Noninvasive Prenatal Diagnosis of SEA-Thalassemia by Combining 1000 Genomes Database and Relative Haplotype Dosage.

To explore a noninvasive method for diagnosis of SEA-thalassemia and to investigate whether the regional factors affect the accuracy of this method. The method involved using a public database and bioinformatics software to construct parental haplotypes for proband and predicting fetal genotypes using relative haplotype dosage. We screened and downloaded sequencing data of couples who were both SEA-thalassemia carriers from the China National Genebank public data platform, and matched the sequencing data format with that of the reference panel using Ubuntu system tools. We then used Beagle software to construct parental haplotypes, predicted fetal haplotypes by relative haplotype dosage. Finally, we used Hidden Markov Model and Viterbi algorithm to determine fetal pathogenic haplotypes. All noninvasive fetal genotype diagnosis results were compared with gold standard gap-PCR electrophoresis results. Our method was successful in diagnosing 13 families with SEA-thalassemia carriers. The best diagnostic results were obtained when Southern Chinese Han was used as the reference panel, and 10 families showed full agreement between our noninvasive diagnostic results and the gap-PCR electrophoresis results. The accuracy of our method was higher when using a Chinese Han as the reference panel for haplotype construction in the Southern Chinese Han region as opposed to Beijing Chinese region. The combined use of public databases and relative haplotype dosage for diagnosing SEA-thalassemia is a feasible approach. Our method produces the best noninvasive diagnostic results when the test samples and population reference panel are closely matched in both ethnicity and geography. When constructing parental haplotypes with our method, it is important to consider the effect of region in addition to population background alone.

Research Progress of Cell-Free Fetal DNA in Non-Invasive Prenatal Diagnosis of Thalassemia.

Thalassemia is a genetic disease that seriously affects the health of the fetus. At present, invasive prenatal diagnosis is the main method of thalassemia screening, but invasive prenatal diagnosis has the risk of fetal abortion. The discovery of cell-free fetal DNA (cffDNA) in the peripheral blood of pregnant women provides the possibility for non-invasive prenatal diagnosis (NIPD). Rapid and efficient capture of mutational information on cffDNA in maternal plasma can help prevent the birth of children with thalassemia major. Currently, strategies for cffDNA-based NIPD of thalassemia include the detection of paternal mutations in maternal plasma, detection of a proportion of wild and mutant alleles in maternal plasma, linkage disequilibrium single nucleotide polymorphism (SNP) based on pedigree probands, and prediction of fetal genotypes by bioinformatics combined with population information. Therefore, this paper will focus on the above aspects, in order to provide an essential reference to the prevention and treatment of thalassemia.