Global identification of human papillomavirus integration sites in uterine cervical cancer cell lines by next-generation sequencing

2016 ◽  
Author(s):  
Noriyuki Yokomichi
Keyword(s):  
Cervical Cancer ◽  
Human Papillomavirus ◽  
Next Generation Sequencing ◽  
Cell Lines ◽  
Cancer Cell ◽  
Uterine Cervical Cancer ◽  
Next Generation ◽  
Integration Sites ◽  
Global Identification ◽  
Generation Sequencing

Discovering HPV16 and HPV18 infection status and cancer gene variations in cervical cancer patient specimens by using Next-generation sequencing.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e13040-e13040
Author(s):  
Bo Meng ◽  
Lili Quan ◽  
Wenjuan Yang ◽  
Jidong Lang ◽  
Lanyou Chen ◽  
...  
Keyword(s):  
Cervical Cancer ◽  
Next Generation Sequencing ◽  
Human Genome ◽  
Gene List ◽  
Cervical Cancer Patient ◽  
Cancer Gene ◽  
Next Generation ◽  
Genetic Event ◽  
Integration Sites ◽  
Generation Sequencing

e13040 Background: Human papillomavirus (HPV) infection has been reported as an important cause of cervical cancer for many years. HPV16 and HPV18 are the two most prevalent types in cervical cancer5. Integration of HPV DNA is a crucial genetic event in cervical carcinogenesis. Therefore, it is important to know the HPV integration hot spots in human genome to predict the cervical cancer development status of patients. Although many studies have addressed the HPV integration sites in human genome, it is still a technique barrier to precisely determine the HPV integration sites of each patient, especially at early disease development stage with limited integration sites existing. Methods: To solve this problem, we first designed HPV probes to capture HPV integrated sequences of genome using next generation sequencing (NGS). And then we analyzed the integration sites by two methods with the NGS results, HPV Detector. We applied the study on 17 patient samples, 15 of them were found HPV16 positive and 2 of them were found HPV18 positive. Among them 16 were detected with HPV integration sites. Results: The results indicated that different samples showed different numbers of integration sites with limited overlapped positions in genome. The integrated positions of HPV16/18 located in all the genes of the virus, but mostly distributed in gene E1, L1 and L2. We identified integration sites HPV16 E6/GATC， E6/WWTR1， L2/DGKB, E1/EHHADH, ect. Some of the integrated sites in human genome are belong to intergenic region. We also used cancer gene panel, which cover 143 cancer related genes exon regions, to identify the mutation sites of each samples. We summed up a highly occurred mutated cancer gene list, which include ALK, NF1, PIK3R1, ROS1, TSC1, TSC2, ect. Most of them are either cancer driver genes or have been found highly related to cervical cancer. Further study is still carrying on. Conclusions: In conclusion, our HPV probe could successfully detect HPV16 and HPV18 in patient samples and enrich HPV integration sites in human genome of cervical samples significantly. It could provide detailed information for cervical cancer discovery and early detection.

scholarly journals Frequent Mutations in TP53 and CDKN2A Found by Next-Generation Sequencing of Head and Neck Cancer Cell Lines

2012 ◽  
Vol 138 (8) ◽  
pp. 732 ◽  
Author(s):  
Anthony C. Nichols ◽  
John Yoo ◽  
David A. Palma ◽  
Kevin Fung ◽  
Jason H. Franklin ◽  
...  
Keyword(s):  
Head And Neck Cancer ◽  
Next Generation Sequencing ◽  
Head And Neck ◽  
Cell Lines ◽  
Cancer Cell ◽  
Neck Cancer ◽  
Cancer Cell Lines ◽  
Next Generation ◽  
Frequent Mutations ◽  
Generation Sequencing

Comparison of three human papillomavirus DNA detection methods: Next generation sequencing, multiplex-PCR and nested-PCR followed by Sanger based sequencing

2015 ◽  
Vol 88 (5) ◽  
pp. 888-894 ◽  
Author(s):  
Allex Jardim da Fonseca ◽  
Renata Silva Galvão ◽  
Angelica Espinosa Miranda ◽  
Luiz Carlos de Lima Ferreira ◽  
Zigui Chen
Keyword(s):  
Human Papillomavirus ◽  
Next Generation Sequencing ◽  
Multiplex Pcr ◽  
Nested Pcr ◽  
Dna Detection ◽  
Detection Methods ◽  
Next Generation ◽  
Papillomavirus Dna ◽  
Generation Sequencing

scholarly journals Human papillomavirus genotyping by Linear Array and Next-Generation Sequencing in cervical samples from Western Mexico

2015 ◽  
Vol 12 (1) ◽  
Author(s):  
María Guadalupe Flores-Miramontes ◽  
Luis Alberto Torres-Reyes ◽  
Liliana Alvarado-Ruíz ◽  
Salvador Angel Romero-Martínez ◽  
Verenice Ramírez-Rodríguez ◽  
...  
Keyword(s):  
Human Papillomavirus ◽  
Next Generation Sequencing ◽  
Linear Array ◽  
Next Generation ◽  
Western Mexico ◽  
Generation Sequencing

