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  1. AU="Cogan, Joy D"
  2. AU="Ainola, Carmen"
  3. AU="Santilli, María C"
  4. AU="Wang, Rui-Hua"
  5. AU="Irish, Ashley"
  6. AU="Derminassian, Andrew D"
  7. AU="Kim, Dalsik"
  8. AU="Shiner, Yotam"
  9. AU="Ali, Mir Mohammad"
  10. AU="Weck Melanie"
  11. AU=Martinez-Riera Jose Ramon AU=Martinez-Riera Jose Ramon
  12. AU="Spano, Luana"
  13. AU="Macomb, Christopher V"
  14. AU="Cylwik, Jolanta"
  15. AU="Mirzabeigi, Parastoo"
  16. AU="Lesage, C"
  17. AU=Kim Donghyun AU=Kim Donghyun
  18. AU="Weisburd, Ben"
  19. AU="van den Berg, Linda M"
  20. AU="Kurochkina, Yu D"
  21. AU="H Cao"
  22. AU="Elias, Rui"
  23. AU="Hofstaedter, Ferdinand"
  24. AU="Ross, Ashley E"
  25. AU="Luque Alarcón, Mónica"

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  1. Artikel ; Online: Lessons learned: next-generation sequencing applied to undiagnosed genetic diseases.

    Schuler, Bryce A / Nelson, Erica T / Koziura, Mary / Cogan, Joy D / Hamid, Rizwan / Phillips, John A

    The Journal of clinical investigation

    2022  Band 132, Heft 7

    Abstract: Rare genetic disorders, when considered together, are relatively common. Despite advancements in genetics and genomics technologies as well as increased understanding of genomic function and dysfunction, many genetic diseases continue to be difficult to ... ...

    Abstract Rare genetic disorders, when considered together, are relatively common. Despite advancements in genetics and genomics technologies as well as increased understanding of genomic function and dysfunction, many genetic diseases continue to be difficult to diagnose. The goal of this Review is to increase the familiarity of genetic testing strategies for non-genetics providers. As genetic testing is increasingly used in primary care, many subspecialty clinics, and various inpatient settings, it is important that non-genetics providers have a fundamental understanding of the strengths and weaknesses of various genetic testing strategies as well as develop an ability to interpret genetic testing results. We provide background on commonly used genetic testing approaches, give examples of phenotypes in which the various genetic testing approaches are used, describe types of genetic and genomic variations, cover challenges in variant identification, provide examples in which next-generation sequencing (NGS) failed to uncover the variant responsible for a disease, and discuss opportunities for continued improvement in the application of NGS clinically. As genetic testing becomes increasingly a part of all areas of medicine, familiarity with genetic testing approaches and result interpretation is vital to decrease the burden of undiagnosed disease.
    Mesh-Begriff(e) Genetic Testing/methods ; Genomics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Phenotype ; Undiagnosed Diseases
    Sprache Englisch
    Erscheinungsdatum 2022-03-26
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Review ; Research Support, N.I.H., Extramural
    ZDB-ID 3067-3
    ISSN 1558-8238 ; 0021-9738
    ISSN (online) 1558-8238
    ISSN 0021-9738
    DOI 10.1172/JCI154942
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel ; Online: Undiagnosed Disease Network collaborative approach in diagnosing rare disease in a patient with a mosaic CACNA1D variant.

    Ezell, Kimberly M / Tinker, Rory J / Furuta, Yutaka / Gulsevin, Alican / Bastarache, Lisa / Hamid, Rizwan / Cogan, Joy D / Rives, Lynette / Neumann, Serena / Corner, Brian / Kozuria, Mary / Phillips, John A

    American journal of medical genetics. Part A

    2024  , Seite(n) e63597

    Abstract: The Undiagnosed Disease Network (UDN) is comprised of clinical and research experts collaborating to diagnose rare disease. The UDN is funded by the National Institutes of Health and includes 12 different clinical sites (About Us, 2022). Here we ... ...

