Simultaneous detection of microsatellite repeats and SNPs in the macrophage migration inhibitory factor (MIF) gene by thin-film biosensor chips and application to rural field studies.
Microsatellite repeat and single nucleotide polymorphisms (SNPs) are abundant sources of genetic variation, but existing methodologies cannot simultaneously detect these variants in a facile or inexpensive way. We describe herein a thin-film biosensor chip based on an allele-discriminating oligonucleotide array that enables genotyping for both microsatellite repeats and SNPs in a single analysis. We validated this methodology for the functionally polymorphic -794 CATT(5-8) repeat and -173 G/C SNP present in the promoter of the human gene for macrophage migration inhibitory factor (MIF). In a comparison of 30 samples collected at a rural hospital in Zambia, we observed a 100% concordance for both the CATT repeat and G/C SNP between the biosensor methodology and the conventional capillary electrophoresis. The biosensor chips are low in cost and once printed, they are robust and require no instrumentation for analysis. When combined with multiple displacement amplification, this methodology can be utilized in primitive settings for the genotyping of nanogram quantities of DNA present in blood, dried and stored on filter paper samples. We applied this methodology to a field study of MIF genotype in children with malaria, and provide first evidence for a potential association between MIF alleles and malaria infection. We also present data supporting significant population stratification of the low- versus high-expression forms of MIF that may bear on the role of this gene in infectious diseases.
Zhong
Xiao-bo
XB
Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA. xzhong@kumc.edu
Leng
Lin
L
Beitin
Anna
A
Chen
Rui
R
McDonald
Courtney
C
Hsiao
Betty
B
Jenison
Robert D
RD
Kang
Insoo
I
Park
Sung-Hwan
SH
Lee
Annette
A
Gregersen
Peter
P
Thuma
Philip
P
Bray-Ward
Patricia
P
Ward
David C
DC
Bucala
Richard
R
D015374:Biosensing Techniques / Q000379:methods*; D002648:Child; D005787:Gene Frequency; D006801:Humans; D008263:Macrophage Migration-Inhibitory Factors / Q000235:genetics*; D008288:Malaria / Q000235:genetics; D018895:Microsatellite Repeats; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D011401:Promoter Regions, Genetic; D012423:Rural Health
D008263:Macrophage Migration-Inhibitory Factors