhance its own survival.
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Affiliation(s)
- Netha Ulahannan
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States of America
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Ronald Cutler
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Reanna Doña-Termine
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Claudia A. Simões-Pires
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - N. Ari Wijetunga
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Matthew McKnight Croken
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Andrew D. Johnston
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Yu Kong
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Shahina B. Maqbool
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Masako Suzuki
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - John M. Greally
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States of America
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24
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Ellingford JM, Ahn JW, Bagnall RD, Baralle D, Barton S, Campbell C, Downes K, Ellard S, Duff-Farrier C, FitzPatrick DR, Greally JM, Ingles J, Krishnan N, Lord J, Martin HC, Newman WG, O’Donnell-Luria A, Ramsden SC, Rehm HL, Richardson E, Singer-Berk M, Taylor JC, Williams M, Wood JC, Wright CF, Harrison SM, Whiffin N. Recommendations for clinical interpretation of variants found in non-coding regions of the genome. Genome Med 2022; 14:73. [PMID: 35850704 PMCID: PMC9295495 DOI: 10.1186/s13073-022-01073-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 06/16/2022] [Indexed: 01/28/2023] Open
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.
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Affiliation(s)
- Jamie M. Ellingford
- grid.5379.80000000121662407Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, M13 9PT UK ,grid.498924.a0000 0004 0430 9101Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL UK ,grid.498322.6Genomics England, London, UK
| | - Joo Wook Ahn
- grid.24029.3d0000 0004 0383 8386Cambridge Genomics Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | - Richard D. Bagnall
- grid.1013.30000 0004 1936 834XAgnes Ginges Centre for Molecular Cardiology at Centenary Institute, University of Sydney, Sydney, Australia
| | - Diana Baralle
- grid.5491.90000 0004 1936 9297School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK ,grid.430506.40000 0004 0465 4079Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Stephanie Barton
- grid.498924.a0000 0004 0430 9101Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL UK
| | - Chris Campbell
- grid.498924.a0000 0004 0430 9101Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL UK
| | - Kate Downes
- grid.24029.3d0000 0004 0383 8386Cambridge Genomics Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | - Sian Ellard
- grid.8391.30000 0004 1936 8024Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK ,grid.419309.60000 0004 0495 6261South West Genomic Laboratory Hub, Exeter Genomic Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Celia Duff-Farrier
- grid.418484.50000 0004 0380 7221South West NHS Genomic Laboratory Hub, Bristol Genetics Laboratory, North Bristol NHS Trust, Bristol, UK
| | - David R. FitzPatrick
- grid.417068.c0000 0004 0624 9907MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - John M. Greally
- grid.251993.50000000121791997Department of Pediatrics, Division of Pediatric Genetic, Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert, Einstein College of Medicine, Bronx, NY USA
| | - Jodie Ingles
- grid.1005.40000 0004 4902 0432Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, Australia ,grid.1058.c0000 0000 9442 535XCentre for Population Genomics, Murdoch Children’s Research Institute, Melbourne, Australia
| | - Neesha Krishnan
- grid.1005.40000 0004 4902 0432Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, Australia ,grid.1058.c0000 0000 9442 535XCentre for Population Genomics, Murdoch Children’s Research Institute, Melbourne, Australia
| | - Jenny Lord
- grid.5491.90000 0004 1936 9297School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Hilary C. Martin
- grid.10306.340000 0004 0606 5382Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - William G. Newman
- grid.5379.80000000121662407Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, M13 9PT UK ,grid.498924.a0000 0004 0430 9101Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL UK
| | - Anne O’Donnell-Luria
- grid.66859.340000 0004 0546 1623Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.2515.30000 0004 0378 8438Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA USA ,grid.32224.350000 0004 0386 9924Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA USA
| | - Simon C. Ramsden
- grid.498924.a0000 0004 0430 9101Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL UK
| | - Heidi L. Rehm
- grid.66859.340000 0004 0546 1623Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.32224.350000 0004 0386 9924Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA USA
| | - Ebony Richardson
- grid.1005.40000 0004 4902 0432Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, Australia ,grid.1058.c0000 0000 9442 535XCentre for Population Genomics, Murdoch Children’s Research Institute, Melbourne, Australia
| | - Moriel Singer-Berk
- grid.66859.340000 0004 0546 1623Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Jenny C. Taylor
- grid.4991.50000 0004 1936 8948National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN UK ,grid.4991.50000 0004 1936 8948Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN UK
| | - Maggie Williams
- grid.418484.50000 0004 0380 7221South West NHS Genomic Laboratory Hub, Bristol Genetics Laboratory, North Bristol NHS Trust, Bristol, UK
| | - Jordan C. Wood
- grid.66859.340000 0004 0546 1623Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Caroline F. Wright
- grid.8391.30000 0004 1936 8024Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Steven M. Harrison
- grid.66859.340000 0004 0546 1623Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.465138.d0000 0004 0455 211XAmbry Genetics, Aliso Viejo, CA USA
| | - Nicola Whiffin
- grid.66859.340000 0004 0546 1623Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.4991.50000 0004 1936 8948Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN UK
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25
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Myer PA, Lee JK, Madison RW, Pradhan K, Newberg JY, Isasi CR, Klempner SJ, Frampton GM, Ross JS, Venstrom JM, Schrock AB, Das S, Augenlicht L, Verma A, Greally JM, Raj SM, Goel S, Ali SM. The Genomics of Colorectal Cancer in Populations with African and European Ancestry. Cancer Discov 2022; 12:1282-1293. [PMID: 35176763 DOI: 10.1158/2159-8290.cd-21-0813] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/28/2021] [Accepted: 02/11/2022] [Indexed: 11/16/2022]
Abstract
Blacks have a higher incidence of colorectal cancer (CRC) and worse survival rates when compared to Whites. Comprehensive genomic profiling was performed in 46,140 colorectal adenocarcinoma cases. Ancestry-informative markers identified 5,301 patients of African descent (AFR) and 33,770 patients of European descent (EUR). AFR were younger, had fewer MSI-H tumors, and had significantly more frequent alterations in KRAS, APC, and PIK3CA. AFR had increased frequency of KRAS mutations specifically KRAS G12D and KRAS G13. There were no differences in rates of actionable kinase driver alterations (HER2, MET, NTRK, ALK, ROS1, RET). In patients with young onset CRC (<50 years), AFR and EUR had similar frequency of MSI-H and TMB-H tumors, and strikingly different trends in APC mutations by age, as well as differences in MAPK pathway alterations. These findings inform treatment decisions, impact prognosis, and underscore the need for model systems representative of our diverse US population.
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Affiliation(s)
| | | | | | - Kith Pradhan
- Albert Einstein College of Medicine, bronx, United States
| | | | | | | | | | | | - Jeffrey M Venstrom
- University of California, San Francisco, San Francisco, CA, United States
| | | | - Sudipto Das
- Royal College of Surgeons in Ireland, Dublin, Ireland
| | | | - Amit Verma
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York, United States
| | - John M Greally
- Albert Einstein College of Medicine, Bronx, United States
| | | | - Sanjay Goel
- Montefiore Medical Center, and Albert Einstein College of Medicine, Bronx, NY, United States
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26
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Lundy K, Greally JF, Essilfie-Bondzie G, Olivier JB, Doña-Termine R, Greally JM, Suzuki M. Vitamin D Deficiency During Development Permanently Alters Liver Cell Composition and Function. Front Endocrinol (Lausanne) 2022; 13:860286. [PMID: 35634491 PMCID: PMC9133936 DOI: 10.3389/fendo.2022.860286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 03/21/2022] [Indexed: 01/19/2023] Open
Abstract
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. We tested the histopathology and the transcriptomic profiles of livers from male C57BL/6J mice exposed to prenatal vitamin D deficiency through a maternal dietary intervention model. We found that prenatal vitamin D deficiency increases the prevalence of histopathological changes in the liver, and alters its gene expression profile. Cell subtype proportion analysis showed that the liver of prenatal vitamin D deficiency alters non-parenchymal cells of the liver, specifically macrophages, a subset of endothelial cells, and dendritic cells. Our results indicate the long-term memory of prenatal vitamin D deficiency exposure in the adult liver, a potential contributor to offspring health risks.
