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  1. AU="Anne Slavotinek"
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  1. Article ; Online: Use of PTC124 for nonsense suppression therapy targeting BMP4 nonsense variants in vitro and the bmp4st72 allele in zebrafish.

    Max Krall / Stephanie Htun / Anne Slavotinek

    PLoS ONE, Vol 14, Iss 4, p e

    2019  Volume 0212121

    Abstract: Nonsense suppression therapy (NST) utilizes compounds such as PTC124 (Ataluren) to induce translational read-through of stop variants by promoting the insertion of near cognate, aminoacyl tRNAs that yield functional proteins. We used NST with PTC124 to ... ...

    Abstract Nonsense suppression therapy (NST) utilizes compounds such as PTC124 (Ataluren) to induce translational read-through of stop variants by promoting the insertion of near cognate, aminoacyl tRNAs that yield functional proteins. We used NST with PTC124 to determine if we could successfully rescue nonsense variants in human Bone Morphogenetic Protein 4 (BMP4) in vitro and in a zebrafish bmp4 allele with a stop variant in vivo. We transfected 293T/17 cells with wildtype or mutant human BMP4 cDNA containing p.Arg198* and p.Glu213* and exposed cells to 0-20 μM PTC124. Treatment with 20 μM PTC124 produced a small, non-significant increase in BMP4 when targeting the p.Arg198* allele, but not the p.Glu213* allele, as measured with an In-cell ELISA assay. We then examined the ability of PTC124 to rescue the ventral tail fin defects associated with homozygosity for the p.Glu209* allele of bmp4 (bmp4st72/st72) in Danio rerio. We in-crossed bmp4st72/+ heterozygous fish and found a statistically significant increase in homozygous larvae without tail fin and ventroposterior defects, consistent with phenotypic rescue, after treatment of dechorionated larvae with 0.5 μM PTC124. We conclude that treatment with PTC124 can rescue bmp4 nonsense variants, but that the degree of rescue may depend on sequence specific factors and the amount of RNA transcript available for rescue. Our work also confirms that zebrafish show promise as a useful animal model for assessing the efficacy of PTC124 treatment on nonsense variants.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2019-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Genetic ancestry and diagnostic yield of exome sequencing in a diverse population

    Yusuph Mavura / Nuriye Sahin-Hodoglugil / Ugur Hodoglugil / Mark Kvale / Pierre-Marie Martin / Jessica Van Ziffle / W. Patrick Devine / Sara L. Ackerman / Barbara A. Koenig / Pui-Yan Kwok / Mary E. Norton / Anne Slavotinek / Neil Risch

    npj Genomic Medicine, Vol 9, Iss 1, Pp 1-

    2024  Volume 14

    Abstract: Abstract It has been suggested that diagnostic yield (DY) from Exome Sequencing (ES) may be lower among patients with non-European ancestries than those with European ancestry. We examined the association of DY with estimated continental/subcontinental ... ...

    Abstract Abstract It has been suggested that diagnostic yield (DY) from Exome Sequencing (ES) may be lower among patients with non-European ancestries than those with European ancestry. We examined the association of DY with estimated continental/subcontinental genetic ancestry in a racially/ethnically diverse pediatric and prenatal clinical cohort. Cases (N = 845) with suspected genetic disorders underwent ES for diagnosis. Continental/subcontinental genetic ancestry proportions were estimated from the ES data. We compared the distribution of genetic ancestries in positive, negative, and inconclusive cases by Kolmogorov–Smirnov tests and linear associations of ancestry with DY by Cochran-Armitage trend tests. We observed no reduction in overall DY associated with any genetic ancestry (African, Native American, East Asian, European, Middle Eastern, South Asian). However, we observed a relative increase in proportion of autosomal recessive homozygous inheritance versus other inheritance patterns associated with Middle Eastern and South Asian ancestry, due to consanguinity. In this empirical study of ES for undiagnosed pediatric and prenatal genetic conditions, genetic ancestry was not associated with the likelihood of a positive diagnosis, supporting the equitable use of ES in diagnosis of previously undiagnosed but potentially Mendelian disorders across all ancestral populations.
    Keywords Medicine ; R ; Genetics ; QH426-470
    Language English
    Publishing date 2024-01-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Publisher Correction

    Joseph T. Shieh / Monica Penon-Portmann / Karen H. Y. Wong / Michal Levy-Sakin / Michelle Verghese / Anne Slavotinek / Renata C. Gallagher / Bryce A. Mendelsohn / Jessica Tenney / Daniah Beleford / Hazel Perry / Stephen K. Chow / Andrew G. Sharo / Steven E. Brenner / Zhongxia Qi / Jingwei Yu / Ophir D. Klein / David Martin / Pui-Yan Kwok /
    Dario Boffelli

    npj Genomic Medicine, Vol 6, Iss 1, Pp 1-

    Application of full-genome analysis to diagnose rare monogenic disorders

    2021  Volume 1

    Keywords Medicine ; R ; Genetics ; QH426-470
    Language English
    Publishing date 2021-10-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Application of full-genome analysis to diagnose rare monogenic disorders

