title: Detection and analysis of human papillomavirus (HPV) DNA in breast cancer patients by an effective method of HPV capture.
abstract: Despite an increase in the number of molecular epidemiological studies conducted in recent years to evaluate the association between human papillomavirus (HPV) and the risk of breast carcinoma, these studies remain inconclusive. Here we aim to detect HPV DNA in various tissues from patients with breast carcinoma using the method of HPV capture combined with massive paralleled sequencing (MPS). To validate the confidence of our methods, 15 cervical cancer samples were tested by PCR and the new method. Results showed that there was 100% consistence between the two methods.DNA from peripheral blood, tumor tissue, adjacent lymph nodes and adjacent normal tissue were collected from seven malignant breast cancer patients, and HPV type 16 (HPV16) was detected in 1/7, 1/7, 1/7 and 1/7 of patients respectively. Peripheral blood, tumor tissue and adjacent normal tissue were also collected from two patients with benign breast tumor, and 1/2, 2/2 and 2/2 was detected to have HPV16 DNA respectively. MPS metrics including mapping ratio, coverage, depth and SNVs were provided to characterize HPV in samples. The average coverage was 69% and 61.2% for malignant and benign samples respectively. 126 SNVs were identified in all 9 samples. The maximum number of SNVs was located in the gene of E2 and E4 among all samples. Our study not only provided an efficient method to capture HPV DNA, but detected the SNVS, coverage, SNV type and depth. The finding has provided further clue of association between HPV16 and breast cancer.
authors.affiliation: Department of Vascular and Endocrine Surgery, Xijing Hospital, Fourth Military Medical University, Xi An, China.
authors.forename: Ting
authors.initials: T
authors.lastname: Wang
authors.affiliation: BGI-Shenzhen, Shenzhen, China; Division of Genomics and Bioinformatics, CUHK-BGI Innovation Institute of Trans-omics, The Chinese University of Hong Kong, Hong Kong, China.
authors.forename: Xi
authors.initials: X
authors.lastname: Zeng
authors.affiliation: BGI-Shenzhen, Shenzhen, China; School of Bioscience and Bioengineering, South China University of Technology, Guang Zhou, Chinah.
authors.forename: Weiyang
authors.initials: W
authors.lastname: Li
authors.affiliation: Department of Vascular and Endocrine Surgery, Xijing Hospital, Fourth Military Medical University, Xi An, China.
authors.forename: Haijun
authors.initials: H
authors.lastname: Zhu
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Guan
authors.initials: G
authors.lastname: Wang
authors.affiliation: BGI-Shenzhen, Shenzhen, China; Department of Biology, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Xiao
authors.initials: X
authors.lastname: Liu
authors.affiliation: Department of Vascular and Endocrine Surgery, Xijing Hospital, Fourth Military Medical University, Xi An, China.
authors.forename: Yonggang
authors.initials: Y
authors.lastname: Lv
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Jinghua
authors.initials: J
authors.lastname: Wu
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Xuehan
authors.initials: X
authors.lastname: Zhuang
authors.affiliation: Department of Vascular and Endocrine Surgery, Xijing Hospital, Fourth Military Medical University, Xi An, China.
authors.forename: Juliang
authors.initials: J
authors.lastname: Zhang
authors.affiliation: BGI-Shenzhen, Shenzhen, China; School of Bioscience and Bioengineering, South China University of Technology, Guang Zhou, Chinah.
authors.forename: Yi
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: BGI-Shenzhen, Shenzhen, China; School of Bioscience and Bioengineering, South China University of Technology, Guang Zhou, Chinah.
authors.forename: Haodong
authors.initials: H
authors.lastname: Huang
authors.affiliation: Department of Vascular and Endocrine Surgery, Xijing Hospital, Fourth Military Medical University, Xi An, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Fan
authors.affiliation: Department of Vascular and Endocrine Surgery, Xijing Hospital, Fourth Military Medical University, Xi An, China.
authors.forename: Qing
authors.initials: Q
authors.lastname: Yao
authors.affiliation: Department of Vascular and Endocrine Surgery, Xijing Hospital, Fourth Military Medical University, Xi An, China.
authors.forename: Chenyang
authors.initials: C
authors.lastname: He
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Xiuqing
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Department of Nephrology, Xijing Hospital, Fourth Military Medical University, Xi An, China.
authors.forename: Chen
authors.initials: C
authors.lastname: Huang
authors.affiliation: Department of Vascular and Endocrine Surgery, Xijing Hospital, Fourth Military Medical University, Xi An, China.
authors.forename: Jianghao
authors.initials: J
authors.lastname: Chen
authors.affiliation: Department of Vascular and Endocrine Surgery, Xijing Hospital, Fourth Military Medical University, Xi An, China.
authors.forename: Ling
authors.initials: L
authors.lastname: Wang
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D001943:Breast Neoplasms / Q000821:virology*; D004279:DNA, Viral / Q000235:genetics*; D005260:Female; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008875:Middle Aged; D027383:Papillomaviridae / Q000235:genetics* / Q000302:isolation & purification*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D002583:Uterine Cervical Neoplasms / Q000821:virology
chemical_list: D004279:DNA, Viral