LIVIVO - Search results -

Search results

Result 1 - 10 of total 33

Search options

Book: Precision medicine in practice

Schmidt, Ryan J.

molecular diagnosis enabling precision therapies

(Clinics in laboratory medicine ; volume 40, number 2 (June 2020))

2020

Author's details	editor Ryan J. Schmidt
Series title	Clinics in laboratory medicine ; volume 40, number 2 (June 2020)
Collection
Language	English
Size	x Seiten, Seite 114-230, Illustrationen
Publisher	Elsevier
Publishing place	Philadelphia, Pennsylvania
Publishing country	United States
Document type	Book
HBZ-ID	HT020524713
ISBN	978-0-323-75845-1 ; 0-323-75845-2
Database	Catalogue ZB MED Medicine, Health

In stock of ZB MED Cologne/Königswinter

Shelf mark	Loan status	Location
Zs A 1695 -40,2-	not available for loan	Zeitschriften-Lesesaal

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Precision Medicine Exits the Hype Cycle and Enters into Productive Clinical Use.

Schmidt, Ryan J

Clinics in laboratory medicine

2020 Volume 40, Issue 2, Page(s) ix–x

MeSH term(s)	Genetics, Medical ; Humans ; Precision Medicine
Language	English
Publishing date	2020-05-20
Publishing country	United States
Document type	Editorial
ZDB-ID	604580-7
ISSN	1557-9832 ; 0272-2712
ISSN (online)	1557-9832
ISSN	0272-2712
DOI	10.1016/j.cll.2020.04.001
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 1695: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Hidden cargo: The impact of historical shipping trade on the recent-past and contemporary non-native flora of northeastern United States.

Schmidt, Ryan J / King, Megan R / Aronson, Myla F J / Struwe, Lena

American journal of botany

2023 Volume 110, Issue 9, Page(s) e16224

Abstract: Premise: Understanding establishment and spread of non-native plants is important in the face of a homogenizing global flora. While many studies focus on successful, invasive species, fewer have studied failed plant introductions. Until the early 1900s, ...

Abstract	Premise: Understanding establishment and spread of non-native plants is important in the face of a homogenizing global flora. While many studies focus on successful, invasive species, fewer have studied failed plant introductions. Until the early 1900s, large quantities of ship ballast, often containing foreign plant propagules, were deposited in New Jersey (USA). The resulting ballast flora is documented in extensive herbarium records, providing us a unique opportunity to analyze successes and failures of novel plant species introductions. Methods: We used digitized specimens from 75 herbaria to study 264 non-native species introduced into New Jersey through 19th century ballast deposition. We used spatial (density-based clustering; HDBSCAN) and temporal analyses of species retention and geographic spread to quantify disappearance rate, survival, and dispersion through time and define trajectory groups. Results: Four distinct trajectory groups were identified: waif (only present during import; 32% of species), short-term (disappeared quickly; 20%), established-limited spread (survives locally, 30%), and established-widespread (widespread, 18%). Species disappearance rate was highest during ballast deposition and decreased soon after deposition stopped around 1900. Spatial patterns showed a strong association with 19th century railroads for inland dispersal from ports. The disappearance rate and spatial analyses are robust to herbarium collection bias. Conclusions: This study using New Jersey as a model is one of the few documenting multispecies successes and failures in inadvertent plant introductions. Results reveal distinct trends in species establishment and geographic spread and highlight the utility of herbarium specimens in answering questions that span large time scales.
MeSH term(s)	Ships ; Plants ; Introduced Species ; New England ; New Jersey
Language	English
Publishing date	2023-09-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2935-x
ISSN	1537-2197 ; 0002-9122
ISSN (online)	1537-2197
ISSN	0002-9122
DOI	10.1002/ajb2.16224
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Bonn / Germany

Z 4' 49/55: Show issues

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Hidden cargo: The impact of historical shipping trade on the recent‐past and contemporary non‐native flora of northeastern United States

Schmidt, Ryan J. / King, Megan R. / Aronson, Myla F. J. / Struwe, Lena

American Journal of Botany. 2023 Sept., v. 110, no. 9 p.e16224-

2023

Abstract: PREMISE: Understanding establishment and spread of non‐native plants is important in the face of a homogenizing global flora. While many studies focus on successful, invasive species, fewer have studied failed plant introductions. Until the early 1900s, ... ...