Photogem Induces Necrosis in Various Uterine Cervical Cancer Cell Lines by PDT

2003 ◽  
Vol 35 (6) ◽  
pp. 549-556 ◽  
Author(s):  
Su Mi Bae ◽  
Seung Won Huh ◽  
Eun Kyung Park ◽  
Keun Ho Lee ◽  
Joon Mo Lee ◽  
...  
Keyword(s):  
Cervical Cancer ◽  
Cell Lines ◽  
Cancer Cell ◽  
Cancer Cell Lines ◽  
Uterine Cervical Cancer ◽  
Cervical Cancer Cell

scholarly journals Evaluation of TypeSeq, a Novel High-Throughput, Low-Cost, Next-Generation Sequencing-Based Assay for Detection of 51 Human Papillomavirus Genotypes

2019 ◽  
Vol 220 (10) ◽  
pp. 1609-1619 ◽  
Author(s):  
Sarah Wagner ◽  
David Roberson ◽  
Joseph Boland ◽  
Aimée R Kreimer ◽  
Meredith Yeager ◽  
...  
Keyword(s):  
Human Papillomavirus ◽  
Next Generation Sequencing ◽  
High Throughput ◽  
Vaccine Efficacy ◽  
Linear Array ◽  
Human Papillomaviruses ◽  
Next Generation ◽  
Hpv Genotyping ◽  
Positive Agreement ◽  
Generation Sequencing

AbstractBackgroundHuman papillomaviruses (HPV) cause over 500 000 cervical cancers each year, most of which occur in low-resource settings. Human papillomavirus genotyping is important to study natural history and vaccine efficacy. We evaluated TypeSeq, a novel, next-generation, sequencing-based assay that detects 51 HPV genotypes, in 2 large international epidemiologic studies.MethodsTypeSeq was evaluated in 2804 cervical specimens from the Study to Understand Cervical Cancer Endpoints and Early Determinants (SUCCEED) and in 2357 specimens from the Costa Rica Vaccine Trial (CVT). Positive agreement and risks of precancer for individual genotypes were calculated for TypeSeq in comparison to Linear Array (SUCCEED). In CVT, positive agreement and vaccine efficacy were calculated for TypeSeq and SPF10-LiPA.ResultsWe observed high overall and positive agreement for most genotypes between TypeSeq and Linear Array in SUCCEED and SPF10-LiPA in CVT. There was no significant difference in risk of precancer between TypeSeq and Linear Array in SUCCEED or in estimates of vaccine efficacy between TypeSeq and SPF10-LiPA in CVT.ConclusionsThe agreement of TypeSeq with Linear Array and SPF10-LiPA, 2 well established standards for HPV genotyping, demonstrates its high accuracy. TypeSeq provides high-throughput, affordable HPV genotyping for world-wide studies of cervical precancer risk and of HPV vaccine efficacy.

scholarly journals Differential Regulation of Telomeric Complex by BCR-ABL1 Kinase in Human Cellular Models of Chronic Myeloid Leukemia—From Single Cell Analysis to Next-Generation Sequencing

Genes ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 1145
Author(s):  
Anna Deregowska ◽  
Monika Pepek ◽  
Katarzyna Pruszczyk ◽  
Marcin M. Machnicki ◽  
Maciej Wnuk ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Chronic Myeloid Leukemia ◽  
Telomere Length ◽  
Cell Lines ◽  
Copy Number ◽  
Myeloid Leukemia ◽  
Telomere Maintenance ◽  
Next Generation ◽  
Cellular Models ◽  
Generation Sequencing

Telomeres are specialized nucleoprotein complexes, localized at the physical ends of chromosomes, that contribute to the maintenance of genome stability. One of the features of chronic myeloid leukemia (CML) cells is a reduction in telomere length which may result in increased genomic instability and progression of the disease. Aberrant telomere maintenance in CML is not fully understood and other mechanisms such as the alternative lengthening of telomeres (ALT) are involved. In this work, we employed five BCR-ABL1-positive cell lines, namely K562, KU-812, LAMA-84, MEG-A2, and MOLM-1, commonly used in the laboratories to study the link between mutation, copy number, and expression of telomere maintenance genes with the expression, copy number, and activity of BCR-ABL1. Our results demonstrated that the copy number and expression of BCR-ABL1 are crucial for telomere lengthening. We observed a correlation between BCR-ABL1 expression and telomere length as well as shelterins upregulation. Next-generation sequencing revealed pathogenic variants and copy number alterations in major tumor suppressors, such as TP53 and CDKN2A, but not in telomere-associated genes. Taken together, we showed that BCR-ABL1 kinase expression and activity play a crucial role in the maintenance of telomeres in CML cell lines. Our results may help to validate and properly interpret results obtained by many laboratories employing these in vitro models of CML.

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