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  1. Article ; Online: FOCAD Indel in a Family With Juvenile Polyposis Syndrome.

    MacFarland, Suzanne P / Xie, Hongbo / Dent, Maiah H / Greed, Bridgid / Plon, Sharon E / Scollon, Sarah R / Brodeur, Garrett M / Howe, James R

    Journal of pediatric gastroenterology and nutrition

    2022  Volume 75, Issue 1, Page(s) 56–58

    Abstract: Juvenile polyposis syndrome (JPS) is a childhood polyposis syndrome with up to a 50% lifetime risk of gastrointestinal cancer. Germline pathogenic variants in BMPR1A and SMAD4 are responsible for around 40% of cases of JPS, but for the majority of ... ...

    Abstract Juvenile polyposis syndrome (JPS) is a childhood polyposis syndrome with up to a 50% lifetime risk of gastrointestinal cancer. Germline pathogenic variants in BMPR1A and SMAD4 are responsible for around 40% of cases of JPS, but for the majority of individuals, the underlying genetic cause is unknown. We identified a family for which polyposis spanned four generations, and the proband had a clinical diagnosis of JPS. Next-generation sequencing was conducted, followed by Sanger sequencing confirmation. We identified an internal deletion of the FOCAD gene in all family members tested that altered the reading frame and is predicted to be pathogenic. We conclude that inactivation of the FOCAD gene is likely to cause JPS in this family.
    MeSH term(s) Child ; Gastrointestinal Neoplasms ; Germ-Line Mutation ; Humans ; Intestinal Polyposis/congenital ; Intestinal Polyposis/genetics ; Neoplastic Syndromes, Hereditary/genetics
    Chemical Substances FOCAD protein, human
    Language English
    Publishing date 2022-06-17
    Publishing country United States
    Document type Journal Article ; 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.0000000000003470
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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  2. Article: Germline pathogenic variants in 786 neuroblastoma patients.

    Kim, Jung / Vaksman, Zalman / Egolf, Laura E / Kaufman, Rebecca / Evans, J Perry / Conkrite, Karina L / Danesh, Arnavaz / Lopez, Gonzalo / Randall, Michael P / Dent, Maiah H / Farra, Lance M / Menghani, Neil / Dymek, Malwina / Desai, Heena / Hausler, Ryan / Auvil, Jaime Guidry / Gerhard, Daniela S / Hakonarson, Hakon / Maxwell, Kara N /
    Cole, Kristina A / Pugh, Trevor J / Bosse, Kristopher R / Khan, Javed / Wei, Jun S / Maris, John M / Stewart, Douglas R / Diskin, Sharon J

    medRxiv : the preprint server for health sciences

    2023  

    Abstract: Importance: Neuroblastoma accounts for 12% of childhood cancer deaths. The genetic contribution of rare pathogenic germline variation in patients without a family history remains unclear.: Objective: To define the prevalence, spectrum, and clinical ... ...

    Abstract Importance: Neuroblastoma accounts for 12% of childhood cancer deaths. The genetic contribution of rare pathogenic germline variation in patients without a family history remains unclear.
    Objective: To define the prevalence, spectrum, and clinical significance of pathogenic germline variation in cancer predisposition genes (CPGs) in neuroblastoma patients.
    Design setting and participants: Germline DNA sequencing was performed on the peripheral blood from 786 neuroblastoma patients unselected for family history. Rare variants mapping to CPGs were evaluated for pathogenicity and the percentage of cases harboring pathogenic (P) or likely pathogenic (LP) variants was quantified. The frequency of CPG P-LP variants in neuroblastoma cases was compared to two distinct cancer-free control cohorts to assess enrichment. Matched tumor DNA sequencing was evaluated for "second hits" at CPGs and germline DNA array data from 5,585 neuroblastoma cases and 23,505 cancer-free control children was analyzed to identify rare germline copy number variants (CNVs) affecting genes with an excess burden of P-LP variants in neuroblastoma. Neuroblastoma patients with germline P-LP variants were compared to those without P-LP variants to test for association with clinical characteristics, tumor features, and patient survival.
    Main outcomes and measures: Rare variant prevalence, pathogenicity, enrichment, and association with clinical characteristics, tumor features, and patient survival.
    Results: We observed 116 P-LP variants in CPGs involving 13.9% (109/786) of patients, representing a significant excess burden of P-LP variants compared to controls (9.1%; P = 5.14 × 10
    Conclusions and relevance: Neuroblastoma patients harboring germline P-LP variants in CPGs have worse overall survival and
    Language English
    Publishing date 2023-01-25
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.01.23.23284864
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Germline pathogenic variants in neuroblastoma patients are enriched in BARD1 and predict worse survival.

