OBJECTIVE: To diagnose a 46,XN,del(11)(q14q22) fetus by non-invasive prenatal testing (NIPT), karyotype analysis and whole genome sequencing (WGS). METHODS: Peripheral blood sample of the gravida was taken for NIPT screening. Blood samples of the gravida, her husband, and umbilical cord blood were also taken for chromosome karyotyping and whole genome sequencing (WGS). RESULTS: NIPT screening indicated the fetus has carried partial deletion of chromosome 11, while no chromosomal abnormality was found with the cord blood sample due to the low resolution of G-banding analysis. WGS analysis of the cord blood indicated 46,XN,del(11q14.3q22.1). seq[GRCh37/hg19] (90 623 404-97 469 319)×1, 6.85 Mb. The karyotype of the fetus was eventually determined as 46,XN,del(11)(q14q22). Karyotyping analysis suggested that the gravida and her husband were 46,XX,del(11)(q14q22)[8]/46,XX[92] and 46,XY, respectively. However, neither of them was found to harbor the del(11)(q14q22) by WGS. CONCLUSION The abnormal karyotype of the fetus has derived from its mother's low percentage mosaicism. Combined NIPT, karyotyping analysis and WGS can detect chromosomal disorders with accuracy.

We report a case of a pregnant woman with 46,XX karyotype and positive sex-determining region on the Y chromosome ( SRY) gene and her female fetus. Ultrasound examination at 12 +6 gestational weeks indicated a thickened fetal nuchal translucency, and 46, XX with a positive SRY gene was detected in the fetus through quantitative fluorescent-polymerase chain reaction and amniotic fluid karyotype. However, the ultrasound showed that the gender of the fetus was female, which was inconsistent with the phenotype of male syndrome with 46, XX combining positive SRY gene. The fluorescent in situ hybridization (FISH) revealed that the short arm of the Y chromosome translocated to the long arm of one of the X chromosomes, namely Yp11.3-Xq28. In addition, a copy number variation at Yp11.31p11.2 copy (about 1 MB) was found by chromosomal microarray analysis, which validated the result of FISH and was consistent with the mother. After genetic counseling, the parents chose to continue the pregnancy to full term, and no abnormalities were found in the infant during the follow-up.