| 1. |
- Arroyo Mühr, Laila Sara, et al.
(författare)
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Does human papillomavirus-negative condylomata exist?
- 2015
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Ingår i: Virology. - : Elsevier BV. - 1096-0341 .- 0042-6822. ; 485, s. 283-288
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Tidskriftsartikel (refereegranskat)abstract
- Condylomata acuminata is caused by human papillomavirus (HPV). PCR with consensus primers will typically detect HPV in >96% of condylomata. Metagenomic sequencing has found that some "HPV-negative" condylomata do indeed contain HPV. We wished to perform a renewed evaluation of the "HPV-negative" condylomata using deeper metagenomics sequencing. Sequencing of whole genome amplified DNA from 40 apparently "HPV-negative" condylomata detected HPV in 37/40 specimens. We found 75 different HPV types, out of which 43 represented novel putative HPV types. Three types were cloned and established as HPV types 200, 201 and 202. Molluscum contagiosum virus was detected in 24 of the 40 samples. In summary, deep sequencing enables detection of HPV in almost all condylomata. "HPV-negative" condylomata might largely be explained by clinical misdiagnosis or the presence of viral variants, distantly related HPV types and/or low viral loads.
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| 2. |
- Bzhalava, Davit, et al.
(författare)
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Deep sequencing extends the diversity of human papillomaviruses in human skin.
- 2014
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 4:Jul 24
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Tidskriftsartikel (refereegranskat)abstract
- Most viruses in human skin are known to be human papillomaviruses (HPVs). Previous sequencing of skin samples has identified 273 different cutaneous HPV types, including 47 previously unknown types. In the present study, we wished to extend prior studies using deeper sequencing. This deeper sequencing without prior PCR of a pool of 142 whole genome amplified skin lesions identified 23 known HPV types, 3 novel putative HPV types and 4 non-HPV viruses. The complete sequence was obtained for one of the known putative types and almost the complete sequence was obtained for one of the novel putative types. In addition, sequencing of amplimers from HPV consensus PCR of 326 skin lesions detected 385 different HPV types, including 226 previously unknown putative types. In conclusion, metagenomic deep sequencing of human skin samples identified no less than 396 different HPV types in human skin, out of which 229 putative HPV types were previously unknown.
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| 3. |
- Bzhalava, Davit, et al.
(författare)
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Phylogenetically diverse TT virus viremia among pregnant women
- 2012
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Ingår i: Virology. - : Elsevier BV. - 1096-0341 .- 0042-6822. ; 432:2, s. 427-434
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Tidskriftsartikel (refereegranskat)abstract
- Infections during pregnancy have been suggested to be involved in childhood leukemias. We used high-throughput sequencing to describe the viruses most readily detectable in serum samples of pregnant women. Serum DNA of 112 mothers to leukemic children was amplified using whole genome amplification. Sequencing identified one TT virus (TTV) isolate belonging to a known type and two putatively new TTVs. For 22 mothers, we also performed ITV amplification by general primer PCR before sequencing. This detected 39 TTVs, two of which were identical to the Tilts found after whole genome amplification. Altogether, we found 40 TTV isolates, 29 of which were putatively new types (similarities ranging from 89% to 69%). In conclusion, high throughput sequencing is useful to describe the known or unknown viruses that are present in serum samples of pregnant women. (C) 2012 Elsevier Inc. All rights reserved.
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| 4. |
- Bzhalava, Davit, et al.
(författare)
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Risk of second cancers after the diagnosis of Merkel cell carcinoma in Scandinavia.