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Affiliation(s)
- Kassidy Lundy
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States
| | | | | | - Josephine B. Olivier
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Reanna Doña-Termine
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States
| | - John M. Greally
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Masako Suzuki
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States
- *Correspondence: Masako Suzuki,
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27
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Myer PA, Kim H, Blümel AM, Finnegan E, Kel A, Thompson TV, Greally JM, Prehn JHM, O’Connor DP, Friedman RA, Floratos A, Das S. Master Transcription Regulators and Transcription Factors Regulate Immune-Associated Differences Between Patients of African and European Ancestry With Colorectal Cancer. Gastro Hep Advances 2022; 1:328-341. [PMID: 35711675 PMCID: PMC9151447 DOI: 10.1016/j.gastha.2022.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 01/20/2022] [Indexed: 11/21/2022]
Abstract
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.
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28
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Foox J, Nordlund J, Lalancette C, Gong T, Lacey M, Lent S, Langhorst BW, Ponnaluri VKC, Williams L, Padmanabhan KR, Cavalcante R, Lundmark A, Butler D, Mozsary C, Gurvitch J, Greally JM, Suzuki M, Menor M, Nasu M, Alonso A, Sheridan C, Scherer A, Bruinsma S, Golda G, Muszynska A, Łabaj PP, Campbell MA, Wos F, Raine A, Liljedahl U, Axelsson T, Wang C, Chen Z, Yang Z, Li J, Yang X, Wang H, Melnick A, Guo S, Blume A, Franke V, Ibanez de Caceres I, Rodriguez-Antolin C, Rosas R, Davis JW, Ishii J, Megherbi DB, Xiao W, Liao W, Xu J, Hong H, Ning B, Tong W, Akalin A, Wang Y, Deng Y, Mason CE. The SEQC2 epigenomics quality control (EpiQC) study. Genome Biol 2021; 22:332. [PMID: 34872606 PMCID: PMC8650396 DOI: 10.1186/s13059-021-02529-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 10/28/2021] [Indexed: 11/10/2022] Open
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.
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Affiliation(s)
- Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA
| | - Jessica Nordlund
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
| | - Claudia Lalancette
- BRCF Epigenomics Core, University of Michigan Medicine, Ann Arbor, MI, 48109, USA
| | - Ting Gong
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, 96813, USA
| | | | - Samantha Lent
- AbbVie Genomics Research Center, 1 N. Waukegan Rd, North Chicago, IL, 60036, USA
| | | | | | | | | | - Raymond Cavalcante
- BRCF Epigenomics Core, University of Michigan Medicine, Ann Arbor, MI, 48109, USA
| | - Anders Lundmark
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
| | - Daniel Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - Christopher Mozsary
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - Justin Gurvitch
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - John M Greally
- Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Masako Suzuki
- Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Mark Menor
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, 96813, USA
| | - Masaki Nasu
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, 96813, USA
| | - Alicia Alonso
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - Caroline Sheridan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
- Division of Hematology/Oncology, Department of Medicine, Epigenomics Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Andreas Scherer
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | | | - Gosia Golda
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Agata Muszynska
- Małopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Paweł P Łabaj
- Małopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Frank Wos
- New York Genome Center, New York, NY, 10013, USA
| | - Amanda Raine
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
| | - Ulrika Liljedahl
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
| | - Tomas Axelsson
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
| | - Charles Wang
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
| | - Zhong Chen
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
| | - Zhaowei Yang
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jing Li
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiaopeng Yang
- Department of Neurology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450014, China
| | - Hongwei Wang
- Development of Medicine, the University of Chicago, Chicago, IL, 60637, USA
| | - Ari Melnick
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - Shang Guo
- Department of Neurology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450014, China
| | - Alexander Blume
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Vedran Franke
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Inmaculada Ibanez de Caceres
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
- Cancer Epigenetics Laboratory, INGEMM, IdiPAZ, Madrid, Spain
| | - Carlos Rodriguez-Antolin
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
- Cancer Epigenetics Laboratory, INGEMM, IdiPAZ, Madrid, Spain
| | - Rocio Rosas
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
- Cancer Epigenetics Laboratory, INGEMM, IdiPAZ, Madrid, Spain
| | - Justin Wade Davis
- AbbVie Genomics Research Center, 1 N. Waukegan Rd, North Chicago, IL, 60036, USA
| | | | - Dalila B Megherbi
- CMINDS Research Center, Francis College of Engineering, University of Massachusetts Lowell, Lowell, MA, 01854, USA
| | - Wenming Xiao
- Center for Devices and Radiological Health, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA
| | - Will Liao
- New York Genome Center, New York, NY, 10013, USA
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | - Baitang Ning
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | - Altuna Akalin
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Yunliang Wang
- Department of Neurology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450014, China.
| | - Youping Deng
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, 96813, USA.
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA.
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA.
- The Feil Family Brain and Mind Research Institute, New York, New York, USA.
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
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29
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Pearson NM, Stolte C, Shi K, Beren F, Abul-Husn NS, Bertier G, Brown K, Diaz GA, Odgis JA, Suckiel SA, Horowitz CR, Wasserstein M, Gelb BD, Kenny EE, Gagnon C, Jobanputra V, Bloom T, Greally JM. GenomeDiver: a platform for phenotype-guided medical genomic diagnosis. Genet Med 2021; 23:1998-2002. [PMID: 34113009 PMCID: PMC8488006 DOI: 10.1038/s41436-021-01219-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/11/2022] Open
Abstract
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. Methods: GenomeDiver uses genomic data to prompt reverse phenotyping of patients undergoing genetic testing, enriching the amount and quality of structured phenotype data for the diagnostic laboratory, and helping clinicians to explore and flag diseases potentially causing their patient’s presentation. Results: We show how GenomeDiver communicates the clinician’s informed insights to the diagnostic lab in the form of HPO terms for interpretation of genomic sequencing data. We describe our user-driven design process, the engineering of the software for efficiency, security and portability, and examples of the performance of GenomeDiver using genomic testing data. Conclusions: GenomeDiver is a first step in a new approach to genomic diagnostics that enhances laboratory-clinician interactions, with the goal of directly engaging clinicians to improve the outcome of genomic diagnostic testing.
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Affiliation(s)
| | - Christian Stolte
- New York Genome Center, New York, NY, USA.,Stolte Design, Islesboro, ME, USA
| | - Kevin Shi
- New York Genome Center, New York, NY, USA
| | - Faygel Beren
- Columbia University, Graduate School of Arts and Sciences, New York, NY, USA
| | - Noura S Abul-Husn
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Kaitlyn Brown
- Division of Genetics, Department of Pediatrics, Children's Hospital at Montefiore, Bronx, NY, USA
| | - George A Diaz
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jacqueline A Odgis
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sabrina A Suckiel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Melissa Wasserstein
- Division of Genetics, Department of Pediatrics, Children's Hospital at Montefiore, Bronx, NY, USA.,Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Bruce D Gelb
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | - Toby Bloom
- New York Genome Center, New York, NY, USA.,eGenesis, Inc., Cambridge, MA, USA
| | - John M Greally
- Division of Genetics, Department of Pediatrics, Children's Hospital at Montefiore, Bronx, NY, USA. .,Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA. .,Center for Epigenomics, Albert Einstein College of Medicine, Bronx, NY, USA.