    Joseph T. Shieh / Monica Penon-Portmann / Karen H. Y. Wong / Michal Levy-Sakin / Michelle Verghese / Anne Slavotinek / Renata C. Gallagher / Bryce A. Mendelsohn / Jessica Tenney / Daniah Beleford / Hazel Perry / Stephen K. Chow / Andrew G. Sharo / Steven E. Brenner / Zhongxia Qi / Jingwei Yu / Ophir D. Klein / David Martin / Pui-Yan Kwok /
    Dario Boffelli

    npj Genomic Medicine, Vol 6, Iss 1, Pp 1-

    2021  Volume 10

    Abstract: Abstract Current genetic testenhancer and narrows the diagnostic intervals for rare diseases provide a diagnosis in only a modest proportion of cases. The Full-Genome Analysis method, FGA, combines long-range assembly and whole-genome sequencing to ... ...

    Abstract Abstract Current genetic testenhancer and narrows the diagnostic intervals for rare diseases provide a diagnosis in only a modest proportion of cases. The Full-Genome Analysis method, FGA, combines long-range assembly and whole-genome sequencing to detect small variants, structural variants with breakpoint resolution, and phasing. We built a variant prioritization pipeline and tested FGA’s utility for diagnosis of rare diseases in a clinical setting. FGA identified structural variants and small variants with an overall diagnostic yield of 40% (20 of 50 cases) and 35% in exome-negative cases (8 of 23 cases), 4 of these were structural variants. FGA detected and mapped structural variants that are missed by short reads, including non-coding duplication, and phased variants across long distances of more than 180 kb. With the prioritization algorithm, longer DNA technologies could replace multiple tests for monogenic disorders and expand the range of variants detected. Our study suggests that genomes produced from technologies like FGA can improve variant detection and provide higher resolution genome maps for future application.
    Keywords Medicine ; R ; Genetics ; QH426-470
    Subject code 572
    Language English
    Publishing date 2021-09-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Author Correction

    Anne Slavotinek / Shannon Rego / Nuriye Sahin-Hodoglugil / Mark Kvale / Billie Lianoglou / Tiffany Yip / Hannah Hoban / Simon Outram / Beatrice Anguiano / Flavia Chen / Jeremy Michelson / Roberta M. Cilio / Cynthia Curry / Renata C. Gallagher / Marisa Gardner / Rachel Kuperman / Bryce Mendelsohn / Elliott Sherr / Joseph Shieh /
    Jonathan Strober / Allison Tam / Jessica Tenney / William Weiss / Amy Whittle / Garrett Chin / Amanda Faubel / Hannah Prasad / Yusuph Mavura / Jessica Van Ziffle / W. Patrick Devine / Ugur Hodoglugil / Pierre-Marie Martin / Teresa N. Sparks / Barbara Koenig / Sara Ackerman / Neil Risch / Pui-Yan Kwok / Mary E. Norton

    npj Genomic Medicine, Vol 8, Iss 1, Pp 1-

    Diagnostic yield of pediatric and prenatal exome sequencing in a diverse population

    2023  Volume 1

    Keywords Medicine ; R ; Genetics ; QH426-470
    Language English
    Publishing date 2023-10-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Diagnostic yield of pediatric and prenatal exome sequencing in a diverse population

    Anne Slavotinek / Shannon Rego / Nuriye Sahin-Hodoglugil / Mark Kvale / Billie Lianoglou / Tiffany Yip / Hannah Hoban / Simon Outram / Beatrice Anguiano / Flavia Chen / Jeremy Michelson / Roberta M. Cilio / Cynthia Curry / Renata C. Gallagher / Marisa Gardner / Rachel Kuperman / Bryce Mendelsohn / Elliott Sherr / Joseph Shieh /
    Jonathan Strober / Allison Tam / Jessica Tenney / William Weiss / Amy Whittle / Garrett Chin / Amanda Faubel / Hannah Prasad / Yusuph Mavura / Jessica Van Ziffle / W. Patrick Devine / Ugur Hodoglugil / Pierre-Marie Martin / Teresa N. Sparks / Barbara Koenig / Sara Ackerman / Neil Risch / Pui-Yan Kwok / Mary E. Norton

    npj Genomic Medicine, Vol 8, Iss 1, Pp 1-

    2023  Volume 10

    Abstract: Abstract The diagnostic yield of exome sequencing (ES) has primarily been evaluated in individuals of European ancestry, with less focus on underrepresented minority (URM) and underserved (US) patients. We evaluated the diagnostic yield of ES in a cohort ...

