tangwei1129/livercancervirscan

Liver Cancer Virscan

A Viral Exposure Signature Defines Early Onset of Hepatocellular Carcinoma PDF Download

Jinping Liu, Wei Tang, Anuradha Budhu, Marshonna Forgues, Maria O Hernandez, Julián Candia, Yujin Kim, Elise D Bowman, Stefan Ambs, Yongmei Zhao, Bao Tran, Xiaolin Wu, Christopher Koh, Pallavi Surana, T Jake Liang, Maria Guarnera, Dean Mann, Manoj Rajaure, Tim F Greten, Zhanwei Wang, Herbert Yu, Xin Wei Wang

PMID: 32526205 DOI: 10.1016/j.cell.2020.05.038

Abstract Hepatocellular carcinoma (HCC) is an aggressive malignancy with its global incidence and mortality rate continuing to rise, although early detection and surveillance are suboptimal. We performed serological profiling of the viral infection history in 899 individuals from an NCI-UMD case-control study using a synthetic human virome, VirScan. We developed a viral exposure signature and validated the results in a longitudinal cohort with 173 at-risk patients who had long-term follow-up for HCC development. Our viral exposure signature significantly associated with HCC status among at-risk individuals in the validation cohort (area under the curve: 0.91 [95% CI 0.87-0.96] at baseline and 0.98 [95% CI 0.97-1] at diagnosis). The signature identified cancer patients prior to a clinical diagnosis and was superior to alpha-fetoprotein. In summary, we established a viral exposure signature that can predict HCC among at-risk patients prior to a clinical diagnosis, which may be useful in HCC surveillance.

livercancervirscan's Issues

calc_zipval.py

Hello,

I am encountering the below error when attempting to generate p-values form the counts file:

module load python/3.7 && python bin/calc_zipval.py count/VC03_IDX192_S192.count.csv.gz count/INPUT.count.csv.gz log > pvalues/VC03_IDX192_S192.zipval.csv

Traceback (most recent call last):
File "bin/calc_zipval.py", line 133, in
pvals = calc_pvals(in_, out, zigp, param_models)
File "bin/calc_zipval.py", line 101, in calc_pvals
params_fits = fit_models(in_, out, model)
File "bin/calc_zipval.py", line 22, in fit_models
grouped = filtered.groupby(in_.ix[filtered.index])
File "/usr/local/Anaconda/envs/py3.7/lib/python3.7/site-packages/pandas/core/generic.py", line 5487, in getattr
return object.getattribute(self, name)
AttributeError: 'Series' object has no attribute 'ix'

Is there a coding update to the calc_zpal.py script needed due to deprecation of functions calls?

My INPUT.counts.csv.gz file head looks as follows:

id,INPUT
tile1,600
tile2,620
tile3,330
tile4,235
tile5,1732
tile6,1268
tile7,960
tile8,232
tile9,7

My sample file hear looks as follows:

id,SAMPLE_ID
tile1,51
tile2,36
tile3,18
tile4,3
tile5,110
tile6,75
tile7,40
tile8,8
tile9,0

My bin dir has the following saved therein:

calc_zipval.py
generalizedpoisson.py
zigp.py

Thanks ... best,

Kory Johnson