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30
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Suzuki M, Wang T, Garretto D, Isasi CR, Cardoso WV, Greally JM, Quadro L. Disproportionate Vitamin A Deficiency in Women of Specific Ethnicities Linked to Differences in Allele Frequencies of Vitamin A-Related Polymorphisms. Nutrients 2021; 13:nu13061743. [PMID: 34063790 PMCID: PMC8223783 DOI: 10.3390/nu13061743] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 11/16/2022] Open
Abstract
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. Results: Non-Hispanic Black and Hispanic pregnant women showed high VAD prevalence in both datasets. Interestingly, the VAD prevalence for Hispanic pregnant women significantly differed between datasets (p = 1.973 × 10−10, 95%CI 0.04–0.22). Alleles known to confer the risk of low serum retinol (rs10882272 C and rs738409 G) showed higher frequencies in the race/ethnicity groups with more VAD. Moreover, minor allele frequencies of a set of 39 previously reported SNPs associated with vitamin A metabolism were significantly different between the populations of different ancestries than those of randomly selected SNPs (p = 0.030). Conclusions: Our analysis confirmed that VAD prevalence varies between different ethnic groups/races and may be causally associated with genetic variants conferring risk for low retinol levels. Assessing genetic variant information prior to performing an effective nutrient supplementation program will help us plan more effective food-based interventions.
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Affiliation(s)
- Masako Suzuki
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Diana Garretto
- Department of Obstetrics and Gynecology and Women's Health, Stony Brook University Medical Center, Stony Brook, NY 11794, USA
| | - Carmen R Isasi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Wellington V Cardoso
- Columbia Center for Human Development, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - John M Greally
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Loredana Quadro
- Department of Food Science and Rutgers Center for Lipid Research, and New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, NJ 08901, USA
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31
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Abstract
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.
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Affiliation(s)
- Devin Rocks
- Department of Biological Sciences, Fordham University, Bronx, NY, USA
| | - Ivana Jaric
- Department of Biological Sciences, Fordham University, Bronx, NY, USA
| | - Lydia Tesfa
- Flow Cytometry Core Facility, Albert Einstein College of Medicine, Bronx, NY, USA
| | - John M Greally
- Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Masako Suzuki
- Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Marija Kundakovic
- Department of Biological Sciences, Fordham University, Bronx, NY, USA
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32
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Odgis JA, Gallagher KM, Suckiel SA, Donohue KE, Ramos MA, Kelly NR, Bertier G, Blackburn C, Brown K, Fielding L, Lopez J, Aguiniga KL, Maria E, Rodriguez JE, Sebastin M, Teitelman N, Watnick D, Yelton NM, Abhyankar A, Abul-Husn NS, Baum A, Bauman LJ, Beal JC, Bloom T, Cunningham-Rundles C, Diaz GA, Dolan S, Ferket BS, Jobanputra V, Kovatch P, McDonald TV, McGoldrick PE, Rhodes R, Rinke ML, Robinson M, Rubinstein A, Shulman LH, Stolte C, Wolf SM, Yozawitz E, Zinberg RE, Greally JM, Gelb BD, Horowitz CR, Wasserstein MP, Kenny EE. Correction to: The NYCKidSeq project: study protocol for a randomized controlled trial incorporating genomics into the clinical care of diverse New York City children. Trials 2021; 22:146. [PMID: 33593377 PMCID: PMC7885500 DOI: 10.1186/s13063-021-05057-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Jacqueline A Odgis
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Katie M Gallagher
- Department of Pediatrics, Division of Pediatric Genetic, Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert, Einstein College of Medicine, Bronx, NY, USA
| | - Sabrina A Suckiel
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Katherine E Donohue
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michelle A Ramos
- Department of Population, Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nicole R Kelly
- Department of Pediatrics, Division of Pediatric Genetic, Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert, Einstein College of Medicine, Bronx, NY, USA
| | - Gabrielle Bertier
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christina Blackburn
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kaitlyn Brown
- Department of Pediatrics, Division of Pediatric Genetic, Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert, Einstein College of Medicine, Bronx, NY, USA
| | - Lena Fielding
- Molecular Diagnostics, New York, Genome Center, New York, NY, USA
| | - Jessenia Lopez
- Department of Pediatrics, Division of Pediatric Genetic, Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert, Einstein College of Medicine, Bronx, NY, USA
| | - Karla Lopez Aguiniga
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Estefany Maria
- Department of Pediatrics, Division of Pediatric Genetic, Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert, Einstein College of Medicine, Bronx, NY, USA
| | - Jessica E Rodriguez
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Monisha Sebastin
- Department of Pediatrics, Division of Pediatric Genetic, Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert, Einstein College of Medicine, Bronx, NY, USA
| | - Nehama Teitelman
- Department of Pediatrics, Division of, Pediatric Academic Medicine, Children's Hospital at Montefiore/Montefiore, Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Dana Watnick
- Department of Pediatrics, Division of, Pediatric Academic Medicine, Children's Hospital at Montefiore/Montefiore, Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Nicole M Yelton
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Noura S Abul-Husn
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aaron Baum
- Department of Health System, Design and Global Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laurie J Bauman
- Department of Pediatrics, Division of, Pediatric Academic Medicine, Children's Hospital at Montefiore/Montefiore, Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jules C Beal
- Department of Pediatrics, Division of Child Neurology, Weill Cornell Medical, New York, NY, USA
| | - Toby Bloom
- Molecular Diagnostics, New York, Genome Center, New York, NY, USA
| | - Charlotte Cunningham-Rundles
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Pediatrics, Icahn School, of Medicine at Mount Sinai, New York, NY, USA
| | - George A Diaz
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Pediatrics, Icahn School, of Medicine at Mount Sinai, New York, NY, USA
| | - Siobhan Dolan
- Department of Obstetrics and Gynecology and Women's Health (Reproductive and Medical Genetics), Albert Einstein College of Medicine, Bronx, NY, USA
| | - Bart S Ferket
- Department of Population, Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vaidehi Jobanputra
- Molecular Diagnostics, New York, Genome Center, New York, NY, USA.,Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Patricia Kovatch
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Scientific Computing and Data Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas V McDonald
- Department of Medicine (Cardiology), Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Patricia E McGoldrick
- Department of Pediatrics, Division of Child Neurology, New York Medical College, Valhalla, NY, USA.,Pediatric Neurology
- Boston Children's Health Physicians/Maria Fareri Children's Hospital, Hawthorne, NY, USA
| | - Rosamond Rhodes
- Department of Medical Education, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael L Rinke
- Department of Pediatrics, Division of Pediatric Genetic, Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert, Einstein College of Medicine, Bronx, NY, USA
| | | | - Arye Rubinstein
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Lisa H Shulman
- Department of Pediatrics, Division of Pediatric Genetic, Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert, Einstein College of Medicine, Bronx, NY, USA
| | - Christian Stolte
- Molecular Diagnostics, New York, Genome Center, New York, NY, USA
| | - Steven M Wolf
- Department of Pediatrics, Division of Child Neurology, New York Medical College, Valhalla, NY, USA.,Pediatric Neurology
- Boston Children's Health Physicians/Maria Fareri Children's Hospital, Hawthorne, NY, USA
| | - Elissa Yozawitz
- Department of Pediatrics, Division of Pediatric Genetic, Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert, Einstein College of Medicine, Bronx, NY, USA.,Isabelle Rapin Division of Child Neurology of the Saul R Korey Department of Neurology at Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Randi E Zinberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John M Greally
- Department of Pediatrics, Division of Pediatric Genetic, Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert, Einstein College of Medicine, Bronx, NY, USA
| | - Bruce D Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Pediatrics, Icahn School, of Medicine at Mount Sinai, New York, NY, USA.,Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carol R Horowitz
- Department of Population, Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melissa P Wasserstein
- Department of Pediatrics, Division of Pediatric Genetic, Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert, Einstein College of Medicine, Bronx, NY, USA
| | - Eimear E Kenny
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Suckiel SA, Odgis JA, Gallagher KM, Rodriguez JE, Watnick D, Bertier G, Sebastin M, Yelton N, Maria E, Lopez J, Ramos M, Kelly N, Teitelman N, Beren F, Kaszemacher T, Davis K, Laguerre I, Richardson LD, Diaz GA, Pearson NM, Ellis SB, Stolte C, Robinson M, Kovatch P, Horowitz CR, Gelb BD, Greally JM, Bauman LJ, Zinberg RE, Abul-Husn NS, Wasserstein MP, Kenny EE. GUÍA: a digital platform to facilitate result disclosure in genetic counseling. Genet Med 2021; 23:942-949. [PMID: 33531665 PMCID: PMC8105171 DOI: 10.1038/s41436-020-01063-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 11/24/2020] [Accepted: 11/30/2020] [Indexed: 02/06/2023] Open
Abstract
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. Development was informed by formative qualitative research involving parents (N = 22) whose children underwent genomic testing. Participants enrolled in the NYCKidSeq pilot study (N = 18) completed structured feedback interviews post–result disclosure using GUÍA. Genetic specialists, researchers, patients, and community stakeholders provided their perspectives on GUÍA’s design to ensure technical, cultural, and literacy appropriateness. Results NYCKidSeq participants responded positively to the use of GUÍA to deliver their children’s results. All participants (N = 10) with previous experience with genetic testing felt GUÍA improved result disclosure, and 17 (94%) participants said the content was clear. Conclusion GUÍA communicates complex genomic information in an understandable and personalized manner. Initial piloting demonstrated GUÍA’s utility for families enrolled in the NYCKidSeq pilot study. Findings from the NYCKidSeq clinical trial will provide insight into GUÍA’s effectiveness in communicating results among diverse, multilingual populations.
