Quantifying sequencing error and effective sequencing depth of liquid biopsy NGS with UMI error correction

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt

Standard

Quantifying sequencing error and effective sequencing depth of liquid biopsy NGS with UMI error correction. / Frank, Malene Støchkel; Fuß, Janina; Steiert, Tim Alexander; Streleckiene, Greta; Gehl, Julie; Forster, Michael.

I: BioTechniques, Bind 70, Nr. 4, 2021, s. 226-232.

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt

Harvard

Frank, MS, Fuß, J, Steiert, TA, Streleckiene, G, Gehl, J & Forster, M 2021, 'Quantifying sequencing error and effective sequencing depth of liquid biopsy NGS with UMI error correction', BioTechniques, bind 70, nr. 4, s. 226-232. https://doi.org/10.2144/btn-2020-0124

APA

Frank, M. S., Fuß, J., Steiert, T. A., Streleckiene, G., Gehl, J., & Forster, M. (2021). Quantifying sequencing error and effective sequencing depth of liquid biopsy NGS with UMI error correction. BioTechniques, 70(4), 226-232. https://doi.org/10.2144/btn-2020-0124

Vancouver

Frank MS, Fuß J, Steiert TA, Streleckiene G, Gehl J, Forster M. Quantifying sequencing error and effective sequencing depth of liquid biopsy NGS with UMI error correction. BioTechniques. 2021;70(4):226-232. https://doi.org/10.2144/btn-2020-0124

Author

Frank, Malene Støchkel ; Fuß, Janina ; Steiert, Tim Alexander ; Streleckiene, Greta ; Gehl, Julie ; Forster, Michael. / Quantifying sequencing error and effective sequencing depth of liquid biopsy NGS with UMI error correction. I: BioTechniques. 2021 ; Bind 70, Nr. 4. s. 226-232.

Bibtex

@article{5d8caf4b6b1e48959feb514e5a0fbe94,
title = "Quantifying sequencing error and effective sequencing depth of liquid biopsy NGS with UMI error correction",
abstract = "Liquid biopsies are a minimally invasive method to diagnose and longitudinally monitor tumor mutations in patients when tissue biopsies are difficult (e.g., in lung cancer). The percentage of cell-free tumor DNA in blood plasma ranges from more than 65% to 0.1% or lower. To reliably diagnose tumor mutations at 0.1%, there are two options: unrealistically large volumes of patient blood or library preparation and sequencing depth optimized to low-input DNA. Here, we assess two library preparation methods and analysis workflows to determine feasibility and reliability based on standards with known allelic frequency (0 and 0.13% in PIK3CA). However, the implementation for patients is still costly and requires elaborate setups.",
keywords = "cell-free DNA, low allele frequency, next-generation sequencing, unique molecular identifier (UMI)",
author = "Frank, {Malene St{\o}chkel} and Janina Fu{\ss} and Steiert, {Tim Alexander} and Greta Streleckiene and Julie Gehl and Michael Forster",
year = "2021",
doi = "10.2144/btn-2020-0124",
language = "English",
volume = "70",
pages = "226--232",
journal = "BioTechniques",
issn = "0736-6205",
publisher = "Informa Healthcare",
number = "4",

}

RIS

TY - JOUR

T1 - Quantifying sequencing error and effective sequencing depth of liquid biopsy NGS with UMI error correction

AU - Frank, Malene Støchkel

AU - Fuß, Janina

AU - Steiert, Tim Alexander

AU - Streleckiene, Greta

AU - Gehl, Julie

AU - Forster, Michael

PY - 2021

Y1 - 2021

N2 - Liquid biopsies are a minimally invasive method to diagnose and longitudinally monitor tumor mutations in patients when tissue biopsies are difficult (e.g., in lung cancer). The percentage of cell-free tumor DNA in blood plasma ranges from more than 65% to 0.1% or lower. To reliably diagnose tumor mutations at 0.1%, there are two options: unrealistically large volumes of patient blood or library preparation and sequencing depth optimized to low-input DNA. Here, we assess two library preparation methods and analysis workflows to determine feasibility and reliability based on standards with known allelic frequency (0 and 0.13% in PIK3CA). However, the implementation for patients is still costly and requires elaborate setups.

AB - Liquid biopsies are a minimally invasive method to diagnose and longitudinally monitor tumor mutations in patients when tissue biopsies are difficult (e.g., in lung cancer). The percentage of cell-free tumor DNA in blood plasma ranges from more than 65% to 0.1% or lower. To reliably diagnose tumor mutations at 0.1%, there are two options: unrealistically large volumes of patient blood or library preparation and sequencing depth optimized to low-input DNA. Here, we assess two library preparation methods and analysis workflows to determine feasibility and reliability based on standards with known allelic frequency (0 and 0.13% in PIK3CA). However, the implementation for patients is still costly and requires elaborate setups.

KW - cell-free DNA

KW - low allele frequency

KW - next-generation sequencing

KW - unique molecular identifier (UMI)

U2 - 10.2144/btn-2020-0124

DO - 10.2144/btn-2020-0124

M3 - Journal article

C2 - 33512245

AN - SCOPUS:85104369522

VL - 70

SP - 226

EP - 232

JO - BioTechniques

JF - BioTechniques

SN - 0736-6205

IS - 4

ER -

ID: 261055473