    Kim, Jung / Vaksman, Zalman / Egolf, Laura E / Kaufman, Rebecca / Evans, J Perry / Conkrite, Karina L / Danesh, Arnavaz / Lopez, Gonzalo / Randall, Michael P / Dent, Maiah H / Farra, Lance M / Menghani, Neil L / Dymek, Malwina / Desai, Heena / Hausler, Ryan / Hicks, Belynda / Auvil, Jaime Guidry / Gerhard, Daniela S / Hakonarson, Hakon /
    Maxwell, Kara N / Cole, Kristina A / Pugh, Trevor J / Bosse, Kristopher R / Khan, Javed / Wei, Jun S / Maris, John M / Stewart, Douglas R / Diskin, Sharon J

    Journal of the National Cancer Institute

    2023  Volume 116, Issue 1, Page(s) 149–159

    Abstract: Background: Neuroblastoma is an embryonal cancer of the developing sympathetic nervous system. The genetic contribution of rare pathogenic or likely pathogenic germline variants in patients without a family history remains unclear.: Methods: Germline ...

    Abstract Background: Neuroblastoma is an embryonal cancer of the developing sympathetic nervous system. The genetic contribution of rare pathogenic or likely pathogenic germline variants in patients without a family history remains unclear.
    Methods: Germline DNA sequencing was performed on 786 neuroblastoma patients. The frequency of rare cancer predisposition gene pathogenic or likely pathogenic variants in patients was compared with 2 cancer-free control cohorts. Matched tumor DNA sequencing was evaluated for second hits, and germline DNA array data from 5585 neuroblastoma patients and 23 505 cancer-free control children were analyzed to identify rare germline copy number variants. Patients with germline pathogenic or likely pathogenic variants were compared with those without to test for association with clinical characteristics, tumor features, and survival.
    Results: We observed 116 pathogenic or likely pathogenic variants involving 13.9% (109 of 786) of neuroblastoma patients, representing a statistically significant excess burden compared with cancer-free participants (odds ratio [OR] = 1.60, 95% confidence interval [CI] = 1.27 to 2.00). BARD1 harbored the most statistically significant enrichment of pathogenic or likely pathogenic variants (OR = 32.30, 95% CI = 6.44 to 310.35). Rare germline copy number variants disrupting BARD1 were identified in patients but absent in cancer-free participants (OR = 29.47, 95% CI = 1.52 to 570.70). Patients harboring a germline pathogenic or likely pathogenic variant had a worse overall survival compared with those without (P = 8.6 x 10-3).
    Conclusions: BARD1 is an important neuroblastoma predisposition gene harboring both common and rare germline pathogenic or likely pathogenic variations. The presence of any germline pathogenic or likely pathogenic variant in a cancer predisposition gene was independently predictive of worse overall survival. As centers move toward paired tumor-normal sequencing at diagnosis, efforts should be made to centralize data and provide an infrastructure to support cooperative longitudinal prospective studies of germline pathogenic variation.
    MeSH term(s) Child ; Humans ; Genetic Predisposition to Disease ; Prospective Studies ; BRCA1 Protein/genetics ; Germ-Line Mutation ; Neuroblastoma/genetics ; Tumor Suppressor Proteins/genetics ; Ubiquitin-Protein Ligases/genetics
    Chemical Substances BRCA1 Protein ; BARD1 protein, human (EC 2.3.2.27) ; Tumor Suppressor Proteins ; Ubiquitin-Protein Ligases (EC 2.3.2.27)
    Language English
    Publishing date 2023-09-11
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2992-0
    ISSN 1460-2105 ; 0027-8874 ; 0198-0157
    ISSN (online) 1460-2105
    ISSN 0027-8874 ; 0198-0157
    DOI 10.1093/jnci/djad183
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  4. Article ; Online: Corrigendum: Transcriptomic profiling of 39 commonly-used neuroblastoma cell lines.

    Harenza, Jo Lynne / Diamond, Maura A / Adams, Rebecca N / Song, Michael M / Davidson, Heather L / Hart, Lori S / Dent, Maiah H / Fortina, Paolo / Reynolds, C Patrick / Maris, John M

    Scientific data

    2017  Volume 4, Page(s) 170183

    Abstract: This corrects the article DOI: 10.1038/sdata.2017.33. ...

    Abstract This corrects the article DOI: 10.1038/sdata.2017.33.
    Language English
    Publishing date 2017-12-05
    Publishing country England
    Document type Journal Article ; Published Erratum
    ZDB-ID 2775191-0
    ISSN 2052-4463 ; 2052-4463
    ISSN (online) 2052-4463
    ISSN 2052-4463
    DOI 10.1038/sdata.2017.183
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  5. Article ; Online: Transcriptomic profiling of 39 commonly-used neuroblastoma cell lines.

