Download Mutation identification by whole genome sequencing

BIO421
Advanced Genetics
Finish SNP Mapping; Begin Mutation
Detection Through Whole Genome Sequencing
Lecture 7
I. We will continue with SNP mapping, and then move on to:
II. Mutation Detection Through Whole Genome Sequencing
A. Sequencing Methods
1. Conventional Sanger Sequencing
a. dideoxy nucleotide triphosphates (ddNTPs), the key to the Sanger method
1) they terminate DNA polymerization because they lack a 3’ –OH
2) each ddNPT (i.e. ddATP, ddCTP, etc.) has its own charateristic fluorphore
b. protocol
1) combine DNA plus a short primer sequence that provides a 3’ -OH
2) add Polymerase, dNTPs, a small amount of ddNTPs
3) allow primers to anneal, polymerase to synthesize DNA, heat to melt dsDNA,
and repeat multiple times
4) run in an analyzer to separate DNA products of different sizes and detect them
by fluorescence
5) Obtain sequence
2. Next Generation Sequencing by the Illumina method
a. Completed in a flow cell. 8 lanes on each cell can produce 12 billion bases of
sequence information
b. Genomic DNA is fragmented, bound to the surface of the flow cell, and each
fragment amplified to produce a cluster of identical fragments.
c. Each cluster is sequenced using a specially designed nucleotide
1) The sequencing nucleotide has a specific fluorophore for each of the 4 bases
(ie. A – green, T – red, etc.). The fluorophores can be cleaved off after laser
illumination to excite the fluorophores.
2) The sequencing nucleotide has the 3’ –OH blocked so that polymerization
adds on only a single nucleotide. The blocking agent can be chemically
removed after the fluorescence is detected.
3) The sequencing reaction is repeated 72 times to obtain 72 bases of DNA
sequence for each fragment.