Use Of Whole-genome Sequencing Research Articles

Oxford Nanopore Technology-Based Identification of an Acanthamoeba castellanii Endosymbiosis in Microbial Keratitis

(1) Background: Microbial keratitis is a serious eye infection that carries a significant risk of vision loss. Acanthamoeba spp. are known to cause keratitis and their bacterial endosymbionts can increase virulence and/or treatment resistance and thus significantly worsen the course of the disease. (2) Methods and Results: In a suspected case of Acanthamoeba keratitis, in addition to Acanthamoeba spp., an endosymbiont of acanthamoebae belonging to the taxonomic order of Holosporales was detected by chance in a bacterial 16S rDNA-based pan-PCR and subsequently classified as Candidatus Paracaedibacter symbiosus through an analysis of an enlarged 16S rDNA region. We used Oxford Nanopore Technology to evaluate the usefulness of whole-genome sequencing (WGS) as a one-step diagnostics method. Here, Acanthamoeba castellanii and the endosymbiont Candidatus Paracaedibacter symbiosus could be directly detected at the species level. No other microbes were identified in the specimen. (3) Conclusions: We recommend the introduction of WGS as a diagnostic approach for keratitis to replace the need for multiple species-specific qPCRs in future routine diagnostics and to enable an all-encompassing characterisation of the polymicrobial community in one step.

Identifying barriers and opportunities to facilitate the uptake of whole genome sequencing in paediatric haematology and oncology practice

BackgroundThe clinical utility of whole genome sequencing (WGS) in paediatric cancer has been demonstrated in recent years. WGS has been routinely available in the National Health Service (NHS) England for all children with cancer in England since 2021, but its uptake has been variable geographically. To explore the underlying barriers to routine use of WGS in this population across England and more widely in the United Kingdom (UK) and the Republic of Ireland (ROI), a one-day workshop was held in Cambridge, United Kingdom in October 2022.MethodsFollowing a series of talks, delegates participated in open, round-table discussions to outline local and broader challenges limiting routine WGS for diagnostic work-up for children with cancer in their Principal Treatment Centres (PTCs) and Genomic Laboratory Hubs (GLHs). Within smaller groups, delegates answered structured questions regarding clinical capability, education and training needs, and workforce competence and requirements. Data was recorded, centrally collated, and analysed following the event using thematic analysis.ResultsSixty participants attended the workshop with broad representation from the 20 PTCs across the UK and ROI and the seven GLHs in England. All healthcare professionals involved in the WGS pathway were represented, including paediatric oncologists, clinical geneticists, clinical scientists, and histopathologists. The main themes highlighted by the group in ensuring equitable access to WGS identified were: lack of knowledge equity between NHS trusts, with a perception of WGS being for research only; and perception of lack of financial support for the clinical process surrounding WGS, including lack of time to take informed consent from patients. The latter also included limited trained staff available for data interpretation, affecting the turnaround time for reporting. Finally, the need for an integrated digital pathway to order, track, and return data to clinicians was highlighted.ConclusionAt the workshop, the general motivation for including WGS in the diagnostic work up for children with cancer was high throughout the UK, however a perceived lack of resources and education opportunities limit the widespread use of this commissioned assay. This workshop has led to some recommendations to increase access to WGS in this population in England and more widely in the devolved national of the UK and the ROI.

The potential clinical utility of Whole Genome Sequencing for patients with cancer: evaluation of a regional implementation of the 100,000 Genomes Project.

