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CDSD_AP2

Asaf Poran
CDSD 04/27/2015
Motivation : Intelligent Design 2.0
An endless estimated number of enemies (estimated 10^15).
We want to have "The Great Book of How to Kill All Diseases".
The length of the (exonic) gene coding the enemy-sensing receptor is ~1000 nucleotides long

10^18 bases long genome to encode all of the required receptors.
Identification of Antigen-Specific B Cell Receptor Sequences Using Public Repertoire Analysis
(Wikipedia)
Signal to
the immune
system
Identification of Antigen-Specific B Cell Receptor Sequences Using Public Repertoire Analysis
From: Laboratory for Systems and Synthetic Immunology, ETH Zurich
Identification of Antigen-Specific B Cell Receptor Sequences Using Public Repertoire Analysis
And Even More Diversity - Somatic Hypermutation
Why It’s Called Adaptive Immunity
T=0
Introduction
of Antigen
T=7+ days
Study of the BCR Repertoire
What happens to the repertoires of different individuals when vaccinated with the same antigen?
Are there public repertoires- overlap between people?
5 individuals were vaccinated with a mix of:
Haemophilus influenzae type B (Hib)
serogroup C meningococcal (MenC)
tetanus toxoid (TT)
B cells were extracted from blood samples at Day 0 and Day 7 postvaccination.
BCR=B cell Receptor
Increased Clonality Postvaccination
Naiïve B Cells

Plasma Cells (Antibody
Producing B cells)
Critique #1
Wrong Index measurement –Should use Shannon’s enthropy / gini coefficient
Figure S1C
Public CDR3 Are Enriched for Hib-specific Sequences
CDR3=Complementarity determining region 3, the interesting part of the sequence
Figure 2
Increase in Hib-Specific Frequency
Hib=Haemophilus influenzae type B
MenC=serogroup C meningococcal
TT=tetanus toxoid
Figure 5
Critique #2
“for sequences not present at baseline, fold change was calculated as 1.5 times the frequency postvaccination”
Increase in Mutation Number
Figure 6
Hib=Haemophilus influenzae type B
TT=tetanus toxoid
Critique #3
Statistical testing
No normalization
No hypothesis as to why TT>Hib - artifact?
Errors About Errors
Critique #4
Sequencing Errors?!
Diagnostics in Plant Breeding, Springer
The study presents means of mutation numbers ranging from 9.8 to 20.5.

The length of the average V segment is 350nt.
Thus, the expected mean number of “mutations” due to sequencing errors is 1.4-5.25!
Summary
A very interesting application of high-throughput sequencing in the field of B cell repertoires.
A good demonstration of the existence of public repertoires and the convergence of repertoires towards a "common enemy".
Hold great promise for diagnosis of the immune state, previous exposure to antigen, vaccine design, cancer immunotherapy, etc.
Thank you!
These antigens were chosen for the study since past work has determined that theHib-Specific BCRs have a strong motif in their CDR3 region.
This motif could be used to detect BCRs that are targeting theHibantigen.
1. This is a billion times longer than our entire genome.
2. If a new bug comes along, we need to add new entries to the book.
Even if we:
exclude outer-space pathogens and other rare terrestrial pathogens (reduce by a 1000)
assume that an average receptor is good for a 1000 similar enemies

We reduce the problem to a receptor genome that is still a 1000 times the length of our genome.
47 sequences found in two samples or more
However, the paper lacks greatly in the quantitative analysis of the data and lacks controls and crucial corrections.
Hib=Haemophilus influenzae type B
MenC=serogroup C meningococcal
TT=tetanus toxoid
50% of the public CDR3 sequences are Hib-Specific!
"Fifty Years of B Lymphocytes", Nature 2015
Dreamstime image bank
Almudena R, Nature 2004
47 sequences were found to be shared by at least two people

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