DOI: 10.5061/dryad.7pj51v0
title: Data from: Automated size selection for short cell-free DNA fragments enriches for circulating tumor DNA and improves error correction during next generation sequencing

description: Circulating tumor-derived cell-free DNA (ctDNA) enables non-invasive
 diagnosis, monitoring, and treatment susceptibility testing in human
 cancers. However, accurate detection of variant alleles, particularly
 during untargeted searches, remains a principal obstacle to widespread
 application of cell-free DNA in clinical oncology. In this study,
 isolation of short cell-free DNA fragments is shown to enrich for tumor
 variants and improve correction of PCR- and sequencing-associated errors.
 Subfractions of the mononucleosome of circulating cell-free DNA (ccfDNA)
 were isolated from patients with melanoma, pancreatic ductal
 adenocarcinoma, and colorectal adenocarcinoma using a
 high-throughput-capable automated gel-extraction platform. Using a
 128-gene (128 kb) custom next-generation sequencing panel, variant alleles
 were on average 2-fold enriched in the short fraction (median insert size:
 ~142 bp) compared to the original ccfDNA sample, while 0.7-fold reduced in
 the fraction corresponding to the principal peak of the mononucleosome
 (median insert size: ~167 bp). Size-selected short fractions compared to
 the original ccfDNA yielded significantly larger family sizes (i.e., PCR
 duplicates) during in silico consensus sequence interpretation via unique
 molecular identifiers. Increments in family size were associated with a
 progressive reduction of PCR and sequencing errors. Although consensus
 read depth also decreased at larger family sizes, the variant allele
 frequency in the short ccfDNA fraction remained consistent, while variant
 detection in the original ccfDNA was commonly lost at family sizes
 necessary to minimize errors. These collective findings support the
 automated extraction of short ccfDNA fragments to enrich for ctDNA while
 concomitantly reducing false positives through in silico error correction.
description: READMEBuffy coat DNA
 sequencing files - C114145X13.tar.gzBuffy coat DNA sequencing files - C214145X15.tar.gzBuffy coat DNA sequencing files - C314145X17.tar.gzBuffy coat DNA sequencing files - M114145X1.tar.gzBuffy coat DNA sequencing files - M214145X3.tar.gzBuffy coat DNA sequencing files - M314145X5.tar.gzBuffy coat DNA sequencing files - M514145X9.tar.gzBuffy coat DNA sequencing files - M614145X11.tar.gzBuffy coat DNA sequencing files - M814153X15.tar.gzBuffy coat DNA sequencing files - P114145X19.tar.gzBuffy coat DNA sequencing files - P214145X21.tar.gzUnselected cell-free DNA sequencing files - C114145X14.tar.gzUnselected cell-free DNA sequencing files - C214145X16.tar.gzUnselected cell-free DNA sequencing files - C314145X18.tar.gzUnselected cell-free DNA sequencing files - M114145X2.tar.gzUnselected cell-free DNA sequencing files - M214145X4.tar.gzUnselected cell-free DNA sequencing files - M314145X6.tar.gzUnselected cell-free DNA sequencing files - M514145X10.tar.gzUnselected cell-free DNA sequencing files - M614145X12.tar.gzUnselected cell-free DNA sequencing files - M814153X16.tar.gzUnselected cell-free DNA sequencing files - P114145X20.tar.gzUnselected cell-free DNA sequencing files - P214145X22.tar.gz"Short" cell-free DNA sequencing files - C114401X9.tar.gz"Short" cell-free DNA sequencing files - C214401X10.tar.gz"Short" cell-free DNA sequencing files - C314543X8.tar.gz"Short" cell-free DNA sequencing files - M114401X1.tar.gz"Short" cell-free DNA sequencing files - M214401X2.tar.gz"Short" cell-free DNA sequencing files - M314401X3.tar.gz"Short" cell-free DNA sequencing files - M514401X5.tar.gz"Short" cell-free DNA sequencing files - M614574X3.tar.gz"Short" cell-free DNA sequencing files - M814574X1.tar.gz"Short" cell-free DNA sequencing files - P114401X12.tar.gz"Short" cell-free DNA sequencing files - P214574X5.tar.gz"Medium" cell-free DNA sequencing files - C114401X25.tar.gz"Medium" cell-free DNA sequencing files - C214574X2.tar.gz"Medium" cell-free DNA sequencing files - C314401X27.tar.gz"Medium" cell-free DNA sequencing files - M114401X17.tar.gz"Medium" cell-free DNA sequencing files - M214401X18.tar.gz"Medium" cell-free DNA sequencing files - M314401X19.tar.gz"Medium" cell-free DNA sequencing files - M514401X21.tar.gz"Medium" cell-free DNA sequencing files - M614574X4.tar.gz"Medium" cell-free DNA sequencing files - M814401X24.tar.gz"Medium" cell-free DNA sequencing files - P114574X8.tar.gz"Medium" cell-free DNA sequencing files - P214401X29.tar.gz"Long" cell-free DNA sequencing files - C114431X9.tar.gz"Long" cell-free DNA sequencing files - C214431X10.tar.gz"Long" cell-free DNA sequencing files - C314431X11.tar.gz"Long" cell-free DNA sequencing files - M114431X1.tar.gz"Long" cell-free DNA sequencing files - M214431X2.tar.gz"Long" cell-free DNA sequencing files - M314431X3.tar.gz"Long" cell-free DNA sequencing files - M514431X5.tar.gz"Long" cell-free DNA sequencing files - M614543X7.tar.gz"Long" cell-free DNA sequencing files - M814431X8.tar.gz"Long" cell-free DNA sequencing files - P114431X12.tar.gz"Long" cell-free DNA sequencing files - P214431X13.tar.gz