Evidence map›Paper›PMID 31442674›Full record

ArticleThe Journal of molecular diagnostics : JMD2019

Analytical Comparison of Methods for Extraction of Short Cell-Free DNA from Urine.

Amy Oreskovic, Norman D Brault, Nuttada Panpradist, James J Lai, Barry R Lutz

Open access · greenAbstract readComparative Study
PubMed Full text at PMC Publisher
In one paragraph

Article in The Journal of molecular diagnostics : JMD, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
40citing papers in PubMed, 1 pooled it
2.8field-weighted citation impact, top 8% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

40 citing papers in PubMed, 1 synthesis or guideline pooled it, 67 citations in OpenAlex.

  1. Pooled it
  2. Review
  3. Article
  4. Article
  5. Article
  6. Article
  7. Review
  8. Article
  9. Review
  10. Article
  11. A rapid purification method for trace amounts of cell-free DNA in urine.Analytical sciences : the international journal of the Japan Society for Analytical Chemistry · 2025
    Article
  12. Article
  13. Article
  14. Review
  15. Article
  16. Cell-Free DNA DetectsAmerican journal of respiratory and critical care medicine · 2023
    Article
  17. Article
  18. Article
  19. Review
  20. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors at 1 institution in 1 country.

Amy OreskovicDepartment of Bioengineering, University of Washington, Seattle, Washington.
Norman D BraultDepartment of Bioengineering, University of Washington, Seattle, Washington.
Nuttada PanpradistDepartment of Bioengineering, University of Washington, Seattle, Washington.
James J LaiDepartment of Bioengineering, University of Washington, Seattle, Washington.
Barry R LutzDepartment of Bioengineering, University of Washington, Seattle, Washington. Electronic address: blutz@uw.edu.
University of Washington · US

Funding

Point-of-care diagnosis of pulmonary TB from urine samplesR21AI125975 · NIAID · UNIVERSITY OF WASHINGTON · PI LUTZ, BARRY RYAN · 2016 to 2017
$425k
NIAID NIH HHS R21 AI125975
6 · The paper itself

Abstract

Urine cell-free DNA (cfDNA) is a valuable noninvasive biomarker for cancer mutation detection, infectious disease diagnosis (eg, tuberculosis), organ transplantation monitoring, and prenatal screening. Conventional silica DNA extraction does not efficiently capture urine cfDNA, which is dilute (ng/mL) and highly fragmented [30 to 100 nucleotides (nt)]. The clinical sensitivity of urine cfDNA detection increases with decreasing target length, motivating use of sample preparation methods designed for short fragments. We compared the analytical performance of two published protocols (Wizard resin/guanidinium thiocyanate and Q Sepharose), three commercial kits (Norgen, QIAamp, and MagMAX), and an in-house sequence-specific hybridization capture technique. Dependence on fragment length (25 to 150 nt), performance at low concentrations (10 copies/mL), tolerance to variable urine conditions, and susceptibility to PCR inhibition were characterized. Hybridization capture and Q Sepharose performed best overall (60% to 90% recovery), although Q Sepharose had reduced recovery (<10%) of the shortest 25-nt fragment. Wizard resin/guanidinium thiocyanate recovery was dependent on pH and background DNA concentration and was limited to <35%, even under optimal conditions. The Norgen kit led to consistent PCR inhibition but had high recovery of short fragments. The QIAamp and MagMAX kits had minimal recovery of fragments <150 and <80 nt, respectively. Urine cfDNA extraction methods differ widely in ability to capture short, dilute cfDNA in urine; using suboptimal methods may profoundly impair clinical results.

Indexed as

Anion Exchange ResinsCell-Free Nucleic AcidsGuanidinesHumansReagent Kits, DiagnosticReal-Time Polymerase Chain ReactionSepharoseThiocyanatesUrinalysisUrineAnion Exchange ResinsCell-Free Nucleic AcidsGuanidinesguanidine thiocyanateReagent Kits, DiagnosticSepharoseThiocyanates

Identifiers

PMID31442674
PMCPMC6854475
OpenAlexW2969642969

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.