    Harenza, Jo Lynne / Diamond, Maura A / Adams, Rebecca N / Song, Michael M / Davidson, Heather L / Hart, Lori S / Dent, Maiah H / Fortina, Paolo / Reynolds, C Patrick / Maris, John M

    Scientific data

    2017  Volume 4, Page(s) 170033

    Abstract: Neuroblastoma cell lines are an important and cost-effective model used to study oncogenic drivers of the disease. While many of these cell lines have been previously characterized with SNP, methylation, and/or mRNA expression microarrays, there has not ... ...

    Abstract Neuroblastoma cell lines are an important and cost-effective model used to study oncogenic drivers of the disease. While many of these cell lines have been previously characterized with SNP, methylation, and/or mRNA expression microarrays, there has not been an effort to comprehensively sequence these cell lines. Here, we present raw whole transcriptome data generated by RNA sequencing of 39 commonly-used neuroblastoma cell lines. These data can be used to perform differential expression analysis based on a genetic aberration or phenotype in neuroblastoma (e.g., MYCN amplification status, ALK mutation status, chromosome arm 1p, 11q and/or 17q status, sensitivity to pharmacologic perturbation). Additionally, we designed this experiment to enable structural variant and/or long-noncoding RNA analysis across these cell lines. Finally, as more DNase/ATAC and histone/transcription factor ChIP sequencing is performed in these cell lines, our RNA-Seq data will be an important complement to inform transcriptional targets as well as regulatory (enhancer or repressor) elements in neuroblastoma.
    Language English
    Publishing date 2017--28
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2775191-0
    ISSN 2052-4463 ; 2052-4463
    ISSN (online) 2052-4463
    ISSN 2052-4463
    DOI 10.1038/sdata.2017.33
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  6. Article ; Online: Colonoids From Patients With Pediatric Inflammatory Bowel Disease Exhibit Decreased Growth Associated With Inflammation Severity and Durable Upregulation of Antigen Presentation Genes.

    Kelsen, Judith R / Dawany, Noor / Conrad, Maire A / Karakasheva, Tatiana A / Maurer, Kelly / Wei, Jane M / Uman, Selen / Dent, Maiah H / Behera, Rithika / Bryant, Laura M / Ma, Xianghui / Moreira, Leticia / Chatterji, Priya / Shraim, Rawan / Merz, Audrey / Mizuno, Rei / Simon, Lauren A / Muir, Amanda B / Giraudo, Claudio /
    Behrens, Edward M / Whelan, Kelly A / Devoto, Marcella / Russo, Pierre A / Andres, Sarah F / Sullivan, Kathleen E / Hamilton, Kathryn E

    Inflammatory bowel diseases

    2020  Volume 27, Issue 2, Page(s) 256–267

    Abstract: Background: Defining epithelial cell contributions to inflammatory bowel disease (IBD) is essential for the development of much needed therapies for barrier repair. Children with very early onset (VEO)-IBD have more extensive, severe, and refractory ... ...

    Abstract Background: Defining epithelial cell contributions to inflammatory bowel disease (IBD) is essential for the development of much needed therapies for barrier repair. Children with very early onset (VEO)-IBD have more extensive, severe, and refractory disease than older children and adults with IBD and, in some cases, have defective barrier function. We therefore evaluated functional and transcriptomic differences between pediatric IBD (VEO and older onset) and non-IBD epithelium using 3-dimensional, biopsy-derived organoids.
    Methods: We measured growth efficiency relative to histopathological and clinical parameters in patient enteroid (ileum) and colonoid (colon) lines. We performed RNA-sequencing on patient colonoids and subsequent flow cytometry after multiple passages to evaluate changes that persisted in culture.
    Results: Enteroids and colonoids from pediatric patients with IBD exhibited decreased growth associated with histological inflammation compared with non-IBD controls. We observed increased LYZ expression in colonoids from pediatric IBD patients, which has been reported previously in adult patients with IBD. We also observed upregulation of antigen presentation genes HLA-DRB1 and HLA-DRA, which persisted after prolonged passaging in patients with pediatric IBD.
    Conclusions: We present the first functional evaluation of enteroids and colonoids from patients with VEO-IBD and older onset pediatric IBD, a subset of which exhibits poor growth. Enhanced, persistent epithelial antigen presentation gene expression in patient colonoids supports the notion that epithelial cell-intrinsic differences may contribute to IBD pathogenesis.
    MeSH term(s) Antigen Presentation ; Child ; Humans ; Inflammation ; Inflammatory Bowel Diseases/genetics ; Organoids/growth & development ; Organoids/physiopathology ; Up-Regulation
    Language English
    Publishing date 2020-06-07
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1340971-2
    ISSN 1536-4844 ; 1078-0998
    ISSN (online) 1536-4844
    ISSN 1078-0998
    DOI 10.1093/ibd/izaa145
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    Zs.A 4530: Show issues Location:
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  7. Article ; Online: Variants in STXBP3 are Associated with Very Early Onset Inflammatory Bowel Disease, Bilateral Sensorineural Hearing Loss and Immune Dysregulation.

