Bioinformatics Seminars

Bioinformatics Seminar

Time: 10:45am Tuesdays.
Level 7 Seminar Room 2, WEHI1

29 August 2017

Counting T-cell clonotypes

Terry Speed
WEHI Bioinformatics

T-cell receptor loci undergo combinatorial rearrangement, generating a diverse immune receptor repertoire,
which is vital for recognition of potential antigens. My collaborators use a multiplex PCR with a mixture of
primers targeting the rearranged variable and joining segments to capture receptor diversity. Differential
hybridization kinetics introduces significant amplification biases that alters the composition of sequence
libraries prepared by multiplex PCR. Their solution is to spike in to each sample a collection of synthetic
templates embodying the full set of forward and reverse primers used to amplify the receptors, and scale
counts by factors derived from the spike counts.

This talk is about understanding and possibly improving that scaling.

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