Are whole-exome and whole-genome sequencing approaches cost-effective? A systematic review of the literature

Schwarze, Katharina; Buchanan, James; Taylor, Jenny C.; Wordsworth, Sarah

doi:10.1038/gim.2017.247

Cited by 401 publications

(219 citation statements)

References 41 publications

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“…However, the most important challenge for this technology is the interpretation and computation of the huge set of data. In addition, WGS requires significant computer resources and well-trained bioinformaticians [135].…”

Section: Mrsa Typing Methods and Techniquesmentioning

confidence: 99%

Methicillin-Resistant Staphylococcus aureus ST80 Clone: A Systematic Review

Mairi

Touati

Lavigne

2020

Toxins

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This review assessed the molecular characterization of the methicillin-resistant Staphylococcus aureus (MRSA)-ST80 clone with an emphasis on its proportion of total MRSA strains isolated, PVL production, spa-typing, antibiotic resistance, and virulence. A systematic review of the literature was conducted on MRSA-ST80 clone published between 1 January 2000 and 31 August 2019. Citations were chosen for a review of the full text if we found evidence that MRSA-ST80 clone was reported in the study. For each isolate, the country of isolation, the sampling period, the source of isolation (the type of infection, nasal swabs, or extra-human), the total number of MRSA strains isolated, number of MRSA-ST80 strains, antibiotic resistance patterns, PVL production, virulence genes, and spa type were recorded. The data from 103 articles were abstracted into an Excel database. Analysis of the data showed that the overall proportion of MRSA-ST80 has been decreasing in many countries in recent years. The majority of MRSA-ST80 were PVL positive with spa-type t044. Only six reports of MRSA-ST80 in extra-human niches were found. This review summarizes the rise of MRSA-ST80 and the evidence that suggests that it could be in decline in many countries.

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Section: Mrsa Typing Methods and Techniquesmentioning

confidence: 99%

Methicillin-Resistant Staphylococcus aureus ST80 Clone: A Systematic Review

Mairi

Touati

Lavigne

2020

Toxins

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“…However, such literature on WES utilization lacks clear presentation of cost data, is limited by small cohort sizes, and use outcome measures that are difficult to translate into health economic policy (Schwarze, Buchanan, Taylor, & Wordsworth, 2018 (Eldomery et al, 2017;Wenger et al, 2017). As more patients undergo testing, further phenotype-genotype correlations will be established, advances are made in bioinformatics tools, and knowledge about the genetic basis of disease expands.…”

Section: Ta B L E 2 (Continued)mentioning

confidence: 99%

Yield of whole exome sequencing in undiagnosed patients facing insurance coverage barriers to genetic testing

Reuter

Kohler

Bonner

et al. 2019

Journal of Genetic Counseling

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Background Despite growing evidence of diagnostic yield and clinical utility of whole exome sequencing (WES) in patients with undiagnosed diseases, there remain significant cost and reimbursement barriers limiting access to such testing. The diagnostic yield and resulting clinical actions of WES for patients who previously faced insurance coverage barriers have not yet been explored. Methods We performed a retrospective descriptive analysis of clinical WES outcomes for patients facing insurance coverage barriers prior to clinical WES and who subsequently enrolled in the Undiagnosed Diseases Network (UDN). Clinical WES was completed as a result of participation in the UDN. Payer type, molecular diagnostic yield, and resulting clinical actions were evaluated. Results Sixty‐six patients in the UDN faced insurance coverage barriers to WES at the time of enrollment (67% public payer, 26% private payer). Forty‐two of 66 (64%) received insurance denial for clinician‐ordered WES, 19/66 (29%) had health insurance through a payer known not to cover WES, and 5/66 (8%) had previous payer denial of other genetic tests. Clinical WES results yielded a molecular diagnosis in 23 of 66 patients (35% [78% pediatric, 65% neurologic indication]). Molecular diagnosis resulted in clinical actions in 14 of 23 patients (61%). Conclusions These data demonstrate that a substantial proportion of patients who encountered insurance coverage barriers to WES had a clinically actionable molecular diagnosis, supporting the notion that WES has value as a covered benefit for patients who remain undiagnosed despite objective clinical findings.

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“…This is comparable to other targeted sequencing methods such as WES or Haloplex-based sequencing. smMIPs-based ABCA4 sequencing is a cost-effective method compared to Sanger sequencing (≥€500 for 50 exons) and WES, since it costs~€20 for reagents only (excluding the smMIPs design and synthesis) to sequence ABCA4 50 exons and 12 deep-intronic regions which are 25-50-fold less than Sanger sequencing or WES (Schwarze, Buchanan, Taylor, & Wordsworth, 2018). Other advantages of smMIPs are the low input of DNA per patient.…”

Section: Deep-intronic Variants Identification and In Vitro Assessmentmentioning

confidence: 99%

Cost‐effective molecular inversion probe‐based ABCA4 sequencing reveals deep‐intronic variants in Stargardt disease

et al. 2019

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Purpose Stargardt disease (STGD1) is caused by biallelic mutations in ABCA4, but many patients are genetically unsolved due to insensitive mutation‐scanning methods. We aimed to develop a cost‐effective sequencing method for ABCA4 exons and regions carrying known causal deep‐intronic variants. Methods Fifty exons and 12 regions containing 14 deep‐intronic variants of ABCA4 were sequenced using double‐tiled single molecule Molecular Inversion Probe (smMIP)‐based next‐generation sequencing. DNAs of 16 STGD1 cases carrying 29 ABCA4 alleles and of four healthy persons were sequenced using 483 smMIPs. Thereafter, DNAs of 411 STGD1 cases with one or no ABCA4 variant were sequenced. The effect of novel noncoding variants on splicing was analyzed using in vitro splice assays. Results Thirty‐four ABCA4 variants previously identified in 16 STGD1 cases were reliably identified. In 155/411 probands (38%), two causal variants were identified. We identified 11 deep‐intronic variants present in 62 alleles. Two known and two new noncanonical splice site variants showed splice defects, and one novel deep‐intronic variant (c.4539+2065C>G) resulted in a 170‐nt mRNA pseudoexon insertion (p.[Arg1514Lysfs*35,=]). Conclusions smMIPs‐based sequence analysis of coding and selected noncoding regions of ABCA4 enabled cost‐effective mutation detection in STGD1 cases in previously unsolved cases.

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Are whole-exome and whole-genome sequencing approaches cost-effective? A systematic review of the literature

Cited by 401 publications

References 41 publications

Methicillin-Resistant Staphylococcus aureus ST80 Clone: A Systematic Review

Methicillin-Resistant Staphylococcus aureus ST80 Clone: A Systematic Review

Yield of whole exome sequencing in undiagnosed patients facing insurance coverage barriers to genetic testing

Cost‐effective molecular inversion probe‐based ABCA4 sequencing reveals deep‐intronic variants in Stargardt disease

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