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  1. Article ; Online: Magnitude of Mendelian versus complex inheritance of rare disorders.

    Chakravarti, Aravinda

    American journal of medical genetics. Part A

    2021  Volume 185, Issue 11, Page(s) 3287–3293

    Abstract: In medical genetics, the vast majority of patients with a currently known genetic basis harbor a rare deleterious allele explaining its Mendelian inheritance. Increasingly, for these phenotypes, we recognize exceptions to Mendelian expectations from non- ... ...

    Abstract In medical genetics, the vast majority of patients with a currently known genetic basis harbor a rare deleterious allele explaining its Mendelian inheritance. Increasingly, for these phenotypes, we recognize exceptions to Mendelian expectations from non-penetrance of clinical disease to significant inter-individual variation in clinical manifestations, likely reflecting the actions of additional modifier genes. Despite recent progress, we still remain ignorant about the molecular basis for many rare disorders presumed to be Mendelian. The molecular evidence increasingly suggests a role for multiple genes in some of these cases, but for how many? In this article, I discuss why equating a phenotype as Mendelian or complex may be short-sighted or even erroneous. As we learn more about the functions of the human genome with its genes in networks, we should view the phenotype of an individual patient as arising from his or her total genomic deleterious burden in a set of functionally inter-related genes affecting that phenotype. This can sometimes arise from deleterious allele(s) at a single gene (Mendelian inheritance) creating a specific biochemical deficiency (or excess) but could just as frequently arise from the cumulative effects of multiple disease alleles (complex inheritance) leading to the same biochemical deficiency (or excess).
    MeSH term(s) Alleles ; Genetic Diseases, Inborn/genetics ; Genetic Predisposition to Disease ; Genetics, Medical ; Genome, Human/genetics ; Humans ; Multifactorial Inheritance/genetics ; Mutation/genetics ; Rare Diseases/genetics
    Language English
    Publishing date 2021-08-21
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    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.62463
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Commentary: The central questions of human genetics: Richard Lewontin's 1968 senior lecture in Victor McKusick's Bar Harbor short course.

    Chakravarti, Aravinda

    International journal of epidemiology

    2016  Volume 45, Issue 3, Page(s) 668–672

    Language English
    Publishing date 2016-06
    Publishing country England
    Document type Journal Article
    ZDB-ID 187909-1
    ISSN 1464-3685 ; 0300-5771
    ISSN (online) 1464-3685
    ISSN 0300-5771
    DOI 10.1093/ije/dyw184
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Perspectives on Human Variation through the Lens of Diversity and Race.

    Chakravarti, Aravinda

    Cold Spring Harbor perspectives in biology

    2015  Volume 7, Issue 9, Page(s) a023358

    Abstract: Human populations, however defined, differ in the distribution and frequency of traits they display and diseases to which individuals are susceptible. These need to be understood with respect to three recent advances. First, these differences are ... ...

    Abstract Human populations, however defined, differ in the distribution and frequency of traits they display and diseases to which individuals are susceptible. These need to be understood with respect to three recent advances. First, these differences are multicausal and a result of not only genetic but also epigenetic and environmental factors. Second, the actions of genes, although crucial, turn out to be quite dynamic and modifiable, which contrasts with the classical view that they are inflexible machines. Third, the diverse human populations across the globe have spent too little time apart from our common origin 50,000 years ago to have developed many individually adapted traits. Human trait and disease differences by continental ancestry are thus as much the result of nongenetic as genetic forces.
    MeSH term(s) Continental Population Groups ; Evolution, Molecular ; Genetic Variation ; Humans ; Precision Medicine
    Language English
    Publishing date 2015-09-01
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 1943-0264
    ISSN (online) 1943-0264
    DOI 10.1101/cshperspect.a023358
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Book ; Conference proceedings: Human population genetics

    Chakravarti, Aravinda

    the Pittsburgh symposium ; [papers pres. at a Symposium on Human Population Genetics, held at ... Pittsburgh, Oct. 3 - 5, 1982]

    1984  

    Event/congress Symposium on Human Population Genetics (1982, PittsburghPa.)
    Author's details ed. by Aravinda Chakravarti
    Keywords Genetics, Population / congresses ; Populationsgenetik ; Mathematisches Modell
    Subject Bevölkerungsgenetik ; Evolutionsgenetik
    Size XI, 377 S. : graph. Darst.
    Publisher Van Nostrand Reinhold
    Publishing place New York u.a.
    Publishing country Great Britain
    Document type Book ; Conference proceedings
    Note Includes bibliographies and index
    HBZ-ID HT002850728
    ISBN 0-442-21745-5 ; 978-0-442-21745-7
    Database Catalogue ZB MED Medicine, Health

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  5. Article ; Online: 2013 William Allan Award: My multifactorial journey.