Abstract	PREMISE: Understanding establishment and spread of non‐native plants is important in the face of a homogenizing global flora. While many studies focus on successful, invasive species, fewer have studied failed plant introductions. Until the early 1900s, large quantities of ship ballast, often containing foreign plant propagules, were deposited in New Jersey (USA). The resulting ballast flora is documented in extensive herbarium records, providing us a unique opportunity to analyze successes and failures of novel plant species introductions. METHODS: We used digitized specimens from 75 herbaria to study 264 non‐native species introduced into New Jersey through 19th century ballast deposition. We used spatial (density‐based clustering; HDBSCAN) and temporal analyses of species retention and geographic spread to quantify disappearance rate, survival, and dispersion through time and define trajectory groups. RESULTS: Four distinct trajectory groups were identified: waif (only present during import; 32% of species), short‐term (disappeared quickly; 20%), established–limited spread (survives locally, 30%), and established–widespread (widespread, 18%). Species disappearance rate was highest during ballast deposition and decreased soon after deposition stopped around 1900. Spatial patterns showed a strong association with 19th century railroads for inland dispersal from ports. The disappearance rate and spatial analyses are robust to herbarium collection bias. CONCLUSIONS: This study using New Jersey as a model is one of the few documenting multispecies successes and failures in inadvertent plant introductions. Results reveal distinct trends in species establishment and geographic spread and highlight the utility of herbarium specimens in answering questions that span large time scales.
Keywords	flora ; herbaria ; imports ; introduced species ; invasive species ; models ; New Jersey
Language	English
Dates of publication	2023-09
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	2935-x
ISSN	1537-2197 ; 0002-9122
ISSN (online)	1537-2197
ISSN	0002-9122
DOI	10.1002/ajb2.16224
Database	NAL-Catalogue (AGRICOLA)

In stock of ZB MED Bonn / Germany

Z 4' 49/55: Show issues

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾
- See ZB MED holdings
- Order with fees

Article: Developing dashboards for performance improvement in cytopathology.

Horback, Katharine / Sundling, Kaitlin E / Schmidt, Ryan J / Cibas, Edmund S

Journal of the American Society of Cytopathology

2021 Volume 10, Issue 6, Page(s) 535–542

Abstract: Introduction: Cytopathology has well-defined and objective quality metrics for monitoring the performance of cytopathologists (CPs) and cytotechnologists (CTs). We transformed these metrics into dashboards for real-time visualization and on-demand ... ...

Abstract	Introduction: Cytopathology has well-defined and objective quality metrics for monitoring the performance of cytopathologists (CPs) and cytotechnologists (CTs). We transformed these metrics into dashboards for real-time visualization and on-demand feedback. Methods: Dashboards were constructed with data from the previous 10 calendar years using the software Tableau. The dashboards for CPs were designed to display 2 gynecologic metrics and 1 nongynecologic metric: the ASCUS:SIL ratio, the percentage of high-risk human papillomavirus (HPV)-positive ASCUS interpretations (HPV+ ASCUS rate), and the proportion of AUS/FLUS thyroid interpretations. CT dashboards were designed to include these plus 2 others: the percentage of Papanicolaou tests referred for CP review and the percentage of Papanicolaou tests interpreted as unsatisfactory. Established professional benchmarks or standard deviations were used to set color-coded "goal," "borderline," and "attention" zones. Results: Personal dashboards were successfully developed and implemented for CPs and CTs in the laboratory, with results that are automatically updated every week, requiring minimal curation. Each CP and CT has a unique link that allows them access to their results at any time. Color-coded displays show the individual their quality metrics over the past 10 years, with a snapshot of data from the past 3 months. The laboratory director has a unique link that allows the director access to results for each individual and the laboratory in aggregate. Conclusions: Personalized dashboards enable individuals to access their performance metrics on demand and examine recent performance as well as patterns over time. This facilitates self-motivation to improve performance and adhere to professional benchmarks.
MeSH term(s)	Biopsy, Fine-Needle ; Cell Biology/standards ; Cervix Uteri/pathology ; Female ; Humans ; Papanicolaou Test ; Quality Improvement ; Thyroid Gland/pathology ; Vaginal Smears
Language	English
Publishing date	2021-07-18
Publishing country	United States
Document type	Journal Article
ISSN	2213-2945
ISSN	2213-2945
DOI	10.1016/j.jasc.2021.07.001
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Recommendations for Next-Generation Sequencing Germline Variant Confirmation: A Joint Report of the Association for Molecular Pathology and National Society of Genetic Counselors.

Crooks, Kristy R / Farwell Hagman, Kelly D / Mandelker, Diana / Santani, Avni / Schmidt, Ryan J / Temple-Smolkin, Robyn L / Lincoln, Stephen E

The Journal of molecular diagnostics : JMD

2023 Volume 25, Issue 7, Page(s) 411–427

Abstract: Clinical laboratory implementation of next-generation sequencing (NGS)-based constitutional genetic testing has been rapid and widespread. In the absence of widely adopted comprehensive guidance, there remains substantial variability among laboratories ... ...