    Abstract The Undiagnosed Disease Network (UDN) is comprised of clinical and research experts collaborating to diagnose rare disease. The UDN is funded by the National Institutes of Health and includes 12 different clinical sites (About Us, 2022). Here we highlight the success of collaborative efforts within the UDN Clinical Site at Vanderbilt University Medical Center (VUMC) in utilizing a cohort of experts in bioinformatics, structural biology, and genetics specialists in diagnosing rare disease. Our UDN team identified a de novo mosaic CACNA1D variant c.2299T>C in a 5-year-old female with a history of global developmental delay, dystonia, dyskinesis, and seizures. Using a collaborative multidisciplinary approach, our VUMC UDN team diagnosed the participant with Primary Aldosteronism, Seizures, and Neurologic abnormalities (PASNA) OMIM: 615474 due to a rare mosaic CACNA1D variant (O'Neill, 2013). Interestingly, this patient was mosaic, a phenotypic trait previously unreported in PASNA cases. This report highlights the importance of a multidisciplinary approach in diagnosing rare disease.
    Sprache Englisch
    Erscheinungsdatum 2024-03-21
    Erscheinungsland United States
    Dokumenttyp Case Reports
    ZDB-ID 2108614-X
    ISSN 1552-4833 ; 0148-7299 ; 1552-4825
    ISSN (online) 1552-4833
    ISSN 0148-7299 ; 1552-4825
    DOI 10.1002/ajmg.a.63597
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  3. Artikel ; Online: A medical odyssey of a 72-year-old man with Charcot-Marie-Tooth disease type 2 newly diagnosed with biallelic variants in SORD gene causing sorbitol dehydrogenase deficiency.

    Furuta, Yutaka / Nelson, Erica T / Neumann, Serena M / Phillips, John A / Hamid, Rizwan / Tinker, Rory J / Cogan, Joy D / Rives, Lynette / Newman, John H

    American journal of medical genetics. Part A

    2023  Band 191, Heft 12, Seite(n) 2873–2877

    Abstract: A 72-year-old man was referred to the Undiagnosed Diseases Network (UDN) because of gradual progressive weakness in both lower extremities for the past 45 years. He was initially diagnosed as having Charcot-Marie-Tooth disease type 2 (CMT2) without a ... ...

    Abstract A 72-year-old man was referred to the Undiagnosed Diseases Network (UDN) because of gradual progressive weakness in both lower extremities for the past 45 years. He was initially diagnosed as having Charcot-Marie-Tooth disease type 2 (CMT2) without a defined molecular genetic cause. Exome sequencing (ES) failed to detect deleterious neuromuscular variants. Very recently, biallelic variants in sorbitol dehydrogenase (SORD) were discovered to be a novel cause of inherited neuropathies including CMT2 or distal hereditary motor neuropathy (dHMN) referred to as Sorbitol Dehydrogenase Deficiency with Peripheral Neuropathy (SORDD, OMIM 618912). The most common variant identified was c.757delG; p.A253Qfs*27. Through the Vanderbilt UDN clinical site, this patient was formally diagnosed with SORDD after the identification of homozygosity for the above SORD frameshift through UDN Genome Sequencing (GS). His medical odyssey was solved by GS and detection of extremely high levels of sorbitol. The diagnosis provided him the opportunity to receive potential treatment with an investigational drug in a clinical trial for SORDD. We suggest that similar studies be considered in other individuals thought to possibly have CMT2 or dHMN.
    Mesh-Begriff(e) Humans ; Male ; Aged ; Charcot-Marie-Tooth Disease/diagnosis ; Charcot-Marie-Tooth Disease/genetics ; L-Iditol 2-Dehydrogenase/genetics ; Mutation
    Chemische Substanzen L-Iditol 2-Dehydrogenase (EC 1.1.1.14)
    Sprache Englisch
    Erscheinungsdatum 2023-08-25
    Erscheinungsland United States
    Dokumenttyp Case Reports ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2108614-X
    ISSN 1552-4833 ; 0148-7299 ; 1552-4825
    ISSN (online) 1552-4833
    ISSN 0148-7299 ; 1552-4825
    DOI 10.1002/ajmg.a.63383
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  4. Artikel ; Online: Probable digenic inheritance of Diamond-Blackfan anemia.