    Chakravarti, Aravinda

    American journal of human genetics

    2014  Volume 94, Issue 3, Page(s) 326–333

    MeSH term(s) Genetic Linkage ; Genetics, Medical/history ; History, 20th Century ; History, 21st Century ; Humans ; India ; Statistics as Topic/history ; United States
    Language English
    Publishing date 2014-03-04
    Publishing country United States
    Document type Address ; Autobiography ; Historical Article ; Journal Article ; Portrait
    ZDB-ID 219384-x
    ISSN 1537-6605 ; 0002-9297
    ISSN (online) 1537-6605
    ISSN 0002-9297
    DOI 10.1016/j.ajhg.2013.11.014
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Profile of Mary-Claire King, 2014 Lasker-Koshland Special Achievement in Medical Science awardee.

    Chakravarti, Aravinda

    Proceedings of the National Academy of Sciences of the United States of America

    2014  Volume 111, Issue 50, Page(s) 17690–17692

    MeSH term(s) Awards and Prizes ; Evolution, Molecular ; Genes, BRCA1 ; Genetics/history ; History, 20th Century ; History, 21st Century ; Human Rights Abuses/prevention & control ; Regulatory Sequences, Nucleic Acid/genetics
    Language English
    Publishing date 2014-12-16
    Publishing country United States
    Document type Biography ; Historical Article ; Journal Article ; Portraits
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.1418785111
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Book: Human variation

    Chakravarti, Aravinda

    a genetic perspective on diversity, race, and medicine

    2014  

    Author's details edited by Aravinda Chakravarti, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine
    MeSH term(s) Genetic Variation ; Population Groups/genetics
    Language English
    Size viii, 131 pages :, illustrations ;, 26 cm
    Document type Book
    ISBN 9781621820901 ; 1621820904 ; 9781936113255 ; 1936113252
    Database Catalogue of the US National Library of Medicine (NLM)

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  8. Article ; Online: A gene regulatory network explains RET-EDNRB epistasis in Hirschsprung disease.

    Chatterjee, Sumantra / Chakravarti, Aravinda

    Human molecular genetics

    2019  Volume 28, Issue 18, Page(s) 3137–3147

    Abstract: Disruptions in gene regulatory networks (GRNs), driven by multiple deleterious variants, potentially underlie complex traits and diseases. Hirschsprung disease (HSCR), a multifactorial disorder of enteric nervous system (ENS) development, is associated ... ...

    Abstract Disruptions in gene regulatory networks (GRNs), driven by multiple deleterious variants, potentially underlie complex traits and diseases. Hirschsprung disease (HSCR), a multifactorial disorder of enteric nervous system (ENS) development, is associated with at least 24 genes and seven chromosomal loci, with RET and EDNRB as its major genes. We previously demonstrated that RET transcription in the ENS is controlled by an extensive GRN involving the transcription factors (TFs) RARB, GATA2 and SOX10 and other HSCR genes. We now demonstrate, using human and mouse cellular and animal models, that EDNRB is transcriptionally regulated in the ENS by GATA2, SOX10 and NKX2.5 TFs. Significantly, RET and EDNRB expression is regulated by their shared use of GATA2 and SOX10, and in turn, these TFs are controlled by EDNRB and RET in a dose-dependent manner. This study expands the ENS development GRN to include both RET and EDNRB, uncovers the mechanistic basis for RET-EDNRB epistasis and emphasizes how functionally different genes associated with a complex disorder can be united through a common GRN.
    MeSH term(s) Animals ; Disease Models, Animal ; Enhancer Elements, Genetic ; Epigenesis, Genetic ; Epistasis, Genetic ; Gene Expression Regulation ; Gene Regulatory Networks ; Genetic Association Studies ; Genetic Predisposition to Disease ; Hirschsprung Disease/genetics ; Humans ; Mice ; Models, Biological ; Proto-Oncogene Proteins c-ret/genetics ; Receptor, Endothelin B/genetics ; Regulatory Sequences, Nucleic Acid ; Transcription Factors/metabolism
    Chemical Substances EDNRB protein, human ; Receptor, Endothelin B ; Transcription Factors ; Proto-Oncogene Proteins c-ret (EC 2.7.10.1)
    Language English
    Publishing date 2019-07-18
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 1108742-0
    ISSN 1460-2083 ; 0964-6906
    ISSN (online) 1460-2083
    ISSN 0964-6906
    DOI 10.1093/hmg/ddz149
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Identifying Needs, Challenges, and Benefits Among Adults and Parents of Children With Hirschsprung Disease.

