RESUMO
In well-screened populations, most cervical cancers arise from small groups of women with inadequate screening. The present study aims to assess whether registry-based cancer risk assessment could be used to increase screening intensity among high-risk women. The National Cervical Screening Registry identified the 28,689 women residents in Sweden who had either no previous cervical screening or a screening history indicating high risk. We invited these women by SMS and/or physical letter to order a free human papillomavirus (HPV) self-sampling kit. The Swedish national HPV reference laboratory performed extended HPV genotyping and referred high-risk HPV-positive women to their regional gynecologist. A total of 3691/28,689 (12.9%) women ordered a self-sampling kit and 10.0% (2853/28,689) returned a sample for testing. Participation among women who had never attended screening was low, albeit improved. Up to 22.5% of women in other high-risk groups attended. High-risk HPV types were detected in 8.3% of samples. High-risk HPV-positive women (238/2853) were referred without further triaging and severe cervical precancer or cancer (HSIL+) in histopathology were detected in 36/158 (23%) of biopsied women. Repeat invitations gave modest additional participation. Nationwide contacting of women with high risk for cervical cancer with personal invitations to order HPV self-sampling kits resulted in high yield of detected CIN2+. Further efforts to improve risk-stratified screening strategies should be directed to improving (i) the precision of the risk-stratification algorithm, (ii) the convenience for the women to participate and, (iii) ensuring that screen-positive women are followed-up.
RESUMO
The International Human Papillomavirus (HPV) Reference Center (IHRC) confirms and assigns type numbers to novel HPV types, maintains a reference clone repository, and issues international proficiency panels for HPV screening and genotyping. Furthermore, the Center coordinates the Global HPV Reference Laboratory Network that promotes collaboration and international exchange of experiences among national HPV reference laboratories, to further international standardization and quality assurance in the HPV field. The established HPV types (n = 225) belong to 5 different genera: alpha (n = 65), beta (n = 54), gamma (n = 102), mu (n = 3) and nu (n = 1). Since the last published IHRC overview in 2018, 6 novel types have been established, with 5/6 belonging to the gamma genus and 1/6 to beta genus. Also, 474 reference clones have been provided to 55 different research laboratories and the global proficiency program for HPV genotyping has seen an increasing proficiency (despite a decrease seen in 2019), from 68% proficiency in 2017 to 77.3% in 2022. The first proficiency study for HPV screening found an international proficiency of up to 77%. In summary, increasing complexity of the HPVs and demands on quality assurance in the era of cervical cancer elimination requires international efforts to support proficiency and recognized quality and order among HPV types.
Assuntos
Infecções por Papillomavirus , Neoplasias do Colo do Útero , Feminino , Humanos , Papillomavirus Humano , Infecções por Papillomavirus/diagnóstico , Papillomaviridae/genética , Padrões de Referência , Programas de Rastreamento , Neoplasias do Colo do Útero/diagnóstico , Neoplasias do Colo do Útero/prevenção & controleRESUMO
The recommendation for cervical screening is that it should be based on human papillomavirus (HPV) molecular testing. For all screening programs, attention to quality assurance is required to fully realize the benefits. Internationally recognized quality assurance recommendations for HPV-based screening are needed that are ideally applicable for a variety of settings, including in low- and middle-income countries. We summarize the main points of quality assurance for HPV screening, with a focus on the selection, implementation, and use of an HPV screening test, quality assurance systems (including internal quality control and external quality assessment), and staff competence. While we recognize that it might not be possible to fulfill all points in all settings, an awareness of the issues is essential.
