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| 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.
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| 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.
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| Web link |
http://10.1186/s13059-024-03262-2
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| Contributor(s) |
Cui X, Nie J, Kowitwanich K, Beadell A, West-Szymanski D, Zhang W, Chen M, He C |
| Citation(s) |
38877540 |
| |
| Submission date |
Oct 15, 2021 |
| Last update date |
Jul 24, 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 |
| |
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| Platforms (3) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (106)
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| Relations |
| BioProject |
PRJNA771691 |
| SRA |
SRP341621 |
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