Abstract	Clinical laboratory implementation of next-generation sequencing (NGS)-based constitutional genetic testing has been rapid and widespread. In the absence of widely adopted comprehensive guidance, there remains substantial variability among laboratories in the practice of NGS. One issue of sustained discussion in the field is whether and to what extent orthogonal confirmation of genetic variants identified by NGS is necessary or helpful. The Association for Molecular Pathology Clinical Practice Committee convened the NGS Germline Variant Confirmation Working Group to assess current evidence regarding orthogonal confirmation and to establish recommendations for standardizing orthogonal confirmation practices to support quality patient care. On the basis of the results of a survey of the literature, a survey of laboratory practices, and subject expert matter consensus, eight recommendations are presented, providing a common framework for clinical laboratory professionals to develop or refine individualized laboratory policies and procedures regarding orthogonal confirmation of germline variants detected by NGS.
MeSH term(s)	Humans ; Pathology, Molecular ; Counselors ; Genetic Testing/methods ; High-Throughput Nucleotide Sequencing/methods ; Germ Cells
Language	English
Publishing date	2023-05-17
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2000060-1
ISSN	1943-7811 ; 1525-1578
ISSN (online)	1943-7811
ISSN	1525-1578
DOI	10.1016/j.jmoldx.2023.03.012
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 5146: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: VarGrouper: A Bioinformatic Tool for Local Haplotyping of Deletion-Insertion Variants from Next-Generation Sequencing Data after Variant Calling.

Schmidt, Ryan J / Macleay, Allison / Le, Long Phi

The Journal of molecular diagnostics : JMD

2019 Volume 21, Issue 3, Page(s) 384–389

Abstract: Accurate genetic variant representation through nomenclature and annotation is essential for understanding functional consequence and properly noting the presence of variants across time, assays, and laboratories. Current variant calling algorithms ... ...

Abstract	Accurate genetic variant representation through nomenclature and annotation is essential for understanding functional consequence and properly noting the presence of variants across time, assays, and laboratories. Current variant calling algorithms detect single deletion-insertion variants as multiple indel and/or substitution variants from next-generation sequencing data. Consequently, these variants are separately annotated in bioinformatics pipelines, leading to inaccurate variant representation. We developed a bioinformatic solution to this problem-VarGrouper-that automatically recognizes individual variants that arise from a deletion-insertion variant and aggregates them into a single variant that can be properly annotated. This tool has been integrated into our routine clinical molecular diagnostics workflow for DNA sequencing of solid tumors. Over an 11-month period, VarGrouper variants were reported by all attending molecular pathologists involved in interpretation and represented 4.1% of all variants reported; 10.9% of cases with reportable variants contained at least one VarGrouper variant. VarGrouper improves the practice of molecular diagnostics by increasing the accuracy and consistency of variant annotation. VarGrouper is freely available for use by the molecular diagnostic community.
MeSH term(s)	Algorithms ; Base Sequence ; Computational Biology/methods ; Haplotypes/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; INDEL Mutation/genetics ; Software
Language	English
Publishing date	2019-02-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2000060-1
ISSN	1943-7811 ; 1525-1578
ISSN (online)	1943-7811
ISSN	1525-1578
DOI	10.1016/j.jmoldx.2018.12.003
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 5146: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: PLAG1 Immunohistochemical Staining Is a Surrogate Marker for

Warren, Mikako / Tiwari, Nishant / Sy, Sabrina / Raca, Gordana / Schmidt, Ryan J / Pawel, Bruce

Pediatric and developmental pathology : the official journal of the Society for Pediatric Pathology and the Paediatric Pathology Society

2021 Volume 25, Issue 2, Page(s) 134–140

Abstract: Background: The hallmark of lipoblastoma is a PLAG1 fusion. PLAG1 protein overexpression has been reported in sporadic PLAG1-rearranged lipoblastomas.: Methods: We evaluated the utility of PLAG1 immunohistochemical staining (IHC) in 34 pediatric ... ...

