FastViFi: Fast and accurate detection of (Hybrid) Viral DNA and RNA

Javadzadeh, Sara; Rajkumar, Utkrisht; Nguyen, Nam; Sarmashghi, Shahab; Luebeck, Jens; Shang, Jingbo; Bafna, Vineet

doi:10.1093/nargab/lqac032

Cited by 2 publications

(1 citation statement)

References 42 publications

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“…HPV typing and HPV integration detection were performed with FastViFi. [24] The dominant HPV type was determined as the type with the most read evidence. HPV integration sites were identified with chimeric reads mapping to both human and HPV genomes.…”

Section: Hpv Typing and Hpv Integration Detectionmentioning

confidence: 99%

Whole genome sequencing in high-grade cervical intraepithelial neoplasia patients from different ethnic groups in China

Wang,

Li,

Zhao

et al. 2023

Medicine

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Cervical cancer (CC) is the fourth most common cancer in women worldwide. It develops through precancerous lesions (cervical intraepithelial neoplasia (CIN), graded from low-grade (CIN1) to high-grade (CIN2-3)). It is well established that precancerous and cancerous cervical lesions are caused by a persistent infection with high-risk types of the human papilloma virus (hrHPV). To have a deeper understanding of the pathogenesis of CIN and CC, we systematically analyzed the landscape of genomic alterations and HPV integration profiles in high-grade CIN2/3. We performed deep whole genome sequencing on exfoliated cervical cells and matched peripheral blood samples from a cohort of 51 Chinese patients (of whom 35 were HPV+) with high-grade CIN from 3 ethnic groups and constructed strict integrated workflow of genomic analysis. In addition, the HPV types and integration breakpoints in the exfoliated cervical cells from these patients were examined. Genomic analysis identified 6 significantly mutated genes (SMGs), including CDKN2A, PIK3CB, FAM20A, RABEP1, TMPRSS2 and SS18L1, in 51 CIN2/3 samples. As none of them had previously been identified as SMGs in the Cancer Genome Atlas cervical squamous cell carcinoma and endocervical adenocarcinoma (TCGA-CESC) cohort, future studies with larger sample size of CINs may be needed to validate our findings. Mutational signature analysis showed that mutational signatures of CINs were dramatically different from CCs, highlighting their different mutational processes and etiologies. Moreover, non-silent somatic mutations were detected in all of the CIN2/3 samples, and 88% of these mutations occurred in genes that also mutated in CCs of TCGA cohort. CIN2 samples had significantly less non-silent mutations than CIN3 samples (P = .0006). Gene ontology and pathway level analysis revealed that functions of mutated genes were significantly associated with tumorigenesis, thus these genes may be involved in the development and progression of CC. HPV integration breakpoints occurred in 28.6% of the CIN2/3 samples with HPV infection. Integrations of common high risk HPV types in CCs, including HPV16, 52, 58 and 68, also occurred in the CIN samples. Our results lay the groundwork for a deeper understanding of the molecular mechanisms underlying the pathogenesis of CC and pave the way for new tools for screening, diagnosis and treatment of cervical precancerous and cancerous lesions.

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Section: Hpv Typing and Hpv Integration Detectionmentioning

confidence: 99%

Whole genome sequencing in high-grade cervical intraepithelial neoplasia patients from different ethnic groups in China

Wang,

Li,

Zhao

et al. 2023

Medicine

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RE.GA.IN.: the Real-world Gastritis Initiative–updating the updates

Rugge,

Genta,

Malfertheiner

et al. 2024

Gut

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At the end of the last century, a far-sighted ‘working party’ held in Sydney, Australia addressed the clinicopathological issues related to gastric inflammatory diseases. A few years later, an international conference held in Houston, Texas, USA critically updated the seminal Sydney classification. In line with these initiatives, Kyoto Global Consensus Report, flanked by the Maastricht-Florence conferences, added new clinical evidence to the gastritis clinicopathological puzzle.The most relevant topics related to the gastric inflammatory diseases have been addressed by the Real-world Gastritis Initiative (RE.GA.IN.), from disease definitions to the clinical diagnosis and prognosis. This paper reports the conclusions of the RE.GA.IN. consensus process, which culminated in Venice in November 2022 after more than 8 months of intense global scientific deliberations. A forum of gastritis scholars from five continents participated in the multidisciplinary RE.GA.IN. consensus. After lively debates on the most controversial aspects of the gastritis spectrum, the RE.GA.IN. Faculty amalgamated complementary knowledge to distil patient-centred, evidence-based statements to assist health professionals in their real-world clinical practice. The sections of this report focus on: the epidemiology of gastritis;Helicobacter pylorias dominant aetiology of environmental gastritis and as the most important determinant of the gastric oncogenetic field; the evolving knowledge on gastric autoimmunity; the clinicopathological relevance of gastric microbiota; the new diagnostic horizons of endoscopy; and the clinical priority of histologically reporting gastritis in terms of staging. The ultimate goal of RE.GA.IN. was and remains the promotion of further improvement in the clinical management of patients with gastritis.

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FastViFi: Fast and accurate detection of (Hybrid) Viral DNA and RNA

Cited by 2 publications

References 42 publications

Whole genome sequencing in high-grade cervical intraepithelial neoplasia patients from different ethnic groups in China

Whole genome sequencing in high-grade cervical intraepithelial neoplasia patients from different ethnic groups in China

RE.GA.IN.: the Real-world Gastritis Initiative–updating the updates

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