Assuntos
Infecções por Papillomavirus , Neoplasias do Colo do Útero , Feminino , Humanos , Neoplasias do Colo do Útero/diagnóstico , Papillomavirus Humano , Detecção Precoce de Câncer , Colo do Útero , Programas de Rastreamento , Papillomaviridae , Esfregaço VaginalRESUMO
For head-to-head comparison of human papillomavirus (HPV) antibody levels induced by different vaccines, 25-year-old vaccine-naive women were given either the bivalent (n = 188) or the nonavalent HPV vaccine (n = 184). Six months after vaccination antibodies against pseudovirions from 17 different HPV types (HPV6/11/16/18/31/33/35/39/45/51/52/56/58/59/66/68/73) were measured. Antibodies against HPV16/18 were higher after bivalent HPV vaccination (mean international units [IU] 1140.1 and 170.5 for HPV16 and 18, respectively) than after nonavalent vaccination (265.1 and 22.3 IUs, respectively). The bivalent vaccine commonly induced antibodies against the nonvaccine HPV types 31/33/35/45 or 58. The nonavalent vaccine induced higher antibodies against HPV6/11/31/33/45/52/58 and 35.
Assuntos
Alphapapillomavirus , Infecções por Papillomavirus , Vacinas contra Papillomavirus , Neoplasias do Colo do Útero , Adulto , Anticorpos Antivirais , Formação de Anticorpos , Feminino , Papillomavirus Humano 16 , Papillomavirus Humano 18 , Humanos , Papillomaviridae , Infecções por Papillomavirus/prevenção & controle , Vacinas CombinadasRESUMO
BACKGROUND: Whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positivity among asymptomatic subjects reflects past or future disease may be difficult to ascertain. METHODS: We tested 9449 employees at Karolinska University Hospital, Stockholm, Sweden for SARS-CoV-2 RNA and antibodies, linked the results to sick leave records, and determined associations with past or future sick leave using multinomial logistic regression. RESULTS: Subjects with high amounts of SARS-CoV-2 virus, indicated by polymerase chain reaction (PCR) cycle threshold (Ct) value, had the highest risk for sick leave in the 2 weeks after testing (odds ratio [OR], 11.97; 95% confidence interval [CI], 6.29-22.80) whereas subjects with low amounts of virus had the highest risk for sick leave in the 3 weeks before testing (OR, 6.31; 95% CI, 4.38-9.08). Only 2.5% of employees were SARS-CoV-2 positive while 10.5% were positive by serology and 1.2% were positive in both tests. Serology-positive subjects were not at excess risk for future sick leave (OR, 1.06; 95% CI, .71-1.57). CONCLUSIONS: High amounts of SARS-CoV-2 virus, as determined using PCR Ct values, was associated with development of sickness in the next few weeks. Results support the concept that PCR Ct may be informative when testing for SARS-CoV-2. Clinical Trials Registration. NCT04411576.
Assuntos
Doenças Assintomáticas , COVID-19/epidemiologia , COVID-19/virologia , Pessoal de Saúde , SARS-CoV-2 , Adulto , Idoso , Anticorpos Antivirais , COVID-19/diagnóstico , Progressão da Doença , Feminino , Hospitais Universitários , Humanos , Masculino , Programas de Rastreamento , Pessoa de Meia-Idade , Reação em Cadeia da Polimerase , RNA Viral , SARS-CoV-2/genética , Testes Sorológicos , Licença Médica/estatística & dados numéricos , Suécia/epidemiologia , Adulto JovemRESUMO
Nonmelanoma skin cancer (NMSC) has a greatly increased incidence among the immunosuppressed and the DNA of human papillomavirus (HPV) is commonly found in these tumors. To investigate if there are any actively transcribed HPV infections in these tumors, we identified all skin cancers diagnosed after solid organ transplantation in Sweden during 1964-2011 (n = 7614 NMSCs) and requested the diagnostic tumor blocks from the corresponding pathology archives. For the present study, we selected diagnostic specimens from 345 NMSC and performed whole genome transcriptome analysis using NovaSeq (Illumina), in comparison with three cervical cancers. Although we obtained an abundance of high-quality paired reads per sample (median of 35 million reads), only 15 NMSC specimens contained HPV transcription. Three specimens had transcription of oncogenic anogenital HPVs (HPV16 and 56), six tumors had transcription of HPVs from the beta-2 species (three HPV38, two with HPV23 and one with HPV107) and then there was one observation each of transcription of HPVs 3, 26, 57, 147, 158, 168 and of two nonestablished HPV types belonging to the gamma genus. In conclusion, transcription of specific HPV types can be found in NMSC among the immunosuppressed, but this is not common.
