Modeling Survival Data: Extending the Cox Model

Lin, Haiqun; Zelterman, Daniel

doi:10.1198/tech.2002.s656

Cited by 133 publications

(106 citation statements)

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“…Population structure was estimated by using PCA, and the first five principal components were included in the regression analyses. The Cox model estimated hazard ratio (HR) and 95% confidence interval (CI) for individual sample and meta‐analysis between samples was performed under fixed‐effect model using R package survival (version 2.44‐1.1) [ 46 ] and Metafor (version 2.0‐0). [ 47 ] Bonferroni correction was used to adjust for multiple comparisons.…”

Section: Methodsmentioning

confidence: 99%

Germline Polymorphisms and Length of Survival of Nasopharyngeal Carcinoma: An Exome‐Wide Association Study in Multiple Cohorts

et al. 2020

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Germline polymorphisms are linked with differential survival outcomes in cancers but are not well studied in nasopharyngeal carcinoma (NPC). Here, a two-phase association study is conducted to discover germline polymorphisms that are associated with the prognosis of NPC. The discovery phase includes two consecutive hospital cohorts of patients with NPC from Southern China. Exome-wide genotypes at 246 173 single nucleotide polymorphisms (SNPs) are determined, followed by survival analysis for each SNP under Cox proportional hazard regression model. Candidate SNP is replicated in another two independent cohorts from Southern China and Singapore. Meta-analysis of all samples (n = 5553) confirms that the presence of rs1131636-T, located in the 3′-UTR of RPA1, confers an inferior overall survival (HR = 1.33, 95% CI = 1.20-1.47, P = 6.31 × 10 −8 ). Bioinformatics and biological assays show that rs1131636 has regulatory effects on upstream RPA1. Functional studies further demonstrate that RPA1 promotes the growth, invasion, migration, and radioresistance of NPC cells. Additionally, miR-1253 is identified as a suppressor for RPA1 expression, likely through regulation of its binding affinity to rs1131636 locus. Collectively, these findings provide a promising biomarker aiding in stratifying patients with poor survival, as well as a potential drug target for NPC.

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Section: Methodsmentioning

confidence: 99%

Germline Polymorphisms and Length of Survival of Nasopharyngeal Carcinoma: An Exome‐Wide Association Study in Multiple Cohorts

et al. 2020

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“…For hierarchical clustering, Ward's method was used to compute the distances. A Kaplan-Meier survival estimation was created using a Cox model implemented in the CRAN package survival [23]. MYCN status prediction was performed using the partial least-square classifier with a 10-fold cross-validation implemented in the R package caret [24].…”

Section: Methodsmentioning

confidence: 99%

Measuring Transcription Rate Changes via Time-Course 4-Thiouridine Pulse-Labelling Improves Transcriptional Target Identification

Schwarzl

Higgins

Kölch

et al. 2015

Journal of Molecular Biology

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“…Comparisons of survival were carried out using Revolution R Open (version 8.0.2) with a checkpoint date of April 20th 2015 and the “survival” package(24). The threshold for statistical significance was set at 0.05.…”

Section: Methodsmentioning

confidence: 99%

Two-mAb cocktail protects macaques against the Makona variant of Ebola virus

Qiu

Audet

Liao³

et al. 2016

Sci. Transl. Med.

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The 2014–15 Ebola virus (EBOV) outbreak in West Africa highlighted the urgent need for specific therapeutic interventions for infected patients. The human-mouse chimeric monoclonal antibody (mAb) cocktail ZMapp™, previously shown to be efficacious in EBOV (variant Kikwit) lethally infected nonhuman primates (NHPs) when administration was initiated up to 5 days, was used in some patients during the outbreak. Here we show that a two-antibody cocktail, MIL77E, is fully protective in NHPs when administered at 50 mg/kg 3 days after challenge with a lethal dose of EBOV, variant Makona, the virus responsible for the ongoing 2014–15 outbreak, while a similar formulation of ZMapp™ protected 2 of 3 NHPs. The chimeric MIL77E mAb cocktail is produced in engineered CHO cells and is based on mAbs c13C6 and c2G4 from ZMapp™. The use of only 2 antibodies in MIL77E opens the door to a pan-ebolavirus cocktail.

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Modeling Survival Data: Extending the Cox Model

Cited by 133 publications

References 0 publications

Germline Polymorphisms and Length of Survival of Nasopharyngeal Carcinoma: An Exome‐Wide Association Study in Multiple Cohorts

Germline Polymorphisms and Length of Survival of Nasopharyngeal Carcinoma: An Exome‐Wide Association Study in Multiple Cohorts

Measuring Transcription Rate Changes via Time-Course 4-Thiouridine Pulse-Labelling Improves Transcriptional Target Identification

Two-mAb cocktail protects macaques against the Makona variant of Ebola virus

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