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  1. Article ; Online: Publisher Correction

    Nathaly M. Sweeney / Shareef A. Nahas / Shimul Chowdhury / Sergey Batalov / Michelle Clark / Sara Caylor / Julie Cakici / John J. Nigro / Yan Ding / Narayanan Veeraraghavan / Charlotte Hobbs / David Dimmock / Stephen F. Kingsmore

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

    Rapid whole genome sequencing impacts care and resource utilization in infants with congenital heart disease

    2021  Volume 1

    Keywords Medicine ; R ; Genetics ; QH426-470
    Language English
    Publishing date 2021-05-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Author Correction

    Nathaly M. Sweeney / Shareef A. Nahas / Shimul Chowdhury / Sergey Batalov / Michelle Clark / Sara Caylor / Julie Cakici / John J. Nigro / Yan Ding / Narayanan Veeraraghavan / Charlotte Hobbs / David Dimmock / Stephen F. Kingsmore

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

    Rapid whole genome sequencing impacts care and resource utilization in infants with congenital heart disease

    2021  Volume 1

    Keywords Medicine ; R ; Genetics ; QH426-470
    Language English
    Publishing date 2021-05-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Diagnosis and treatment of a boy with IPEX syndrome presenting with diabetes in early infancy

    Sejal Kadakia / Lauge Farnaes / David Dimmock / Shimul Chowdhury / Yan Ding / Eric J. Anderson / Stephen Kingsmore / Ron S. Newfield

    Clinical Case Reports, Vol 7, Iss 11, Pp 2123-

    2019  Volume 2127

    Abstract: Abstract IPEX syndrome (Immune dysregulation, Polyendocrinopathy, X‐linked) should be tested for in males under 6 months old presenting with diabetes, even without other IPEX features. Early diagnosis and bone marrow transplantation can improve outcomes. ...

    Abstract Abstract IPEX syndrome (Immune dysregulation, Polyendocrinopathy, X‐linked) should be tested for in males under 6 months old presenting with diabetes, even without other IPEX features. Early diagnosis and bone marrow transplantation can improve outcomes.
    Keywords autoimmunity ; bone marrow transplantation ; diabetes mellitus ; infant ; X‐linked ; Medicine ; R ; Medicine (General) ; R5-920
    Language English
    Publishing date 2019-11-01T00:00:00Z
    Publisher Wiley
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Partially automated whole-genome sequencing reanalysis of previously undiagnosed pediatric patients can efficiently yield new diagnoses

    Kiely N. James / Michelle M. Clark / Brandon Camp / Cyrielle Kint / Peter Schols / Sergey Batalov / Benjamin Briggs / Narayanan Veeraraghavan / Shimul Chowdhury / Stephen F. Kingsmore

    npj Genomic Medicine, Vol 5, Iss 1, Pp 1-

    2020  Volume 8

    Abstract: Abstract To investigate the diagnostic and clinical utility of a partially automated reanalysis pipeline, forty-eight cases of seriously ill children with suspected genetic disease who did not receive a diagnosis upon initial manual analysis of whole- ... ...

    Abstract Abstract To investigate the diagnostic and clinical utility of a partially automated reanalysis pipeline, forty-eight cases of seriously ill children with suspected genetic disease who did not receive a diagnosis upon initial manual analysis of whole-genome sequencing (WGS) were reanalyzed at least 1 year later. Clinical natural language processing (CNLP) of medical records provided automated, updated patient phenotypes, and an automated analysis system delivered limited lists of possible diagnostic variants for each case. CNLP identified a median of 79 new clinical features per patient at least 1 year later. Compared to a standard manual reanalysis pipeline, the partially automated pipeline reduced the number of variants to be analyzed by 90% (range: 74%-96%). In 2 cases, diagnoses were made upon reinterpretation, representing an incremental diagnostic yield of 4.2% (2/48, 95% CI: 0.5–14.3%). Four additional cases were flagged with a possible diagnosis to be considered during subsequent reanalysis. Separately, copy number analysis led to diagnoses in two cases. Ongoing discovery of new disease genes and refined variant classification necessitate periodic reanalysis of negative WGS cases. The clinical features of patients sequenced as infants evolve rapidly with age. Partially automated reanalysis, including automated re-phenotyping through CNLP, has the potential to identify molecular diagnoses with reduced expert labor intensity.
    Keywords Medicine ; R ; Genetics ; QH426-470
    Subject code 610
    Language English
    Publishing date 2020-08-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Best practices for the interpretation and reporting of clinical whole genome sequencing