Assuntos
Alphapapillomavirus/genética , Carcinoma de Células Escamosas/virologia , Perfilação da Expressão Gênica/métodos , Transplante de Órgãos/efeitos adversos , Infecções por Papillomavirus/diagnóstico , Neoplasias Cutâneas/virologia , Proteínas Virais/genética , Idoso , Alphapapillomavirus/classificação , Carcinoma de Células Escamosas/genética , Feminino , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Hospedeiro Imunocomprometido/genética , Masculino , Pessoa de Meia-Idade , Infecções por Papillomavirus/complicações , Análise de Sequência de RNA , Neoplasias Cutâneas/genética , Suécia , Transcrição Gênica , Sequenciamento do ExomaRESUMO
BACKGROUND: Human papillomavirus (HPV) is a necessary cause of cervical cancer, although some invasive cervical cancers may test negative by HPV PCR. We previously requested all invasive cervical cancers in Sweden during 10 years and subjected them to PCR. We also optimised methods for deep sequencing of formalin-fixed paraffin-embedded samples. METHODS: Using Novaseq 6000, we simultaneously sequenced total DNA and cDNA from 392 HPV PCR-negative cervical cancers. Non-human reads were queried against all known HPVs. The complete database now contains PCR and/or deep sequencing data on 2850 invasive cervical cancers. RESULTS: HPV sequences were detected in 169/392 of HPV PCR-negative cervical cancers. Overall, 30 different HPV types were detected, but only 5 types were present in proportions above 3% of cancers. More than 92% of tumours were HPV-positive in PCR and/or sequencing (95% confidence interval: 91.1-93.1%). Exploring possible reasons for failure to previously detect HPV suggest that more sensitive type-specific PCRs for HPV 31, 33, 45 and 73 targeting retained regions of HPV would have detected most of these (117/392). CONCLUSIONS: Unbiased deep sequencing provides comprehensive data on HPV types in cervical cancers and appears to be an important tool for quality assurance of HPV screening.
Assuntos
Alphapapillomavirus/isolamento & purificação , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Neoplasias do Colo do Útero/virologia , Adulto , Idoso , Idoso de 80 Anos ou mais , Intervalos de Confiança , DNA Viral/isolamento & purificação , Feminino , Sequenciamento de Nucleotídeos em Larga Escala/estatística & dados numéricos , Humanos , Pessoa de Meia-Idade , Resultados Negativos/estatística & dados numéricos , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Suécia , Neoplasias do Colo do Útero/patologiaRESUMO
Introduction. Cervical cancer is caused by human papillomavirus (HPV), but some cases may test HPV-negative. We previously tested 2850 Swedish cases and found that 394/2850 (13.8â%) cases tested HPV DNA-negative by PCR. Sequencing is the most thorough method to assess HPV status.Aim. We wished to assess whether deep sequencing might detect HPV sequences among these HPV-negative cervical cancer specimens, and to increase the likelihood of detecting transcriptionally active infections.Methodology. Out of the 2850 cancer cases, we sequenced a random sample of 92 HPV PCR-negative cervical cancers and 34 HPV PCR-positive cervical cancers. Four pools of blank blocks were sequenced as negative controls. To enrich for mRNA - a hallmark of active viral infection - the samples were extracted, reverse-transcribed, rRNA-depleted and then sequenced using the NovaSeq 6000 system (Illumina, USA). High-quality reads were aligned to the human genome and non-human reads were queried against HPV proteins.Results. We obtained a median of 23 million paired reads per sample. HPV was detected in 31/34 HPV PCR-positive cases. Among cases negative for HPV by PCR, 48/92 (52.2â%) contained HPV sequences, with HPV33 being the most commonly detected type among these (14/48 cases, 29.2â%). Comparison of the ratio of exon and intron sequences found that the sequenced material contained both DNA and RNA. Splice junctions were detected in 12 cases.Conclusion. Apparently, some cervical cancers contain HPV that is difficult to detect by PCR. Sequencing may be a helpful tool for additional quality assurance for HPV testing methods.