- 2011
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Ingår i: British Journal of Cancer. - : Springer Science and Business Media LLC. - 1532-1827 .- 0007-0920. ; 104, s. 178-180
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Tidskriftsartikel (refereegranskat)abstract
- Background:Merkel cell carcinoma (MCC) is an aggressive neuroendocrine tumour of the skin that has been associated with a new tumour virus, the MCC polyomavirus.Methods:To investigate whether MCC may have a shared aetiology with other cancers, we investigated the risk of second cancers after the diagnosis of MCC using the national cancer registries in Denmark, Norway and Sweden.Results:The overall cancer incidence was increased among patients diagnosed with MCC compared with the general population in these countries (79 secondary cancers total, Standardized Incidence Ratio (SIR) 1.38 (95% confidence interval (CI): 1.10-1.72); 49 secondary cancer in females, SIR 1.7 (95% CI: 1.29-2.25); 30 secondary cancers in males and SIR 1.05 (95% CI: 0.73-1.5)). There were significantly increased incidence ratios for non-melanoma skin cancers (34 secondary cancers, SIR 8.35 (95% CI: 5.97-11.68)), melanoma of skin (6 secondary cancers, SIR 4.29 (95% CI: 1.93-9.56)) and laryngeal cancer (2 secondary cancers, SIR 9.51 (95% CI: 2.38-38)). The SIRs for these three cancer sites were also elevated on restricting the follow-up to cancers occurring at least one year after MCC diagnosis.Conclusions:Patients diagnosed with MCC are at increased risk of a second cancer, particularly, other skin cancers. Conceivable explanations include the impact of increased surveillance of the skin and shared causative factors, for example, ultraviolet light exposure or MCC polyomavirus infection.British Journal of Cancer advance online publication, 16 November 2010; doi:10.1038/sj.bjc.6605989 www.bjcancer.com.
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| 5. |
- Bzhalava, Davit
(författare)
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Studies on tumor virus epidemiology
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The causal relationship between several virus infections and human cancers are well established. However, it is also possible that additional cancers may be caused by known or yet unknown viruses. The present thesis has sought to both further elucidate known relationships between virus and cancer as well as to provide a basis for further exploration in the area of infections and cancer. Infections during pregnancy have been suspected to be involved in the etiology of childhood leukemias. However, no specific infectious agent is yet linked to the etiology of these diseases. As a basis for further studies in this area, we applied high-throughput next generation sequencing (NGS) technology to describe the viruses most readily detectable in serum samples of mothers to leukemic children. The most common viruses found were TT viruses, including several previously not described TT viruses. Merkel cell polyomavirus (MCV) is found in Merkel cell carcinoma (MCC), a rare and aggressive neuroendocrine tumor of the skin. To explore whether MCV infection might be associated with additional cancers, we investigated whether MCC patients are at excess risk of other cancers, using population-based Nordic cancer registries. Bidirectional evaluation of excess risk of other diseases among MCC patients revealed that they are at increased risk of other skin cancers as a second cancer, compared to the general Nordic population. Shared causative factors, such as exposure to ultraviolet light and/or MCV infection are among the possible explanations. Also, impact of increased surveillance of the skin should be noted as an explanation of the excess risk. Cutaneous human papillomaviruses (HPV) are suspected to be involved in the etiology of non-melanoma skin cancer (NMSC). To evaluate whether there are any consistent association between cutaneous HPV infections and skin cancer, we conducted a systematic review and meta-analysis of studies that investigated HPV prevalences among cases of skin lesions and their healthy controls. We found that HPV species Beta-1, Beta-2, Beta-3 and Gamma-1 were more frequently detected in squamous cell carcinoma (SCC) compared to healthy controls. To provide clues about possible carcinogenicity of 47 mucosal HPV types, out of which 12 are established as causes of cervical cancer, we also investigated the prevalence of 47 mucosal HPV types across the entire range of cervical diagnoses from normal to cervical cancer. To investigate diversity of HPVs in skin lesions with increased sensitivity, different sample types from different skin lesion were subjected to high-throughput NGS after PCR amplification. Conventional molecular detection methods such as PCR are biased towards the primers used. Thus they might miss viruses that are divergent from the primer sequences. We also investigated whether NGS technology can be used to assess presence of virus DNA in an unbiased manner, both in skin lesions as well as in condylomas that were classified as “HPV negative” by conventional PCR methods. Unbiased sequencing identified two putatively new HPV types that were missed by NGS after PCR amplification. The advantage of unbiased sequencing over conventional molecular detection methods was further demonstrated in the study of “HPV negative” condylomas. We found several known as well as several putatively novel HPV types in condylomas that were previously found to be HPV negative by PCR. In conclusion, we have used registry linkage studies, systematic reviews and metaanalyses and modern NGS technology applied to biobanked specimens to extend our knowledge of the epidemiology of cancer-associated viruses and to provide a basis for further exploration in this area.
