LABS: linear amplification-based bisulfite sequencing for ultrasensitive cancer detection from cell-free DNA

Xiao-Long Cui; Ji Nie; Houxiang Zhu; Krissana Kowitwanich; Alana V Beadell; Diana C West-Szymanski; Zhou Zhang; Urszula Dougherty; Akushika Kwesi; Zifeng Deng; Yan Li; Danqing Meng; Kevin Roggin; Teresa Barry; Ryan Owyang; Ben Fefferman; Chang Zeng; Lu Gao; Carolyn W T Zhao; Yuri Malina; Jiangbo Wei; Melanie Weigert; Wenjun Kang; Ajay Goel; Brian C-H Chiu; Marc Bissonnette; Wei Zhang; Mengjie Chen; Chuan He

doi:10.1186/s13059-024-03262-2

LABS: linear amplification-based bisulfite sequencing for ultrasensitive cancer detection from cell-free DNA

Genome Biol. 2024 Jun 14;25(1):157. doi: 10.1186/s13059-024-03262-2.

Authors

Xiao-Long Cui^#^{1

2

3}, Ji Nie^#^{1

2}, Houxiang Zhu^#^{4

5}, Krissana Kowitwanich^{1

2}, Alana V Beadell^{1

2}, Diana C West-Szymanski^{1

2

4}, Zhou Zhang³, Urszula Dougherty⁴, Akushika Kwesi⁴, Zifeng Deng⁴, Yan Li^{4

5}, Danqing Meng⁶, Kevin Roggin⁷, Teresa Barry⁴, Ryan Owyang^{1

2}, Ben Fefferman^{1

2}, Chang Zeng³, Lu Gao^{1

2

4}, Carolyn W T Zhao^{1

2}, Yuri Malina^{1

2}, Jiangbo Wei^{1

2}, Melanie Weigert⁸, Wenjun Kang^{4

5}, Ajay Goel⁹, Brian C-H Chiu¹⁰, Marc Bissonnette⁴, Wei Zhang^#^{11

12}, Mengjie Chen^#^{13

14}, Chuan He^#^{15

16}

Affiliations

¹ Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
² Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
³ Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
⁴ Department of Medicine, The University of Chicago, Chicago, IL, USA.
⁵ Department of Human Genetics, The University of Chicago, Chicago, IL, USA.
⁶ Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
⁷ Department of Surgery, The University of Chicago, Chicago, IL, USA.
⁸ Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, The University of Chicago, Chicago, IL, USA.
⁹ City of Hope Comprehensive Cancer Center, Duarte, CA, USA.
¹⁰ Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA.
¹¹ Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. [email protected].
¹² The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. [email protected].
¹³ Department of Medicine, The University of Chicago, Chicago, IL, USA. [email protected].
¹⁴ Department of Human Genetics, The University of Chicago, Chicago, IL, USA. [email protected].
¹⁵ Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA. [email protected].
¹⁶ Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA. [email protected].

^# Contributed equally.

Abstract

Methylation-based liquid biopsies show promises in detecting cancer using circulating cell-free DNA; however, current limitations impede clinical application. Most assays necessitate substantial DNA inputs, posing challenges. Additionally, underrepresented tumor DNA fragments may go undetected during exponential amplification steps of traditional sequencing methods. Here, we report linear amplification-based bisulfite sequencing (LABS), 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.

Keywords: Bisulfite sequencing; Cancer detection; Cell-free DNA; Linear amplification; Low-input DNA.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.
Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural

MeSH terms

Cell-Free Nucleic Acids
Circulating Tumor DNA / genetics
DNA Copy Number Variations
DNA Methylation*
DNA, Neoplasm / genetics
Humans
Neoplasms* / genetics
Nucleic Acid Amplification Techniques / methods
Sequence Analysis, DNA* / methods
Sulfites*

Substances

Sulfites
Cell-Free Nucleic Acids
hydrogen sulfite
DNA, Neoplasm
Circulating Tumor DNA

Abstract

Publication types

MeSH terms

Substances

Grants and funding