    Christina A. Austin-Tse / Vaidehi Jobanputra / Denise L. Perry / David Bick / Ryan J. Taft / Eric Venner / Richard A. Gibbs / Ted Young / Sarah Barnett / John W. Belmont / Nicole Boczek / Shimul Chowdhury / Katarzyna A. Ellsworth / Saurav Guha / Shashikant Kulkarni / Cherisse Marcou / Linyan Meng / David R. Murdock / Atteeq U. Rehman /
    Elizabeth Spiteri / Amanda Thomas-Wilson / Hutton M. Kearney / Heidi L. Rehm / Medical Genome Initiative*

    npj Genomic Medicine, Vol 7, Iss 1, Pp 1-

    2022  Volume 13

    Abstract: Abstract Whole genome sequencing (WGS) shows promise as a first-tier diagnostic test for patients with rare genetic disorders. However, standards addressing the definition and deployment practice of a best-in-class test are lacking. To address these gaps, ...

    Abstract Abstract Whole genome sequencing (WGS) shows promise as a first-tier diagnostic test for patients with rare genetic disorders. However, standards addressing the definition and deployment practice of a best-in-class test are lacking. To address these gaps, the Medical Genome Initiative, a consortium of leading health care and research organizations in the US and Canada, was formed to expand access to high quality clinical WGS by convening experts and publishing best practices. Here, we present best practice recommendations for the interpretation and reporting of clinical diagnostic WGS, including discussion of challenges and emerging approaches that will be critical to harness the full potential of this comprehensive test.
    Keywords Medicine ; R ; Genetics ; QH426-470
    Language English
    Publishing date 2022-04-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Best practices for the analytical validation of clinical whole-genome sequencing intended for the diagnosis of germline disease

    Christian R. Marshall / Shimul Chowdhury / Ryan J. Taft / Mathew S. Lebo / Jillian G. Buchan / Steven M. Harrison / Ross Rowsey / Eric W. Klee / Pengfei Liu / Elizabeth A. Worthey / Vaidehi Jobanputra / David Dimmock / Hutton M. Kearney / David Bick / Shashikant Kulkarni / Stacie L. Taylor / John W. Belmont / Dimitri J. Stavropoulos / Niall J. Lennon /
    Medical Genome Initiative

    npj Genomic Medicine, Vol 5, Iss 1, Pp 1-

    2020  Volume 12

    Abstract: Abstract Whole-genome sequencing (WGS) has shown promise in becoming a first-tier diagnostic test for patients with rare genetic disorders; however, standards addressing the definition and deployment practice of a best-in-class test are lacking. To ... ...

    Abstract Abstract Whole-genome sequencing (WGS) has shown promise in becoming a first-tier diagnostic test for patients with rare genetic disorders; however, standards addressing the definition and deployment practice of a best-in-class test are lacking. To address these gaps, the Medical Genome Initiative, a consortium of leading healthcare and research organizations in the US and Canada, was formed to expand access to high-quality clinical WGS by publishing best practices. Here, we present consensus recommendations on clinical WGS analytical validation for the diagnosis of individuals with suspected germline disease with a focus on test development, upfront considerations for test design, test validation practices, and metrics to monitor test performance. This work also provides insight into the current state of WGS testing at each member institution, including the utilization of reference and other standards across sites. Importantly, members of this initiative strongly believe that clinical WGS is an appropriate first-tier test for patients with rare genetic disorders, and at minimum is ready to replace chromosomal microarray analysis and whole-exome sequencing. The recommendations presented here should reduce the burden on laboratories introducing WGS into clinical practice, and support safe and effective WGS testing for diagnosis of germline disease.
    Keywords Medicine ; R ; Genetics ; QH426-470
    Language English
    Publishing date 2020-10-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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    Inter-library loan at ZB MED

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  7. Article ; Online: Rapid whole-genome sequencing decreases infant morbidity and cost of hospitalization

    Lauge Farnaes / Amber Hildreth / Nathaly M. Sweeney / Michelle M. Clark / Shimul Chowdhury / Shareef Nahas / Julie A. Cakici / Wendy Benson / Robert H. Kaplan / Richard Kronick / Matthew N. Bainbridge / Jennifer Friedman / Jeffrey J. Gold / Yan Ding / Narayanan Veeraraghavan / David Dimmock / Stephen F. Kingsmore

    npj Genomic Medicine, Vol 3, Iss 1, Pp 1-

    2018  Volume 8

    Abstract: Neonatology: Rapid sequencing of sick babies is useful and cost-effective Rapid whole-genome testing for babies in intensive care yields improved health outcomes and lowers medical costs. Stephen Kingsmore from Rady Children’s Institute for Genomic ... ...

