Due to the explosion of cancer genome data and the urgent needs for cancer treatment, it is becoming increasingly important and necessary to easily and timely analyze and annotate cancer genomes. However, tumor heterogeneity is recognized as a serious barrier to annotate cancer genomes at the individual patient level. In addition, the interpretation and analysis of cancer multi-omics data rely heavily on existing database resources that are often located in different data centers or research institutions, which poses a huge challenge for data parsing. Here we present CCAS (Cancer genome Consensus Annotation System, https://ngdc.cncb.ac.cn/ccas/#/home), a one-stop and comprehensive annotation system for the individual patient at multi-omics level. CCAS integrates 20 widely recognized resources in the field to support data annotation of 10 categories of cancers covering 395 subtypes. Data from each resource are manually curated and standardized by using ontology frameworks. CCAS accepts data on single nucleotide variant/insertion or deletion, expression, copy number variation, and methylation level as input files to build a consensus annotation. Outputs are arranged in the forms of tables or figures and can be searched, sorted, and downloaded. Expanded panels with additional information are used for conciseness, and most figures are interactive to show additional information. Moreover, CCAS offers multidimensional annotation information, including mutation signature pattern, gene set enrichment analysis, pathways and clinical trial related information. These are helpful for intuitively understanding the molecular mechanisms of tumors and discovering key functional genes.

Omics

10.3389/fgene.2022.956781

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Citations (2)

Case of Hermansky–Pudlak syndrome 1 in a Japanese infant

The Journal of Dermatology (2015)

Mari Tanaka Liping Yang Mari Wataya‐Kaneda Tamio Suzuki Ken Okamura

10.1111/1346-8138.12937

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Citations (1)

The clinical efficacy and safety of single-agent pembrolizumab in patients with recurrent granulosa cell tumors of the ovary: a case series from a phase II basket trial

Investigational New Drugs (2021)

Jeffrey How Amir A. Jazaeri Shannon N. Westin Anil K. Sood Lois M. Ramondetta

10.1007/s10637-020-01043-9

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Citations (16)

Comparison of the efficacy and safety of first-line treatments based on clinicopathological characteristics for patients with advanced epidermal growth factor receptor mutated non-small-cell lung cancer: A systematic review and network meta-analysis

Critical Reviews in Oncology/Hematology (2022)

Fei Yang Wengang Zhang Xiaoling Shang Ni Liu Xinchun Ma

Osimertinib

Regimen

Pemetrexed

Progression-free survival

Clinical endpoint

10.1016/j.critrevonc.2022.103760

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Citations (9)

Laser microdissection and microarray analysis of breast tumors reveal ER-α related genes and pathways

Oncogene (2005)

Fei Yang John A. Foekens Jingxue Yu Anieta M. Sieuwerts Mieke Timmermans

Laser capture microdissection

Microdissection

10.1038/sj.onc.1209165

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[Diagnosis and treatment of intracranial hemangiopericytoma].

PubMed (2005)

Fei Yang Qiwu Xu Rong Xie Liang Gao

To summarize the experience in diagnosis and treatment of intracranial hemangiopericytoma (HPC).The clinical data of 63 patients, 37 males and 26 females, aged 41 (14 - 77), with intracranial HPC were studied retrospectively.Fifty-eight patients underwent total excision of tumor and 5 patients underwent subtotal excision. Thirty-eight patients were followed up for 3 to 84 months (on average: 25 months), of which 34 underwent conventional external beam radiotherapy as an adjuvant measure after the first operation. Six patients who had local recurrence received second operation. Two patients had metastases to the spine.Complete excision followed with radiotherapy can delay the recurrence of HPC, a malignant tumor with rich blood supply, and improve the prognosis. Pre-operative embolization of the feeding artery may be helpful to the surgery and abundant transfusion should be ready intra-operatively.

Hemangiopericytoma

Adjuvant radiotherapy

Blood supply

Intracranial tumor

Source

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Immunohistochemical analysis of rhododendrol-induced leukoderma in improved and aggravated cases

Journal of Dermatological Science (2020)

Masahito Yasuda Akiko Sekiguchi Chikako Kishi Sayaka Toki Noriko Arase

Depigmentation

Melanocyte

Hypopigmentation

10.1016/j.jdermsci.2020.06.011

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Gender difference in knowledge of tuberculosis and associated health-care seeking behaviors: a cross-sectional study in a rural area of China

BMC Public Health (2008)

Jianming Wang Fei Yang Hongbing Shen Biao Xu

Abstract Background Tuberculosis (TB) detection under the national TB control program in China follows passive case-finding guidelines, which could be influenced by the accessibility of health service and patient's health-care seeking behaviors. One intriguing topic is the correlation between men and women's knowledge on TB and their health-care seeking behaviors. Methods Two cross-sectional studies were separately carried out in Yangzhong County, a rural area of China. One study, by using systematic sampling method, including 1,200 subjects, was conducted to investigate the TB knowledge among general population. Another study in the same source population screened 33,549 people aged 15 years or over among 20 stratified cluster-sampled villages for identifying prolonged cough patients at households and individual interviews were then carried out. Gender difference in the knowledge of TB and health-care seeking behaviors was analyzed particularly. Results Among general population, only 16.0% (men 17.1% vs. women 15.0%) knew the prolonged cough with the duration of 3 weeks or longer was a symptom for suspicious TB. Fewer women than men knew the local appointed health facility for TB diagnosis and treatment as well as the current free TB service policy. Moreover, women were less likely to learn information about TB and share it with others on their own initiatives. On the contrary, after the onset of the prolonged cough, women (79.2%) were more likely to seek health-care than men (58.6%) did. However, a large part of women preferred to visit the lower level non-hospital health facilities at first such as village clinics and drugstores. Conclusion TB and DOTS program were not well known by rural Chinese. Gender issues should be considered to reduce diagnostic delay of TB and improve both men and women's access to qualified health facility for TB care. Strengthening awareness of TB and improving the accessibility of health-care service is essential in TB control strategy, especially under the current vertical TB control system.

Biostatistics

Cross-sectional study

Stratified Sampling

10.1186/1471-2458-8-354

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Citations (119)