A genome-wide association study of nasopharyngeal carcinoma identifies three new susceptibility loci

Bei, Jin Xin; Li, Yi; Jia, Wei Hua; Feng, Bing; Zhou, Gangqiao; Chen, Li Zhen; Feng, Qi Sheng; Low, Hui Qi; Zhang, Hongxing; He, Fuchu; Tai, E. Shyong; Kang, Tiebang; Liu, Edison T.; Liu, Jing; Zeng, Yi Xin

doi:10.1038/ng.601

Cited by 353 publications

(341 citation statements)

References 44 publications

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“…And we conducted a sequencing‐based association analysis through LRT and the Fisher's exact test and identified 5066 SNPs with significant evidence ( P < .05, Figure 1A,B, Table S2). Notably, these variants include most of signals previously reported by two GWAS efforts6, 7 and our previous study (Table S3),5 indicating the reliability of our results.…”

Section: Resultssupporting

confidence: 86%

“…As shown in Table S7, very low correlations were identified between rs117560607 with those SNPs, with the largest R 2 of 0.0339 between rs117565607 and rs3129055 (near HLA‐F gene), and SNP rs3129055 was found to have a significant association with NPC in the Taiwanese population 6. The lowest correlation was found between rs117565607 and rs28421666 with R 2 of 0.0002, which was near HLA‐DQ/DR gene 7. These results suggested that the genetic effect of rs117565607 was independent of the previously reported signals.…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, we calculated the linkage disequilibrium (LD) between the top SNP rs117565607 with the previously reported SNPs5, 6, 7 associated with NPC in MHC region in the 1000 Genomes Project Phase 3 data. As shown in Table S7, very low correlations were identified between rs117560607 with those SNPs, with the largest R 2 of 0.0339 between rs117565607 and rs3129055 (near HLA‐F gene), and SNP rs3129055 was found to have a significant association with NPC in the Taiwanese population 6.…”

Section: Discussionmentioning

confidence: 99%

“…Since the 1970s, numerous efforts have been made to reveal the association of the MHC with NPC, hypothesizing that some MHC loci or genes may play major roles in the genetic predisposition to NPC, probably either by modulating innate and adaptive immune responses or as genetic markers of predisposition loci in close linkage 2, 5. This was also strongly supported by two genomewide association studies (GWAS)6, 7 and our recent association study 5. Despite the success of GWAS in identifying genetic variations, the variations in the genome have small effect sizes and only explain a modest fraction of the predicted genetic variance 8.…”

Section: Introductionmentioning

confidence: 96%

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A regulatory mutant on TRIM26 conferring the risk of nasopharyngeal carcinoma by inducing low immune response

et al. 2018

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The major histocompatibility complex (MHC) is most closely associated with nasopharyngeal carcinoma (NPC), but the complexity of its genome structure has proven challenging for the discovery of causal MHC loci or genes. We conducted a targeted MHC sequencing in 40 Cantonese NPC patients followed by a two‐stage replication in 1065 NPC cases and 2137 controls of Southern Chinese descendent. Quantitative RT‐PCR analysis (qRT‐PCR) was used to detect gene expression status in 108 NPC and 43 noncancerous nasopharyngeal (NP) samples. Luciferase reporter assay and chromatin immunoprecipitation (ChIP) were used to assess the transcription factor binding site. We discovered that a novel SNP rs117565607_A at TRIM26 displayed the strongest association (OR = 1.909, Pcombined = 2.750 × 10−19). We also observed that TRIM26 was significantly downregulated in NPC tissue samples with genotype AA/AT than TT. Immunohistochemistry (IHC) test also found the TRIM26 protein expression in NPC tissue samples with the genotype AA/AT was lower than TT. According to computational prediction, rs117565607 locus was a binding site for the transcription factor Yin Yang 1 (YY1). We observed that the luciferase activity of YY1 which is binding to the A allele of rs117565607 was suppressed. ChIP data showed that YY1 was binding with T not A allele. Significance analysis of microarray suggested that TRIM26 downregulation was related to low immune response in NPC. We have identified a novel gene TRIM26 and a novel SNP rs117565607_A associated with NPC risk by regulating transcriptional process and established a new functional link between TRIM26 downregulation and low immune response in NPC.