Abstract	Background: The hallmark of lipoblastoma is a PLAG1 fusion. PLAG1 protein overexpression has been reported in sporadic PLAG1-rearranged lipoblastomas. Methods: We evaluated the utility of PLAG1 immunohistochemical staining (IHC) in 34 pediatric lipomatous tumors, correlating the results with histology and conventional cytogenetics, FISH and/or next generation sequencing (NGS) results. Results: The study included 24 lipoblastomas, divided into 2 groups designated as "Lipoblastoma 1" with both lipoblastoma histology and PLAG1 rearrangement (n = 16) and "Lipoblastoma 2" with lipoblastoma histology but without PLAG1 cytogenetic rearrangement (n = 8), and 10 lipomas with neither lipoblastoma histology nor a PLAG1 rearrangement. Using the presence of a fusion as the "gold standard" for diagnosing lipoblastoma (Lipoblastoma 1), the sensitivity of PLAG1 IHC was 94%. Using histologic features alone (Lipoblastoma 1 + 2), the sensitivity was 96%. Specificity, as defined by the ability to distinguish lipoma from lipoblastoma, was 100%, as there were no false positives in the lipoma group. Conclusions: Cytogenetics/molecular testing is expensive and may not be ideal for detecting PLAG1 fusions because PLAG1 fusions are often cytogenetically cryptic and NGS panels may not include all partner genes. PLAG1 IHC is an inexpensive surrogate marker of PLAG1 fusions and may be useful in distinguishing lipoblastomas from lipomas.
MeSH term(s)	Biomarkers ; Child ; DNA-Binding Proteins/genetics ; Gene Fusion ; Humans ; In Situ Hybridization, Fluorescence ; Lipoblastoma/diagnosis ; Lipoblastoma/genetics ; Transcription Factors/genetics
Chemical Substances	Biomarkers ; DNA-Binding Proteins ; PLAG1 protein, human ; Transcription Factors
Language	English
Publishing date	2021-10-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	1463498-3
ISSN	1615-5742 ; 1093-5266
ISSN (online)	1615-5742
ISSN	1093-5266
DOI	10.1177/10935266211043366
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 5063: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Contamination Assessment for Cancer Next-Generation Sequencing.

Li, Yvonne Y / Schmidt, Ryan J / Manning, Danielle K / Jia, Yonghui / Dong, Fei

Archives of pathology & laboratory medicine

2021 Volume 146, Issue 2, Page(s) 227–232

Abstract: Context.—: The presence of allogeneic contamination impacts clinical reporting in cancer next-generation sequencing specimens. Although consensus guidelines recommend the identification of contaminating DNA as a part of quality control, implementation ... ...

Abstract	Context.—: The presence of allogeneic contamination impacts clinical reporting in cancer next-generation sequencing specimens. Although consensus guidelines recommend the identification of contaminating DNA as a part of quality control, implementation of contamination assessment methods in clinical molecular diagnostic laboratories has not been reported in the literature. Objective.—: To develop and implement a method to assess allogeneic contamination in clinical cancer next-generation sequencing specimens. Design.—: We describe a method to detect contamination based on the evaluation of single-nucleotide polymorphic sites from tumor-only specimens. We validate this method and apply it to a large cohort of cancer sequencing specimens. Results.—: Identification of specimen contamination was validated via in silico and in vitro mixtures, and reference range and reproducibility were established in a panel of normal specimens. The algorithm accurately detects an episode of systemic contamination due to reagent impurity. We prospectively applied this algorithm across 7571 clinical cancer specimens from a targeted next-generation sequencing panel, in which 262 specimens (3.5%) were predicted to be affected by greater than 5% contamination. Conclusions.—: Allogeneic contamination can be inferred from intrinsic cancer next-generation sequencing data without paired normal sequencing. The adoption of this approach can be useful as a quality control measure for laboratories performing clinical next-generation sequencing.
MeSH term(s)	High-Throughput Nucleotide Sequencing/methods ; Humans ; Neoplasms/diagnosis ; Neoplasms/genetics ; Pathology, Molecular ; Polymorphism, Single Nucleotide ; Reproducibility of Results
Language	English
Publishing date	2021-05-17
Publishing country	United States
Document type	Journal Article
ZDB-ID	194119-7
ISSN	1543-2165 ; 0363-0153 ; 0096-8528 ; 0003-9985
ISSN (online)	1543-2165
ISSN	0363-0153 ; 0096-8528 ; 0003-9985
DOI	10.5858/arpa.2020-0679-OA
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Ud II Zs.36: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: m.3685T > C is a novel mitochondrial DNA variant that causes Leigh syndrome.

Jean, Jeffrey / Christodoulou, Eirini / Gai, Xiaowu / Tamrazi, Benita / Vera, Moin / Mitchell, Wendy G / Schmidt, Ryan J

Cold Spring Harbor molecular case studies

2022 Volume 8, Issue 2

Abstract: Variants in the mitochondrial genome can result in dysfunction of Complex I within the electron transport chain, thus causing disruptions in oxidative phosphorylation. Pathogenic variants in ... ...

Abstract	Variants in the mitochondrial genome can result in dysfunction of Complex I within the electron transport chain, thus causing disruptions in oxidative phosphorylation. Pathogenic variants in the
MeSH term(s)	DNA, Mitochondrial/genetics ; Female ; Humans ; Lactic Acid ; Leigh Disease/genetics ; Mitochondrial Diseases/genetics ; Mutation ; Seizures
Chemical Substances	DNA, Mitochondrial ; Lactic Acid (33X04XA5AT)
Language	English
Publishing date	2022-03-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	2835759-0
ISSN	2373-2873 ; 2373-2873
ISSN (online)	2373-2873
ISSN	2373-2873
DOI	10.1101/mcs.a006136
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

To top

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Bonn / Germany

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Bonn / Germany

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito