Analysis of microbial sequences in plasma cell-free DNA for early-onset breast cancer patients and healthy females

Abstract

Background

Cell-free circulating DNA (cfDNA) is becoming a useful biopsy for noninvasive diagnosis of diseases. Microbial sequences in plasma cfDNA may provide important information to improve prognosis and treatment. We have developed a stringent method to identify microbial species via microbial cfDNA in the blood plasma of early-onset breast cancer (EOBC) patients and healthy females. Empirically, microbe-originated sequence reads were identified by mapping non-human PE reads in cfDNA libraries to microbial databases. Those mapped concordantly to unique microbial species were assembled into contigs, which were subsequently aligned to the same databases. Microbial species uniquely aligned were identified and compared across all individuals on MCRPM (Microbial CfDNA Reads Per Million quality PE reads) basis.

Results

The predominant microbial cfDNAs in all plasma samples examined are originated from bacteria and these bacteria were limited to only a few genera. Among those, Acinetobacter johnsonii XBB1 and low levels of Mycobacterium spp. were commonly found in all healthy females, but also present in an EOBC patient. Compared to those in healthy counterparts, bacterial species in EOBC patients are more diverse and more likely to present at high levels. Among these three EOBC patients tested, a patient who has record high titer (2,724 MCRPM) of Pseudomonas mendocina together with 8.82 MCRPM of Pannonibacter phragmitetus has passed away; another patient infected by multiple Sphingomonas species remains alive; while the third patient who has similar microbial species (Acinetobacter johnsonii XBB1) commonly seen in normal controls is having a normal life.

Conclusions

Our preliminary data on the profiles of microbial cfDNA sequences suggested that it may have some prognostic value in cancer patients. Validation in larger number of patients is warranted.

 

Microbial Data

5 individuals hg19 unmapped paired-end (PE) reads for the study

IDTypeR1R2
BBCNormalR1.fastqR2.fastq
EJCNormalR1.fastqR2.fastq
BC0145EOBCR1.fastqR2.fastq
BC0190EOBCR1.fastqR2.fastq
CGBC0025EOBCR1.fastqR2.fastq

BBC is normal Taiwanese and at age 40 or younger.
EJC is normal Taiwanese and at age 40 or younger.
BC0145 was suffering from breast cancer(subtype :LB) age 40 or younger in Taiwan.
BC0190 was suffering from breast cancer(subtype :LB) age 40 or younger in Taiwan.
GCBC0025 was suffering from breast cancer(subtype :LB) age 40 or younger in Taiwan.