Base composition analysis of human mitochondrial DNA using electrospray ionization mass spectrometry: a novel tool for the identification and differentiation of humans.
In traditional approaches, mitochondrial DNA (mtDNA) variation is exploited for forensic identity testing by sequencing the two hypervariable regions of the human mtDNA control region. To reduce time and labor, single nucleotide polymorphism (SNP) assays are being sought to possibly replace sequencing. However, most SNP assays capture only a portion of the total variation within the desired regions, require a priori knowledge of the position of the SNP in the genome, and are generally not quantitative. Furthermore, with mtDNA, the clustering of SNPs complicates the design of SNP extension primers or hybridization probes. This article describes an automated electrospray ionization mass spectrometry method that can detect a number of clustered SNPs within an amplicon without a priori knowledge of specific SNP positions and can do so quantitatively. With this technique, the base composition of a PCR amplicon, less than 140 nucleotides in length, can be calculated. The difference in base composition between two samples indicates the presence of an SNP. Therefore, no post-PCR analytical construct needs to be developed to assess variation within a fragment. Of the 2754 different mtDNA sequences in the public forensic mtDNA database, nearly 90% could be resolved by the assay. The mass spectrometer is well suited to characterize and quantitate heteroplasmic samples or those containing mixtures. This makes possible the interpretation of mtDNA mixtures (as well as mixtures when assaying other SNPs). This assay can be expanded to assess genetic variation in the coding region of the mtDNA genome and can be automated to facilitate analysis of a large number of samples such as those encountered after a mass disaster.
Hall
Thomas A
TA
Ibis Therapeutics, A Division of Isis Pharmaceuticals, 1891 Rutherford Road, Carlsbad, CA 92008, USA.
Budowle
Bruce
B
Jiang
Yun
Y
Blyn
Lawrence
L
Eshoo
Mark
M
Sannes-Lowery
Kristin A
KA
Sampath
Rangarajan
R
Drader
Jared J
JJ
Hannis
James C
JC
Harrell
Patina
P
Samant
Vivek
V
White
Neill
N
Ecker
David J
DJ
Hofstadler
Steven A
SA
D001331:Automation; D001482:Base Composition; D001483:Base Sequence; D004247:DNA / Q000097:blood; D004262:DNA Restriction Enzymes / Q000378:metabolism; D004272:DNA, Mitochondrial / Q000737:chemistry*; D030561:Databases, Nucleic Acid; D044707:Forensic Sciences / Q000379:methods*; D006801:Humans; D010865:Pilot Projects; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D012680:Sensitivity and Specificity; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods*
D004272:DNA, Mitochondrial; D004247:DNA; D004262:DNA Restriction Enzymes