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Affiliation(s)
- Sabrina A Suckiel
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jaqueline A Odgis
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Katie M Gallagher
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore and The Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jessica E Rodriguez
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dana Watnick
- Department of Pediatrics, Division of Pediatric Academic Medicine, Children's Hospital at Montefiore and The Albert Einstein College of Medicine, Bronx, NY, USA
| | - Gabrielle Bertier
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Monisha Sebastin
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore and The Albert Einstein College of Medicine, Bronx, NY, USA
| | - Nicole Yelton
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Estefany Maria
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore and The Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jessenia Lopez
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore and The Albert Einstein College of Medicine, Bronx, NY, USA
| | - Michelle Ramos
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nicole Kelly
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore and The Albert Einstein College of Medicine, Bronx, NY, USA
| | - Nehama Teitelman
- Department of Pediatrics, Division of Pediatric Academic Medicine, Children's Hospital at Montefiore and The Albert Einstein College of Medicine, Bronx, NY, USA
| | - Faygel Beren
- Molecular Diagnostics, New York Genome Center, New York, NY, USA
| | - Tom Kaszemacher
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kojo Davis
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Irma Laguerre
- The Children's Cultural Center of Native America, New York, NY, USA
| | - Lynne D Richardson
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Emergency Medicine, Icahn School of Medicine at Mount Sinai at Mount Sinai, New York, NY, USA
| | - George A Diaz
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Stephen B Ellis
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christian Stolte
- Molecular Diagnostics, New York Genome Center, New York, NY, USA
| | - Mimsie Robinson
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Patricia Kovatch
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Scientific Computing and Data Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carol R Horowitz
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bruce D Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John M Greally
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore and The Albert Einstein College of Medicine, Bronx, NY, USA
| | - Laurie J Bauman
- Department of Pediatrics, Division of Pediatric Academic Medicine, Children's Hospital at Montefiore and The Albert Einstein College of Medicine, Bronx, NY, USA
| | - Randi E Zinberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Noura S Abul-Husn
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melissa P Wasserstein
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore and The Albert Einstein College of Medicine, Bronx, NY, USA
| | - Eimear E Kenny
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Odgis JA, Gallagher KM, Suckiel SA, Donohue KE, Ramos MA, Kelly NR, Bertier G, Blackburn C, Brown K, Fielding L, Lopez J, Aguiniga KL, Maria E, Rodriguez JE, Sebastin M, Teitelman N, Watnick D, Yelton NM, Abhyankar A, Abul-Husn NS, Baum A, Bauman LJ, Beal JC, Bloom T, Cunningham-Rundles C, Diaz GA, Dolan S, Ferket BS, Jobanputra V, Kovatch P, McDonald TV, McGoldrick PE, Rhodes R, Rinke ML, Robinson M, Rubinstein A, Shulman LH, Stolte C, Wolf SM, Yozawitz E, Zinberg RE, Greally JM, Gelb BD, Horowitz CR, Wasserstein MP, Kenny EE. The NYCKidSeq project: study protocol for a randomized controlled trial incorporating genomics into the clinical care of diverse New York City children. Trials 2021; 22:56. [PMID: 33446240 PMCID: PMC7807444 DOI: 10.1186/s13063-020-04953-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 12/08/2020] [Indexed: 12/18/2022] Open
Abstract
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. METHODS The NYCKidSeq project is a randomized controlled trial recruiting 1130 children and young adults predominantly from Harlem and the Bronx with suspected genetic disorders in three disease categories: neurologic, cardiovascular, and immunologic. Two clinical genetic tests will be performed for each participant, either proband, duo, or trio whole-genome sequencing (depending on sample availability) and proband targeted gene panels. Clinical utility, cost, and diagnostic yield of both testing modalities will be assessed. This study will evaluate the use of a novel, digital platform (GUÍA) to digitize the return of genomic results experience and improve participant understanding for English- and Spanish-speaking families. Surveys will collect data at three study visits: baseline (0 months), result disclosure visit (ROR1, + 3 months), and follow-up visit (ROR2, + 9 months). Outcomes will assess parental understanding of and attitudes toward receiving genomic results for their child and behavioral, psychological, and social impact of results. We will also conduct a pilot study to assess a digital tool called GenomeDiver designed to enhance communication between clinicians and genetic testing labs. We will evaluate GenomeDiver's ability to increase the diagnostic yield compared to standard practices, improve clinician's ability to perform targeted reverse phenotyping, and increase the efficiency of genetic testing lab personnel. DISCUSSION The NYCKidSeq project will contribute to the innovations and best practices in communicating genomic test results to diverse populations. This work will inform strategies for implementing genomic medicine in health systems serving diverse populations using methods that are clinically useful, technologically savvy, culturally sensitive, and ethically sound. TRIAL REGISTRATION ClinicalTrials.gov NCT03738098 . Registered on November 13, 2018 Trial Sponsor: Icahn School of Medicine at Mount Sinai Contact Name: Eimear Kenny, PhD (Principal Investigator) Address: Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Pl., Box 1003, New York, NY 10029 Email: eimear.kenny@mssm.edu.
