NDLI: BasePhasing: a highly efficient approach for preimplantation genetic haplotyping in clinical application of balanced translocation carriers

Content Provider	Springer Nature : BioMed Central
Author	Zhang, Shuo Zhao, Dingding Zhang, Jun Mao, Yan Kong, Lingyin Zhang, Yueping Liang, Bo Sun, Xiaoxi Xu, Congjian
Abstract	Background Preimplantation genetic testing (PGT) has already been applied in chromosomally balanced translocation carriers to improve the clinical outcome of assisted reproduction. However, traditional methods could not further distinguish embryos carrying a translocation from those with a normal karyotype prior to implantation. Methods To solve this problem, we developed a method named “Chromosomal Phasing on Base level” (BasePhasing), which based on Infinium Asian Screening Array-24 v1.0 (ASA) and a specially phasing pipeline. Firstly, by comparing the number of single nucleotide polymorphism (SNP) loci in different minor allele frequencies (MAFs) and in 2Mbp continuous windows of ASA chip and karyomap-12 chip, we verified whether ASA could be adopted for genome-wide haplotype linkage analysis. Besides, the whole gene amplification (WGA) of 3–10 cells of GM16457 cell line was used to verify whether ASA chip could be used for testing of WGA products. Finally, two balanced translocation families were utilized to carry out BasePhasing and to validate the feasibility of its clinical application. Results The average number of SNP loci in each window of ASA (473.2) was twice of that of Karyomap-12 (201.2). The coincidence rate of SNP loci in genomic DNA and WGA products was about 97%. The 5.3Mbp deletion was detected positively in cell line GM16457 of both genomic DNA and WGA products, and haplotype linkage analysis was performed in genome wide successfully. In the two balanced translocation families, 18 blastocysts were analyzed, in which 8 were unbalanced and the other 10 were balanced or normal chromosomes. Two embryos were transferred back to the patients successfully, and prenatal cytogenetic analysis of amniotic fluid was performed in the second trimester. The results predicted by BasePhasing and prenatal diagnosis were totally consistent. Conclusions Infinium ASA bead chip based BasePhasing pipeline shows good performance in balanced translocation carrier testing. With the characteristics of simple operation procedure and accurate results, we demonstrate that BasePhasing is one of the most suitable methods to distinguish between balanced and structurally normal chromosome embryos from translocation carriers in PGT at present.
Related Links	https://bmcmedgenomics.biomedcentral.com/counter/pdf/10.1186/s12920-019-0495-6.pdf
Ending Page	10
Page Count	10
Starting Page	1
File Format	HTM / HTML
ISSN	17558794
DOI	10.1186/s12920-019-0495-6
Journal	BMC Medical Genomics
Issue Number	1
Volume Number	12
Language	English
Publisher	BioMed Central
Publisher Date	2019-03-18
Access Restriction	Open
Subject Keyword	Human Genetics Microarrays Gene Expression Preimplantation genetic testing Balanced translocation Infinium Asian screening Array-24 Preimplantation genetic haplotyping BasePhasing
Content Type	Text
Resource Type	Article
Subject	Genetics (clinical) Genetics
Journal Impact Factor	2.1/2023
5-Year Journal Impact Factor	2.5/2023

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