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To delineate cytogenetic and molecular abnormalities of a fetus carrying a de novo 46,X,der(X),t(X;Y)(p22.3;p11.2).G-banded karyotyping and next-generation sequencing (NGS) were used to analyze the fetus, his father and sister. Single nucleotide polymorphism-based arrays (SNP-array), multiple PCR and fluorescence in situ hybridization (FISH) were utilized to verify the result.G-banded karyotyping at 320 bands showed that the fetus had a normal karyotype, while NGS has identified a 3.58 Mb microdeletion at Xp22.33 and a Y chromosomal segment of about 10 Mb at Yp11.32p11.2. With the sequencing results, high-resolution karyotyping at 550-750 bands level has determined the fetus to be 46,X,der(X)t(X;Y)(p22.3;p11.2). The result was confirmed by PCR amplification of the SRY gene, FISH and SNP-array assays. The karyotypes of his father and sister were both normal. His sister also showed no amplification of the SRY gene, and her NGS results were normal too, suggesting that the karyotype of the fetus was de novo.Combined karyotyping, NGS, SNP-array, PCR and FISH assay can facilitate diagnosis of XX disorder of sex development.

To explore the origin and mechanism of small supernumerary marker chromosomes (sSMC) in order to facilitate genetic counseling.Chromosome karyotypes of two fetuses and their immediate family members were analyzed by conventional G banding. High-throughput whole genome sequencing was used to determine the origin of sSMCs.Fetus 1 was shown to have a karyotype of 47,XY,+mar but with normal FISH and B ultrasound findings. Its father also had a 47,XY,+mar karyotype with normal FISH results and clinical phenotype. High-throughput genome sequencing revealed that fetus 1 and its father were both 46,XY,dup(21)(q11.2;q21.1) with a 6.2 Mb duplication of the long arm of chromosome 21. The fetus was born with normal phenotype and developed well. Its grandmother also had a karyotype of 46,XX,t(15;21)(q13;p13) with normal FISH result and clinical phenotype. The karyotypes of its mother and grandfather were both normal. Analysis of fetus 2 showed a 47,XY,+mar karyotype with normal FISH results. High-throughput genome sequencing suggested a molecular karyotype of 46,XX. The fetus was born with normal phenotype and developed well. The karyotypes of its parents were both normal.Considering their variable origins, identification of sSMC should combine conventional G banding analyses with high-throughput whole genome sequencing for precise delineation of the chromosomes.