    Abstract Abstract The diagnostic yield of exome sequencing (ES) has primarily been evaluated in individuals of European ancestry, with less focus on underrepresented minority (URM) and underserved (US) patients. We evaluated the diagnostic yield of ES in a cohort of predominantly US and URM pediatric and prenatal patients suspected to have a genetic disorder. Eligible pediatric patients had multiple congenital anomalies and/or neurocognitive disabilities and prenatal patients had one or more structural anomalies, disorders of fetal growth, or fetal effusions. URM and US patients were prioritized for enrollment and underwent ES at a single academic center. We identified definitive positive or probable positive results in 201/845 (23.8%) patients, with a significantly higher diagnostic rate in pediatric (26.7%) compared to prenatal patients (19.0%) (P = 0.01). For both pediatric and prenatal patients, the diagnostic yield and frequency of inconclusive findings did not differ significantly between URM and non-URM patients or between patients with US status and those without US status. Our results demonstrate a similar diagnostic yield of ES between prenatal and pediatric URM/US patients and non-URM/US patients for positive and inconclusive results. These data support the use of ES to identify clinically relevant variants in patients from diverse populations.
    Keywords Medicine ; R ; Genetics ; QH426-470
    Subject code 610
    Language English
    Publishing date 2023-05-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Correction to

    Eden V. Haverfield / Edward D. Esplin / Sienna J. Aguilar / Kathryn E. Hatchell / Kelly E. Ormond / Andrea Hanson-Kahn / Paldeep S. Atwal / Sarah Macklin-Mantia / Stephanie Hines / Caron W.-M. Sak / Steven Tucker / Steven B. Bleyl / Peter J. Hulick / Ora K. Gordon / Lea Velsher / Jessica Y. J. Gu / Scott M. Weissman / Teresa Kruisselbrink / Christopher Abel /
    Michele Kettles / Anne Slavotinek / Bryce A. Mendelsohn / Robert C. Green / Swaroop Aradhya / Robert L. Nussbaum

    BMC Medicine, Vol 19, Iss 1, Pp 1-

    Physician-directed genetic screening to evaluate personal risk for medically actionable disorders: a large multi-center cohort study

    2021  Volume 1

    Keywords Medicine ; R
    Language English
    Publishing date 2021-11-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Physician-directed genetic screening to evaluate personal risk for medically actionable disorders

    Eden V. Haverfield / Edward D. Esplin / Sienna J. Aguilar / Kathryn E. Hatchell / Kelly E. Ormond / Andrea Hanson-Kahn / Paldeep S. Atwal / Sarah Macklin-Mantia / Stephanie Hines / Caron W.-M. Sak / Steven Tucker / Steven B. Bleyl / Peter J. Hulick / Ora K. Gordon / Lea Velsher / Jessica Y. J. Gu / Scott M. Weissman / Teresa Kruisselbrink / Christopher Abel /
    Michele Kettles / Anne Slavotinek / Bryce A. Mendelsohn / Robert C. Green / Swaroop Aradhya / Robert L. Nussbaum

    BMC Medicine, Vol 19, Iss 1, Pp 1-

    a large multi-center cohort study

    2021  Volume 10

    Abstract: Abstract Background The use of proactive genetic screening for disease prevention and early detection is not yet widespread. Professional practice guidelines from the American College of Medical Genetics and Genomics (ACMG) have encouraged reporting ... ...

    Abstract Abstract Background The use of proactive genetic screening for disease prevention and early detection is not yet widespread. Professional practice guidelines from the American College of Medical Genetics and Genomics (ACMG) have encouraged reporting pathogenic variants that confer personal risk for actionable monogenic hereditary disorders, but only as secondary findings from exome or genome sequencing. The Centers for Disease Control and Prevention (CDC) recognizes the potential public health impact of three Tier 1 actionable disorders. Here, we report results of a large multi-center cohort study to determine the yield and potential value of screening healthy individuals for variants associated with a broad range of actionable monogenic disorders, outside the context of secondary findings. Methods Eligible adults were offered a proactive genetic screening test by health care providers in a variety of clinical settings. The screening panel based on next-generation sequencing contained up to 147 genes associated with monogenic disorders within cancer, cardiovascular, and other important clinical areas. Sequence and intragenic copy number variants classified as pathogenic, likely pathogenic, pathogenic (low penetrance), or increased risk allele were considered clinically significant and reported. Results were analyzed by clinical area and severity/burden of disease using chi-square tests without Yates’ correction. Results Among 10,478 unrelated adults screened, 1619 (15.5%) had results indicating personal risk for an actionable monogenic disorder. In contrast, only 3.1 to 5.2% had clinically reportable variants in genes suggested by the ACMG version 2 secondary findings list to be examined during exome or genome sequencing, and 2% had reportable variants related to CDC Tier 1 conditions. Among patients, 649 (6.2%) were positive for a genotype associated with a disease of high severity/burden, including hereditary cancer syndromes, cardiovascular disorders, or malignant hyperthermia susceptibility. Conclusions This ...
    Keywords Cardiovascular disorders ; Clinical genetics ; Hereditary cancer syndromes ; Monogenic disorders ; Population screening ; Proactive genetic screening ; Medicine ; R
    Subject code 610 ; 616
    Language English
    Publishing date 2021-08-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Dominant ARF3 variants disrupt Golgi integrity and cause a neurodevelopmental disorder recapitulated in zebrafish

