Benchmarking nanopore sequencing and rapid genomics feasibility: validation at a quaternary hospital in New Zealand DOI Creative Commons
Denis M. Nyaga, Peter Tsai,

Clare Gebbie

et al.

npj Genomic Medicine, Journal Year: 2024, Volume and Issue: 9(1)

Published: Nov. 8, 2024

Approximately 200 critically ill infants and children in New Zealand are high-dependency care, many suspected of having genetic conditions, requiring scalable genomic testing. We adopted an acute care genomics protocol from accredited laboratory established a clinical pipeline using Oxford Nanopore Technologies PromethION 2 solo system Fabric GEM™ software. Benchmarking the was performed Global Alliance for Genomics Health benchmarking tools Genome Bottle samples (HG002-HG007). Evaluation single nucleotide variants resulted precision recall 0.997 0.992, respectively. Small indel identification approached 0.922 0.838. Large variations Coriell Copy Number Variation Reference Panel 1 were reliably detected with ~2 M long reads. Finally, we present results obtained fourteen trio samples, ten which processed parallel clinically short-read rapid testing (Newborn Programme; NCT06081075; 2023-10-12).

Language: Английский

Rapid genomic sequencing for genetic disease diagnosis and therapy in intensive care units: a review DOI Creative Commons
Stephen F. Kingsmore, Russell Nofsinger,

Kasia Ellsworth

et al.

npj Genomic Medicine, Journal Year: 2024, Volume and Issue: 9(1)

Published: Feb. 27, 2024

Abstract Single locus (Mendelian) diseases are a leading cause of childhood hospitalization, intensive care unit (ICU) admission, mortality, and healthcare cost. Rapid genome sequencing (RGS), ultra-rapid (URGS), rapid exome (RES) diagnostic tests for genetic ICU patients. In 44 studies children in ICUs with unknown etiology, 37% received diagnosis, 26% had consequent changes management, net costs were reduced by $14,265 per child tested URGS, RGS, or RES. URGS outperformed RGS RES faster time to higher rate diagnosis clinical utility. Diagnostic outcomes will improve as methods evolve, decrease, testing is implemented within precision medicine delivery systems attuned needs. currently performed <5% the ~200,000 likely benefit annually due lack payor coverage, inadequate reimbursement, hospital policies, hospitalist unfamiliarity, under-recognition possible diseases, current formatting rather than system. The gap between actual optimal increasing since expanded use lags growth those through new therapies. There sufficient evidence conclude that should be considered all uncertain etiology at admission. Minimally, ordered early during admissions critically ill infants suspected diseases.

Language: Английский

Citations

24
Concordance of whole-genome long-read sequencing with standard clinical testing for Prader-Willi and Angelman syndromes DOI
Cate Paschal, Miranda Galey, Anita Beck

et al.

Journal of Molecular Diagnostics, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Language: Английский

Citations

1
Applications of advanced technologies for detecting genomic structural variation DOI Creative Commons
Vincent A. Laufer, Thomas W. Glover, Thomas E. Wilson

et al.

Mutation Research/Reviews in Mutation Research, Journal Year: 2023, Volume and Issue: 792, P. 108475 - 108475

Published: July 1, 2023

Language: Английский

Citations

7
Potential clinical applications of advanced genomic analysis in cerebral palsy DOI Creative Commons
Sara A. Lewis,

Andrew Ruttenberg,

Tuğçe Iyiyol

et al.

EBioMedicine, Journal Year: 2024, Volume and Issue: 106, P. 105229 - 105229

Published: July 5, 2024

Cerebral palsy (CP) has historically been attributed to acquired insults, but emerging research suggests that genetic variations are also important causes of CP. While microarray and whole-exome sequencing based studies have the primary methods for establishing new CP-gene relationships providing a etiology individual patients, cause their condition remains unknown many patients with Recent advancements in genomic technologies offer additional opportunities uncover human genomes, transcriptomes, epigenomes previously escaped detection. In this review, we outline use these state-of-the-art address molecular diagnostic challenges experienced by individuals We explore importance identifying whenever possible, given potential medicine provide treat CP more precise ways.

Language: Английский

Citations

1
Moving Beyond Oxford Nanopore Standard Procedures: New Insights from Water and Multiple Fish Microbiomes DOI Open Access

Ricardo Domingo-Bretón,

Federico Moroni, Socorro Toxqui-Rodríguez

et al.

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(23), P. 12603 - 12603

Published: Nov. 23, 2024

Oxford Nanopore Technology (ONT) allows for the rapid profiling of aquaculture microbiomes. However, not all experimental and downstream methodological possibilities have been benchmarked. Here, we aimed to offer novel insights into use different library preparation methods (standard-RAP native barcoding-LIG), primers (V3-V4, V1-V3, V1-V9), basecalling models (fast-FAST, high-HAC, super-accuracy-SUP) implemented in ONT elucidate microbiota associated with aquatic environment farmed fish, including faeces, skin, intestinal mucus. Microbial DNA from water faeces samples could be amplified regardless library-primer strategy, but only LIG V1-V3/V1-V9 case skin intestine Low taxonomic assignment levels were favoured by full-length V1-V9 primers, though silico hybridisation revealed a lower number potential matching sequences SILVA database, especially evident increase Actinobacteriota real datasets. SUP execution allowed higher median Phred quality (24) than FAST (11) HAC (17), its time (6-8 h) was comparison other (0.6-7 h). Altogether, optimised water- fish-related microbial analyses, validating, first time, strategy. We consider that LIG-V1-V9-HAC is optimal time/cost-effective option amplify environmental samples. V1-V3 help maximise dataset microbiome diversity, representing an alternative when long amplicon become compromised and/or high host loads interfere PCR amplification/sequencing procedures, gut

Language: Английский

Citations

1
Benchmarking nanopore sequencing and rapid genomics feasibility: validation at a quaternary hospital in New Zealand DOI Creative Commons
Denis M. Nyaga, Peter Tsai,

Clare Gebbie

et al.

npj Genomic Medicine, Journal Year: 2024, Volume and Issue: 9(1)

Published: Nov. 8, 2024

Approximately 200 critically ill infants and children in New Zealand are high-dependency care, many suspected of having genetic conditions, requiring scalable genomic testing. We adopted an acute care genomics protocol from accredited laboratory established a clinical pipeline using Oxford Nanopore Technologies PromethION 2 solo system Fabric GEM™ software. Benchmarking the was performed Global Alliance for Genomics Health benchmarking tools Genome Bottle samples (HG002-HG007). Evaluation single nucleotide variants resulted precision recall 0.997 0.992, respectively. Small indel identification approached 0.922 0.838. Large variations Coriell Copy Number Variation Reference Panel 1 were reliably detected with ~2 M long reads. Finally, we present results obtained fourteen trio samples, ten which processed parallel clinically short-read rapid testing (Newborn Programme; NCT06081075; 2023-10-12).

Language: Английский

Citations

1