3018 Functional intronic ERCC1 polymorphism from RegulomeDB can predict survival in lung cancer after surgery

Lee, S.Y.; Hong, Mi Jeong; Jung, Deuk Kju; Jin, Congguo; Do, Soon; Park, J.Y.

doi:10.1016/s0959-8049(15)30059-9

Cited by 2 publications

(2 citation statements)

References 26 publications

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“…Many non-coding variants that have been assigned dbSNP identifiers are annotated by the Regulome database project based on whether they are located in and have a potential disruptive effect on regulatory elements and intergenic regions in the human genome, including regions of DNAase hypersensitivity, transcription factor binding sites, and biochemically characterized promoter regions. For example, this database was used to identify a functional intronic polymorphism that is predictive for post-surgery lung cancer survival (34). SNP identifiers can be submitted to the RegulomeDB (35) web server at www.regulomedb.org, which will assign them a category based on likely functional impact.…”

Section: Identifying Candidate Function-impacting Variantsmentioning

confidence: 99%

A Practical Guide To Filtering and Prioritizing Genetic Variants

Dashti

Gamieldien

2017

BioTechniques

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Next-generation sequencing (NGS) of whole genomes and exomes is a powerful tool in biomedical research and clinical diagnostics. However, the vast amount of data produced by NGS introduces new challenges and opportunities, many of which require novel computational and theoretical approaches when it comes to identifying the causal variant(s) for a disease of interest. While workflows and associated software to process raw data and produce high-confidence variant calls have significantly improved, filtering tens of thousands of candidates to identify a subset relevant to a specific study is still a complex exercise best left to bioinformaticists. However, as this prioritization procedure requires biological/biomedical reasoning, biologists and clinicians are increasingly motivated to handle the task themselves. Here, we describe a set of guidelines, tools, and online resources that can be used to identify functional variants from whole-genome and whole-exome variant calls and then prioritize these variants with potential associations to phenotypes of interest. Insights gained from a recently published analysis of protein-coding gene variation in >60,000 humans by the Exome Aggregation Consortium (ExAC) are also taken into account.

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Section: Identifying Candidate Function-impacting Variantsmentioning

confidence: 99%

A Practical Guide To Filtering and Prioritizing Genetic Variants

Dashti

Gamieldien

2017

BioTechniques

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“…In pancreatic cancers, SNPs in the APC and CD24 genes may predict the progress of the disease [11]. In lung cancer, ERCC1 variant rs2298881 affects the prognosis of lung cancer after surgery by regulating the expression of the gene [12]. Numerous similar reports have been published.…”

Section: Introductionmentioning

confidence: 98%

ATXN7 Gene Variants and Expression Predict Post-Operative Clinical Outcomes in Hepatitis B Virus-Related Hepatocellular Carcinoma

Han

Liu²,

Liu³

et al. 2016

Cell Physiol Biochem

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Background/Aims: Hepatocellular carcinoma (HCC) is a lethal disease with nearly equal morbidity and mortality. Thus, the discovery and application of more useful predictive biomarkers for improving therapeutic effects and prediction of clinical outcomes is of crucial significance. Methods: A total of 475 HBV-related HCC patients were enrolled. Ataxin 7 (ATXN7) single nucleotide polymorphisms (SNPs) were genotyped by Sanger DNA sequencing after PCR amplification. The associations between ATXN7 SNPs and mRNA expression with the prognosis of HBV-related HCC were analyzed. Results: In all, rs3774729 was significantly associated with overall survival (OS) of HBV-related HCC (P = 0.013, HR = 0.66, 95% CI: 0.48-0.94). And patients with the AA genotype and a high level of serum alpha fetoprotein (AFP) had significantly worse OS when compared to patients with AG/GG genotypes and a low level of AFP (adjusted P = 0.007, adjusted HR = 1.83, 95% CI = 1.18-2.82). Furthermore, low expression of ATXN7 was significantly associated with poor recurrence-free survival (RFS) and OS (P = 0.007, HR = 2.38, 95% CI = 1.27-4.45 and P = 0.025, HR = 1.75, 95% CI = 1.18-2.62). Conclusion: ATXN7 may be a potential predictor of post-operative prognosis of HBV-related HCC.

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3018 Functional intronic ERCC1 polymorphism from RegulomeDB can predict survival in lung cancer after surgery

Cited by 2 publications

References 26 publications

A Practical Guide To Filtering and Prioritizing Genetic Variants

A Practical Guide To Filtering and Prioritizing Genetic Variants

ATXN7 Gene Variants and Expression Predict Post-Operative Clinical Outcomes in Hepatitis B Virus-Related Hepatocellular Carcinoma

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