The 100,000 Genomes Project established infrastructure for Whole Genome Sequencing (WGS) in the United Kingdom. A retrospective study of cancer patients recruited to the 100,000 Genomes Project by the West Midlands Genomics Medicine Centre, evaluating clinical relevance of results. After excluding samples with no sequencing data (1678/4851; 34.6%), 3166 sample sets (germline and somatic) from 3067 participants were sequenced. Results of 1256 participants (41.0%) were interpreted (excluding participants who died (308/3067; 10.0%) or were clinically excluded (1503/3067; 49.0%)). Of these, 323 (25.7%) had no variants in genes which may alter management (Domain 1 genes). Of the remaining 933 participants, 552 (59.2%) had clinical recommendations made (718 recommendations in total). These included therapeutic recommendations (377/933; 40.4%), such as clinical trial, unlicensed or licensed therapies or high TMB recommendations, and germline variants warranting clinical genetics review (85/933; 9.1%). At the last follow up, 20.2% of all recommendations were followed (145/718). However, only a small proportion of therapeutic recommendations were followed (5.1%, 25/491). The 100,000 Genomes Project has established infrastructure and regional experience to support personalised cancer care. The majority of those with successful sequencing had actionable variants. Ensuring GTAB recommendations are followed will maximise benefits for patients.

Sheeppox virus genome sequences from the European outbreaks in Spain, Bulgaria, and Greece in 2022–2024

In 2022-2024, three outbreaks of sheeppox (SPP) were reported in the European Union. These occurred in Spain, Bulgaria, and Greece and had serious economic consequences due to animal losses and trade restrictions. Five sheeppox virus (SPPV) whole-genome sequences (WGSs) were determined from samples collected during these outbreaks and analyzed in the context of all other published WGSs. Sheeppox virus strains can be divided in two, or possibly three, main groups. The isolates from the recent outbreaks belong to clade A2, which includes strains historically circulating in the Middle East and Northern Africa. Sequence divergence was low among the isolates that caused the recent European outbreaks. These results highlight the need for more regular and dense surveillance in under-sampled areas and the use of WGS to increase the chance of pinpointing the origin of an introduction, identifying potential introduction routes, and providing insights into SPPV evolution.

Evaluation of whole genome sequencing utility in identifying driver alterations in cancer genome

In cancer genome analysis, identifying pathogenic alterations and assessing their effects on oncogenic processes is important. Although whole exome sequencing (WES) can effectively detect such changes, driver alterations could not be identified in 27.8% of the cases, according to a previous study. The objectives of the present study were to evaluate the utility of whole genome sequencing (WGS) and clarify its differences with WES in terms of driver alteration detection. For this purpose, WGS analysis was conducted on 177 driverless WES samples, selected from 5,480 fresh frozen samples derived from 5,140 Japanese patients with cancer. These samples were selected as primary tumor, both WES and transcriptome profiling were performed, estimated tumor content of ≥ 30%, and no driver alterations were identified by WES. WGS identified driver and likely driver alterations in 68.4 and 22.6% of the samples, respectively. The most frequent alteration type was oncogene amplification, followed by tumor suppressor gene deletion and small variants located outside the coding region. In the remaining 9.0% of samples, no such signals were identified; therefore, further investigations are required. The current study clearly demonstrated the role and utility of WGS in identifying genomic alterations that contribute to tumorigenesis.

Re-updating the taxonomy of Kluyvera genus for a better understanding of CTX-M β-lactamase origin.

The taxonomic definitions within the Kluyvera genus are still unclear, as several deposits might belong to misidentified species or genus or genome assemblies comprehend large indeterminate nucleotide zones. In this study, we performed a comparative phylogenomic analysis of Kluyvera chromosomes and other selected Enterobacterales. We also included the genomic analysis of chromosomal blaCTX-M/KLU from Kluyvera isolates and assigned the plasmid-encoded blaCTX/M genes. The study allowed us to propose a new Kluyvera genomospecies and to better define Kluyvera genomosp. 5. Two new CTX-M sub-groups could also be suggested. Even if no chromosomal blaCTX-M/KLU gene can be found in K. intermedia and Kluyvera genomosp. 6, accurate identification can be achieved by using these gene sequences in the remaining strains.IMPORTANCEThe use of whole-genome sequencing (WGS) accelerated the identification of new Kluyvera species proposals, but a rigorous analysis of these sequences is needed for a better definition, including preexisting, and even established species. Kluyvera genomosp. 5 could be more clearly defined, and, among isolates that do not produce a chromosome-encoded CTX-M enzyme, true K. intermedia should be kept within the genus as well as a new genomospecies (Kluyvera genomosp. 6) different from K. intermedia. We could clean up true Kluyvera from those that deserved transfer to other genera, and some deposits as K. ascorbata, K. cryocrescens, K. georgiana, and several Kluyvera sp. to the real species. Two new sub-groups of CTX-M enzymes could be proposed. The accurate identification of the chromosome-encoded blaCTX-M/KLU gene in Kluyvera isolates could be a useful taxonomic tool to guide the species classification.