Assuntos
Sequenciamento de Nucleotídeos em Larga Escala/métodos , Resultados Negativos , Papillomaviridae/genética , Infecções por Papillomavirus/diagnóstico , Reação em Cadeia da Polimerase/métodos , Neoplasias do Colo do Útero/virologia , Adulto , Idoso , Idoso de 80 Anos ou mais , Colo do Útero/patologia , Colo do Útero/virologia , DNA Viral/genética , Feminino , Genótipo , Humanos , Pessoa de Meia-Idade , Infecções por Papillomavirus/virologia , Análise de Sequência de DNA , SuéciaRESUMO
BACKGROUND: HPV genomic variation may be involved in viral carcinogenesis. METHODS: In a national register-based nested case-control study, we retrieved archival smears from baseline cytologically normal women who later developed cancer in situ (CIS), squamous cervical cancer (SCC) or remained free of disease. These smears were previously HPV tested by PCR and HPV16 was the strongest risk factor. We now used the Illumina NextSeq platform to sequence HPV16 genomes in cervical smears from 242 women who later developed CIS/CIN3 (n = 134), SCC (n = 92) or remained healthy (n = 16). RESULTS: The median sequence depth per sample was high (11,288×). For 218/242 samples (>90%), we covered ≥80% of the complete HPV16 genome with sequencing median depths of >200×. We identified a wide range of unique isolates and 147 novel SNPs across the 218 samples. Most women (97%) had HPV16 lineage A infection, with the sublineages being A1 (66.1%), A2 (28.9%) and A4 (1.8%), respectively. The least variable gene was the E7 (3.4% variability), where 170/204 case women (83%) displayed a fully conserved sequence. There were no obvious differences by disease outcome (CIS or SCC). CONCLUSIONS: We found a high number of novel SNPs. The E7 gene was hypovariable both among women later developing CIN3/CIS, and SCC, respectively.
Assuntos
Carcinoma in Situ/virologia , Genoma Viral , Papillomavirus Humano 16/genética , Invasividade Neoplásica , Neoplasias do Colo do Útero/virologia , Adolescente , Adulto , Carcinoma in Situ/diagnóstico , Carcinoma in Situ/epidemiologia , Estudos de Casos e Controles , Feminino , Humanos , Mutação INDEL , Pessoa de Meia-Idade , Polimorfismo de Nucleotídeo Único , Estudos Prospectivos , Sistema de Registros , Suécia/epidemiologia , Neoplasias do Colo do Útero/diagnóstico , Neoplasias do Colo do Útero/epidemiologia , Esfregaço Vaginal , Adulto JovemRESUMO
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 are increased has been inconsistent. To provide a reliable and generalizable estimate, with high statistical power and long follow-up time, we assessed cancer risks using comprehensive, population-based registries in two different countries and from two different immunosuppressed patient groups (solid organ transplant recipients (OTRs) and long-term dialysis patients (LDPs)). National registries in Denmark and Sweden identified 20,804 OTRs and 31,140 LDPs that were followed up using national cancer registries. Standardized incidence ratios (SIR) compared to the general population were estimated. We found highly similar results, both for the two different countries and for the two different immunosuppressed cohorts, namely an increased incidence for the following specific cancer forms: Non-melanoma skin cancer (NMSC), non-Hodgkin's lymphoma and cancers of the lip, kidney, larynx and thyroid. The SIR for overall cancer among OTRs was 3.5 [n = 2,142, 95% CI, 3.4-3.7] in Sweden, 2.9 [n = 1,110, 95% CI, 2.8-3.1] in Denmark and 1.6 [n = 1,713, 95% CI, 1.5-1.6] among LDP. The SIR for NMSC among OTRs was 44.7 [n = 994, 95% CI, 42-47.5] in Sweden and 41.5 [n = 445, 95% CI, 37.8-45.5] in Denmark. The increased SIR for NMSC among LDPs was 5.3 [n = 304, 95% CI, 4.7-5.9]). In summary, an increased SIR for a specific, similar set of cancer forms is consistently found among the immunosuppressed. Conceivable explanations include surveillance bias and immunosuppression-related susceptibility to viral infections.
