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Series GSE186007 Query DataSets for GSE186007
Status Public on Apr 24, 2024
Title LABS: linear amplification-based bisulfite sequencing for ultrasensitive cancer detection from cell-free DNA
Organisms Homo sapiens; Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary Methylation-based liquid biopsies show promise in detecting cancer from circulating cell-free DNA, but current limitations impede clinical application. Most assays necessitate substantial DNA inputs, posing challenges. Underrepresented tumor DNA fragments may go undetected during exponential amplification steps of traditional sequencing methods. Here we report LABS (Linear Amplification based Bisulfite Sequencing), enabling linear amplification of bisulfite-treated DNA fragments in a genome-wide, unbiased fashion, detecting cancer abnormalities with sub-nanogram inputs. Applying LABS to 100 patient samples revealed cancer-specific patterns, copy number alterations, and enhanced cancer detection accuracy by identifying tissue-of-origin and immune cell composition.
 
Overall design For method validation, we compared our LABS method with two commonly used commercial methods: EpiGnome and MethylC-seq. For clinical usage, we collected cfDNA samples from 50 CRC, 16 PDAC, and 34 control patients.
 
Contributor(s) Cui X, Nie J, Kowitwanich K, Beadell A, West-Szymanski D, Zhang W, Chen M, He C
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Submission date Oct 15, 2021
Last update date Apr 26, 2024
Contact name Xiaolong Cui
E-mail(s) xiaolong.cui@northwestern.edu
Organization name Northwestern University
Department Department of Preventive Medicine
Street address 680 N Lake Shore Drive
City Chicago
State/province IL
ZIP/Postal code 60611
Country USA
 
Platforms (3)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (106)
GSM5628822 10pg rep1
GSM5628823 10pg rep2
GSM5628824 20pg rep1
Relations
BioProject PRJNA771691
SRA SRP341621

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE186007_RAW.tar 16.9 Gb (http)(custom) TAR (of COV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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