Detection of circulating tumor DNA by tumor-informed whole-genome sequencing enables prediction of recurrence in stage III colorectal cancer patients

IntroductionCirculating tumor (ctDNA) can be used to detect residual disease after cancer treatment. Detecting low-level ctDNA is challenging, due to the limited number of recoverable ctDNA fragments at any target loci. In response, we applied tumor-informed whole-genome sequencing (WGS), leveraging thousands of mutations for ctDNA detection. MethodsPerformance was evaluated in serial plasma samples (n = 1283) from 144 stage III colorectal cancer patients. Tumor/normal WGS was used to establish a patient-specific mutational fingerprint, which was searched for in 20x WGS plasma profiles. For reproducibility, paired aliquots of 172 plasma samples were analyzed in two independent laboratories. De novo variant calling was performed for serial plasma samples with a ctDNA level > 10 % (n = 17) to explore genomic evolution. ResultsWGS-based ctDNA detection was prognostic of recurrence: post-operation (Hazard ratio [HR] 6.75, 95 %CI 3.18–14.3, p < 0.001), post-adjuvant chemotherapy (HR 28.9, 95 %CI 10.1–82.8; p < 0.001), and during surveillance (HR 22.8, 95 %CI 13.7–37.9, p < 0.0001). The 3-year cumulative incidence of ctDNA detection in recurrence patients was 95 %. ctDNA was detected a median of 8.7 months before radiological recurrence. The independently analyzed plasma aliquots showed excellent agreement (Cohens Kappa=0.9, r = 0.99). Genomic characterization of serial plasma revealed significant evolution in mutations and copy number alterations, and the timing of mutational processes, such as 5-fluorouracil-induced mutations. ConclusionOur study supports the use of WGS for sensitive ctDNA detection and demonstrates that post-treatment ctDNA detection is highly prognostic of recurrence. Furthermore, plasma WGS can identify genomic differences distinguishing the primary tumor and relapsing metastasis, and monitor treatment-induced genomic changes.

1204P Real-world utility of whole genome sequencing for patients with cancer: Evaluation of a regional implementation of the 100,000 genomes project

1204P Real-world utility of whole genome sequencing for patients with cancer: Evaluation of a regional implementation of the 100,000 genomes project

Rapid Whole Genome Characterization of High-Risk Pathogens Using Long-Read Sequencing to Identify Potential Healthcare Transmission.

