Clinical Application Of Whole-genome Sequencing Research Articles

Clinical application of whole-genome sequencing in the management of extensively drug-resistant tuberculosis: a case report

BackgroundWhole-genome sequencing (WGS)-based prediction of drug resistance in Mycobacterium tuberculosis has the potential to guide clinical decisions in the design of optimal treatment regimens.MethodsWe utilized WGS to investigate drug resistance mutations in a 32-year-old Tanzanian male admitted to Kibong’oto Infectious Diseases Hospital with a history of interrupted multidrug-resistant tuberculosis treatment for more than three years. Before admission, he received various all-oral bedaquiline-based multidrug-resistant tuberculosis treatment regimens with unfavourable outcomes.ResultsDrug susceptibility testing of serial M. tuberculosis isolates using Mycobacterium Growth Incubator Tubes culture and WGS revealed resistance to first-line anti-TB drugs, bedaquiline, and fluoroquinolones but susceptibility to linezolid, clofazimine, and delamanid. WGS of serial cultured isolates revealed that the Beijing (Lineage 2.2.2) strain was resistant to bedaquiline, with mutations in the mmpR5 gene (Rv0678. This study also revealed the emergence of two distinct subpopulations of bedaquiline-resistant tuberculosis strains with Asp47f and Glu49fs frameshift mutations in the mmpR5 gene, which might be the underlying cause of prolonged resistance. An individualized regimen comprising bedaquiline, delamanid, pyrazinamide, ethionamide, and para-aminosalicylic acid was designed. The patient was discharged home at month 8 and is currently in the ninth month of treatment. He reported no cough, chest pain, fever, or chest tightness but still experienced numbness in his lower limbs.ConclusionWe propose the incorporation of WGS in the diagnostic framework for the optimal management of patients with drug-resistant and extensively drug-resistant tuberculosis.

Clinical application of whole-genome sequencing of solid tumors for precision oncology

Genomic alterations in tumors play a pivotal role in determining their clinical trajectory and responsiveness to treatment. Targeted panel sequencing (TPS) has served as a key clinical tool over the past decade, but advancements in sequencing costs and bioinformatics have now made whole-genome sequencing (WGS) a feasible single-assay approach for almost all cancer genomes in clinical settings. This paper reports on the findings of a prospective, single-center study exploring the real-world clinical utility of WGS (tumor and matched normal tissues) and has two primary objectives: (1) assessing actionability for therapeutic options and (2) providing clarity for clinical questions. Of the 120 patients with various solid cancers who were enrolled, 95 (79%) successfully received genomic reports within a median of 11 working days from sampling to reporting. Analysis of these 95 WGS reports revealed that 72% (68/95) yielded clinically relevant insights, with 69% (55/79) pertaining to therapeutic actionability and 81% (13/16) pertaining to clinical clarity. These benefits include the selection of informed therapeutics and/or active clinical trials based on the identification of driver mutations, tumor mutational burden (TMB) and mutational signatures, pathogenic germline variants that warrant genetic counseling, and information helpful for inferring cancer origin. Our findings highlight the potential of WGS as a comprehensive tool in precision oncology and suggests that it should be integrated into routine clinical practice to provide a complete image of the genomic landscape to enable tailored cancer management.

Real-time whole genome sequencing to control a Streptococcus pyogenes outbreak at a national orthopaedic hospital

Whole genome sequencing (WGS) of Streptococcus pyogenes linked to invasive disease has been used to identify and investigate outbreaks. The clinical application of WGS in real-time for outbreak control is seldom employed. A fatal case of bacteraemia at a national orthopaedic hospital prompted an outbreak investigation to identify carriers and halt transmission using real-time WGS. Retrospective surveillance was conducted to identify patients with Streptococcus pyogenes infections in the last year. Upon contact tracing, four patients and 179 staff were screened for Streptococcus pyogenes carriage. All isolates identified were emm-typed. WGS was performed in real-time on a subset of isolates. Twelve isolates of Streptococcus pyogenes from the index case, two patients and eight staff were identified. Six isolates were emm 1.0, including the index case and five staff isolates. The remaining isolates belonged to distinct emm types. WGS analysis was undertaken on the six emm 1.0 isolates. Five were indistinguishable by single nucleotide polymorphism (SNP) analysis, with 0 SNP distance, and one had one SNP difference, supporting the hypothesis of recent local transmission. All screen-positive healthcare workers were offered treatment with penicillin or clindamycin. No further cases were identified. The increased molecular discrimination of WGS confirmed the clustering of these cases and the outbreak was contained. This demonstrates the clinical utility of WGS in managing outbreaks of invasive Streptococcus pyogenes in real-time and we recommend its implementation as a routine clinical service.

Clinical application of whole-genome sequencing in patients with primary immunodeficiency

This report illustrates the value of whole genome sequencing (WGS) in elucidating the genetic cause of disease in patients with primary immunodeficiency (PID). As sequencing costs decline, we predict that utilization of next generation sequencing (NGS) in the clinical setting will increase.

