Open AccessQuantifying sequencing error and effective sequencing depth of liquid biopsy NGS with UMI error correction
Author(s) -
Malene S. Frank,
Janina Fuß,
Tim Alexander Steiert,
Greta Streleckienė,
Julie Gehl,
Michael Förster
Publication year - 2021
Publication title -
biotechniques/biotechniques
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.617
H-Index - 131
eISSN - 1940-9818
pISSN - 0736-6205
DOI - 10.2144/btn-2020-0124
Subject(s) - liquid biopsy , dna sequencing , biopsy , dna , circulating tumor dna , computational biology , workflow , computer science , cancer , pathology , biology , medicine , genetics , database
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.