Assuntos
Neoplasias/epidemiologia , Transplante de Órgãos/estatística & dados numéricos , Complicações Pós-Operatórias/epidemiologia , Diálise Renal/estatística & dados numéricos , Adulto , Idoso , Dinamarca/epidemiologia , Suscetibilidade a Doenças , Feminino , Seguimentos , Humanos , Hospedeiro Imunocomprometido , Incidência , Nefropatias/imunologia , Nefropatias/cirurgia , Nefropatias/terapia , Masculino , Pessoa de Meia-Idade , Especificidade de Órgãos , Complicações Pós-Operatórias/imunologia , Sistema de Registros , Risco , Suécia/epidemiologia , Imunologia de TransplantesRESUMO
Most cancer forms known to be caused by viruses are increased among the immunosuppressed, but several cancer forms without established viral etiology are also increased, notably nonmelanoma skin carcinoma (NMSC). We followed all 13,429 solid organ transplantation patients in Sweden for cancer occurrence after transplantation. We requested these tumor specimens and sequenced the first 89 specimens received (62 NMSCs, 27 other cancers). The sequences were analyzed for viruses based on two bioinformatics algorithms (paracel-blast (sensitive for detection of known viruses) and hidden Markov model (HMM; sensitive for distantly related viruses)). Among the 62 NMSCs, the virus family detected in the largest proportion of specimens was Mimiviridae (9/62 NMSCs). The majority of the virus-related reads belonged to Papillomaviridae. The HMM analysis identified 86 additional previously not described viral contigs related to 11 virus families, with reads related to Mimiviridae being the most common (detected in 28/62 NMSCs) with the most prevalent contig (Mimivirus SE906, 1937 bp) detected in 17/62 NMSCs. Among the 27 other cancers, viral sequences were detected in only 5 specimens by blast analysis, compared to in all 27 specimens by HMM (Mimiviridae, Poxviridae, Phycodnaviridae and virus-related sequences yet unclassified to any family). 99% of the virus reads belonged to a single previously not described sequence (Mimivirus SE996, 911 bp). A multitude of viruses is readily detectable in specimens with cancers occurring among the immunosuppressed, with sequences related to Mimiviridae being the most prevalent. Further research would be needed to elucidate the biological significance of the viruses.
Assuntos
Neoplasias/imunologia , Transplante de Órgãos/efeitos adversos , Análise de Sequência de DNA/métodos , Viroses/epidemiologia , Vírus/classificação , Algoritmos , Biologia Computacional/métodos , Humanos , Hospedeiro Imunocomprometido , Cadeias de Markov , Mimiviridae/genética , Mimiviridae/isolamento & purificação , Neoplasias/virologia , Papillomaviridae/genética , Papillomaviridae/isolamento & purificação , Suécia , Vírus/genéticaRESUMO
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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Leucemia/epidemiologia , Complicações Infecciosas na Gravidez/virologia , Efeitos Tardios da Exposição Pré-Natal/epidemiologia , Viremia/complicações , Estudos de Casos e Controles , Feminino , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Leucemia/etiologia , Gravidez , Efeitos Tardios da Exposição Pré-Natal/virologia , Fatores de RiscoRESUMO
HPV vaccination with concomitant HPV-based screening of young women has been proposed for faster cervical cancer elimination. We describe the baseline results of a population-based trial of this strategy to reduce the incidence of HPV. All 89,547 women born 1994-1999 and resident in the capital region of Sweden were personally invited to concomitant HPV vaccination and HPV screening with 26,125 women (29.2%) enrolled between 2021-05-03 and 2022-12-31. Baseline HPV genotyping of cervical samples from the study participants finds, compared to pre-vaccination prevalences, a strong decline of HPV16 and 18 in birth cohorts previously offered vaccination, some decline for cross-protected HPV types but no decline for HPV types not targeted by vaccines. Our dynamic transmission modelling predicts that the trial could reduce the incidence of high-risk HPV infections among the 1994-1998 cohorts by 62-64% in 3 years. Baseline results are prevalences of HPV infection, validated transmission model projections, and power estimates for evaluating HPV incidence reductions at follow-up (+/-0.1% with 99.9% confidence). In conclusion, concomitant HPV vaccination and HPV screening appears to be a realistic option for faster cervical cancer elimination. Clinicaltrials.gov identifier: NCT04910802; EudraCT number: 2020-001169-34.