    Furuta, Yutaka / Tinker, Rory J / Gulsevin, Alican / Neumann, Serena M / Hamid, Rizwan / Cogan, Joy D / Rives, Lynette / Liu, Qi / Chen, Hua-Chang / Joos, Karen M / Phillips, John A

    American journal of medical genetics. Part A

    2023  Band 194, Heft 3, Seite(n) e63454

    Abstract: A 26-year-old female proband with a clinical diagnosis and consistent phenotype of Diamond-Blackfan anemia (DBA, OMIM 105650) without an identified genotype was referred to the Undiagnosed Diseases Network. DBA is classically associated with monoallelic ... ...

    Abstract A 26-year-old female proband with a clinical diagnosis and consistent phenotype of Diamond-Blackfan anemia (DBA, OMIM 105650) without an identified genotype was referred to the Undiagnosed Diseases Network. DBA is classically associated with monoallelic variants that have an autosomal-dominant or -recessive mode of inheritance. Intriguingly, her case was solved by a detection of a digenic interaction between non-allelic RPS19 and RPL27 variants. This was confirmed with a machine learning structural model, co-segregation analysis, and RNA sequencing. This is the first report of DBA caused by a digenic effect of two non-allelic variants demonstrated by machine learning structural model. This case suggests that atypical phenotypic presentations of DBA may be caused by digenic inheritance in some individuals. We also conclude that a machine learning structural model can be useful in detecting digenic models of possible interactions between products encoded by alleles of different genes inherited from non-affected carrier parents that can result in DBA with an unrealized 25% recurrence risk.
    Mesh-Begriff(e) Humans ; Female ; Adult ; Anemia, Diamond-Blackfan/diagnosis ; Anemia, Diamond-Blackfan/genetics ; Ribosomal Proteins/genetics ; Genotype ; Alleles ; Phenotype ; Base Sequence ; Mutation
    Chemische Substanzen Ribosomal Proteins
    Sprache Englisch
    Erscheinungsdatum 2023-10-27
    Erscheinungsland United States
    Dokumenttyp Case Reports
    ZDB-ID 2108614-X
    ISSN 1552-4833 ; 0148-7299 ; 1552-4825
    ISSN (online) 1552-4833
    ISSN 0148-7299 ; 1552-4825
    DOI 10.1002/ajmg.a.63454
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  5. Artikel ; Online: The contribution of mosaicism to genetic diseases and de novo pathogenic variants.

    Tinker, Rory J / Bastarache, Lisa / Ezell, Kimberly / Kobren, Shilpa Nadimpalli / Esteves, Cecilia / Rosenfeld, Jill A / Macnamara, Ellen F / Hamid, Rizwan / Cogan, Joy D / Rinker, David / Mukharjee, Souhrid / Glass, Ian / Dipple, Katrina / Phillips, John A

    American journal of medical genetics. Part A

    2023  Band 191, Heft 10, Seite(n) 2482–2492

    Abstract: The contribution of mosaicism to diagnosed genetic disease and presumed de novo variants (DNV) is under investigated. We determined the contribution of mosaic genetic disease (MGD) and diagnosed parental mosaicism (PM) in parents of offspring with ... ...

    Abstract The contribution of mosaicism to diagnosed genetic disease and presumed de novo variants (DNV) is under investigated. We determined the contribution of mosaic genetic disease (MGD) and diagnosed parental mosaicism (PM) in parents of offspring with reported DNV (in the same variant) in the (1) Undiagnosed Diseases Network (UDN) (N = 1946) and (2) in 12,472 individuals electronic health records (EHR) who underwent genetic testing at an academic medical center. In the UDN, we found 4.51% of diagnosed probands had MGD, and 2.86% of parents of those with DNV exhibited PM. In the EHR, we found 6.03% and 2.99% and (of diagnosed probands) had MGD detected on chromosomal microarray and exome/genome sequencing, respectively. We found 2.34% (of those with a presumed pathogenic DNV) had a parent with PM for the variant. We detected mosaicism (regardless of pathogenicity) in 4.49% of genetic tests performed. We found a broad phenotypic spectrum of MGD with previously unknown phenotypic phenomena. MGD is highly heterogeneous and provides a significant contribution to genetic diseases. Further work is required to improve the diagnosis of MGD and investigate how PM contributes to DNV risk.
    Mesh-Begriff(e) Humans ; Mosaicism ; Genetic Variation ; Genetic Testing ; Exome ; Parents
    Sprache Englisch
    Erscheinungsdatum 2023-05-29
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 2108614-X
    ISSN 1552-4833 ; 0148-7299 ; 1552-4825
    ISSN (online) 1552-4833
    ISSN 0148-7299 ; 1552-4825
    DOI 10.1002/ajmg.a.63309
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  6. Artikel ; Online: TBX4 Transcription Factor Is a Positive Feedback Regulator of Itself and Phospho-SMAD1/5.