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| 6. |
- Bzhalava, Davit, et al.
(författare)
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Unbiased Approach for Virus Detection in Skin Lesions
- 2013
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Ingår i: PLOS ONE. - : Public Library of Science. - 1932-6203. ; 8:6
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Tidskriftsartikel (refereegranskat)abstract
- To assess presence of virus DNA in skin lesions, swab samples from 82 squamous cell carcinomas of the skin (SCCs), 60 actinic keratoses (AKs), paraffin-embedded biopsies from 28 SCCs and 72 kerathoacanthomas (KAs) and fresh-frozen biopsies from 92 KAs, 85 SCCs and 92 AKs were analyzed by high throughput sequencing (HTS) using 454 or Ion Torrent technology. We found total of 4,284 viral reads, out of which 4,168 were Human Papillomavirus (HPV)-related, belonging to 15 known (HPV8, HPV12, HPV20, HPV36, HPV38, HPV45, HPV57, HPV59, HPV104, HPV105, HPV107, HPV109, HPV124, HPV138, HPV147), four previously described putative (HPV 915 F 06 007 FD1, FA73, FA101, SE42) and two putatively new HPV types (SE46, SE47). SE42 was cloned, sequenced, designated as HPV155 and found to have 76% similarity to the most closely related known HPV type. In conclusion, an unbiased approach for viral DNA detection in skin tumors has found that, although some new putative HPVs were found, known HPV types constituted most of the viral DNA.
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| 7. |
- Bzhalava, Davit, et al.
(författare)
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Viremia during pregnancy and risk of childhood leukemia and lymphomas in the offspring: Nested case-control study.
- 2016
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Ingår i: International Journal of Cancer. - : Wiley. - 0020-7136 .- 1097-0215. ; 138:9, s. 2212-2220
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Tidskriftsartikel (refereegranskat)abstract
- A possible role for infections of the pregnant mother in the development of childhood acute leukemias and lymphomas has been suggested. However, no specific infectious agent has been identified. Offspring of 74,000 mothers who had serum samples taken during pregnancy and stored in a large-scale biobank were followed up to the age of 15 years (750,000 person years) through over-generation linkages between the biobank files, the Swedish national population and cancer registers to identify incident leukemia/lymphoma cases in the offspring. First-trimester sera from mothers of 47 cases and 47 matched controls were retrieved and analyzed using next generation sequencing. Anelloviruses were the most common viruses detected, found in 37/47 cases and in 40/47 controls, respectively (OR: 0.6, 95% CI: 0.2-1.9). None of the detected viruses was associated with leukemia/lymphoma in the offspring. Viremia during pregnancy was common, but no association with leukemia/lymphoma risk in the offspring was found.
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| 8. |
- de la Rua Martinez, Javier, et al.
(författare)
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The Hopsworks Feature Store for Machine Learning
- 2024
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Ingår i: SIGMOD-Companion 2024 - Companion of the 2024 International Conferaence on Management of Data. - : Association for Computing Machinery (ACM). ; , s. 135-147
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Konferensbidrag (refereegranskat)abstract
- Data management is the most challenging aspect of building Machine Learning (ML) systems. ML systems can read large volumes of historical data when training models, but inference workloads are more varied, depending on whether it is a batch or online ML system. The feature store for ML has recently emerged as a single data platform for managing ML data throughout the ML lifecycle, from feature engineering to model training to inference. In this paper, we present the Hopsworks feature store for machine learning as a highly available platform for managing feature data with API support for columnar, row-oriented, and similarity search query workloads. We introduce and address challenges solved by the feature stores related to feature reuse, how to organize data transformations, and how to ensure correct and consistent data between feature engineering, model training, and model inference. We present the engineering challenges in building high-performance query services for a feature store and show how Hopsworks outperforms existing cloud feature stores for training and online inference query workloads.
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| 9. |
- Ekström, Johanna, et al.