Clinical Application of Whole-Genome Sequencing

Stunning advances have been made over the last 5 years in the ability to rapidly and inexpensively detect variation in the human genome. In the mid-2000s massively parallel detection of single-nucleotide polymorphisms (SNPs) on gene chips (genotyping) burst on to the scene, launching the era of genome-wide association studies and high-profile direct-to-consumer marketing of genetic testing of questionable clinical value.1 More recently, substantial credible evidence has been accumulating for the research and clinical value of whole-exome sequencing (WES) for conditions ranging from cancer to developmental delay to mendelian disorders.2- 5 Whole-exome sequencing uses high-throughput sequencing technologies to determine the arrangement of DNA base pairs specifying the protein coding regions of an individual’s genome, also known as the exome. As remarkable as SNP genotyping and WES technologies are, they are both interim methods for detecting DNA variation. Assuming perfect technical accuracy, both are limited in the extent of variation that they can discover in a patient. In the case of SNP genotyping, this is because of the type of known variations the platforms can detect and in WES because the exome comprises about 1% of the entire genome.

Currents in Contemporary Bioethics

From the earliest days of the Human Genome Project, the holy grail of genomics was the ability to perform whole-genome sequencing quickly, accurately, and relatively inexpensively so that the benefits of genomics would be widely available in clinical settings. Although the mythical $1,000 genome sequence seemed elusive for many years, next-generation sequencing technologies and other recent advances clearly indicate that inexpensive whole-genome sequencing is at hand.Whole-genome sequencing has demonstrable value in elucidating the genetic etiology of rare disorders, in identifying atypical variants in common diseases, in determining pharmacogenomically appropriate drugs and dosages, in performing tumor genome sequencing, and in aiding other clinical applications for the diagnosis and treatment of individuals who are symptomatic or whose family health history places them at substantial risk. Undoubtedly, the clinical applications of wholegenome sequencing will increase in the future.

Genomics of AML: Clinical Applications of Next-Generation Sequencing

In the past decade, a series of technological advances have revolutionized our ability to interrogate cancer genomes, culminating in whole-genome sequencing, which provides genome-wide coverage at a single base-pair resolution. As sequencing technologies improve and costs decrease, it is likely that whole-genome sequencing of cancer cells will become commonplace in the diagnostic workup of patients with acute myelogenous leukemia (AML) and other cancers. The unprecedented molecular characterization provided by whole-genome sequencing offers the potential for an individualized approach to treatment in AML, bringing us one step closer to personalized medicine. In this chapter, we discuss how next-generation sequencing is being used to study cancer genomes. Recent publications of whole-genome sequencing in AML are reviewed and current limitations of whole-genome sequencing are examined, as well as current and potential future clinical applications of whole-genome sequencing.

Challenges in the clinical application of whole-genome sequencing

Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine (E A Ashley MRCP, M T Wheeler MD), Department of Medicine (Prof R B Altman MD), Department of Bioengineering (Prof R B Altman), Division of Medical Genetics (Prof L Hudgins MD), Department of Pediatrics (A J Butte MD), and Department of Genetics (T E Klein PhD, K E Ormond MSc, Prof R B Altman), Stanford University School of Medicine, Stanford, CA, USA; and Center for Law and Biosciences, Stanford University School of Law, Stanford, CA, USA (Prof H T Greely JD)

The $1000 genome: why would you do it?

The prospect of whole genome sequencing (WGS) at a reasonable cost and with accuracy sufficient for clinical diagnostics is tantalising to laymen and professionals alike. In the presentation I will offer a perspective of an academic medical geneticist directing a comprehensive genetic health service for a small country. The cost of WGS is falling rapidly and when the cost of determining an individual genome sequence falls to a price of around $1000 this technology will be applied to a large number of individuals for research and clinical diagnostics. It is even proposed that determining a person’s genome sequence may in the future become a first step upon entering a health insurance or a clinical facility similar to routine blood tests. We don’t at this junction comprehend the extent of the human genomic variation. In early clinical applications of WGS we are likely to be faced with new genetic variation including millions of single nucleotide polymorphisms (SNP), hundreds of thousands of insertion/deletion polymorphisms and thousands of structural variants. The functional significance of recurrent variations is expected to be sorted out eventually with association studies involving whole genomes sequences. However, given the accuracy of DNA replication and the number of cell divisions between zygote and gametes it is expected that each individual has in the order of 50-100 de novo mutations. Many of these are private and eventually eliminated in future generations. The reliable interpretation of their significance will require a deeper than current understanding of the structure-function and copy number relationships of DNA sequences. In short, the advice to those considering clinical WGS is: Be careful. You will be faced with thousands and thousands of novel sequence variants of uncertain clinical significance. We most often don’t know how to interpret their significance. Take for instance missense mutations. Thousands will be present in a genomic sequence. One can look at whether it is a known mutation in a database, evaluate the change in chemical class of amino acids, analyse whether the change involves a critical site, or if the sequence is conserved by interspecies comparison. Computer programs are available to assist in this work. One can also do segregation studies of the variation in the family. These methods are often not reliable in predicting pathogenicity as will be illustrated with examples from my own practice. WGS by its nature involves diagnostic testing, predictive testing, susceptibility testing, pharmacogenetic testing, and carrier testing all in one. The pre- and post-test genetic counselling will be time consuming and complex as will the postanalytical phase of assigning significance to the findings and reporting them. Besides the health implications, privacy issues and risk of unfair discrimination need to be addressed. The associated work is likely to cost much more than the $1000 for determining the sequence! Clinical WGS will presumably first be applied to individuals with a serious condition, which is presumably genetic, but has resisted conventional diagnostic measures. The need to understand the condition, establish prognosis, contemplate therapy as well as to determine recurrence risks is very strong. Often this need will be stronger than any possible disadvantage of WGS. Medical geneticists are currently regularly faced with distressed families where a diagnosis could not be made. They look forward to adding WGS to their armamentarium.