To evaluate the detection ability and efficiency of single nucleotide polymorphisms array (SNP-array) and next generation sequencing (NGS) in preimplantation genetic testing (PGT).

Totally 188 couples who carried pathogenic gene mutation and requested preimplantation genetic testing for monogenic (PGT-M) treatment were retrospectively analyzed in the Reproductive Center of Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region during January 2020 and August 2022. After ovulation induction, insemination was conducted by intracytoplasmic sperm injection (ICSI) and cultured in vitro, 995 blastocysts were harvested and biopsied. After whole genome amplification (WGA) of the genetic material from embryonic cell samples, their carrying status of mutations and chromosome copy number variations (CNVs) were analyzed by SNP-array or NGS, respectively, and along with mutation direct detection by Sanger sequencing or Gap-PCR. The relationship between female age and the number of blastocysts was analyzed, as well as the proportion of embryos carrying mutations and pathogenic CNVs. The detection success rate and accuracy of different molecular diagnostic techniques used in PGT were compared. Amniocentesis prenatal diagnosis was performed in the second trimester after successful intrauterine transfer of embryos.

1) A total of 924 embryo samples were successfully performed genetic testing, with a total success rate of 92.9%, and 389 embryos (42.1%) can be transferred according to these results. 2) In detecting deletional α-thalassemia, the success rate of Gap-PCR [84.9% (465/548)] was lower than that of SNP-array [98.7% (81/82)] and NGS [92.5% (431/466)]. However, the success rate of direct mutation detection by Sanger sequencing [98.5% (440/447)] was not significantly different from that by SNP-array [95.6% (110/115)] and NGS [96.1% (319/332)]. There were 38 embryo samples with direct mutation detection results inconsistent with those based on SNP haplotyping. In addition, 4 embryo samples failed SNP haplotyping due to chromosomal recombination. 3) Compared with NGS, SNP-array had a lower success rate [83.7% (165/197)] in detecting CNVs, but it could find out more types of chromosomal abnormalities. 4) A total of 152 embryo transfers were performed, 107 patients got clinical pregnancies, 69 patients completed amniocentesis prenatal diagnosis, and 42 healthy infants were delivered.

In considering the detection efficiency, SNP-array is suitable for analyzing embryos which carry multiple pathogenic genes, rare monogenic or deletion mutations, whereas NGS is suitable for detecting common types of mutations. Meanwhile, using Sanger sequencing and Gap-PCR to directly detect the mutations can improve the success rate and accuracy of PGT. Our findings would provide a basis for PGT technicians to select appropriate detection platforms based on the type of mutations and the situation of patients.

Preimplantation genetic testing; SNP haplotyping; Next generation sequencing