(författare)
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Diversity of human papillomaviruses in skin lesions
- 2013
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Ingår i: Virology. - : Elsevier BV. - 0042-6822 .- 1096-0341. ; 447:1-2, s. 300-311
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Tidskriftsartikel (refereegranskat)abstract
- Pools of frozen biopsies from patients with squamous cell carcinoma (SCC) (n=29) actinic keratosis (AK) (n=31), keratoacanthoma (n=91) and swab samples from 84 SCCs and 91 AKs were analysed with an extended HPV general primer PCR and high-throughput sequencing of amplimers. We found 273 different HPV isolates (87 known HPV types, 139 previously known HPV sequences (putative types) and 47 sequences from novel putative HPV types). Among the new sequences, five clustered in genus Betapapillomavirus and 42 in genus Gammapapillomavirus. Resequencing of the three pools between 21 to 70 times resulted in the detection of 283 different known or putative HPV types, with 156 different sequences found in only one of the pools. Type-specific PCRs for 37 putative types from an additional 296 patients found only two of these putative types. In conclusion, skin lesions contain a large diversity of HPV types, but most appeared to be rare infections. (C) 2013 Elsevier Inc. All rights reserved.
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| 10. |
- Ekström, Johanna, et al.
(författare)
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High throughput sequencing reveals diversity of human papillomaviruses in cutaneous lesions.
- 2011
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Ingår i: International Journal of Cancer. - : Wiley. - 0020-7136 .- 1097-0215. ; 129, s. 2643-2650
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Tidskriftsartikel (refereegranskat)abstract
- There are at least 120 completely characterized human papillomavirus (HPV) types and putative new types are continuously found. Both squamous cell carcinoma of the skin (SCC) and other skin lesions commonly contain multiple cutaneous HPV types. The objective of this study was to achieve an improved resolution of the diversity of HPV types in lesions such as SCCs, actinic keratoses (AKs) and keratoacanthomas (KAs). Fresh frozen biopsies from 37 SCC lesions, 36 AK lesions and 92 KA lesions and swab samples from the top of the lesion from 86 SCCs and 92 AKs were amplified using the general HPV primers FAP and mixed to three pools followed by high throughput sequencing. We obtained 2196 reads with homology to HPV. In the pool of SCC/AK biopsies 48 different HPV types were found. Eighty-three types were found in the pool of SCC/AK swab samples and 64 types in the KA biopsies, respectively. For 9 novel putative HPV types most of the amplimer sequence was obtained, whereas for an additional 35 novel putative HPV types only partial amplimer sequences were obtained. Most of the novel putative types belonged to the genus Gamma. In conclusion, high throughput sequencing was an effective means to identify both known and previously unknown HPV types in putatively HPV-associated lesions and has revealed an extended diversity of HPV types.
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| 11. |
- Forslund, Ola, et al.
(författare)
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A novel human in vitro papillomavirus type 16 positive tonsil cancer cell line with high sensitivity to radiation and cisplatin
- 2019
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Ingår i: BMC Cancer. - : Springer Science and Business Media LLC. - 1471-2407. ; 19:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Human papillomavirus (HPV) is an established risk factor for oropharyngeal squamous cell carcinoma (OSCC). The aim was to establish cell lines from HPV-positive tonsil carcinomas to be used for treatment development. Methods: Fresh samples from 23 HPV-positive tonsil carcinomas were cultivated in vitro. The established cell line was analyzed for viral characteristics, cell karyotype, TP53 status, and growth capabilities in nude mice. In vitro studies of sensitivities to radiation, cisplatin and cetuximab were performed. Results: After 19 months (eight passages), one cell line, LU-HNSCC-26, was established in vitro and also grew as xenografts. The tumor was from a 48 year old non-smoking man with non-keratinizing, p16 positive tonsil OSCC, stage T2N0M0 with HPV16. It contained 19.5 (CV% 3.7) HPV16 copies/cell (passage 8). The complete HPV16 genome sequence was obtained. Episomal HPV16 was present with an E2/E7 ratio of 1.1 (CV% 2.6). In addition, HPV16 mRNA specific for the intact E2 gene was detected. The viral expression manifested 1.0 (CV% 0.1) E7 mRNA copies per HPV16 genome. The karyotype was determined and the cell line demonstrated wild type TP53. The ID50 for radiation was 0.90 Gy and the IC50 for cisplatin was 0.99 μmol/L. The cell line was inhibited to a maximum of 18% by cetuximab. Conclusions: We established an in vitro tonsil carcinoma cell line containing episomal HPV16. This is an important step towards efficient treatment development.