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Affiliation(s)
- Jacqueline A Odgis
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Katie M Gallagher
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Sabrina A Suckiel
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Katherine E Donohue
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michelle A Ramos
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nicole R Kelly
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Gabrielle Bertier
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christina Blackburn
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kaitlyn Brown
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Lena Fielding
- Molecular Diagnostics, New York Genome Center, New York, NY, USA
| | - Jessenia Lopez
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Karla Lopez Aguiniga
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Estefany Maria
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jessica E Rodriguez
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Monisha Sebastin
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Nehama Teitelman
- Department of Pediatrics, Division of Pediatric Academic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Dana Watnick
- Department of Pediatrics, Division of Pediatric Academic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Nicole M Yelton
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Noura S Abul-Husn
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aaron Baum
- Department of Health System Design and Global Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laurie J Bauman
- Department of Pediatrics, Division of Pediatric Academic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jules C Beal
- Department of Pediatrics, Division of Child Neurology, Weill Cornell Medical, New York, NY, USA
| | - Toby Bloom
- Molecular Diagnostics, New York Genome Center, New York, NY, USA
| | - Charlotte Cunningham-Rundles
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - George A Diaz
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Siobhan Dolan
- Department of Obstetrics and Gynecology and Women's Health (Reproductive and Medical Genetics), Albert Einstein College of Medicine, Bronx, NY, USA
| | - Bart S Ferket
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vaidehi Jobanputra
- Molecular Diagnostics, New York Genome Center, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Patricia Kovatch
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Scientific Computing and Data Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas V McDonald
- Department of Medicine (Cardiology), Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Patricia E McGoldrick
- Department of Pediatrics, Division of Child Neurology, New York Medical College, Valhalla, NY, USA
- Pediatric Neurology, Boston Children's Health Physicians/Maria Fareri Children's Hospital, Hawthorne, NY, USA
| | - Rosamond Rhodes
- Department of Medical Education, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael L Rinke
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Arye Rubinstein
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Lisa H Shulman
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Christian Stolte
- Molecular Diagnostics, New York Genome Center, New York, NY, USA
| | - Steven M Wolf
- Department of Pediatrics, Division of Child Neurology, New York Medical College, Valhalla, NY, USA
- Pediatric Neurology, Boston Children's Health Physicians/Maria Fareri Children's Hospital, Hawthorne, NY, USA
| | - Elissa Yozawitz
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
- Isabelle Rapin Division of Child Neurology of the Saul R Korey Department of Neurology at Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Randi E Zinberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John M Greally
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Bruce D Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carol R Horowitz
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melissa P Wasserstein
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Eimear E Kenny
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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de Torrenté L, Zimmerman S, Suzuki M, Christopeit M, Greally JM, Mar JC. The shape of gene expression distributions matter: how incorporating distribution shape improves the interpretation of cancer transcriptomic data. BMC Bioinformatics 2020; 21:562. [PMID: 33371881 PMCID: PMC7768656 DOI: 10.1186/s12859-020-03892-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 01/15/2023] Open
Abstract
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. Most of the distribution categories contained genes that were significantly enriched for unique biological processes. Different assumptions based on the shape of the expression profile were used to identify genes that could discriminate between patients with good versus poor survival. The prognostic marker genes that were identified when the shape of the distribution was accounted for reflected functional insights into cancer biology that were not observed when standard assumptions were applied. We showed that when multiple types of distributions were permitted, i.e. the shape of the expression profile was used, the statistical classifiers had greater predictive accuracy for determining the prognosis of a patient versus those that assumed only one type of gene expression distribution. CONCLUSIONS Our results highlight the value of studying a gene's distribution shape to model heterogeneity of transcriptomic data and the impact on using analyses that permit more than one type of gene expression distribution. These insights would have been overlooked when using standard approaches that assume all genes follow the same type of distribution in a patient cohort.
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Affiliation(s)
- Laurence de Torrenté
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Samuel Zimmerman
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Masako Suzuki
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Maximilian Christopeit
- Internal Medicine II, Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tuebingen, Otfried-Mueller-Strasse 10, 72076, Tuebingen, Germany
| | - John M Greally
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Jessica C Mar
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA. .,Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, 10461, USA. .,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia.
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36
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Amendola LM, Muenzen K, Biesecker LG, Bowling KM, Cooper GM, Dorschner MO, Driscoll C, Foreman AKM, Golden-Grant K, Greally JM, Hindorff L, Kanavy D, Jobanputra V, Johnston JJ, Kenny EE, McNulty S, Murali P, Ou J, Powell BC, Rehm HL, Rolf B, Roman TS, Van Ziffle J, Guha S, Abhyankar A, Crosslin D, Venner E, Yuan B, Zouk H, Jarvik GP, Jarvik GP. Variant Classification Concordance using the ACMG-AMP Variant Interpretation Guidelines across Nine Genomic Implementation Research Studies. Am J Hum Genet 2020; 107:932-941. [PMID: 33108757 DOI: 10.1016/j.ajhg.2020.09.011] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/29/2020] [Indexed: 12/31/2022] Open
Abstract
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.2.0 genes. After removing duplicates, each of the 158 variants was annotated and independently classified by two additional laboratories using the ACMG-AMP guidelines. Overall concordance across three laboratories was assessed and discordant variants were reviewed via teleconference and email. The submitted variant set included 28 P/LP variants, 96 VUS, and 34 LB/B variants, mostly in cancer (40%) and cardiac (27%) risk genes. Eighty-six (54%) variants reached complete five-category (i.e., P, LP, VUS, LB, B) concordance, and 17 (11%) had a discordance that could affect clinical recommendations (P/LP versus VUS/LB/B). 21% and 63% of variants submitted as P and LP, respectively, were discordant with VUS. Of the 54 originally discordant variants that underwent further review, 32 reached agreement, for a post-review concordance rate of 84% (118/140 variants). This project provides an updated estimate of variant concordance, identifies considerations for LP classified variants, and highlights ongoing sources of discordance. Continued and increased sharing of variant classifications and evidence across laboratories, and the ongoing work of ClinGen to provide general as well as gene- and disease-specific guidance, will lead to continued increases in concordance.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Gail P Jarvik
- Department of Medicine, Division of Medical Genetics, University of Washington Medical Center, Seattle, WA 98195, USA
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Shieh KR, Kratschmer C, Maier KE, Greally JM, Levy M, Golden A. AptCompare: optimized de novo motif discovery of RNA aptamers via HTS-SELEX. Bioinformatics 2020; 36:2905-2906. [PMID: 31999328 DOI: 10.1093/bioinformatics/btaa054] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 12/20/2019] [Accepted: 01/22/2020] [Indexed: 11/14/2022] Open
Abstract
SUMMARY High-throughput sequencing can enhance the analysis of aptamer libraries generated by the Systematic Evolution of Ligands by EXponential enrichment. Robust analysis of the resulting sequenced rounds is best implemented by determining a ranked consensus of reads following the processing by multiple aptamer detection algorithms. While several such approaches have been developed to this end, their installation and implementation is problematic. We developed AptCompare, a cross-platform program that combines six of the most widely used analytical approaches for the identification of RNA aptamer motifs and uses a simple weighted ranking to order the candidate aptamers, all driven within the same GUI-enabled environment. We demonstrate AptCompare's performance by identifying the top-ranked candidate aptamers from a previously published selection experiment in our laboratory, with follow-up bench assays demonstrating good correspondence between the sequences' rankings and their binding affinities. AVAILABILITY AND IMPLEMENTATION The source code and pre-built virtual machine images are freely available at https://bitbucket.org/shiehk/aptcompare. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Kevin R Shieh
- Department of Medicine, Maimonides Medical Center, Brooklyn, NY, USA
| | - Christina Kratschmer
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | | | - John M Greally
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Aaron Golden
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Galway, Ireland
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38
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Piqué DG, Greally JM, Mar JC. Identification of a novel subgroup of endometrial cancer patients with loss of thyroid hormone receptor beta expression and improved survival. BMC Cancer 2020; 20:857. [PMID: 32894083 PMCID: PMC7487950 DOI: 10.1186/s12885-020-07325-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 08/20/2020] [Indexed: 12/28/2022] Open
Abstract
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. Furthermore, there are no tools to systematically identify tumors that lose NHR mRNA expression relative to normal tissue. The development of such an approach could identify sets of NHR-based biomarkers for classifying patients into subgroups with poor survival outcomes. METHODS Here, a new computational method, termed receptLoss, was developed for identifying NHR expression loss in endometrial cancer relative to adjacent normal tissue. When applied to gene expression data from The Cancer Genome Atlas (TCGA), receptLoss identified 6 NHRs that were highly expressed in normal tissue and exhibited expression loss in a subset of endometrial tumors. RESULTS Three of the six identified NHRs - estrogen, progesterone, and androgen receptors - that are known to lose expression in ECs were correctly identified by receptLoss. Additionally, a novel association was found between thyroid hormone receptor beta (THRB) expression loss, increased expression of miRNA-146a, and increased rates of 5-year survival in the EC TCGA patient cohort. THRB expression loss occurs independently of estrogen and progesterone expression loss, suggesting the discovery of a distinct, clinically-relevant molecular subgroup. CONCLUSION ReceptLoss is a novel, open-source software tool to systematically identify NHR expression loss in cancer. The application of receptLoss to endometrial cancer gene expression data identified THRB, a previously undescribed biomarker of survival in endometrial cancer. Applying receptLoss to expression data from additional cancer types could lead to the development of biomarkers of disease progression for patients with any other tumor type. ReceptLoss can be applied to expression data from additional cancer types with the goal of identifying biomarkers of differential survival.
