OBJECTIVETo apply single nucleotide polymorphism microarray (SNP array) for the detection of genome-wide copy number variations(CNVs) in fetuses with malformations and women with an adverse reproductive history, and to explore the correlation of rare CNVs with the clinical manifestations.

METHODSAmniotic fluid and umbilical cord blood samples were collected from 314 women with singleton pregnancy. SNP array was performed on samples where chromosomal abnormalities were excluded after G-banding analysis.

RESULTSPathological CNVs were detected in 8.91% (28/314) of all samples, which included 11 duplications, 9 deletions, 4 loss of heterozygosity (LOH), and 4 conjoined deletions and duplications. The sizes of duplications and deletions were between 0.47 Mb and 16.7 Mb, and between 0.16 Mb and 13.3 Mb, respectively. Fifteen CNVs were mapped to the regions of microdeletion or microduplication syndromes or regions associated with clinical manifestations, while the remainder 13 were considered benign or variant of uncertain significance.

CONCLUSIONA proportion of fetuses with malformations and women with an adverse reproductive history may be attributed to CNVs, half of which are mapped with to the regions of well known syndromes. SNP array may facilitate discovery of new syndromes and provide a basis for genetic counseling and prenatal diagnosis.