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| 12. |
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| 13. |
- Kocjan, Boštjan J, et al.
(författare)
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Molecular methods for identification and characterization of novel papillomaviruses.
- 2015
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Ingår i: Clinical Microbiology and Infection. - : Elsevier BV. - 1469-0691 .- 1198-743X. ; 21:9, s. 808-816
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Forskningsöversikt (refereegranskat)abstract
- Papillomaviruses (PV) are a remarkably heterogeneous family of small DNA viruses that infect a wide variety of vertebrate species and are etiologically linked with the development of various neoplastic changes of the skin and mucosal epithelia. Based on nucleotide similarity, PVs are hierarchically classified into genera, species and types. Novel human PV (HPV) types are given a unique number only after the whole genome has been cloned and deposited with the International HPV Reference Center. As of March 09, 2015, 200 different HPV types, belonging to 49 species, had been recognized by the International HPV Reference Center. In addition, 131 animal PV types identified from 66 different animal species exist. Recent advances in molecular techniques have resulted in an explosive increase in the identification of novel HPV types and novel subgenomic HPV sequences in the last few years. Among PV genera, the Gamma-PV genus has been growing most rapidly in recent years with 80 completely sequenced HPV types, followed by Alpha- and Beta-PV genera that have 65 and 51 recognized HPV types, respectively. We reviewed in detail the contemporary molecular methods most often used for identification and characterization of novel PV types, including polymerase chain reaction, rolling circle amplification and next generation sequencing. Furthermore, we present a short overview of 12 and 10 novel HPV types recently identified in Sweden and Slovenia, respectively. Finally, an update on the International Human Papillomavirus Reference Center is provided.
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| 14. |
- Mercalli, A., et al.
(författare)
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No evidence of enteroviruses in the intestine of patients with type 1 diabetes
- 2012
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Ingår i: Diabetologia. - : Springer Science and Business Media LLC. - 1432-0428 .- 0012-186X. ; 55:9, s. 2479-2488
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Tidskriftsartikel (refereegranskat)abstract
- The purpose of this study was to investigate whether the gut mucosa is a reservoir for enterovirus persistence in patients with type 1 diabetes. Small intestine biopsy samples from 25 individuals at different stages of type 1 diabetes, 21 control individuals and 27 individuals with coeliac disease were analysed for the presence of enterovirus RNA by using both radioactive in-situ hybridisation and real-time RT-PCR and for the presence of enterovirus proteins by immunostaining with antibodies against VP1 and VP4-2-3 capsid proteins and virus polymerase. Lymphocytic enteropathy and serum anti-VP1 antibodies were also evaluated at the time of biopsy. Moreover, high-throughput sequencing was performed to identify viral transcripts or genomes. Enterovirus was not detected by in-situ hybridisation or RT-PCR in any of the individuals tested. Immunohistology revealed a few stained cells in the intestinal epithelium in a low number of individuals, with no difference between diabetic and non-diabetic individuals. Levels of serum IgG against VP1 did not differ between control individuals and those with diabetes or coeliac disease and no evidence of diabetes-related lymphocytic enteropathy was detected. High-throughput sequencing did not reveal specific enterovirus sequences in the gut mucosa of individuals with type 1 diabetes. Prolonged/persistent enterovirus infections in gut mucosa are not common in patients with type 1 diabetes.
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| 15. |
- Muhr, L. Sara Arroyo, et al.