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Affiliation(s)
- Daniel G. Piqué
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461 USA
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461 USA
| | - John M. Greally
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461 USA
| | - Jessica C. Mar
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461 USA
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461 USA
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Building 75, Cnr. College Rd & Cooper Rd, Brisbane, QLD 4072 Australia
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39
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Sato H, Singer RH, Greally JM. Quantitative Kinetic Analyses of Histone Turnover Using Imaging and Flow Cytometry. Bio Protoc 2020; 10:e3738. [PMID: 33043098 DOI: 10.21769/bioprotoc.3738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Dynamic histone changes occur as a central part of chromatin regulation. Deposition of histone variants and post-translational modifications of histones are strongly associated with properties of chromatin status. Characterizing the kinetics of histone variants allows important insights into transcription regulation, chromatin maintenance and other chromatin properties. Here we provide a protocol of quantitative and sensitive approaches to test the timing of incorporation and dissociation of histones using a two-color SNAP-labeling system, labelling pre-existing and newly-incorporated histones distinctly. Together with cell cycle synchronization methods and cell cycle markers, this approach enables a pulse-chase analysis to determine the turnover of histone variants during the cell cycle, detected using imaging or flow cytometry methods at single cell resolution. As well as testing global histone turnover, cell cycle-dependent cellular localization of histone variants can be also addressed using imaging approaches.
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Affiliation(s)
- Hanae Sato
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA.,Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461, USA
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA.,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn. VA 20147, USA
| | - John M Greally
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461, USA
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40
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Rastogi D, Johnston AD, Nico J, Loh LN, Jorge Y, Suzuki M, Macian F, Greally JM. Functional Genomics of the Pediatric Obese Asthma Phenotype Reveal Enrichment of Rho-GTPase Pathways. Am J Respir Crit Care Med 2020; 202:259-274. [PMID: 32255672 DOI: 10.1164/rccm.201906-1199oc] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Rationale: Obesity-related asthma disproportionately affects minority children and is associated with nonatopic T-helper type 1 (Th1) cell polarized inflammation that correlates with pulmonary function deficits. Its underlying mechanisms are poorly understood.Objectives: To use functional genomics to identify cellular mechanisms associated with nonatopic inflammation in obese minority children with asthma.Methods: CD4+ (cluster of differentiation 4-positive) Th cells from 59 obese Hispanic and African American children with asthma and 61 normal-weight Hispanic and African American children with asthma underwent quantification of the transcriptome and DNA methylome and genotyping. Expression and methylation quantitative trait loci revealed the contribution of genetic variation to transcription and DNA methylation. Adjusting for Th-cell subtype proportions discriminated loci where transcription or methylation differences were driven by differences in subtype proportions from loci that were independently associated with obesity-related asthma.Measurements and Main Results: Obese children with asthma had more memory and fewer naive Th cells than normal-weight children with asthma. Differentially expressed and methylated genes and methylation quantitative trait loci in obese children with asthma, independent of Th-cell subtype proportions, were enriched in Rho-GTPase pathways. Inhibition of CDC42 (cell division cycle 42), one of the Rho-GTPases associated with Th-cell differentiation, was associated with downregulation of the IFNγ, but not the IL-4, gene. Differential expression of the RPS27L (40S ribosomal protein S27-like) gene, part of the p53/mammalian target of rapamycin pathway, was due to nonrandom distribution of expression quantitative trait loci variants between groups. Differentially expressed and/or methylated genes, including RPS27L, were associated with pulmonary function deficits in obese children with asthma.Conclusions: We found enrichment of Rho-GTPase pathways in obese asthmatic Th cells, identifying them as a novel therapeutic target for obesity-related asthma, a disease that is suboptimally responsive to current therapies.
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Affiliation(s)
- Deepa Rastogi
- Department of Pediatrics.,Department of Pathology, and
| | - Andrew D Johnston
- Department of Genetics, Albert Einstein College of Medicine, New York, New York
| | | | | | | | - Masako Suzuki
- Department of Genetics, Albert Einstein College of Medicine, New York, New York
| | | | - John M Greally
- Department of Genetics, Albert Einstein College of Medicine, New York, New York
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41
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Johnston AD, Abdulrazak A, Sato H, Maqbool SB, Suzuki M, Greally JM, Simões-Pires CA. A Cellular Stress Response Induced by the CRISPR-dCas9 Activation System Is Not Heritable Through Cell Divisions. CRISPR J 2020; 3:188-197. [PMID: 33560917 DOI: 10.1089/crispr.2019.0077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
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. Here, we show how distinct components of this CRISPR-dCas9 activation system, particularly dCas9 with untargeted gRNAs, upregulate genes associated with transcriptional stress, defense response, and regulation of cell death. Our results highlight a previously undetected acute stress response to CRISPR-dCas9 components in human cells, which is transient and not maintained through cell divisions.
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Affiliation(s)
- Andrew D Johnston
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Alali Abdulrazak
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Hanae Sato
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Shahina B Maqbool
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Masako Suzuki
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - John M Greally
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Claudia A Simões-Pires
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
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42
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Johnston AD, Simões-Pires CA, Suzuki M, Greally JM. High-efficiency genomic editing in Epstein-Barr virus-transformed lymphoblastoid B cells using a single-stranded donor oligonucleotide strategy. Commun Biol 2019; 2:312. [PMID: 31428700 PMCID: PMC6694121 DOI: 10.1038/s42003-019-0559-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 07/29/2019] [Indexed: 12/29/2022] Open
Abstract
While human lymphoblastoid cell lines represent a valuable resource for population genetic studies, they have usually been regarded as difficult for CRISPR-mediated genomic editing because of very inefficient DNA transfection and retroviral or lentiviral transduction in these cells, which becomes a substantial problem when multiple constructs need to be co-expressed. Here we describe a protocol using a single-stranded donor oligonucleotide strategy for 'scarless' editing in lymphoblastoid cells, yielding 12/60 (20%) of clones with homology-directed recombination, when rates of <5-10% are frequently typical for many other cell types. The protocol does not require the use of lentiviruses or stable transfection, permitting lymphoblastoid cell lines to be used for CRISPR-mediated genomic targeting and screening in population genetic studies.
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Affiliation(s)
- Andrew D. Johnston
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Claudia A. Simões-Pires
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Masako Suzuki
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - John M. Greally
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
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43
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Johnston AD, Simões-Pires CA, Thompson TV, Suzuki M, Greally JM. Functional genetic variants can mediate their regulatory effects through alteration of transcription factor binding. Nat Commun 2019; 10:3472. [PMID: 31375681 PMCID: PMC6677801 DOI: 10.1038/s41467-019-11412-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 07/10/2019] [Indexed: 12/23/2022] Open
Abstract
Functional variants in the genome are usually identified by their association with local gene expression, DNA methylation or chromatin states. DNA sequence motif analysis and chromatin immunoprecipitation studies have provided indirect support for the hypothesis that functional variants alter transcription factor binding to exert their effects. In this study, we provide direct evidence that functional variants can alter transcription factor binding. We identify a multifunctional variant within the TBC1D4 gene encoding a canonical NFκB binding site, and edited it using CRISPR-Cas9 to remove this site. We show that this editing reduces TBC1D4 expression, local chromatin accessibility and binding of the p65 component of NFκB. We then used CRISPR without genomic editing to guide p65 back to the edited locus, demonstrating that this re-targeting, occurring ~182 kb from the gene promoter, is enough to restore the function of the locus, supporting the central role of transcription factors mediating the effects of functional variants.
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Affiliation(s)
- Andrew D Johnston
- Center for Epigenomics and Department of Genetics (Division of Genomics), Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Claudia A Simões-Pires
- Center for Epigenomics and Department of Genetics (Division of Genomics), Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Taylor V Thompson
- Center for Epigenomics and Department of Genetics (Division of Genomics), Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Masako Suzuki
- Center for Epigenomics and Department of Genetics (Division of Genomics), Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY, 10461, USA
| | - John M Greally
- Center for Epigenomics and Department of Genetics (Division of Genomics), Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY, 10461, USA.