    Ouahed, Jodie / Kelsen, Judith R / Spessott, Waldo A / Kooshesh, Kameron / Sanmillan, Maria L / Dawany, Noor / Sullivan, Kathleen E / Hamilton, Kathryn E / Slowik, Voytek / Nejentsev, Sergey / Neves, João Farela / Flores, Helena / Chung, Wendy K / Wilson, Ashley / Anyane-Yeboa, Kwame / Wou, Karen / Jain, Preti / Field, Michael / Tollefson, Sophia /
    Dent, Maiah H / Li, Dalin / Naito, Takeo / McGovern, Dermot P B / Kwong, Andrew C / Taliaferro, Faith / Ordovas-Montanes, Jose / Horwitz, Bruce H / Kotlarz, Daniel / Klein, Christoph / Evans, Jonathan / Dorsey, Jill / Warner, Neil / Elkadri, Abdul / Muise, Aleixo M / Goldsmith, Jeffrey / Thompson, Benjamin / Engelhardt, Karin R / Cant, Andrew J / Hambleton, Sophie / Barclay, Andrew / Toth-Petroczy, Agnes / Vuzman, Dana / Carmichael, Nikkola / Bodea, Corneliu / Cassa, Christopher A / Devoto, Marcella / Maas, Richard L / Behrens, Edward M / Giraudo, Claudio G / Snapper, Scott B

    Journal of Crohn's & colitis

    2021  Volume 15, Issue 11, Page(s) 1908–1919

    Abstract: Background and aims: Very early onset inflammatory bowel disease [VEOIBD] is characterized by intestinal inflammation affecting infants and children less than 6 years of age. To date, over 60 monogenic aetiologies of VEOIBD have been identified, many ... ...

    Abstract Background and aims: Very early onset inflammatory bowel disease [VEOIBD] is characterized by intestinal inflammation affecting infants and children less than 6 years of age. To date, over 60 monogenic aetiologies of VEOIBD have been identified, many characterized by highly penetrant recessive or dominant variants in underlying immune and/or epithelial pathways. We sought to identify the genetic cause of VEOIBD in a subset of patients with a unique clinical presentation.
    Methods: Whole exome sequencing was performed on five families with ten patients who presented with a similar constellation of symptoms including medically refractory infantile-onset IBD, bilateral sensorineural hearing loss and, in the majority, recurrent infections. Genetic aetiologies of VEOIBD were assessed and Sanger sequencing was performed to confirm novel genetic findings. Western analysis on peripheral blood mononuclear cells and functional studies with epithelial cell lines were employed.
    Results: In each of the ten patients, we identified damaging heterozygous or biallelic variants in the Syntaxin-Binding Protein 3 gene [STXBP3], a protein known to regulate intracellular vesicular trafficking in the syntaxin-binding protein family of molecules, but not associated to date with either VEOIBD or sensorineural hearing loss. These mutations interfere with either intron splicing or protein stability and lead to reduced STXBP3 protein expression. Knock-down of STXBP3 in CaCo2 cells resulted in defects in cell polarity.
    Conclusion: Overall, we describe a novel genetic syndrome and identify a critical role for STXBP3 in VEOIBD, sensorineural hearing loss and immune dysregulation.
    MeSH term(s) Age of Onset ; Female ; Genetic Variation/genetics ; Hearing Loss, Sensorineural/epidemiology ; Hearing Loss, Sensorineural/genetics ; Humans ; Immune System Diseases/epidemiology ; Immune System Diseases/genetics ; Infant, Newborn ; Inflammatory Bowel Diseases/epidemiology ; Inflammatory Bowel Diseases/genetics ; Male ; Qa-SNARE Proteins/analysis ; Qa-SNARE Proteins/genetics ; Exome Sequencing
    Chemical Substances Qa-SNARE Proteins
    Language English
    Publishing date 2021-04-15
    Publishing country England
    Document type Journal Article
    ZDB-ID 2390120-2
    ISSN 1876-4479 ; 1873-9946
    ISSN (online) 1876-4479
    ISSN 1873-9946
    DOI 10.1093/ecco-jcc/jjab077
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    Zs.A 6634: Show issues Location:
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