Routine use of whole genome sequencing (WGS) has been shown to help identify transmission of pathogens causing healthcare-associated infections (HAIs). However, the current gold standard of short-read, Illumina-based WGS is labor and time-intensive. In light of recent improvements in long-read Oxford Nanopore Technologies (ONT) sequencing, we sought to establish a low resource utilization approach capable of providing accurate WGS-based comparisons of HAI pathogens within a time frame allowing for infection prevention and control (IPC) interventions. WGS was prospectively performed on antimicrobial-resistant pathogens at increased risk of potential healthcare transmission using the ONT MinION sequencer with R10.4.1 flow cells and Dorado basecalling algorithm. Potential transmission was assessed via Ridom SeqSphere+ for core genome multilocus sequence typing and MINTyper for reference-based core genome single nucleotide polymorphisms using previously published cut-off values. The accuracy of our ONT pipeline was determined relative to Illumina-based WGS data generated from the same genomic DNA sample. Over a six-month period, 242 bacterial isolates from 216 patients were sequenced by a single operator. Compared to the Illumina gold-standard data, our ONT pipeline achieved a Q score of 60 for assembled genomes, even with a coverage rate of as low as 40X. The mean time from initiating DNA extraction to complete genetic analysis was 2 days (IQR 2-3.25 days). We identified five potential transmission clusters comprising 21 isolates (8.7% of all sequenced strains). Combining ONT WGS data with epidemiological data, >70% (15/21) of the isolates originated from patients with potential healthcare transmission links. Via a stand-alone ONT pipeline, we detected potentially transmitted HAI pathogens rapidly and accurately, aligning closely with epidemiological data. Our low-resource method has the potential to assist in the efficient detection and deployment of preventative measures against HAI transmission.

EFSA statement on the requirements for whole genome sequence analysis of microorganisms intentionally used in the food chain.

Microorganisms, genetically modified or not, may be used in the food chain either as active agents, biomasses or as production organisms of substances of interest. The placement of such microorganisms or their derived substances/products in the European market may be subject to a premarket authorisation process. The authorisation process requires a risk assessment in order to establish the safety and/or the efficacy of the microorganism(s) when used in the food chain as such, as biomasses or as production strains. This includes a full molecular characterisation of the microorganism(s) under assessment. For certain regulated products, the use of whole genome sequence (WGS) data of the microorganism is established as a requirement for the risk assessment. In this regard, data obtained from WGS analysis can provide information on the unambiguous taxonomic identification of the strains, on the presence of genes of concern (e.g. those encoding virulence factors, resistance to antimicrobials of clinical relevance for humans and animals, production of harmful metabolites or of clinically relevant antimicrobials) and on the characterisation of genetic modification(s) (where relevant). This document provides recommendations to applicants on how to describe and report the results of WGS analyses in the context of an application for market authorisation of a regulated product. Indications are given on how to perform genome sequencing and the quality criteria/thresholds that should be reached, as well as the data and relevant information that need to be reported, if required. This updated document replaces the EFSA 2021 Statement and reflects the current knowledge in technologies and methodologies to be used to generate and analyse WGS data for the risk assessment of microorganisms.

Whole-genome sequencing establishes persistence of biofilm-associated Pseudomonas aeruginosa detected from microbiological surveillance of gastrointestinal endoscopes

BackgroundAn increased incidence of P. aeruginosa in microbiological surveillance (MS) cultures from gastrointestinal endoscopes was detected between March 2020 to March 2023 in Tan Tock Seng Hospital Singapore. The aim of this report is to describe the use of whole-genome sequencing (WGS) in this investigation. MethodsWGS was performed for all P. aeruginosa isolates with pairwise comparison of isolates to assess for genomic linkage. Comprehensive review of reprocessing practices and environmental sampling was performed. FindingsTwenty-two P. aeruginosa isolates were detected from endoscopic MS cultures. Fifteen (68%) isolates were available for WGS. Eighteen pairwise comparisons of isolates were made, of which 10 were found to be genomically linked. One endoscope had P. aeruginosa repeatedly cultured from subsequent MS that were genomically linked and persistent despite repeat endoscopic reprocessing, establishing the persistence of biofilm that could not be eradicated with routine reprocessing. All P. aeruginosa isolates cultured from other different endoscopes were genetically distinct.Investigation into reprocessing practices revealed the use of air/water valves connected to endoscopes during clinical use. Inspection of these valves revealed the presences of cracks and tears. All other environmental samples were negative. ConclusionsThe WGS findings helped to deprioritize common source contamination and supported the hypothesis of biofilm buildup within endoscopes leading to repeatedly positive MS cultures that were genomically linked. This was possibly related to incomplete reprocessing of the damaged air/water valves, resulting in biofilm build up. All faulty valves were changed and subsequently cleaned separately with ultrasonic cleaning followed by sterilization which resolved this incident.