    Abstract Neonatology: Rapid sequencing of sick babies is useful and cost-effective Rapid whole-genome testing for babies in intensive care yields improved health outcomes and lowers medical costs. Stephen Kingsmore from Rady Children’s Institute for Genomic Medicine in San Diego, California, USA, and colleagues retrospectively analyzed a cohort of 42 infants who had their genomes decoded in 2–5 days. This quick turnaround DNA sequencing identified disease-causing genetic defects in 18 infants, 13 of whom then had a change in medical or surgical treatment that helped alleviate symptoms or prevent death. As a result, many of those babies had shorter hospital stays and reduced healthcare costs. By comparison, standard genetic testing yielded a diagnosis in four cases, and prompted change of care for only one individual. The findings confirm Kingsmore’s results from another hospital, and suggest rapid sequencing should be more widely adopted for critically ill infants.
    Keywords Medicine ; R ; Genetics ; QH426-470
    Subject code 360
    Language English
    Publishing date 2018-04-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Artificial intelligence enables comprehensive genome interpretation and nomination of candidate diagnoses for rare genetic diseases

    Francisco M. De La Vega / Shimul Chowdhury / Barry Moore / Erwin Frise / Jeanette McCarthy / Edgar Javier Hernandez / Terence Wong / Kiely James / Lucia Guidugli / Pankaj B. Agrawal / Casie A. Genetti / Catherine A. Brownstein / Alan H. Beggs / Britt-Sabina Löscher / Andre Franke / Braden Boone / Shawn E. Levy / Katrin Õunap / Sander Pajusalu /
    Matt Huentelman / Keri Ramsey / Marcus Naymik / Vinodh Narayanan / Narayanan Veeraraghavan / Paul Billings / Martin G. Reese / Mark Yandell / Stephen F. Kingsmore

    Genome Medicine, Vol 13, Iss 1, Pp 1-

    2021  Volume 19

    Abstract: Abstract Background Clinical interpretation of genetic variants in the context of the patient’s phenotype is becoming the largest component of cost and time expenditure for genome-based diagnosis of rare genetic diseases. Artificial intelligence (AI) ... ...

    Abstract Abstract Background Clinical interpretation of genetic variants in the context of the patient’s phenotype is becoming the largest component of cost and time expenditure for genome-based diagnosis of rare genetic diseases. Artificial intelligence (AI) holds promise to greatly simplify and speed genome interpretation by integrating predictive methods with the growing knowledge of genetic disease. Here we assess the diagnostic performance of Fabric GEM, a new, AI-based, clinical decision support tool for expediting genome interpretation. Methods We benchmarked GEM in a retrospective cohort of 119 probands, mostly NICU infants, diagnosed with rare genetic diseases, who received whole-genome or whole-exome sequencing (WGS, WES). We replicated our analyses in a separate cohort of 60 cases collected from five academic medical centers. For comparison, we also analyzed these cases with current state-of-the-art variant prioritization tools. Included in the comparisons were trio, duo, and singleton cases. Variants underpinning diagnoses spanned diverse modes of inheritance and types, including structural variants (SVs). Patient phenotypes were extracted from clinical notes by two means: manually and using an automated clinical natural language processing (CNLP) tool. Finally, 14 previously unsolved cases were reanalyzed. Results GEM ranked over 90% of the causal genes among the top or second candidate and prioritized for review a median of 3 candidate genes per case, using either manually curated or CNLP-derived phenotype descriptions. Ranking of trios and duos was unchanged when analyzed as singletons. In 17 of 20 cases with diagnostic SVs, GEM identified the causal SVs as the top candidate and in 19/20 within the top five, irrespective of whether SV calls were provided or inferred ab initio by GEM using its own internal SV detection algorithm. GEM showed similar performance in absence of parental genotypes. Analysis of 14 previously unsolved cases resulted in a novel finding for one case, candidates ultimately not ...
    Keywords Medicine ; R ; Genetics ; QH426-470
    Subject code 610
    Language English
    Publishing date 2021-10-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: An automated 13.5 hour system for scalable diagnosis and acute management guidance for genetic diseases

