Genome Sequencing in Prenatal Testing and Screening: Lessons Learned From Broadening the Scope of Prenatal Genetics From Conventional Karyotyping to Whole-Genome Microarray Analysis

ABSTRACT Routine use of whole-genome analysis for infectious diseases can be used to enlighten various scenarios pertaining to public health, including identification of microbial pathogens, relating individual cases to an outbreak of infectious disease, establishing an association between an outbreak of food poisoning and a specific food vehicle, inferring drug susceptibility, source tracing of contaminants, and study of variations in the genome that affect pathogenicity/virulence. We describe the setup, validation, and ongoing verification of a centralized whole-genome-sequencing (WGS) laboratory to carry out sequencing for these public health functions for the National Infection Services, Public Health England, in the United Kingdom. The performance characteristics and quality control metrics measured during validation and verification of the entire end-to-end process (accuracy, precision, reproducibility, and repeatability) are described and include information regarding the automated pass and release of data to service users without intervention.

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Whole-genome microarray analysis and functional characterization reveal distinct gene expression profiles and patterns in two mouse models of ileal inflammation

BMC Genomics ◽

10.1186/1471-2164-13-377 ◽

2012 ◽

Vol 13 (1) ◽

pp. 377 ◽

Cited By ~ 7

Author(s):

Leela Rani Avula ◽

Dries Knapen ◽

Roeland Buckinx ◽

Lucia Vergauwen ◽

Dirk Adriaensen ◽

...

Keyword(s):

Gene Expression ◽

Mouse Models ◽

Microarray Analysis ◽

Expression Profiles ◽

Functional Characterization ◽

Gene Expression Profiles ◽

Whole Genome ◽

Distinct Gene ◽

Whole Genome Microarray

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Whole genome microarray analysis of neural progenitor C17.2 cells during differentiation and validation of 30 neural mRNA biomarkers for estimation of developmental neurotoxicity

PLoS ONE ◽

10.1371/journal.pone.0190066 ◽

2017 ◽

Vol 12 (12) ◽

pp. e0190066 ◽

Cited By ~ 2

Author(s):

Kristina Attoff ◽

Anda Gliga ◽

Jessica Lundqvist ◽

Ulf Norinder ◽

Anna Forsby

Keyword(s):

Microarray Analysis ◽

Neural Progenitor ◽

Developmental Neurotoxicity ◽

Whole Genome ◽

Whole Genome Microarray

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Abstract 4418: Affymetrix whole genome microarray analysis of 24 human tumor xenograft models and the cell lines from which they were developed: Clustering of targets vs tumor tissue of origin

10.1158/1538-7445.am2011-4418 ◽

2011 ◽

Author(s):

Yulia Y. Maxuitenko ◽

Michael S. Koratich ◽

William R. Waud ◽

Murray Stackhouse ◽

Richard D. May ◽

...

Keyword(s):

Cell Lines ◽

Microarray Analysis ◽

Tumor Tissue ◽

Human Tumor ◽

Tumor Xenograft ◽

Whole Genome ◽

Human Tumor Xenograft ◽

Whole Genome Microarray ◽

Xenograft Models ◽

Tissue Of Origin

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531. Practical and Evidence-Based Considerations for Implementation of Bacterial Whole-Genome Sequencing Within Longitudinal Infection Control Practice

Open Forum Infectious Diseases ◽

10.1093/ofid/ofz360.600 ◽

2019 ◽

Vol 6 (Supplement_2) ◽

pp. S255-S255

Author(s):

Donald S Chen ◽

Moira Quinn ◽

Rita M Sussner ◽

Guiqing Wang ◽

John T Fallon ◽

...

Keyword(s):

Infection Control ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Tertiary Care ◽

False Negative ◽

Lessons Learned ◽

Evidence Based ◽

Guidance Document ◽

Whole Genome ◽

Care Hospital

Abstract Background Whole-genome sequencing (WGS) of bacteria is becoming a routine tool within microbiology, yet its utility to help guide infection control (IC) practice longitudinally is underexplored. As with any technology adopted in the hospital, the integration of WGS into IC practice must be carefully managed and considered. We qualitatively report an evidence-based implementation workflow that considers WGS to help proactively guide IC professionals during investigation of infectious outbreaks. Methods We built upon lessons learned in an ongoing surveillance effort at a tertiary care hospital—utilizing retrospective WGS data within the Philips IntelliSpace Epidemiology system—to understand facilitators and barriers to the use of bacterial WGS longitudinally to inform IC workflow. Our team established a 9-month workgroup to study the practical aspects of implementing WGS in routine IC practice. From expert opinion collected via the workgroup, in addition to evidence from the literature, a workflow guidance document and checklist were codified. New ideas included incorporating education to promote the establishment of an IC triage process. Results Facilitators to implementation included ability to display genomic relatedness alongside relevant patient data to enable clinical actionability, ability to pivot time and resources rapidly when infections are a pseudo outbreak (false positive) or missed outbreak (false negative), opportunities for nuanced staff education, and willingness to be a first-of-kind adopter. Barriers were communication of genomic concepts to IC professionals and relevant institutional stakeholders, maintaining sharable notes of active investigations to promote data-sharing practices, and timing and review of relevant interventions into the facility workflow. Strategies to address these issues are considered. Conclusion This study provides a novel framework for adaptation of existing IC workflow strategies to leverage the utility of bacterial WGS, and it presents a schema to effectively engage relevant stakeholders, based on an analysis of the unique challenges inherent within IC practice. It also offers an innovative model for the development and implementation of IC workflows to account for, and adapt to, site-specific conditions. Disclosures All authors: No reported disclosures.

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