Is the $1000 Genome as Near as We Think? A Cost Analysis of Next-Generation Sequencing

Nimwegen, K.J.M. van; Soest, Ronald A. van; Veltman, Joris A.; Nelen, Marcel; Wilt, Gert Jan van der; Vissers, Lisenka E L M; Grutters, Janneke P.C.

doi:10.1373/clinchem.2016.258632

Cited by 130 publications

(120 citation statements)

References 31 publications

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“…59 With future costs to generate WGS data reducing, WGS in large populations of continental Africans with stroke for discovery 39 ; followed by validation in African Americans, is the most plausible approach to discover and pinpoint causal variants for stroke with implications for the entire human race. This is due to the African origin of all humans and the substantially higher heritability of stroke among African ancestry populations.…”

Section: 0 Discussionmentioning

confidence: 99%

Advancing stroke genomic research in the age of Trans-Omics big data science: Emerging priorities and opportunities

Owolabi

Peprah

et al. 2017

Journal of the Neurological Sciences

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Background We systematically reviewed the genetic variants associated with stroke in genome-wide association studies (GWAS) and examined the emerging priorities and opportunities for rapidly advancing stroke research in the era of Trans-Omics science. Methods Using the PRISMA guideline, we searched PubMed and NHGRI- EBI GWAS catalog for stroke studies from 2007 till May 2017. Results We included 31 studies. The major challenge is that the few validated variants could not account for the full genetic risk of stroke and have not been translated for clinical use. None of the studies included continental Africans. Genomic study of stroke among Africans presents a unique opportunity for the discovery, validation, functional annotation, trans-omics study and translation of genomic determinants of stroke with implications for global populations. This is because all humans originated from Africa, a continent with a unique genomic architecture and a distinctive epidemiology of stroke; as well as substantially higher heritability and resolution of fine mapping of stroke genes. Conclusion Understanding the genomic determinants of stroke and the corresponding molecular mechanisms will revolutionize the development of a new set of precise biomarkers for stroke prediction, diagnosis and prognostic estimates as well as personalized interventions for reducing the global burden of stroke.

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Section: 0 Discussionmentioning

confidence: 99%

Advancing stroke genomic research in the age of Trans-Omics big data science: Emerging priorities and opportunities

Owolabi

Peprah

et al. 2017

Journal of the Neurological Sciences

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“…Since the exome contains approximately 30,000 genes, or <2% of the human genome, the exome can be sequenced at a greater depth than the genome at a lower price. The cost of an average exome has been estimated at $800 (38), although the fee for a clinical-grade exome typically exceeds several thousand dollars due to the certifications and regulations applied to clinical testing. A TGP focused on genes specific to a clinical phenotype is even more cost efficient, with studies reporting a range of $250–500 per sample for targeted PID gene panels (39).…”

Section: Ngs Technologiesmentioning

confidence: 99%

Uses of Next-Generation Sequencing Technologies for the Diagnosis of Primary Immunodeficiencies

et al. 2017

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Primary immunodeficiencies (PIDs) are genetic disorders impairing host immunity, leading to life-threatening infections, autoimmunity, and/or malignancies. Genomic technologies have been critical for expediting the discovery of novel genetic defects underlying PIDs, expanding our knowledge of the complex clinical phenotypes associated with PIDs, and in shifting paradigms of PID pathogenesis. Once considered Mendelian, monogenic, and completely penetrant disorders, genomic studies have redefined PIDs as a heterogeneous group of diseases found in the global population that may arise through multigenic defects, non-germline transmission, and with variable penetrance. This review examines the uses of next-generation DNA sequencing (NGS) in the diagnosis of PIDs. While whole genome sequencing identifies variants throughout the genome, whole exome sequencing sequences only the protein-coding regions within a genome, and targeted gene panels sequence only a specific cohort of genes. The advantages and limitations of each sequencing approach are compared. The complexities of variant interpretation and variant validation remain the major challenge in wide-spread implementation of these technologies. Lastly, the roles of NGS in newborn screening and precision therapeutics for individuals with PID are also addressed.

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“…1,[6][7][8] Despite rapid advancements, high reagent costs and time-consuming sample preparation remain a significant obstacle for the full implementation of NGS in clinical practice. 9 Several approaches are available to isolate and purify nucleic acids (NA). 1,8,10 Target sequences can be pulled down from solution via biotinylated probes that are captured by streptavidin-coated solid beads (e.g.…”

Section: Introductionmentioning

confidence: 99%

“…[2][3][4]7 Despite the diverse variety of approaches, current methods have critical shortcomings that require trade-offs between material cost, ease of use, versatility and performance. Commercial kits are expensive, 9,10 due to high costs of recombinant proteins and enzymes. Solid beads are susceptible to non-specific interfacial adsorption of macromolecules, leakage of surface-attached streptavidin, degradation in presence of reducing agents and chelators, or incomplete release of target molecules.…”

Section: Introductionmentioning

confidence: 99%

A smart polymer for sequence-selective binding, pulldown, and release of DNA targets

Krieg

Gupta

Dahl

et al. 2019

Preprint

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Selective isolation of DNA is crucial for applications in biology, bionanotechnology, clinical diagnostics and forensics. We herein report a smart methanol-responsive polymer (MeRPy) that can be programmed to bind and separate single-as well as double-stranded DNA targets. Captured targets are quickly isolated and released back into solution by denaturation (sequence-agnostic) or toehold-mediated strand displacement (sequence-selective). The latter mode allows 99.8% efficient removal of unwanted sequences and 79% recovery of highly pure target sequences. We applied MeRPy for depletion of insulin cDNA from clinical next-generation sequencing (NGS) libraries. This step improved data quality for low-abundance transcripts in expression profiles of pancreatic tissues. Its low cost, scalability, high stability and ease of use make MeRPy suitable for diverse applications in research and clinical laboratories, including enhancement of NGS libraries, extraction of DNA from biological samples, preparative-scale DNA isolations, and sorting of DNA-labeled non-nucleic acid targets.

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Is the $1000 Genome as Near as We Think? A Cost Analysis of Next-Generation Sequencing

Cited by 130 publications

References 31 publications

Advancing stroke genomic research in the age of Trans-Omics big data science: Emerging priorities and opportunities

Advancing stroke genomic research in the age of Trans-Omics big data science: Emerging priorities and opportunities

Uses of Next-Generation Sequencing Technologies for the Diagnosis of Primary Immunodeficiencies

A smart polymer for sequence-selective binding, pulldown, and release of DNA targets

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