Microfluidic chip-based method for genotyping microsatellites, VNTRs and insertion/deletion polymorphisms

Youvraj R. Sohni, James P. Burke, Peter J. Dyck, Dennis J. O'Kane

Research output: Contribution to journalArticle

18 Scopus citations

Abstract

We have developed a method to genotype variable number of tandem repeats (VNTRs) and insertion/deletion polymorphisms using an integrated microfluidic chip-based system. We used this method to analyze a) a highly polymorphic pentanucleotide repeat (CCTTT)n locus within the 5′-putative promoter region of the human inducible nitric oxide synthase gene (iNOS5) which is associated with diabetic complications and infectious diseases; b) a bi-allelic 27 bp VNTR region within intron 4 of endothelial nitric oxide gene (eNOS27) which is associated with hypertension in type 2 diabetes patients with coronary heart disease and excess risk of advanced diabetic nephropathy in type 1 diabetes patients and c) an insertion/deletion polymorphism within the gene encoding angiotensin-converting enzyme (ACE/ID) which is associated with cardiovascular pathology and nitric oxide activity, and is in strong linkage disequilibrium with functional variants. Following amplifications, samples were mixed with gel-dye and markers and loaded into commercially available microfluidic chips designed for DNA sizing applications. In the study (N = 230), 95 (41%) of the DNA samples were homozygous and 135 (59%) were heterozygous for the iNOS5 repeats. For eNOS27, 173 (75%) of the genotyped DNA samples were homozygous for the larger 4b allele and the remaining 57 samples (25%) were heterozygous (4b/4a). No DNA samples were homozygous for the shorter 4a allele with four 27 bp repeats. In case of ACE/ID, 47 (20%) of the DNA samples were homozygous for the insertion, 65 (28%) were homozygous for the deletion and the remaining 118 (51%) were heterozygous. The results obtained were verified by analyzing random amplicons using bi-directional sequencing and GeneScan® 3.0 analyses with 100% concordance being observed. Using the microfluidic chip-based method, separation and DNA sizing and genotyping are rapidly accomplished. The DNA fragments are resolved clearly and the system allows quantitation. Finally, the microfluidic chip-based method may be used for both large- and small-scale genotyping studies.

Original languageEnglish (US)
Pages (from-to)35-40
Number of pages6
JournalClinical Biochemistry
Volume36
Issue number1
DOIs
StatePublished - Jan 1 2003

Keywords

  • Genotyping
  • Microfluidic
  • Microsatellites
  • VNTRs

ASJC Scopus subject areas

  • Clinical Biochemistry

Fingerprint Dive into the research topics of 'Microfluidic chip-based method for genotyping microsatellites, VNTRs and insertion/deletion polymorphisms'. Together they form a unique fingerprint.

  • Cite this