SNPredict: A Machine Learning Approach for Detecting Low Frequency Variants in Cancer

Cancer is a genetic disease caused by the accumulation of DNA variants such as single nucleotide changes or insertions/deletions in DNA. DNA variants can cause silencing of tumor suppressor genes or increase the activity of oncogenes. In order to come up with successful therapies for cancer patients, these DNA variants need to be identified accurately. DNA variants can be identified by comparing DNA sequence of tumor tissue to a non-tumor tissue by using Next Generation Sequencing (NGS) technology. But the problem of detecting variants in cancer is hard because many of these variant occurs only in a small subpopulation of the tumor tissue. It becomes a challenge to distinguish these low frequency variants from sequencing errors, which are common in today\u27s NGS methods. Several algorithms have been made and implemented as a tool to identify such variants in cancer. However, it has been previously shown that there is low concordance in the results produced by these tools. Moreover, the number of false positives tend to significantly increase when these tools are faced with low frequency variants. This study presents SNPredict, a single nucleotide polymorphism (SNP) detection pipeline that aims to utilize the results of multiple variant callers to produce a consensus output with higher accuracy than any of the individual tool with the help of machine learning techniques. By extracting features from the consensus output that describe traits associated with an individual variant call, it creates binary classifiers that predict a SNP’s true state and therefore help in distinguishing a sequencing error from a true variant

Conflict in Cross Border Mergers Effect of Firm and Market Size

This paper tries to analyze the interrelationship between possibilities of conflict in cross border mergers and acquisitions and firm and market characteristics in a two country three firm model. We show that in general an increase in asymmetry across firms reduces the possibility of conflict between jurisdictions over merger review decisions. We also show that possibility of conflict increase with the increase in market asymmetries across countries. We also discuss interaction of asymmetry in firm and market size with the distribution of firms across countries and its effect on the possibilities of conflict.conflict, Cross border mergers, firm size, Market Size

Wage-price dynamics : are they consistent with cost push?

Wages ; Inflation (Finance)

Recursive Competitive Equilibrium

In this article we define a Recursive Competitive Equilibrium, provide an example and review the related literature. The article is an entry prepared for The New Palgrave: A Dictionary of Economics, 2nd Edition (Palgrave Macmillan: New York).

Money growth volatility and high nominal interest rates

The period 1979-86 saw (1) high interest rates, (2) volatile money growth, and (3) new Fed operating procedures. Was the third item the chief cause of the other two? Probably not. For much of the increased monetary volatility stemmed not from the new procedures but rather from the public’s deregulation-induced switching from assets included in M1 to those included in M1 and M2. Moreover it was not monetary volatility as much as deregulation-triggered rises in money demand that contributed to high rates early in the period.Money supply ; Interest rates