A Pilot Study of Noninvasive Prenatal Diagnosis of Alpha- and Beta-Thalassemia with Target Capture Sequencing of Cell-Free Fetal DNA in Maternal Blood

Genet Test Mol Biomarkers. 2017 Jul;21(7):433-439. doi: 10.1089/gtmb.2016.0411. Epub 2017 May 24.


Aims: Thalassemia is a dangerous hematolytic genetic disease. In south China, ∼24% Chinese carry alpha-thalassemia or beta-thalassemia gene mutations. Given the fact that the invasive sampling procedures can only be performed by professionals in experienced centers, it may increase the risk of miscarriage or infection. Thus, most people are worried about the invasive operation. As such, a noninvasive and accurate prenatal diagnosis is needed for appropriate genetic counseling for families with high risks. Here we sought to develop capture probes and their companion analysis methods for the noninvasive prenatal detection of deletional and nondeletional thalassemia.

Materials and methods: Two families diagnosed as carriers of either beta-thalassemia gene or Southeast Asian deletional alpha-thalassemia gene mutation were recruited. The maternal plasma and amniotic fluid were collected for prenatal diagnosis. Probes targeting exons of the genes of interest and the highly heterozygous SNPs within the 1Mb flanking region were designed. The target capture sequencing was performed with plasma DNA from the pregnant woman and genomic DNA from the couples and their children. Then the parental haplotype was constructed by the trios-based strategy. The fetal haplotype was deduced from the parental haplotype with a hidden Markov model-based algorithm.

Results: The fetal genotypes were successfully deduced in both families noninvasively. The noninvasively constructed haplotypes of both fetuses were identical to the invasive prenatal diagnosis results with an accuracy rate of 100% in the target region.

Conclusion: Our study demonstrates that the effective noninvasive prenatal diagnosis of alpha-thalassemia and beta-thalassemia can be achieved with the targeted capture sequencing and the haplotype-assisted analysis method.

Keywords: SNP; massively parallel sequencing; noninvasive prenatal test; target region capture; thalassemia.

MeSH terms

  • Adult
  • Amniotic Fluid
  • China
  • DNA / genetics
  • DNA Probes
  • Female
  • Fetus
  • Genetic Counseling
  • Genotype
  • Haplotypes
  • Humans
  • Pedigree
  • Pilot Projects
  • Polymorphism, Single Nucleotide / genetics
  • Pregnancy
  • Prenatal Diagnosis / methods*
  • Sequence Analysis, DNA / methods
  • alpha-Thalassemia / blood
  • alpha-Thalassemia / diagnosis*
  • alpha-Thalassemia / genetics
  • beta-Thalassemia / blood
  • beta-Thalassemia / diagnosis*
  • beta-Thalassemia / genetics


  • DNA Probes
  • DNA