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Section: Resultssupporting

confidence: 86%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 96%

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A regulatory mutant on TRIM26 conferring the risk of nasopharyngeal carcinoma by inducing low immune response

et al. 2018

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“…PLCγ1 in competition with GRB2 to attach to FGFR2, that provides a binding site for these two proteins, and determines prognosis of recurrence-free survival in lung adenocarcinoma [19,33,41]. Bei et alexplored AgNP-based, SERS applications for biochemical analysis of blood plasma samples and demonstrated the capability of this method to detect nasopharyngeal cancer [91]. …”

Section: Detection Of Other Malignanciesmentioning

confidence: 99%

Application of nanoparticles in cancer detection by Raman scattering based techniques

Ravanshad

Zadeh

Amani

et al. 2017

Nano Reviews & Experiments

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In vitro detection technique Raman spectroscopy (Rs), in one number times another Rs based expert ways of art and so on, are useful instruments for cancer discovery. top gave greater value to Raman spectroscopy sers is a relatively new careful way for in vitro and in vivo discovery that takes away bad points of simple Raman spectroscopy (Rs). Raman spectroscopy (RS) and in particular, multiple RS-based techniques are useful for cancer detection. Surface enhanced Raman spectroscopy (SERS) is a relatively new method for both in vitro and in vivo detection, which eliminates the drawbacks of simple RS. Using nanoparticles has elevated the sensitivity and specificity of SERS. SERS has the potential to increase sensitivity, specificity and spatial resolution in cancer detection, especially in cooperation with other diagnostic imaging tools such as magnetic resonance imaging (MRI) and PET-scan polyethylene terephthalate. Developing a hand held instrument for detecting cancer or other illnesses may also be feasible by using SERS. Frequently, novel nanoparticles are used in SERS. With a focus on nanoparticle utilization, we review the benefits of RS in cancer detection and related biomarkers. With a focus on nanoparticles utilizations, the benefits of RS in cancer detection and related biomarkers were reviewed. In addition, Raman applications to detect some of prevalent were discussed. Also more investigated cancers such as breast and colorectal cancer, multiple nanostructures and their possible special biomarkers, especially as SERS nano-tag have been reviewed. The main purpose of this article is introducing of most popular nanotechnological approaches in cancer detection by using Raman techniques. Moreover, have been caught up on detection and reviewed some of the most prevalent and also more investigated cancers such as breast, colorectal cancer, multiple intriguing nanostructures, especially as SERS nano-tag, special cancer biomarkers and related approaches. The main purpose of this article is to introduce the most popular nanotechnological approaches in cancer detection by using Raman techniques.

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Association of Immigration Status and Chinese and South Asian Ethnicity With Incidence of Head and Neck Cancer

Noel

Sutradhar

et al. 2020

JAMA Otolaryngol Head Neck Surg

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IMPORTANCE Head and neck cancer (HNC) incidence varies worldwide, although it remains one of the most common cancers among those of East Asian and South Asian ethnicity.OBJECTIVE To determine the association of Chinese and South Asian ethnicity, independent of immigration status, with HNC incidence.DESIGN, SETTING, AND PARTICIPANTS This was a retrospective population-based matched cohort study that examined data collected between 1994 and 2017 in Ontario, Canada. Data were analyzed between July 2019 and March 2020. Individuals who immigrated to Canada between 1985 and 2017 were classified as immigrants, whereas Canadian-born individuals and those who immigrated prior to 1985 were classified as long-standing residents. Two separate, matched cohorts were created: an immigration cohort, consisting of immigrants and long-standing residents hard matched on age and sex, and an ethnicity cohort, where participants were further matched on ethnicity (Chinese, South Asian, or non-Chinese/non-South Asian).EXPOSURES Chinese ethnicity, South Asian ethnicity, and immigration status.MAIN OUTCOMES AND MEASURES Patients newly diagnosed with primary HNC were captured in both the immigration and the ethnicity cohorts. Cause-specific hazard models were used to estimate the association of immigration status and ethnicity with HNC incidence. RESULTSIn the immigration cohort, 3 328 434 matched individuals (mean [SD] age, 36.73 [13.46] years; 52.8% female) were followed, across which 3173 unique HNC diagnoses were made. The hazard ratio (HR) for a new diagnosis of oropharynx cancer was lower in immigrants compared with long-standing residents (HR, 0.26 [95% CI, 0.22-0.31]). In the ethnicity cohort, after adjusting for age, sex, rurality, and deprivation, the rate of HNC diagnosis was higher for Chinese individuals (HR, 1.49 [95% CI,) and South Asian individuals (HR, 1.29 [95% CI, 1.14-1.45]), although it was lower for immigrants (HR, 0.48 [95% CI, 0.44-0.52]) when compared with non-Chinese and non-South Asian individuals. There was no difference in the incidence of nasopharynx cancer when comparing immigrants and long-standing residents of Chinese ethnicity.CONCLUSIONS AND RELEVANCE Immigration status appears to offer a protective effect against a diagnosis of HNC. Chinese and South Asian ethnic groups may experience higher HNC incidence when compared with the general Ontario population.

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A genome-wide association study of nasopharyngeal carcinoma identifies three new susceptibility loci

Cited by 353 publications

References 44 publications

A regulatory mutant on TRIM26 conferring the risk of nasopharyngeal carcinoma by inducing low immune response

A regulatory mutant on TRIM26 conferring the risk of nasopharyngeal carcinoma by inducing low immune response

Application of nanoparticles in cancer detection by Raman scattering based techniques

Association of Immigration Status and Chinese and South Asian Ethnicity With Incidence of Head and Neck Cancer

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