A5058484846- Cervical Cancer and HPV Research
- Polyomavirus and related diseases
- Nonmelanoma Skin Cancer Studies
- Plant Virus Research Studies
- Viral-associated cancers and disorders
- Animal Virus Infections Studies
- Genomics and Phylogenetic Studies
- Head and Neck Cancer Studies
- Hepatitis B Virus Studies
- Genital Health and Disease
- Microbial infections and disease research
- Molecular Biology Techniques and Applications
- Bacteriophages and microbial interactions
- Urological Disorders and Treatments
- Cancer-related molecular mechanisms research
- Algorithms and Data Compression
- Acute Lymphoblastic Leukemia research
- Machine Learning in Bioinformatics
- Machine Learning and Data Classification
- Prenatal Screening and Diagnostics
- Reproductive tract infections research
- Big Data and Business Intelligence
- Celiac Disease Research and Management
- Childhood Cancer Survivors' Quality of Life
- Bladder and Urothelial Cancer Treatments
Karolinska Institutet
2011-2019
Karolinska University Hospital
2011-2017
Centre International de Recherche sur le Cancer
2016
Lawrence Berkeley National Laboratory
2013
Lund University
2010-2012
Malmö University
2010
University of Iceland
2009
Finnish Cancer Registry
2009
Icelandic Cancer Society
2009
Tampere University
2009
Most viruses in human skin are known to be papillomaviruses (HPVs). Previous sequencing of samples has identified 273 different cutaneous HPV types, including 47 previously unknown types. In the present study, we wished extend prior studies using deeper sequencing. This without PCR a pool 142 whole genome amplified lesions 23 3 novel putative types and 4 non-HPV viruses. The complete sequence was obtained for one almost addition, amplimers from consensus 326 detected 385 226 conclusion,...
Patients with recurrent respiratory papillomatosis (RRP) in Norway treated between 1987 and 2009 were recruited to this cohort study. They followed from disease onset data recorded until January 2012. Here, we describe the distribution of human papillomavirus (HPV) genotypes, prevalence multiple HPV infections, risk high-grade laryngeal neoplasia tract invasive carcinoma a large patients RRP. We also examined whether genotype, gender, age or clinical course are factors for development....
There are at least 120 completely characterized human papillomavirus (HPV) types and putative new continuously found. Both squamous cell carcinoma of the skin (SCC) other lesions commonly contain multiple cutaneous HPV types. The objective this study was to achieve an improved resolution diversity in such as SCCs, actinic keratoses (AKs) keratoacanthomas (KAs). Fresh frozen biopsies from 37 SCC lesions, 36 AK 92 KA swab samples top lesion 86 SCCs AKs were amplified using general primers FAP...
Immunosuppression involves an inability to control virus infections and increased incidence of virus-associated cancers. Some cancers without known viral etiology are also increased, but data on exactly which cancer forms has been inconsistent. To provide a reliable generalizable estimate, with high statistical power long follow-up time, we assessed risks using comprehensive, population-based registries in two different countries from immunosuppressed patient groups (solid organ transplant...
To assess presence of virus DNA in skin lesions, swab samples from 82 squamous cell carcinomas the (SCCs), 60 actinic keratoses (AKs), paraffin-embedded biopsies 28 SCCs and 72 kerathoacanthomas (KAs) fresh-frozen 92 KAs, 85 AKs were analyzed by high throughput sequencing (HTS) using 454 or Ion Torrent technology. We found total 4,284 viral reads, out which 4,168 Human Papillomavirus (HPV)-related, belonging to 15 known (HPV8, HPV12, HPV20, HPV36, HPV38, HPV45, HPV57, HPV59, HPV104, HPV105,...
Non‐melanoma skin cancers commonly contain Human Papillomavirus (HPV), but the types found have varied depending on polymerase chain reaction (PCR) primer systems used. Whole genome amplified DNA (not by any specific PCR primers) from 91 lesions [41 squamous cell carcinomas (SCCs), 8 keratoacanthomas, 22 actinic keratoses, 3 basal and 17 SCCs in situ ] were sequenced. All samples sequenced both at 160 Mb 1.8 Gb sequencing depth per sample. The sequences 10 different HPVs 47/91 specimens...