(författare)
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Human papillomavirus type 197 is commonly present in skin tumors
- 2015
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Ingår i: International Journal of Cancer. - : Wiley. - 0020-7136 .- 1097-0215. ; 136:11, s. 2546-2555
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Tidskriftsartikel (refereegranskat)abstract
- Non-melanoma skin cancers commonly contain Human Papillomavirus (HPV), but the types found have varied depending on the polymerase chain reaction (PCR) primer systems used. Whole genome amplified DNA (not amplified by any specific PCR primers) from 91 skin lesions [41 squamous cell skin carcinomas (SCCs), 8 keratoacanthomas, 22 actinic keratoses, 3 basal cell carcinomas and 17 SCCs in situ] were sequenced. All samples were sequenced both at 160 Mb and 1.8 Gb sequencing depth per sample. The sequences from 10 different HPVs in 47/91 specimens were found. Sequences represented four established HPV types (HPV types 16, 22, 120, 124), two previously known putative types (present in GenBank) and four previously unknown HPV sequences (new putative types). The most commonly detected virus was cloned, sequenced and designated as HPV197. Type-specific real-time PCR detected HPV197 in 34/91 specimens. For comparison, a pool of the same samples after general primer PCR amplification was also sequenced. This revealed 40 different HPVs, but only two HPV types were detected both with sequencing without prior PCR and with sequencing PCR amplicons, suggesting that sequencing without prior PCR gives a more unbiased representation of the HPVs present. In summary, it was found that HPV can be sequenced from most skin disease specimens and HPV197 appeared to be the most commonly present virus. What's new? Some skin cancers such as squamous cell carcinomas occur more often in immune compromised individuals, pointing to an infectious agent as cause. In an unbiased approach the authors used next-generation sequencing to examine 91 non-melanoma skin cancer lesions. Most skin lesions contained Human Papilloma Virus (HPV). The authors cloned and sequenced a new type, HPV type 197, present in 34 of the 91 skin lesions. HPV197 has only 75% similarity with the most closely related known HPV (HPV178), suggesting a possible new agent involved in the carcinogenesis of non-melanoma skin lesions.
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| 16. |
- Sehic, Daniel, et al.
(författare)
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Absence of Epstein-Barr and Cytomegalovirus Infection in Neuroblastoma Cells by Standard Detection Methodologies.
- 2013
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Ingår i: Pediatric Blood & Cancer. - : Wiley. - 1545-5017 .- 1545-5009. ; 60:9, s. 91-93
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Tidskriftsartikel (refereegranskat)abstract
- Indications exist in the scientific literature that infection with human herpes family viruses may contribute to the pathogenesis of neuroblastoma (NB). However, systematic investigations regarding viral presence in NB cells have been scarcely reported. Here, the presence of DNA from Epstein-Barr virus (EBV) and human cytomegalovirus (HCMV) was assessed by PCR in 12 NBs, supplemented with RNA in situ hybridization, immunohistochemical detection, and high-throughput DNA sequencing. These standard methods did not detect infection by EBV or HCMV in NB cells in any tumor, while occasional immune cells were positive for EBV RNA or HCMV protein in four cases. Pediatr Blood Cancer © 2013 Wiley Periodicals, Inc.
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| 17. |
- Tedeschi, Rosamaria, et al.
(författare)
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No Risk of Maternal EBV Infection for Childhood Leukemia.
- 2009
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Ingår i: Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology. - 1538-7755. ; 18, s. 2790-2792
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Tidskriftsartikel (refereegranskat)abstract
- We performed a large nested case-control study within the Finnish and Icelandic maternity cohorts to verify/falsify the association of maternal EBV infection with an increased risk of acute lymphoblastic leukemia (ALL) in the offspring found in previous studies. All hematologic malignancies diagnosed among children born during 1983 to 2006 in Finland and 1997 to 2005 in Iceland were identified through national cancer registries. For each index mother of a leukemia case, three matched control mothers with cancer-free offspring were identified. First trimester sera from 561 ALL and 144 non-ALL index mothers and from 2,105 control mothers were analyzed for antibodies to EBV viral capsid antigen (IgG and IgM), early antigen (IgG) and ZEBRA protein (IgG). Conditional logistic regression-based estimates of odds ratios and 95% confidence intervals adjusted for birth order and sib-ship size were calculated. Overall, there was no evidence of increased risk of ALL associated to EBV viral capsid antigen IgM (odds ratio, 0.9; 95% confidence interval, 0.5-1.8). The early antigen and ZEBRA antibodies (EBV reactivation markers) were also not associated with risk. The data argue against a role of EBV in ALL. (Cancer Epidemiol Biomarkers Prev 2009;18(10):OF1-3).
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