    Mallory J. Owen / Sebastien Lefebvre / Christian Hansen / Chris M. Kunard / David P. Dimmock / Laurie D. Smith / Gunter Scharer / Rebecca Mardach / Mary J. Willis / Annette Feigenbaum / Anna-Kaisa Niemi / Yan Ding / Luca Van Der Kraan / Katarzyna Ellsworth / Lucia Guidugli / Bryan R. Lajoie / Timothy K. McPhail / Shyamal S. Mehtalia / Kevin K. Chau /
    Yong H. Kwon / Zhanyang Zhu / Sergey Batalov / Shimul Chowdhury / Seema Rego / James Perry / Mark Speziale / Mark Nespeca / Meredith S. Wright / Martin G. Reese / Francisco M. De La Vega / Joe Azure / Erwin Frise / Charlene Son Rigby / Sandy White / Charlotte A. Hobbs / Sheldon Gilmer / Gail Knight / Albert Oriol / Jerica Lenberg / Shareef A. Nahas / Kate Perofsky / Kyu Kim / Jeanne Carroll / Nicole G. Coufal / Erica Sanford / Kristen Wigby / Jacqueline Weir / Vicki S. Thomson / Louise Fraser / Seka S. Lazare

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

    2022  Volume 14

    Abstract: Rapid diagnosis and implementation of treatments is crucial in many genetic conditions. Here the authors describe Genome-to-Treatment, a virtual disease management system that can achieve a rapid diagnosis by expedited whole genome sequencing in 13.5 ... ...

    Abstract Rapid diagnosis and implementation of treatments is crucial in many genetic conditions. Here the authors describe Genome-to-Treatment, a virtual disease management system that can achieve a rapid diagnosis by expedited whole genome sequencing in 13.5 hours and provide guidance to clinicians for possible therapies.
    Keywords Science ; Q
    Language English
    Publishing date 2022-07-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Maternal genome-wide DNA methylation patterns and congenital heart defects.

    Shimul Chowdhury / Stephen W Erickson / Stewart L MacLeod / Mario A Cleves / Ping Hu / Mohammad A Karim / Charlotte A Hobbs

    PLoS ONE, Vol 6, Iss 1, p e

    2011  Volume 16506

    Abstract: The majority of congenital heart defects (CHDs) are thought to result from the interaction between multiple genetic, epigenetic, environmental, and lifestyle factors. Epigenetic mechanisms are attractive targets in the study of complex diseases because ... ...

    Abstract The majority of congenital heart defects (CHDs) are thought to result from the interaction between multiple genetic, epigenetic, environmental, and lifestyle factors. Epigenetic mechanisms are attractive targets in the study of complex diseases because they may be altered by environmental factors and dietary interventions. We conducted a population based, case-control study of genome-wide maternal DNA methylation to determine if alterations in gene-specific methylation were associated with CHDs. Using the Illumina Infinium Human Methylation27 BeadChip, we assessed maternal gene-specific methylation in over 27,000 CpG sites from DNA isolated from peripheral blood lymphocytes. Our study sample included 180 mothers with non-syndromic CHD-affected pregnancies (cases) and 187 mothers with unaffected pregnancies (controls). Using a multi-factorial statistical model, we observed differential methylation between cases and controls at multiple CpG sites, although no CpG site reached the most stringent level of genome-wide statistical significance. The majority of differentially methylated CpG sites were hypermethylated in cases and located within CpG islands. Gene Set Enrichment Analysis (GSEA) revealed that the genes of interest were enriched in multiple biological processes involved in fetal development. Associations with canonical pathways previously shown to be involved in fetal organogenesis were also observed. We present preliminary evidence that alterations in maternal DNA methylation may be associated with CHDs. Our results suggest that further studies involving maternal epigenetic patterns and CHDs are warranted. Multiple candidate processes and pathways for future study have been identified.
    Keywords Medicine ; R ; Science ; Q
    Subject code 610
    Language English
    Publishing date 2011-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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