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44
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Bowler TG, Pradhan K, Kong Y, Bartenstein M, Morrone KA, Sridharan A, Kessel RM, Shastri A, Giricz O, Bhagat TD, Gordon-Mitchell S, Rohanizadegan M, Hooda L, Datt I, Przychodzen BP, Parmar S, Maqbool S, Maciejewski JP, Steidl U, Greally JM, Verma A. Misidentification of MLL3 and other mutations in cancer due to highly homologous genomic regions. Leuk Lymphoma 2019; 60:3132-3137. [PMID: 31288594 DOI: 10.1080/10428194.2019.1630620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The MLL3 gene has been shown to be recurrently mutated in many malignancies including in families with acute myeloid leukemia. We demonstrate that many MLL3 variant calls made by exome sequencing are false positives due to misalignment to homologous regions, including a region on chr21, and can only be validated by long-range PCR. Numerous other recurrently mutated genes reported in COSMIC and TCGA databases have pseudogenes and cannot also be validated by conventional short read-based sequencing approaches. Genome-wide identification of pseudogene regions demonstrates that frequency of these homologous regions is increased with sequencing read lengths below 200 bps. To enable identification of poor quality sequencing variants in prospective studies, we generated novel genome-wide maps of regions with poor mappability that can be used in variant calling algorithms. Taken together, our findings reveal that pseudogene regions are a source of false-positive mutations in cancers.
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Affiliation(s)
- Timothy G Bowler
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Kith Pradhan
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Yu Kong
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
| | | | - Kerry A Morrone
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Ashwin Sridharan
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Rachel M Kessel
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Aditi Shastri
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Orsi Giricz
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Tushar D Bhagat
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
| | | | | | - Lauren Hooda
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Ishan Datt
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
| | | | | | - Shahina Maqbool
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
| | | | - Ulrich Steidl
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - John M Greally
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Amit Verma
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
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45
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Jaric I, Rocks D, Greally JM, Suzuki M, Kundakovic M. Chromatin organization in the female mouse brain fluctuates across the oestrous cycle. Nat Commun 2019; 10:2851. [PMID: 31253786 PMCID: PMC6598989 DOI: 10.1038/s41467-019-10704-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 05/23/2019] [Indexed: 12/12/2022] Open
Abstract
Male and female brains differ significantly in both health and disease, and yet the female brain has been understudied. Sex-hormone fluctuations make the female brain particularly dynamic and are likely to confer female-specific risks for neuropsychiatric disorders. The molecular mechanisms underlying the dynamic nature of the female brain structure and function are unknown. Here we show that neuronal chromatin organization in the female ventral hippocampus of mouse fluctuates with the oestrous cycle. We find chromatin organizational changes associated with the transcriptional activity of genes important for neuronal function and behaviour. We link these chromatin dynamics to variation in anxiety-related behaviour and brain structure. Our findings implicate an immediate-early gene product, Egr1, as part of the mechanism mediating oestrous cycle-dependent chromatin and transcriptional changes. This study reveals extreme, sex-specific dynamism of the neuronal epigenome, and establishes a foundation for the development of sex-specific treatments for disorders such as anxiety and depression. The molecular mechanisms underlying the dynamic nature of the female brain structure and function remain poorly understood. Here the authors characterise chromatin organization in the mouse female ventral hippocampus, finding it fluctuates with the oestrous cycle, and identify changes in chromatin organization associated with the transcription of genes important for neuronal function and behaviour.
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Affiliation(s)
- Ivana Jaric
- Department of Biological Sciences, Fordham University, 441 E. Fordham Road, Bronx, NY, 10458, USA
| | - Devin Rocks
- Department of Biological Sciences, Fordham University, 441 E. Fordham Road, Bronx, NY, 10458, USA
| | - John M Greally
- Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Masako Suzuki
- Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Marija Kundakovic
- Department of Biological Sciences, Fordham University, 441 E. Fordham Road, Bronx, NY, 10458, USA.
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46
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Piqué DG, Andriani GA, Maggi E, Zimmerman SE, Greally JM, Montagna C, Mar JC. Aneuvis: web-based exploration of numerical chromosomal variation in single cells. BMC Bioinformatics 2019; 20:336. [PMID: 31208319 PMCID: PMC6580570 DOI: 10.1186/s12859-019-2842-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 04/22/2019] [Indexed: 01/02/2023] Open
Abstract
Background Numerical chromosomal variation is a hallmark of populations of malignant cells. Identifying the factors that promote numerical chromosomal variation is important for understanding mechanisms of carcinogenesis. However, the ability to quantify and visualize differences in chromosome number between experimentally-defined groups (e.g. control vs treated) obtained from single-cell experiments is currently limited by the lack of user-friendly software. Results Aneuvis is a web application that allows users to determine whether numerical chromosomal variation exists between experimental treatment groups. The web interface allows users to upload molecular cytogenetic or processed single cell whole-genome sequencing data in a cell-by-chromosome matrix format and automatically generates visualizations and summary statistics that reflect the degree of numeric chromosomal variability. Conclusions Aneuvis is the first user-friendly web application to help researchers identify the genetic and environmental perturbations that promote numerical chromosomal variation. Aneuvis is freely available as a web application at https://dpique.shinyapps.io/aneuvis/ and the source code for the application is available at https://github.com/dpique/aneuvis. Electronic supplementary material The online version of this article (10.1186/s12859-019-2842-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel G Piqué
- Department of Systems Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Grasiella A Andriani
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Elaine Maggi
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Samuel E Zimmerman
- Department of Systems Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - John M Greally
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Cristina Montagna
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA. .,Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
| | - Jessica C Mar
- Department of Systems Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA. .,Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, 10461, USA. .,Australian Institute for Bioengineering and Nanotechnology, the University of Queensland, Brisbane, QLD, 4072, Australia.
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47
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Sato H, Wu B, Delahaye F, Singer RH, Greally JM. Retargeting of macroH2A following mitosis to cytogenetic-scale heterochromatic domains. J Cell Biol 2019; 218:1810-1823. [PMID: 31110057 PMCID: PMC6548134 DOI: 10.1083/jcb.201811109] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 03/20/2019] [Accepted: 04/19/2019] [Indexed: 12/12/2022] Open
Abstract
How macroH2A, a histone variant involved in silencing gene expression, is inherited from parent to daughter cells is unclear. Using a combination of imaging, biochemical, and genomic approaches, Sato et al. describe how newly synthesized macroH2A is incorporated predominantly in the G1 phase of human mitosis, targeting heterochromatic regions. The heritability of chromatin states through cell division is a potential contributor to the epigenetic maintenance of cellular memory of prior states. The macroH2A histone variant has properties of a regulator of epigenetic cell memory, including roles controlling gene silencing and cell differentiation. Its mechanisms of regional genomic targeting and maintenance through cell division are unknown. Here, we combined in vivo imaging with biochemical and genomic approaches to show that human macroH2A is incorporated into chromatin in the G1 phase of the cell cycle following DNA replication. The newly incorporated macroH2A retargets the same large heterochromatic domains where macroH2A was already enriched in the previous cell cycle. It remains heterotypic, targeting individual nucleosomes that do not already contain a macroH2A molecule. The pattern observed resembles that of a new deposition of centromeric histone variants during the cell cycle, indicating mechanistic similarities for macrodomain-scale regulation of epigenetic properties of the cell.