Use of Whole Genome Sequencing for Investigation of Potential Hospital-Acquired Vancomycin Resistant Enterococcus

Background: Whole genome sequencing (WGS) is a relatively new method for analyzing outbreaks and modes of transmission, particularly for multidrug resistant bacteria. This study sought to investigate clusters of patients with genetically related Vancomycin-Resistant Enterococcus spp. (VRE) bacteremia for shared hospital environmental exposures. Methods: All VRE blood culture isolates from patients from July 1, 2021 to June 30, 2022 underwent Illumina WGS. Core single nucleotide polymorphisms (SNPs) were identified, and multi-locus sequence typing (MLST) was performed across the VRE isolates. Clusters were defined as isolates with 15 or fewer core genome SNPs and were investigated for potential transmission routes. For each cluster, patients were evaluated in the 12 weeks before and after the first VRE isolate for shared hospital environmental exposures (hospital unit, patient rooms, procedural rooms, and radiology suites). Hospital units were comprised of patient rooms located geographically together on the same floor of the hospital. Results: A total of 82 VRE isolates underwent WGS. Thirty-eight (46%) clustered genetically with at least one other isolate. Clusters included 2 to 15 patients per group and represented 10 distinct MLST subgroups (Figure 1). Nine hundred and thirty-nine hospital environmental exposures were identified across the 38 patients. For each cluster, there was a total of 341 (36.3%) shared exposures. Shared environmental exposures occurred in radiology suites (35, 38.5%), patient rooms (32, 35.6%) and procedural rooms (23, 25.6%). Of the patients who shared the same hospital unit, 10 (31.3%) had the same patient room with 7 (70%) of them being in the emergency department (ED). Overall, the ED represented 7 (21.9%) of the shared hospital units. Each cluster had at least one shared hospital environmental exposure found. Conclusions: Use of WGS can help investigate outbreak clusters of resistant organisms such as VRE. In this study, nearly half of all VRE blood isolates were able to be segregated into clusters with at least one other isolate. Although VRE colonization of hospital rooms is well described, patient rooms represented the smallest proportion of shared hospital environmental exposures. This study thus suggests other environmental transmission routes such as radiology suites and procedural rooms warrant closer investigation.

Whole genome sequencing as a ticket to cancer treatment in the Netherlands: Are inequalities in access to molecular diagnostics unfair?

Whole genome sequencing (WGS) of a tumour may sometimes reveal additional potential targets for medical treatment. Practice variation in the use of WGS is therefore a source of unequal access to targeted therapies and, as a consequence, of disparities in health outcomes. Moreover, this may even be more significant if patients seek access to WGS by paying a relatively limited amount of money out of pocket, and sometimes effectively buy themselves a ticket to (very) expensive publicly funded treatments. Should resulting unequal access to WGS be considered unfair? Drawing from current practice in the Dutch healthcare system, known as egalitarian, we argue that differences in employment of WGS between hospitals are the consequence of the fact that medical innovation and its subsequent uptake inevitably takes time. Consequently, temporal inequalities in access can be deemed acceptable, or at least tolerated, because and insofar as, ultimately, all patients benefit. However, we argue against allowing a practice of out-of-pocket payments for WGS in publicly funded healthcare systems, for four reasons: because allowing private spending favours patients with higher socio-economic status significantly more than practice variation between hospitals does, may lead to displacement of publicly funded health care, does not help to ultimately benefit all, and may undermine the solidaristic ethos essential for egalitarian healthcare systems.

Clinical presentation of early syphilis and genomic sequences of Treponema pallidum strains in patient specimens and isolates obtained by rabbit inoculation.

