Visualizing Coronavirus Phylogenies with Genome Mutation Analysis

In this post, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) responsible for the recent pandemic is analyzed. Several attributes about the presently recorded virus genomes are plotted and genetic mutations in the sequences are traced to identify probable phylogenies among the samples.

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Ancestry Determination via Genetic Variant Analysis

Introduction

Sequencing of the human genome began in 1990 as part of the Human Genome Project. With the technology available at the time, the project was a substantial undertaking. The human genome contains two sets of 23 chromosomes each with roughly 3.2 billion base pairs. A number of institutions, in countries around the world, participated in the project. Thirteen years later the project was complete at a cost of roughly three billion US dollars. The result was the first reference human genome.

Rapid advances in the field of genomics have dramatically lowered the cost of genetic sequencing and have ushered in the age of the once fabled “$1000 genome.” Now, a growing list of companies offer whole genome sequencing for hundreds of dollars with turn around time measured in weeks. This technology enables introspection into the sequences of nucleobases that comprise DNA and thus the genes of anyone curious enough to take the plunge.

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A Method for Addressing Nonhomogeneous Data using an Implicit Hierarchical Linear Model

Datasets containing nonhomogenous groups of samples present a challenge to linear models. In particular, such datasets violate the assumption that there is a linear relationship between the independent and dependent variables. If the data is grouped into distinct clusters, linear models may predict responses that fall in between the clusters. These predictions can be quite far from the targets depending on how the data is structured. In this post, a method is presented for automatically handling nonhomogenous datasets using linear models.

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Decorrelating Features using the Gram-Schmidt Process

A problem that frequently arises when applying linear models is that of multicollinearity. The term multicollinearity describes the phenomenon where one or more features in the data matrix can be accurately predicted using a linear model involving others of the features. The consequences of multicollinearity include numerical instability due to ill-conditioning, and difficulty in interpreting the regression coefficients. An approach to decorrelate features is presented using the Gram-Schmidt process.

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