    Giulia Fasano / Valentina Muto / Francesca Clementina Radio / Martina Venditti / Niloufar Mosaddeghzadeh / Simona Coppola / Graziamaria Paradisi / Erika Zara / Farhad Bazgir / Alban Ziegler / Giovanni Chillemi / Lucia Bertuccini / Antonella Tinari / Annalisa Vetro / Francesca Pantaleoni / Simone Pizzi / Libenzio Adrian Conti / Stefania Petrini / Alessandro Bruselles /
    Ingrid Guarnetti Prandi / Cecilia Mancini / Balasubramanian Chandramouli / Magalie Barth / Céline Bris / Donatella Milani / Angelo Selicorni / Marina Macchiaiolo / Michaela V. Gonfiantini / Andrea Bartuli / Riccardo Mariani / Cynthia J. Curry / Renzo Guerrini / Anne Slavotinek / Maria Iascone / Bruno Dallapiccola / Mohammad Reza Ahmadian / Antonella Lauri / Marco Tartaglia

    Nature Communications, Vol 13, Iss 1, Pp 1-

    2022  Volume 29

    Abstract: Disruptions to the ER-Golgi network can lead to neurodevelopmental disorders, though our understanding of these Golgipathies remains incomplete. Here Lauri, Tartaglia and colleagues show that ARF3 mutations cause a rare pediatric neurological disorder ... ...

    Abstract Disruptions to the ER-Golgi network can lead to neurodevelopmental disorders, though our understanding of these Golgipathies remains incomplete. Here Lauri, Tartaglia and colleagues show that ARF3 mutations cause a rare pediatric neurological disorder and perform detailed molecular characterization in fish.
    Keywords Science ; Q
    Language English
    Publishing date 2022-11-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Exome Sequence Analysis Suggests that Genetic Burden Contributes to Phenotypic Variability and Complex Neuropathy

    Claudia Gonzaga-Jauregui / Tamar Harel / Tomasz Gambin / Maria Kousi / Laurie B. Griffin / Ludmila Francescatto / Burcak Ozes / Ender Karaca / Shalini N. Jhangiani / Matthew N. Bainbridge / Kim S. Lawson / Davut Pehlivan / Yuji Okamoto / Marjorie Withers / Pedro Mancias / Anne Slavotinek / Pamela J. Reitnauer / Meryem T. Goksungur / Michael Shy /
    Thomas O. Crawford / Michel Koenig / Jason Willer / Brittany N. Flores / Igor Pediaditrakis / Onder Us / Wojciech Wiszniewski / Yesim Parman / Anthony Antonellis / Donna M. Muzny / Nicholas Katsanis / Esra Battaloglu / Eric Boerwinkle / Richard A. Gibbs / James R. Lupski

    Cell Reports, Vol 12, Iss 7, Pp 1169-

    2015  Volume 1183

    Abstract: Charcot-Marie-Tooth (CMT) disease is a clinically and genetically heterogeneous distal symmetric polyneuropathy. Whole-exome sequencing (WES) of 40 individuals from 37 unrelated families with CMT-like peripheral neuropathy refractory to molecular ... ...

    Abstract Charcot-Marie-Tooth (CMT) disease is a clinically and genetically heterogeneous distal symmetric polyneuropathy. Whole-exome sequencing (WES) of 40 individuals from 37 unrelated families with CMT-like peripheral neuropathy refractory to molecular diagnosis identified apparent causal mutations in ∼45% (17/37) of families. Three candidate disease genes are proposed, supported by a combination of genetic and in vivo studies. Aggregate analysis of mutation data revealed a significantly increased number of rare variants across 58 neuropathy-associated genes in subjects versus controls, confirmed in a second ethnically discrete neuropathy cohort, suggesting that mutation burden potentially contributes to phenotypic variability. Neuropathy genes shown to have highly penetrant Mendelizing variants (HPMVs) and implicated by burden in families were shown to interact genetically in a zebrafish assay exacerbating the phenotype established by the suppression of single genes. Our findings suggest that the combinatorial effect of rare variants contributes to disease burden and variable expressivity.
    Keywords Biology (General) ; QH301-705.5
    Subject code 610
    Language English
    Publishing date 2015-08-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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