The global resurgence of syphilis necessitates vaccine development. We collected ulcer exudates and blood from 17 primary syphilis (PS) participants and skin biopsies and blood from 51 secondary syphilis (SS) participants in Guangzhou, China for Treponema pallidum subsp. pallidum (TPA) qPCR, whole genome sequencing (WGS), and isolation of TPA in rabbits. TPA DNA was detected in 15 of 17 ulcer exudates and 3 of 17 blood PS specimens. TPA DNA was detected in 50 of 51 SS skin biopsies and 27 of 51 blood specimens. TPA was isolated from 47 rabbits with success rates of 71% (12/17) and 69% (35/51), respectively, from ulcer exudates and SS bloods. We obtained paired genomic sequences from 24 clinical samples and corresponding rabbit isolates. Six SS14- and two Nichols-clade genome pairs contained rare discordances. Forty-one of the 51 unique TPA genomes clustered within SS14 subgroups largely from East Asia, while 10 fell into Nichols C and E subgroups. Our TPA detection rate was high from PS ulcer exudates and SS skin biopsies and over 50% from SS blood, with TPA isolation in over two-thirds of samples. Our results support the use of WGS from rabbit isolates to inform vaccine development.

Phylogenomic reconstruction influenced by assembly and annotation parameters: Using whole genome data to unravel the relationships of Spionidae (Annelida)

AbstractMost efforts at improving accuracy in phylogenomic reconstructions have focused on improving tree‐building methods or orthology determination. Even though the use of whole genome sequence or transcriptome data is increasing, the degree to which accurate genome assembly and annotation influence phylogenetic inference has not been well explored. Here, we use low‐coverage whole genome sequencing of spionid annelids to explore the impact of different assemblers and annotation strategies on tree reconstruction. We also produce a phylogenetic hypothesis that spans the breadth of Spionidae, examining the current systematics of the group, which is based on morphological parsimony analyses and classical taxonomy. Our results show that both assembly and annotation can have important consequences for the pool of loci that may be available for tree reconstruction. When an identical phylogenomic pipeline is used, differences in assembly and annotation can account for variation in reconstructed topologies. Interestingly, the completeness and depth of the data used for training annotation software (i.e. data from model systems) appear to be more important, by some measures, than the degree of phylogenetic relatedness of the organism from which training data are drawn. Despite variation in recovered topologies, the recognised subfamily Spioninae is nested within Nerininae, suggesting that diagnostic characters of Nerininae (e.g. thick egg membrane, short‐headed sperm) are symplesiomorphies of Spionidae rather than apomorphies of a particular subclade. With the increased use of genomic data, our results advocate for a broader consideration of how assembly and annotation may impact data matrices used in phylogenomic analyses.

Whole Genome Sequencing of Mycobacterium tuberculosis under routine conditions in a high-burden area of multidrug-resistant tuberculosis in Peru.

Whole Genome Sequencing (WGS) is a promising tool in the global fight against tuberculosis (TB). The aim of this study was to evaluate the use of WGS in routine conditions for detection of drug resistance markers and transmission clusters in a multidrug-resistant TB hot-spot area in Peru. For this, 140 drug-resistant Mycobacterium tuberculosis strains from Lima and Callao were prospectively selected and processed through routine (GenoType MTBDRsl and BACTEC MGIT) and WGS workflows, simultaneously. Resistance was determined in accordance with the World Health Organization mutation catalogue. Agreements between WGS and BACTEC results were calculated for rifampicin, isoniazid, pyrazinamide, moxifloxacin, levofloxacin, amikacin and capreomycin. Transmission clusters were determined using different cut-off values of Single Nucleotide Polymorphism differences. 100% (140/140) of strains had valid WGS results for 13 anti-TB drugs. However, the availability of final, definitive phenotypic BACTEC MGIT results varied by drug with 10-17% of invalid results for the seven compared drugs. The median time to obtain results of WGS for the complete set of drugs was 11.5 days, compared to 28.6-52.6 days for the routine workflow. Overall categorical agreement by WGS and BACTEC MGIT for the compared drugs was 96.5%. Kappa index was good (0.65≤k≤1.00), except for moxifloxacin, but the sensitivity and specificity values were high for all cases. 97.9% (137/140) of strains were characterized with only one sublineage (134 belonging to "lineage 4" and 3 to "lineage 2"), and 2.1% (3/140) were mixed strains presenting two different sublineages. Clustering rates of 3.6% (5/140), 17.9% (25/140) and 22.1% (31/140) were obtained for 5, 10 and 12 SNP cut-off values, respectively. In conclusion, routine WGS has a high diagnostic accuracy to detect resistance against key current anti-TB drugs, allowing results to be obtained through a single analysis and helping to cut quickly the chain of transmission of drug-resistant TB in Peru.