    Cai, Ying / Yan, Ling / Kielt, Matthew J / Cogan, Joy D / Hedges, Lora K / Nunley, Bethany / West, James / Austin, Eric D / Hamid, Rizwan

    American journal of respiratory cell and molecular biology

    2021  Band 64, Heft 1, Seite(n) 140–143

    Mesh-Begriff(e) Animals ; Cell Line ; Feedback ; Gene Expression Regulation/physiology ; Humans ; Signal Transduction/physiology ; Smad1 Protein/metabolism ; Smad5 Protein/metabolism ; T-Box Domain Proteins/metabolism ; Transcription Factors/metabolism
    Chemische Substanzen Smad1 Protein ; Smad5 Protein ; T-Box Domain Proteins ; Transcription Factors
    Sprache Englisch
    Erscheinungsdatum 2021-01-01
    Erscheinungsland United States
    Dokumenttyp Letter ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1025960-0
    ISSN 1535-4989 ; 1044-1549
    ISSN (online) 1535-4989
    ISSN 1044-1549
    DOI 10.1165/rcmb.2020-0331LE
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  7. Artikel ; Online: Identifying digenic disease genes via machine learning in the Undiagnosed Diseases Network.

    Mukherjee, Souhrid / Cogan, Joy D / Newman, John H / Phillips, John A / Hamid, Rizwan / Meiler, Jens / Capra, John A

    American journal of human genetics

    2021  Band 108, Heft 10, Seite(n) 1946–1963

    Abstract: Rare diseases affect millions of people worldwide, and discovering their genetic causes is challenging. More than half of the individuals analyzed by the Undiagnosed Diseases Network (UDN) remain undiagnosed. The central hypothesis of this work is that ... ...

    Abstract Rare diseases affect millions of people worldwide, and discovering their genetic causes is challenging. More than half of the individuals analyzed by the Undiagnosed Diseases Network (UDN) remain undiagnosed. The central hypothesis of this work is that many of these rare genetic disorders are caused by multiple variants in more than one gene. However, given the large number of variants in each individual genome, experimentally evaluating combinations of variants for potential to cause disease is currently infeasible. To address this challenge, we developed the digenic predictor (DiGePred), a random forest classifier for identifying candidate digenic disease gene pairs by features derived from biological networks, genomics, evolutionary history, and functional annotations. We trained the DiGePred classifier by using DIDA, the largest available database of known digenic-disease-causing gene pairs, and several sets of non-digenic gene pairs, including variant pairs derived from unaffected relatives of UDN individuals. DiGePred achieved high precision and recall in cross-validation and on a held-out test set (PR area under the curve > 77%), and we further demonstrate its utility by using digenic pairs from the recent literature. In contrast to other approaches, DiGePred also appropriately controls the number of false positives when applied in realistic clinical settings. Finally, to enable the rapid screening of variant gene pairs for digenic disease potential, we freely provide the predictions of DiGePred on all human gene pairs. Our work enables the discovery of genetic causes for rare non-monogenic diseases by providing a means to rapidly evaluate variant gene pairs for the potential to cause digenic disease.
    Mesh-Begriff(e) Databases, Genetic ; Disease/genetics ; Genomics/methods ; Humans ; Machine Learning ; Multifactorial Inheritance ; Phenotype ; Rare Diseases/diagnosis ; Rare Diseases/genetics ; Undiagnosed Diseases/diagnosis ; Undiagnosed Diseases/genetics
    Sprache Englisch
    Erscheinungsdatum 2021-09-15
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 219384-x
    ISSN 1537-6605 ; 0002-9297
    ISSN (online) 1537-6605
    ISSN 0002-9297
    DOI 10.1016/j.ajhg.2021.08.010
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  8. Artikel ; Online: Peripheral Blood Telomere Attrition in Persons at Risk for Familial Pulmonary Fibrosis.

