Application of long-read sequencing based haplotype construction in preimplantation genetic testing for a patient with Incontinentia pigmenti
10.3760/cma.j.cn511374-20250414-00220
- VernacularTitle:基于长读长测序技术的单体型构建方案在色素失禁症患者胚胎植入前遗传学检测中的应用
- Author:
Wenjie MA
1
;
Min XIE
;
Kai KANG
;
Mengnan GU
;
Lulu YAN
;
Shanshan WU
;
Haibo LI
;
Jiangyang XUE
Author Information
1. 宁波大学医学部，宁波 315211
- Publication Type:Journal Article
- Keywords:
Long read sequencing technology;
Preimplantation genetic testing;
Incontinentia pigmenti;
Single nucleotide polymorphism;
Pseudogene;
De novo variant
- From:
Chinese Journal of Medical Genetics
2025;42(5):518-524
- CountryChina
- Language:Chinese
-
Abstract:
Objective:To provide preimplantation genetic testing (PGT) for a patient with Incontinentia pigmenti (IP) due to IKBKG gene variant but without family samples through construction of single nucleotide polymorphism (SNP)-based haplotype by Long-read sequencing (LRS) technology. Methods:A female IP patient with a heterozygous IKBKG c. 1167dup variant but without family genetic data who sought genetic counseling at Women and Children′s Hospital of Ningbo University in November 2021 was selected as the study subject. The IKBKG gene has a highly homologous pseudogene IKBKGP1. Genomic DNA was extracted from peripheral blood samples from the couple, and LRS was used to obtain informative SNP loci flanking the variant locus, enabling the construction of SNP haplotype with a long segment spanning from the non-homologous region of IKBKG to the variant site. Trophoblast cells were biopsied from blastocysts fertilized through intracytoplasmic sperm injection, and next-generation sequencing (NGS) was used to determine the SNP information of the embryos. Linkage analysis with the parental SNP haplotypes was conducted to detect the carrier status of the embryos and exclude chromosomal aneuploidies. Sanger sequencing was carried out to validate the result. A euploid embryo without the pathogenic variant was selected for transfer. Prenatal diagnosis was carried out by amniocentesis at mid-trimester to verify the result of PGT, and follow-up was conducted after the baby was born. This study has been approved by the Ethics Committee of the Women and Children′s Hospital of Ningbo University (Ethics No. EC2023-094). Results:In total seven blastocysts were tested, and PGT results indicated that two embryos were euploid and did not carry the pathogenic variant. One euploid embryo was transferred, which resulted in a singleton pregnancy. Amniocentesis at 24 weeks of gestation confirmed that the status of fetal IKBKG gene, and its chromosomal status was consistent with the PGT results. A healthy male infant was born at 38 + 6 weeks of gestation. Conclusion:For IP patients with de novo mutation or without family samples, PGT with LRS can directly construct the SNP-based haplotype while avoiding interference from pseudogenes, providing an effective strategy for PGT.
