Reading about using phylogenetics in court

In my new job at SFSU, I am teaching a seminar on the evolution of human viruses. We are reading one paper every week and every student gets a different assignment for each paper. We’ve done one week now and I am very happy with the results. The paper we read was Metzker et al (PNAS, 2002), it is about using phylogenetic methods in an HIV infection case that went to court (thanks to Graham Coop for suggesting the paper).

I asked the students if I could publish some of their work. Here we go:

Describe the context and main question of the paper

The Metzker et al. study details the first instance of the admission of phylogenetic analysis as forensic evidence in a criminal case. It sought to determine whether scientific support existed for the proposed viral transmission event between the suspect (via injection of blood from an HIV-positive patient) and the victim by inferring phylogenies of the patient, victim, and HIV-infected control strains from the same geographic region using two loci under different selective pressures. In trees generated from both loci, the isolates from the victim clustered with the patient’s, supporting a close relationship between victim and patient HIV strains. Phylogenetic analysis has previously been used in inferring HIV transmission events, notably in the “Florida dentist case”. Five individuals were inferred to have contracted HIV-1 from their dentist based on the distinct clustering of their strains with the dentist’s relative to geographically similar HIV-positive controls.

Roxanne Bantay

Who are the (main) authors of the paper?

Dr. Michael Metzker, the primary author of Molecular evidence of HIV-1 transmission in a criminal case (2012), is an associate professor at Baylor college of Medicine and Rice University where he teaches human genetics. Additionally, he is president & CEO at RedVault Biosciences, a technology company that aims to advance personalized genomic medicine. Metzker is also an active researcher in the field of bioinformatics and next-generation sequencing.

The last author of the preceding publication is Dr. David Hillis, who is a current evolutionary biology professor and former director of the biology and bioinformatics department at the University of Texas (Austin). Hillis’ research focuses on experimental laboratory evolution; he believes that by studying this process we can ultimately gain insight into the underlying mechanisms that drive evolution.

Eduardo Lujan

Explain the main results of the paper using only the 1000 most common English words

This paper is about a doctor who tried to kill his girlfriend by using blood from a sick person. The doctor got the blood from their work and stuck their girlfriend during a fight. The important part of this case is the way that they showed that it really was the doctor who made the woman sick. For this case, tiny changes that happened in the thing that made the woman sick were found. These changes can show which person made the other people sick and show the relationships between all of the sick people.   By looking at these changes and the relationships, they showed that the doctor was the one who was at fault for making the woman sick.

Bradley Bowser

(see http://splasho.com/upgoer5/)

Make a graphical abstract of the paper

Peter Manzo