Assuntos
Infecções por Papillomavirus , Vacinas contra Papillomavirus , Neoplasias do Colo do Útero , Humanos , Feminino , Neoplasias do Colo do Útero/prevenção & controle , Neoplasias do Colo do Útero/virologia , Neoplasias do Colo do Útero/epidemiologia , Infecções por Papillomavirus/epidemiologia , Infecções por Papillomavirus/prevenção & controle , Infecções por Papillomavirus/virologia , Vacinas contra Papillomavirus/imunologia , Vacinas contra Papillomavirus/administração & dosagem , Vacinas contra Papillomavirus/uso terapêutico , Adulto , Suécia/epidemiologia , Adulto Jovem , Vacinação , Adolescente , Incidência , Programas de Rastreamento , Prevalência , Pessoa de Meia-Idade , Detecção Precoce de Câncer , Papillomavirus Humano 16/genética , Papillomavirus Humano 16/imunologia , Papillomavirus Humano 18/genética , Papillomavirus Humano 18/imunologia , Papillomavirus HumanoRESUMO
BACKGROUND: Some high-grade cervical lesions and cervical cancers (HSIL+) test negative for human papillomavirus (HPV). The HPV-negative fraction varies between 0.03 % and 15 % between different laboratories. Monitoring and extended re-analysis of HPV-negative HSIL+ could thus be helpful to monitor performance of HPV testing services. We aimed to a) provide a real-life example of a quality assurance (QA) program based on re-analysis of HPV-negative HSIL+ and b) develop international guidance for QA of HPV testing services based on standardized identification of apparently HPV-negative HSIL+ and extended re-analysis, either by the primary laboratory or by a national HPV reference laboratory (NRL). METHODS: There were 116 initially HPV-negative cervical specimens (31 histopathology specimens and 85 liquid-based cytology samples) sent to the Swedish HPV Reference Laboratory for re-testing. Based on the results, an international QA guidance was developed through an iterative consensus process. RESULT: Standard PCR testing detected HPV in 55.2 % (64/116) of initially "HPV-negative" samples. Whole genome sequencing of PCR-negative samples identified HPV in an additional 7 samples (overall 61.2 % HPV positivity). Reasons for failure to detect HPV in an HSIL+ lesion are listed and guidance to identify cases for extended re-testing, including which information should be included when referring samples to an NRL are presented. CONCLUSION: Monitoring the proportion of and reasons for failure to detect HPV in HSIL+ will help support high performance and quality improvement of HPV testing services. We encourage implementation of QA strategies based on re-analysis of "HPV negative" HSIL+ samples.