    Berrios, Courtney / Bollinger, Juli / Yan, Jia / Biesecker, Barbara / Chakravarti, Aravinda

    Journal of pediatric gastroenterology and nutrition

    2022  Volume 74, Issue 5, Page(s) e103–e108

    Abstract: Abstract: Adults with Hirschsprung disease (HD), unaffected parents of children with HD, and affected adults with an affected child completed a cross-sectional survey with open-ended questions about greatest needs at diagnosis and at current time, ... ...

    Abstract Abstract: Adults with Hirschsprung disease (HD), unaffected parents of children with HD, and affected adults with an affected child completed a cross-sectional survey with open-ended questions about greatest needs at diagnosis and at current time, greatest challenges encountered, and any benefits of having HD or having a child with HD. In the 297 respondents, information and good medical care were common needs at diagnosis and at the time of survey, but the information needed evolved with time. Managing ongoing symptoms was a frequently cited need and challenge, along with managing medical care and the social and emotional impact of HD. Perceived benefits included empathy for others and new perspectives on life. The needs and challenges identified in this study can guide healthcare providers in discussions with families. Provision of information, recommendations, and referrals based on each individual family's needs can support families with HD throughout the lifecycle and facilitate adaptation.
    MeSH term(s) Adult ; Child ; Cross-Sectional Studies ; Family ; Hirschsprung Disease/therapy ; Humans ; Parents/psychology ; Surveys and Questionnaires
    Language English
    Publishing date 2022-02-10
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 603201-1
    ISSN 1536-4801 ; 0277-2116
    ISSN (online) 1536-4801
    ISSN 0277-2116
    DOI 10.1097/MPG.0000000000003411
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  10. Article ; Online: RET enhancer haplotype-dependent remodeling of the human fetal gut development program.

    Chatterjee, Sumantra / Fries, Lauren E / Yaacov, Or / Hu, Nan / Berk-Rauch, Hanna E / Chakravarti, Aravinda

    PLoS genetics

    2023  Volume 19, Issue 11, Page(s) e1011030

    Abstract: Hirschsprung disease (HSCR) is associated with deficiency of the receptor tyrosine kinase RET, resulting in loss of cells of the enteric nervous system (ENS) during fetal gut development. The major contribution to HSCR risk is from common sequence ... ...

    Abstract Hirschsprung disease (HSCR) is associated with deficiency of the receptor tyrosine kinase RET, resulting in loss of cells of the enteric nervous system (ENS) during fetal gut development. The major contribution to HSCR risk is from common sequence variants in RET enhancers with additional risk from rare coding variants in many genes. Here, we demonstrate that these RET enhancer variants specifically alter the human fetal gut development program through significant decreases in gene expression of RET, members of the RET-EDNRB gene regulatory network (GRN), other HSCR genes, with an altered transcriptome of 2,382 differentially expressed genes across diverse neuronal and mesenchymal functions. A parsimonious hypothesis for these results is that beyond RET's direct effect on its GRN, it also has a major role in enteric neural crest-derived cell (ENCDC) precursor proliferation, its deficiency reducing ENCDCs with relative expansion of non-ENCDC cells. Thus, genes reducing RET proliferative activity can potentially cause HSCR. One such class is the 23 RET-dependent transcription factors enriched in early gut development. We show that their knockdown in human neuroblastoma SK-N-SH cells reduces RET and/or EDNRB gene expression, expanding the RET-EDNRB GRN. The human embryos we studied had major remodeling of the gut transcriptome but were unlikely to have had HSCR: thus, genetic or epigenetic changes in addition to those in RET are required for aganglionosis.
    MeSH term(s) Haplotypes ; Humans ; Enhancer Elements, Genetic ; Proto-Oncogene Proteins c-ret/genetics ; Neuroblastoma ; Cell Line, Tumor ; Hirschsprung Disease/genetics ; Fetus ; Gastrointestinal Tract/embryology ; Neural Crest/cytology ; Enteric Nervous System/embryology ; Single-Cell Gene Expression Analysis ; Gene Expression Regulation, Developmental
    Chemical Substances RET protein, human (EC 2.7.10.1) ; Proto-Oncogene Proteins c-ret (EC 2.7.10.1)
    Language English
    Publishing date 2023-11-10
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2186725-2
    ISSN 1553-7404 ; 1553-7390
    ISSN (online) 1553-7404
    ISSN 1553-7390
    DOI 10.1371/journal.pgen.1011030
    Database MEDical Literature Analysis and Retrieval System OnLINE

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