    Salisbury, Margaret L / Markin, Cheryl R / Wu, Pingsheng / Cogan, Joy D / Mitchell, Daphne B / Liu, Qi / Loyd, James E / Lancaster, Lisa H / Kropski, Jonathan A / Blackwell, Timothy S

    American journal of respiratory and critical care medicine

    2022  Band 207, Heft 2, Seite(n) 208–211

    Mesh-Begriff(e) Humans ; Idiopathic Pulmonary Fibrosis ; Mutation ; Telomere/genetics
    Sprache Englisch
    Erscheinungsdatum 2022-05-30
    Erscheinungsland United States
    Dokumenttyp Letter ; Research Support, N.I.H., Extramural
    ZDB-ID 1180953-x
    ISSN 1535-4970 ; 0003-0805 ; 1073-449X
    ISSN (online) 1535-4970
    ISSN 0003-0805 ; 1073-449X
    DOI 10.1164/rccm.202204-0766LE
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  9. Artikel ; Online: HACER: an atlas of human active enhancers to interpret regulatory variants.

    Wang, Jing / Dai, Xizhen / Berry, Lynne D / Cogan, Joy D / Liu, Qi / Shyr, Yu

    Nucleic acids research

    2018  Band 47, Heft D1, Seite(n) D106–D112

    Abstract: Recent studies have shown that disease-susceptibility variants frequently lie in cell-type-specific enhancer elements. To identify, interpret, and prioritize such risk variants, we must identify the enhancers active in disease-relevant cell types, their ... ...

    Abstract Recent studies have shown that disease-susceptibility variants frequently lie in cell-type-specific enhancer elements. To identify, interpret, and prioritize such risk variants, we must identify the enhancers active in disease-relevant cell types, their upstream transcription factor (TF) binding, and their downstream target genes. To address this need, we built HACER (http://bioinfo.vanderbilt.edu/AE/HACER/), an atlas of Human ACtive Enhancers to interpret Regulatory variants. The HACER atlas catalogues and annotates in-vivo transcribed cell-type-specific enhancers, as well as placing enhancers within transcriptional regulatory networks by integrating ENCODE TF ChIP-Seq and predicted/validated chromatin interaction data. We demonstrate the utility of HACER in (i) offering a mechanistic hypothesis to explain the association of SNP rs614367 with ER-positive breast cancer risk, (ii) exploring tumor-specific enhancers in selective MYC dysregulation and (iii) prioritizing/annotating non-coding regulatory regions targeting CCND1. HACER provides a valuable resource for studies of GWAS, non-coding variants, and enhancer-mediated regulation.
    Mesh-Begriff(e) Computational Biology/methods ; Databases, Genetic ; Enhancer Elements, Genetic ; Gene Expression Regulation ; Genetic Variation ; Genomics/methods ; Humans ; Web Browser
    Sprache Englisch
    Erscheinungsdatum 2018-06-14
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gky864
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  10. Artikel ; Online: The Y Chromosome Regulates BMPR2 Expression via SRY: A Possible Reason "Why" Fewer Males Develop Pulmonary Arterial Hypertension.

    Yan, Ling / Cogan, Joy D / Hedges, Lora K / Nunley, Bethany / Hamid, Rizwan / Austin, Eric D

    American journal of respiratory and critical care medicine

    2018  Band 198, Heft 12, Seite(n) 1581–1583

    Mesh-Begriff(e) Bone Morphogenetic Protein Receptors, Type II/genetics ; Chromosomes, Human, Y ; Female ; Humans ; Hypertension, Pulmonary/genetics ; Male ; Sex Factors ; Sex-Determining Region Y Protein/genetics
    Chemische Substanzen Sex-Determining Region Y Protein ; BMPR2 protein, human (EC 2.7.11.30) ; Bone Morphogenetic Protein Receptors, Type II (EC 2.7.11.30)
    Sprache Englisch
    Erscheinungsdatum 2018-10-09
    Erscheinungsland United States
    Dokumenttyp Letter ; Research Support, N.I.H., Extramural
    ZDB-ID 1180953-x
    ISSN 1535-4970 ; 0003-0805 ; 1073-449X
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    ISSN 0003-0805 ; 1073-449X
    DOI 10.1164/rccm.201802-0308LE
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