Assuntos
Infecções por Papillomavirus , Displasia do Colo do Útero , Neoplasias do Colo do Útero , Feminino , Humanos , Displasia do Colo do Útero/diagnóstico , Papillomavirus Humano , Infecções por Papillomavirus/diagnóstico , Programas de Rastreamento/métodos , Papillomaviridae/genéticaRESUMO
BACKGROUND: Colorectal cancer (CRC) is known to present a distinct microbiome profile compared to healthy mucosa. Non-targeted deep-sequencing strategies enable nowadays full microbiome characterization up to species level. AIM: We aimed to analyze both bacterial and viral communities in CRC using these strategies. MATERIALS & METHODS: We analyzed bacterial and viral communities using both DNA and RNA deep-sequencing (Novaseq) in colorectal tissue specimens from 10 CRC patients and 10 matched control patients. Following taxonomy classification using Kraken 2, different metrics for alpha and beta diversities as well as relative and differential abundance were calculated to compare tumoral and healthy samples. RESULTS: No viral differences were identified between tissue types, but bacterial species Polynucleobacter necessarius had a highly increased presence for DNA in tumors (p = 0.001). RNA analyses showed that bacterial species Arabia massiliensis had a highly decreased transcription in tumors (p = 0.002) while Fusobacterium nucleatum transcription was highly increased in tumors (p = 0.002). DISCUSSION: Sequencing of both DNA and RNA enables a wider perspective of micriobiome profiles. Lack of RNA transcription (Polynucleobacter necessarius) casts doubt on possible role of a microorganism in CRC. The association of F. nucleatum mainly with transcription, may provide further insights on its role in CRC. CONCLUSION: Joint assessment of the metagenome (DNA) and the metatranscriptome (RNA) at the species level provided a huge coverage for both bacteria and virus and identifies differential specific bacterial species as tumor associated.
Assuntos
Neoplasias Colorretais , Humanos , Neoplasias Colorretais/patologia , RNA , Bactérias/genética , DNA , Sequenciamento de Nucleotídeos em Larga EscalaRESUMO
BACKGROUND: Although cervical screening using Human Papillomavirus (HPV) testing is globally recommended public health policy, there has been no international proficiency studies specifically targeting HPV testing for cervical screening. OBJECTIVE: To obtain the first global overview of the current proficiency of HPV testing services for cervical cancer screening. STUDY DESIGN: A coded proficiency panel of 12 samples containing HPV types 16, 18, 31, 33, 45, 52, 58 or 35/39/51/56/59/68 in human DNA in varying amounts as well as control. Datasets detecting at least a) 10 International Units (IU) of HPV16 and 18, b) 1000 IU of HPV types 31, 33, 45, 52, 58 and c) having no false positives were considered proficient. RESULTS: In total, 84 laboratories worldwide submitted 158 datasets (some laboratories used >1 HPV testing platform). Of those, 122 (77%) were 100% proficient. Only 14/158 datasets (9%) contained false positive results. Comparison of results with assays approved by the Food and Drug Administration (FDA) suggest that future proficiency requirements should also accommodate assays detecting only 100 IU of HPV16/18. A pool of low oncogenicity HPV types that contributed very little to sensitivity, but adversely affected specificity, was detectable by most datasets. CONCLUSION: Internationally recognized proficiency studies of HPV screening, traceable to international standards, provided an overview of current testing performance. There was a high level of proficiency in terms of sensitivity and few false positives, but specificity was not optimal and further research on optimal specificity of HPV screening tests may be warranted.
Assuntos
Infecções por Papillomavirus , Neoplasias do Colo do Útero , Feminino , Humanos , Detecção Precoce de Câncer , Papillomavirus Humano 16 , Papillomavirus Humano 18 , Papillomavirus Humano , Infecções por Papillomavirus/diagnóstico , Estados Unidos , Neoplasias do Colo do Útero/diagnósticoRESUMO
PURPOSE: Detection of human papillomavirus (HPV) by polymerase chain reaction in invasive cervical cancer is strongly associated with prognosis but previous studies have not considered sequencing efforts. We aimed to assess the association when also including comprehensive analysis of HPV infection by deep sequencing and a longer follow-up period. MATERIALS AND METHODS: We subjected all 392 of 2,845 invasive cervical cancer cases that were polymerase chain reaction-negative for HPV to RNA sequencing on the NovaSeq 6000 platform (Illumina) and identified an additional 169 cases as HPV-positive. We followed all women from date of diagnosis to December 31, 2016, emigration, or death, whichever occurred first. The main outcome was all-cause mortality by December 31, 2016. We calculated 5-year cumulative relative survival ratios compared with the female general population and used Poisson regression to estimate excess hazard ratios of all-cause mortality by infection with any of the 13 most oncogenic (high-risk [hr]) HPV types in the tumor. All models were adjusted for age, time since diagnosis, stage, histology, and education level. RESULTS: The 5-year cumulative relative survival ratio was 0.45 (95% CI, 0.39 to 0.51) in the hrHPV-negative group, and 0.74 (95% CI, 0.72 to 0.75) in the hrHPV-positive group. This translated to a statistically significantly 43% lower excess mortality in the hrHPV-positive group compared with the hrHPV-negative (corresponding to an excess hazard ratio 0.57; 95% CI, 0.48 to 0.69). There was no association between HPV risk group, clade, or number of HPV infections and prognosis. CONCLUSION: hrHPV status is a strong determinant of cervical cancer prognosis over 15 years after diagnosis, above and beyond other established factors.
