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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.
Pages
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Posts
Genetic Risk for Overall Cancer and the Benefit of Adherence to a Healthy Lifestyle: A review
Published:
This post is a review on a paper in American Association of Cancer Research, which describes association of PRS and lifestyle with developement of 20 types of cancer.
Genetic risk, incident gastric cancer, and healthy lifestyle: a meta-analysis of genome-wide association studies and prospective cohort study: A review
Published:
This post is a review on a paper published in Lancet Oncology that discusses PRS applied to gastric cancer.
On cross-ancestry cancer polygenic risk scores: A review
Published:
Today, I’m reviewing a paper that examines the use of PRS across ancestries
Reviewing PRS literature Part 1
Published:
Today I reviewed 10 of papers on PRS literature. Part 1.
Using gnomAD
Published:
This post is a very short learning point on how to identify pathogenic variants in a given gene. I have not yet verified whether this resource is reputable, however I hope that it provides to be a great resource. It was previously used by Joe Park in another area of the PMBB lab, an utilized in his paper in Nature here.
ACMG Clinically Relevant Mutations for Cancer
Published:
Creating a list of clinically relevant pathogenic variants for cancer
Beginning of a quick project
Published:
Below is a post to identify the first few steps in a project in which I aim to identify the proportion of pathogenic variants present in our population.
Subsetting patients by lung cancer histology subtype
Published:
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Creating concise phenotype files for patients in PMBB
Published:
In this posting, I created a script in R that goes through the 3 most important phenotype files in PMBB.
Evaluating PRS in R to calculate “Area Under the Curve” and Odds Ratio
Published:
This post shows the R script I’ve written to calculate AUC and OR for the PRS generated in plink in previous blog posts. It has undergone several iterations as I adjust our desired outcomes.
Creating a PRS based on a list of SNPs and the imputed PMBB dataset
Published:
This post shows the script I wrote to convert LD pruned lists of SNPs, apply them to the Penn Medicine Biobank on a specific population, and use plink -score to create Polygenic Risk scores. Below I have pasted the .sh script I wrote today to create PRS.
Linkage Disequilibrium Pruning on the 1000 genomes dataset
Published:
In this blog post, I’ll outline the script I made to conduct Linkage Disequilibrium Pruning with a given list of SNPs on the 1000 genomes dataset.
Determining the Single Nucleotide Polymorphisms to be used in building Polygenic Risk Scores for Lung Cancer Susceptibility
Published:
This blog post describes how to create a list of SNPs associated with Lung Cancer. This will be used in future steps to build PRSs.
Performance of polygenic risk scores for cancer prediction in a racially diverse academic biobank: Methods part 2
Published:
This blog post is Part 2 of outlining the materials and methods used in our lab’s most recent work on generating polygenic risk scores (PRSs). This article is entitled “Performance of polygenic risk scores for cancer prediction in a racially diverse academic biobank”. It was published in October 2021 and led by Dr. Louise Wang and Heena Desai.
Genetically Informed Ancestry using EIGENSTRAT
Published:
In creating polygenic risk scores in Wang et al., 2021, patient population was subdivided into those with European and African descent.
Genotype Imputation and TOPMed r2
Published:
I have never understood genotype imputation. This blog post serves to describe the concept of genetic imputation and how it’s carried out using TOPMed.
Performance of polygenic risk scores for cancer prediction in a racially diverse academic biobank: Methods Part 1
Published:
This blog post will be Part 1 of outlining the materials and methods used in our lab’s most recent work on generating polygenic risk scores (PRSs). This article is entitled “Performance of polygenic risk scores for cancer prediction in a racially diverse academic biobank”. It was published in October 2021 and led by Dr. Louise Wang and Heena Desai.
What is a VCF file?
Published:
This blog post exists because I tried to create a blog post on study methods and failed.
Initial exploration of Penn Medicine Biobank
Published:
Today I’m exploring the data available within PMBB. This blog is a data dump of the directories and README files, which might not be pleasant to read. However, I’m interested in copying it here as a resource that I can check back on when navigating this complicated database.
Linkage disequilibrium - understanding the evolutionary past and mapping the medical future… A review
Published:
In this blog post, I’ll cover a paper published by Montgomery Slatkin in Nature Reviews genetics in 2008, entitled “Linkage disequilibrium - understanding the evolutionary past and mapping the medical future”. It can be found on Nature’s website here and free on Pubmed here.
At atlas of genetic correlations across human diseases and traits… A review
Published:
In this posting, I’ll review an analytical paper in Nature genetics entitled “An atlas of genetic correlations across human disease and traits”, by Bulik-Sullivan et al. published 2015. It can be found here on Nature’s website and here on PubMed.
Large-scale association analysis identifies new lung cancer susceptibility… A review
Published:
In the upcoming days, I’m going to review background literature on the topic of my future research.
An introduction to the Penn Medicine Biobank
Published:
Welcome to the blog. In this first posting, I aim to describe the Penn Medicine Biobank. Although it remains an unfamiliar resource within Penn Medicine, it contains a fantastic array of electronic health record and genetic information with tremendous research potential.
portfolio
Portfolio item number 1
Short description of portfolio item number 1
Portfolio item number 2
Short description of portfolio item number 2
publications
Paper Title Number 1
Published in Journal 1, 2009
This paper is about the number 1. The number 2 is left for future work.
Recommended citation: Your Name, You. (2009). "Paper Title Number 1." Journal 1. 1(1). http://academicpages.github.io/files/paper1.pdf
Paper Title Number 2
Published in Journal 1, 2010
This paper is about the number 2. The number 3 is left for future work.
Recommended citation: Your Name, You. (2010). "Paper Title Number 2." Journal 1. 1(2). http://academicpages.github.io/files/paper2.pdf
Paper Title Number 3
Published in Journal 1, 2015
This paper is about the number 3. The number 4 is left for future work.
Recommended citation: Your Name, You. (2015). "Paper Title Number 3." Journal 1. 1(3). http://academicpages.github.io/files/paper3.pdf
talks
Talk 1 on Relevant Topic in Your Field
Published:
This is a description of your talk, which is a markdown files that can be all markdown-ified like any other post. Yay markdown!
Conference Proceeding talk 3 on Relevant Topic in Your Field
Published:
This is a description of your conference proceedings talk, note the different field in type. You can put anything in this field.
teaching
Teaching experience 1
Undergraduate course, University 1, Department, 2014
This is a description of a teaching experience. You can use markdown like any other post.
Teaching experience 2
Workshop, University 1, Department, 2015
This is a description of a teaching experience. You can use markdown like any other post.