Feasibility of implementing whole genome sequencing into routine oncology care.

e15181 Background: The promise of precision oncology to deliver improved patient outcomes is dependent on the availability and appropriate interpretation of individual patient tumor sequencing results. While routine use and clinical utility for comprehensive genomic profiling (CGP) is growing, there are limited data in the U.S. to support the use of whole genome sequencing (WGS) outside of limited specific indications (i.e. acute myeloid leukemia, pediatric, sarcoma). This study highlights reports on the feasibility from a pilot project offering paired germline/somatic WGS to a cohort of oncology patients at an academic medical center. Methods: Eligible patients included those with an active cancer diagnosis, available tumor, and a treating provider within Weill Cornell. There were no specific restrictions. Providers selected patients with newly diagnosed metastatic cancers, rare tumors, refractory tumors, and/or those with uninformative germline testing for hereditary cancer. Reportable germline findings were pathogenic or likely pathogenic (P/LP) variants in known cancer predisposition genes and/or genes on the American College of Medical Genetics list of reportable secondary findings. Clinical actionability of somatic results was determined using the cBioPortal Database and Oncology Knowledgebase. Ordering providers disclosed results to patients. Barriers to enrollment were explored and addressed. Results: Between January 2021 and December 2023, 82 patients had germline/somatic WGS. The most common tumors included breast (17%), prostate (11%), renal (10%), lung (7%), bladder (7%), and colon (5%), with 48% of the cohort represented by rare tumors. Six cases (7.3%) had insufficient quantity/quality. WGS detected single nucleotide variants in 84% (n = 69) of cases, with 39% (n = 27) of those having clinical actionability in the patient’s tumor. Additional somatic results included copy number variants in 83% (n = 68) and transcriptome variants in 17% (n = 14). P/LP germline variants were found in 17% (n = 14) of cases. Barriers to enrollment included: difficulty identifying which patients would benefit most from WGS, lengthy in-person consent process, limited access to pretest genetic counseling, and difficulty procuring and processing tissue specimens. Availability of reflexive in-house CGP since August 2022 also resulted in decreased uptake of this service. Several interventions were implemented to address the barriers, resulting in an increase in enrollment. Conclusions: Paired germline/somatic WGS identified clinically relevant variants for patients with diverse tumors. Results were used to direct treatment decisions and determine eligibility for clinical trials as well as inform hereditary cancer predisposition. An assessment period after WGS implementation is needed to improve workflow. Further research aims to determine optimal accessibility and utilization of WGS for oncologic patients.