Assuntos
Alphapapillomavirus , Infecções por Papillomavirus , Displasia do Colo do Útero , Neoplasias do Colo do Útero , Feminino , Humanos , Papillomaviridae/genética , Prognóstico , Neoplasias do Colo do Útero/patologia , Displasia do Colo do Útero/diagnósticoRESUMO
In the era of cervical cancer elimination, accurate and validated pipelines to detect human papillomavirus are essential to elucidate and understand HPV association with human cancers. We aimed to provide an open-source pipeline, "HPV-meta", to detect HPV transcripts in RNA sequencing data, including several steps to warn operators for possible viral contamination. The "HPV-meta" pipeline automatically performs several steps, starting with quality trimming, human genome filtering, HPV detection (blastx), cut-off settlement (10 reads and 690 bp coverage to make an HPV call) and finishing with fasta sequence generation for HPV positive samples. Fasta sequences can then be aligned to assess sequence diversity among HPV positive samples. All RNA sequencing files (n = 10,908) present in the cancer genome atlas (TCGA) were analyzed. "HPV-meta" identified 25 different HPV types being present in 488/10,904 specimens. Validation of results showed 99.98% agreement (10,902/10,904). Multiple alignment from fasta files warned about high sequence identity between several HPV 18 and 38 positive samples, whose contamination had previously been reported. The "HPV-meta" pipeline is a robust and validated pipeline that detects HPV in RNA sequencing data. Obtaining the fasta files enables contamination investigation, a non very rare occurrence in next generation sequencing.
Assuntos
Alphapapillomavirus , Infecções por Papillomavirus , Neoplasias do Colo do Útero , Alphapapillomavirus/genética , Feminino , Humanos , Papillomaviridae/genética , Infecções por Papillomavirus/diagnóstico , RNA , Neoplasias do Colo do Útero/diagnósticoRESUMO
Human papillomavirus (HPV) negative cancers are associated with symptomatic detection, late-stage diagnosis, and worse prognosis. It is thus essential to investigate all possible infectious agents and biomarkers that could early identify these HPV negative cancers. We aimed to analyze and compare the metatranscriptome present in HPV positive and HPV negative cervical cancers. We analyzed the whole RNA sequencing files from 223 HPV negative cervical cancers (negativity established after confirming cervical cancer diagnosis, sample adequacy and subjecting specimens to PCR and unbiased RNA sequencing), 223 HPV positive tumors and 11 blank paraffin block pools (used as controls) using Kraken2 software. Overall, 84 bacterial genera were detected, with 6/84 genera showing a positive median number of reads/sample and being present in both cervical tumor groups (HPV positive and negative). Viral reads belonged to 63 different viral genera, with 6/63 genera showing a positive median annotated read/sample value. No significant difference among genera was detected except for the presence of alpha-papillomaviruses. Metatranscriptome of bacteria and viruses present in HPV positive and HPV negative cervical cancers show no significant difference, except for HPV. Further studies are needed to early identify this biologically distinct group of cervical cancers.