Non-invasive prenatal detection of Trisomy 21 using tandem single nucleotide polymorphisms

Sujana Ghanta, Michael E. Mitchell, Mary Ames, Mats Hidestrand, Pippa Simpson, Mary Goetsch, William G. Thilly, Craig A. Struble, Aoy Tomita-Mitchell

Research output: Contribution to journalArticle

16 Citations (Scopus)

Abstract

Background: Screening tests for Trisomy 21 (T21), also known as Down syndrome, are routinely performed for the majority of pregnant women. However, current tests rely on either evaluating non-specific markers, which lead to false negative and false positive results, or on invasive tests, which while highly accurate, are expensive and carry a risk of fetal loss. We outline a novel, rapid, highly sensitive, and targeted approach to non-invasively detect fetal T21 using maternal plasma DNA. Methods and Findings: Highly heterozygous tandem Single Nucleotide Polymorphism (SNP) sequences on chromosome 21 were analyzed using High-Fidelity PCR and Cycling Temperature Capillary Electrophoresis (CTCE). This approach was used to blindly analyze plasma DNA obtained from peripheral blood from 40 high risk pregnant women, in adherence to a Medical College of Wisconsin Institutional Review Board approved protocol. Tandem SNP sequences were informative when the mother was heterozygous and a third paternal haplotype was present, permitting a quantitative comparison between the maternally inherited haplotype and the paternally inherited haplotype to infer fetal chromosomal dosage by calculating a Haplotype Ratio (HR). 27 subjects were assessable; 13 subjects were not informative due to either low DNA yield or were not informative at the tandem SNP sequences examined. All results were confirmed by a procedure (amniocentesis/CVS) or at postnatal follow-up. Twenty subjects were identified as carrying a disomy 21 fetus (with two copies of chromosome 21) and seven subjects were identified as carrying a T21 fetus. The sensitivity and the specificity of the assay was 100% when HR values lying between 3/5 and 5/3 were used as a threshold for normal subjects. Conclusions: In summary, a targeted approach, based on calculation of Haplotype Ratios from tandem SNP sequences combined with a sensitive and quantitative DNA measurement technology can be used to accurately detect fetal T21 in maternal plasma when sufficient fetal DNA is present in maternal plasma.

Original languageEnglish (US)
Article numbere13184
JournalPLoS One
Volume5
Issue number10
DOIs
StatePublished - 2010
Externally publishedYes

Fingerprint

trisomics
Down Syndrome
Polymorphism
Haplotypes
single nucleotide polymorphism
Single Nucleotide Polymorphism
haplotypes
Nucleotides
DNA
Plasmas
Mothers
Chromosomes, Human, Pair 21
Chromosomes
pregnant women
fetus
Pregnant Women
Fetus
Capillary electrophoresis
chromosomes
Down syndrome

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Ghanta, S., Mitchell, M. E., Ames, M., Hidestrand, M., Simpson, P., Goetsch, M., ... Tomita-Mitchell, A. (2010). Non-invasive prenatal detection of Trisomy 21 using tandem single nucleotide polymorphisms. PLoS One, 5(10), [e13184]. https://doi.org/10.1371/journal.pone.0013184

Non-invasive prenatal detection of Trisomy 21 using tandem single nucleotide polymorphisms. / Ghanta, Sujana; Mitchell, Michael E.; Ames, Mary; Hidestrand, Mats; Simpson, Pippa; Goetsch, Mary; Thilly, William G.; Struble, Craig A.; Tomita-Mitchell, Aoy.

In: PLoS One, Vol. 5, No. 10, e13184, 2010.

Research output: Contribution to journalArticle

Ghanta, S, Mitchell, ME, Ames, M, Hidestrand, M, Simpson, P, Goetsch, M, Thilly, WG, Struble, CA & Tomita-Mitchell, A 2010, 'Non-invasive prenatal detection of Trisomy 21 using tandem single nucleotide polymorphisms', PLoS One, vol. 5, no. 10, e13184. https://doi.org/10.1371/journal.pone.0013184
Ghanta S, Mitchell ME, Ames M, Hidestrand M, Simpson P, Goetsch M et al. Non-invasive prenatal detection of Trisomy 21 using tandem single nucleotide polymorphisms. PLoS One. 2010;5(10). e13184. https://doi.org/10.1371/journal.pone.0013184
Ghanta, Sujana ; Mitchell, Michael E. ; Ames, Mary ; Hidestrand, Mats ; Simpson, Pippa ; Goetsch, Mary ; Thilly, William G. ; Struble, Craig A. ; Tomita-Mitchell, Aoy. / Non-invasive prenatal detection of Trisomy 21 using tandem single nucleotide polymorphisms. In: PLoS One. 2010 ; Vol. 5, No. 10.
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