Noninvasive prenatal diagnosis of β-thalassemia by relative haplotype dosage without analyzing proband

Mol Genet Genomic Med. 2019 Nov;7(11):e963. doi: 10.1002/mgg3.963. Epub 2019 Sep 30.

Abstract

Background: β-thalassemia is one of the most common monogenic diseases in the world. Southeast China is a highly infected area affected by four β-thalassemia mutation types (HBB:c.-78A>G, HBB:c.52A>T, HBB:c.126_129delCTTT, and HBB:c.316-197C>T). Relative haplotype dosage (RHDO), a haplotype-based approach, has shown promise as an application for noninvasive prenatal diagnosis (NIPD); however, additional family members (such as the proband) are required for haplotype construction. The abovementioned circumstances make RHDO-based NIPD cost prohibitive; additionally, the genetic information of the proband is not always available. Thus, it is necessary to find a practical method to solve these problems.

Methods: Targeted sequencing was applied to sequence parental genomic DNA and cell-free fetal DNA (cffDNA). Parental haplotypes were constructed with the SHAPEIT software based on the 1000 Genomes Project (1000G) Phase 3 v5 Southern Han Chinese (CHS) haplotype dataset. Single-nucleotide polymorphisms (SNPs) in the target region were called and classified, and the fetal mutation inheritance status was deduced using the RHDO method.

Results: Construction of the parental haplotypes and detection of the inherited parental mutations were successfully achieved in five families, despite a suspected recombination event. The status of the affected fetuses is consistent with the results of traditional reverse dot blot (RDB) diagnosis.

Conclusion: This research introduced SHAPEIT into the classical RHDO workflow and proved that it is applicable to construct parental haplotypes without information from other family members.

Keywords: cell-free fetal DNA; haplotype; noninvasive prenatal diagnosis; relative haplotype dosage; β-thalassemia.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • China
  • DNA / blood
  • DNA / genetics*
  • Female
  • Genetic Testing
  • Haplotypes
  • Humans
  • Male
  • Mutation*
  • Noninvasive Prenatal Testing / methods*
  • Pedigree
  • Polymorphism, Single Nucleotide*
  • Pregnancy
  • Prenatal Diagnosis / methods*
  • Sequence Analysis, DNA
  • beta-Thalassemia / blood
  • beta-Thalassemia / diagnosis*
  • beta-Thalassemia / genetics

Substances

  • DNA