We tested prostatic secretions from men with and without prostate cancer (13 cases 13 matched controls) or prostatitis (18 18 metagenomic sequencing. A large number (>200) of viral reads was only detected among four (1 patient each positive for Merkel cell polyomavirus, JC polyomavirus Human Papillomavirus types 89 40, respectively). Lower numbers a variety viruses were in all groups. Our knowledge the biology may be furthered by fact that DNA are commonly shed can readily sequencing...
Merkel cell carcinoma (MCC) is an aggressive neuroendocrine tumour of the skin that has been associated with a new virus, MCC polyomavirus. To investigate whether may have shared aetiology other cancers, we investigated risk second cancers after diagnosis using national cancer registries in Denmark, Norway and Sweden. The overall incidence was increased among patients diagnosed compared general population these countries (79 secondary total, Standardized Incidence Ratio (SIR) 1.38 (95%...
Basic Local Alignment Search Tool (BLAST) is an essential algorithm that researchers use for sequence alignment analysis. The National Center Biotechnology Information (NCBI)-BLAST application the most popular implementation of BLAST algorithm. It can run on a single multithreading node. However, volume nucleotide and protein data fast growing, making node insufficient. more important to develop high-performance computing solutions, which could help analyze genetic in scalable way. This...
Most cancer forms known to be caused by viruses are increased among the immunosuppressed, but several without established viral etiology also increased, notably nonmelanoma skin carcinoma (NMSC). We followed all 13,429 solid organ transplantation patients in Sweden for occurrence after transplantation. requested these tumor specimens and sequenced first 89 received (62 NMSCs, 27 other cancers). The sequences were analyzed based on two bioinformatics algorithms (paracel-blast (sensitive...
Human papillomavirus (HPV) is an established risk factor for oropharyngeal squamous cell carcinoma (OSCC). The aim was to establish lines from HPV-positive tonsil carcinomas be used treatment development.Fresh samples 23 were cultivated in vitro. line analyzed viral characteristics, karyotype, TP53 status, and growth capabilities nude mice. In vitro studies of sensitivities radiation, cisplatin cetuximab performed.After 19 months (eight passages), one line, LU-HNSCC-26, also grew as...
Introduction Exploring different sampling sites and methods is of interest for studies the epidemiology HPV infections in male. Expressed prostate secretions (EPS) are obtained during digital rectal examination (DRE), a daily routine urological diagnostic procedure, following massage prostate. Materials Methods Urethral swabs EPS samples were from consecutive sample 752 men (mean age 32.4 years; median life-time sex partners 34) visiting urology outpatient clinics St. Petersburg, Russia...
Detection of the presence known and unknown viruses in biospecimens is today routinely performed using viral metagenomics.Because sequencing speed cost per base rapidly declining with new next generation technologies, such as HiSeq (Illumina), 454 GS FLX (Roche), SOLiD (ABI) Ion Torrent Proton (Life Technologies), bioinformatics analysis a most important increasingly demanding part metagenomics analysis.In this review, we highlight some major challenges commonly adapted tools for metagenomics.
Abstract We performed a large nested case-control study within the Finnish and Icelandic maternity cohorts to verify/falsify association of maternal EBV infection with an increased risk acute lymphoblastic leukemia (ALL) in offspring found previous studies. All hematologic malignancies diagnosed among children born during 1983 2006 Finland 1997 2005 Iceland were identified through national cancer registries. For each index mother case, three matched control mothers cancer-free identified....
A possible role for infections of the pregnant mother in development childhood acute leukemias and lymphomas has been suggested. However, no specific infectious agent identified. Offspring 74,000 mothers who had serum samples taken during pregnancy stored a large-scale biobank were followed up to age 15 years (750,000 person years) through over-generation linkages between files, Swedish national population cancer registers identify incident leukemia/lymphoma cases offspring. First-trimester...