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Affiliation(s)
- Hanae Sato
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, NY.,Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY
| | - Bin Wu
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY.,Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY
| | - Fabien Delahaye
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, NY.,Department of Obstetrics and Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY .,Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY.,Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY.,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA
| | - John M Greally
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, NY
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Kong Y, Rastogi D, Seoighe C, Greally JM, Suzuki M. Insights from deconvolution of cell subtype proportions enhance the interpretation of functional genomic data. PLoS One 2019; 14:e0215987. [PMID: 31022271 PMCID: PMC6483354 DOI: 10.1371/journal.pone.0215987] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 04/11/2019] [Indexed: 02/07/2023] Open
Abstract
Cell subtype proportion variability between samples contributes significantly to the variation of functional genomic properties such as gene expression or DNA methylation. Although the impact of the variation of cell subtype composition on measured genomic quantities is recognized, and some innovative tools have been developed for the analysis of heterogeneous samples, most functional genomics studies using samples with mixed cell types still ignore the influence of cell subtype proportion variation, or just deal with it as a nuisance variable to be eliminated. Here we demonstrate how harvesting information about cell subtype proportions from functional genomics data can provide insights into cellular changes associated with phenotypes. We focused on two types of mixed cell populations, human blood and mouse kidney. Cell type prediction is well developed in the former, but not currently in the latter. Estimating the cellular repertoire is easier when a reference dataset from purified samples of all cell types in the tissue is available, as is the case for blood. However, reference datasets are not available for most other tissues, such as the kidney. In this study, we showed that the proportion of alterations attributable to changes in the cellular composition varies strikingly in the two disorders (asthma and systemic lupus erythematosus), suggesting that the contribution of cell subtype proportion changes to functional genomic properties can be disease-specific. We also showed that a reference dataset from a single-cell RNA-seq study successfully estimated the cell subtype proportions in mouse kidney and allowed us to distinguish altered cell subtype differences between two different knock-out mouse models, both of which had reported a reduced number of glomeruli compared to their wild-type counterparts. These findings demonstrate that testing for changes in cell subtype proportions between conditions can yield important insights in functional genomics studies.
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Affiliation(s)
- Yu Kong
- Department of Genetics and Center for Epigenomics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Deepa Rastogi
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Cathal Seoighe
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland Galway, University Road, Galway, Ireland
| | - John M. Greally
- Department of Genetics and Center for Epigenomics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Masako Suzuki
- Department of Genetics and Center for Epigenomics, Albert Einstein College of Medicine, Bronx, New York, United States of America
- * E-mail:
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Nakahara F, Borger DK, Wei Q, Pinho S, Maryanovich M, Zahalka AH, Suzuki M, Cruz CD, Wang Z, Xu C, Boulais PE, Ma'ayan A, Greally JM, Frenette PS. Engineering a haematopoietic stem cell niche by revitalizing mesenchymal stromal cells. Nat Cell Biol 2019; 21:560-567. [PMID: 30988422 PMCID: PMC6499646 DOI: 10.1038/s41556-019-0308-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 03/07/2019] [Indexed: 12/15/2022]
Abstract
Haematopoietic stem cells (HSCs) are maintained by bone marrow (BM) niches in vivo1,2, but the ability of niche cells to maintain HSCs ex vivo is markedly diminished. Expression of niche factors by Nestin-GFP+ mesenchymal-derived stromal cells (MSCs) is downregulated upon culture, suggesting that transcriptional rewiring may contribute to this reduced HSC maintenance potential. Using an RNA sequencing screen, we identified 5 transcription factors (Klf7, Ostf1, Xbp1, Irf3, Irf7) that restored HSC niche function in cultured BM-derived MSCs. These revitalized MSCs (rMSCs) exhibited enhanced synthesis of HSC niche factors while retaining their mesenchymal differentiation capacity. In contrast to HSCs co-cultured with control MSCs, HSCs expanded with rMSCs showed higher repopulation capacity and protected lethally irradiated recipient mice. Competitive reconstitution assays revealed ~7-fold expansion of functional HSCs by rMSCs. rMSCs prevented the accumulation of DNA damage in cultured HSCs, a hallmark of ageing and replication stress. Analysis of the reprogramming mechanisms uncovered a role for myocyte enhancer factor 2c (Mef2c) in the revitalization of MSCs. These results provide insight in the transcriptional regulation of the niche with implications for stem cell-based therapies.
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Affiliation(s)
- Fumio Nakahara
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY, USA.,Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA.,Department of Hematology and Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Daniel K Borger
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY, USA.,Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Qiaozhi Wei
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY, USA.,Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Sandra Pinho
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY, USA.,Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA.,Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Maria Maryanovich
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY, USA.,Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Ali H Zahalka
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY, USA.,Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Masako Suzuki
- Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Cristian D Cruz
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY, USA.,Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Zichen Wang
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Chunliang Xu
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY, USA.,Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Philip E Boulais
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY, USA.,Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Avi Ma'ayan
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John M Greally
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA.,Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Paul S Frenette
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY, USA. .,Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA. .,Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA.
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50
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Shenoy N, Bhagat TD, Cheville J, Lohse C, Bhattacharyya S, Tischer A, Machha V, Gordon-Mitchell S, Choudhary G, Wong LF, Gross L, Ressigue E, Leibovich B, Boorjian SA, Steidl U, Wu X, Pradhan K, Gartrell B, Agarwal B, Pagliaro L, Suzuki M, Greally JM, Rakheja D, Thompson RH, Susztak K, Witzig T, Zou Y, Verma A. Ascorbic acid-induced TET activation mitigates adverse hydroxymethylcytosine loss in renal cell carcinoma. J Clin Invest 2019; 129:1612-1625. [PMID: 30702441 DOI: 10.1172/jci98747] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 01/24/2019] [Indexed: 12/31/2022] Open
Abstract
Although clear cell renal cell carcinoma (ccRCC) has been shown to result in widespread aberrant cytosine methylation and loss of 5-hydroxymethylcytosine (5hmC), the prognostic impact and therapeutic targeting of this epigenetic aberrancy has not been fully explored. Analysis of 576 primary ccRCC samples demonstrated that loss of 5hmC was strongly associated with aggressive clinicopathologic features and was an independent adverse prognostic factor. Loss of 5hmC also predicted reduced progression-free survival after resection of nonmetastatic disease. The loss of 5hmC in ccRCC was not due to mutational or transcriptional inactivation of ten eleven translocation (TET) enzymes, but to their functional inactivation by l-2-hydroxyglutarate (L2HG), which was overexpressed due to the deletion and underexpression of L2HG dehydrogenase (L2HGDH). Ascorbic acid (AA) reduced methylation and restored genome-wide 5hmC levels via TET activation. Fluorescence quenching of the recombinant TET-2 protein was unaffected by L2HG in the presence of AA. Pharmacologic AA treatment led to reduced growth of ccRCC in vitro and reduced tumor growth in vivo, with increased intratumoral 5hmC. These data demonstrate that reduced 5hmC is associated with reduced survival in ccRCC and provide a preclinical rationale for exploring the therapeutic potential of high-dose AA in ccRCC.
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Affiliation(s)
- Niraj Shenoy
- Albert Einstein College of Medicine, Montefiore Medical Center, New York, New York, USA
| | - Tushar D Bhagat
- Albert Einstein College of Medicine, Montefiore Medical Center, New York, New York, USA
| | | | | | | | | | | | | | - Gaurav Choudhary
- Albert Einstein College of Medicine, Montefiore Medical Center, New York, New York, USA
| | - Li-Fan Wong
- Albert Einstein College of Medicine, Montefiore Medical Center, New York, New York, USA
| | | | - Emily Ressigue
- Albert Einstein College of Medicine, Montefiore Medical Center, New York, New York, USA
| | | | | | - Ulrich Steidl
- Albert Einstein College of Medicine, Montefiore Medical Center, New York, New York, USA
| | | | - Kith Pradhan
- Albert Einstein College of Medicine, Montefiore Medical Center, New York, New York, USA
| | - Benjamin Gartrell
- Albert Einstein College of Medicine, Montefiore Medical Center, New York, New York, USA
| | | | | | - Masako Suzuki
- Albert Einstein College of Medicine, Montefiore Medical Center, New York, New York, USA
| | - John M Greally
- Albert Einstein College of Medicine, Montefiore Medical Center, New York, New York, USA
| | - Dinesh Rakheja
- University of Texas Southwestern Medical School, Dallas, Texas, USA
| | | | - Katalin Susztak
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | | | - Yiyu Zou
- Albert Einstein College of Medicine, Montefiore Medical Center, New York, New York, USA
| | - Amit Verma
- Albert Einstein College of Medicine, Montefiore Medical Center, New York, New York, USA
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