Understanding the potential role of whole genome sequencing (WGS) in managing patients with gonorrhoea: A systematic review of WGS use on human pathogens in individual patient care

The utility of whole genome sequencing (WGS) to inform sexually transmitted infection (STI) patient management is unclear. Timely WGS data might support clinical management of STIs by characterising epidemiological links and antimicrobial resistance profiles. We conducted a systematic review of clinical application of WGS to any human pathogen that may be transposable to gonorrhoea. We searched six databases for articles published between 01/01/2010-06/02/2023 that reported on real/near real-time human pathogen WGS to inform clinical intervention. All article types from all settings were included. Findings were analysed using narrative synthesis. We identified 12,179 articles, of which eight reported applications to inform tuberculosis (n=7) and gonorrhoea (n=1) clinical patient management. WGS data were successfully used as an adjunct to clinical and epidemiological data to enhance contact-tracing (n=2), inform antimicrobial therapy (n=5) and identify cross-contamination (n=1). WGS identified gonorrhoea transmission chains that were not established via partner notification. Future applications could include insights into pathogen exposure detected within sexual networks for targeted patient management. While there was some evidence of WGS use to provide individualised tuberculosis and gonorrhoea treatment, the eight identified studies contained few participants. Future research should focus on testing WGS intervention effectiveness and examining ethical considerations of STI WGS use.

Whole genome sequencing in paediatric channelopathy and cardiomyopathy.

Precision medicine in paediatric cardiac channelopathy and cardiomyopathy has a rapid advancement over the past years. Compared to conventional gene panel and exome-based testing, whole genome sequencing (WGS) offers additional coverage at the promoter, intronic regions and the mitochondrial genome. However, the data on use of WGS to evaluate the genetic cause of these cardiovascular conditions in children and adolescents are limited. In a tertiary paediatric cardiology center, we recruited all patients diagnosed with cardiac channelopathy and cardiomyopathy between the ages of 0 and 18 years old, who had negative genetic findings with prior gene panel or exome-based testing. After genetic counselling, blood samples were collected from the subjects and both their parents for WGS analysis. A total of 31 patients (11 cardiac channelopathy and 20 cardiomyopathy) were recruited. Four intronic splice-site variants were identified in three cardiomyopathy patients, which were not identified in previous whole exome sequencing. These included a pathogenic variant in TAFAZZIN:c.284+5G>A (Barth syndrome), a variant of unknown significance (VUS) in MYBPC3:c.1224-80G>A and 2 compound heterozygous LP variants in LZTR1 (LZTR1:c.1943-256C>T and LZTR1:c1261-3C>G) in a patient with clinical features of RASopathy. There was an additional diagnostic yield of 1.94% using WGS for identification of intronic variants, on top of conventional gene testing. WGS plays a role in identifying additional intronic splice-site variants in paediatric patients with isolated cardiomyopathy. With the demonstrated low extra yield of WGS albeit its ability to provide potential clinically important information, WGS should be considered in selected paediatric cases of cardiac channelopathy and cardiomyopathy in a cost-effective manner.

Application of genomic studies in epidemiological surveillance: A mini-overview

The 21st century has already seen the emergence of several pandemics both in developed and developing nations, including the recent Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic. The recent upsurge in certain diseases clearly indicates the need for continuous epidemiological surveillance and real-time monitoring of infectious diseases. Interestingly, genomics has found extensive application in monitoring infectious diseases through the sequencing of bacteria, parasites, and virus genomes. The continual scrutiny of pathogens and the examination of their genetic similarities and distinctions constitute genomic surveillance. The potential of genomic sequencing lies in its ability to offer a significantly more detailed depiction of the evolution and transmission of antimicrobial resistance (AMR), thus initiating a transformative impact on how public health surveillance networks address bacterial AMR. The utilization of whole-genome sequencing (WGS) stands as a prevalent technique for identifying and tracking pathogens, establishing transmission routes, and managing outbreaks. However, despite several decades of advancements, the seamless integration of genomics into surveillance pipelines faces substantial barriers that necessitate overcoming. Recent advances in genomics and next-generation sequencing approaches provide new paradigms for monitoring transmission pipelines and reducing overall morbidity and mortality. In this mini-review, we highlight the advances in genomics, how they have been critical in epidemiological surveillance and monitoring outbreaks, and how they can help predict and monitor possible future outbreaks.