Chromosomal Microarray Analysis In The Prenatal Genetic Diagnosis Of Fetal Multicystic Dysplastic Kidney

Objective The study was to explore the relationship between copy number variations (CNVs) and multicystic dysplastic kidney (MCDK) and to evaluate the clinical application of chromosomal microarray analysis (CMA) in prenatal genetic diagnosis of MCDK.Methods The study included thirty-seven cases that were diagnosed with MCDKs by prenatal ultrasound in Nanjing Drum Tower Hospital from July 2007 to December 2015 as the MCDKs group. Among them 33 cases were isolated MCDKs and four cases were non-isolated MCDKs that had major malformations other than congenital anomalies of kidney and urinary tract (CAKUT). We made calls to the parents in all the cases to follow up for babies/children born before the technology was induced. We successfully recruited 15 babies/children, measured their growth and development indexes, blood pressure, and serum creatinine, took their urine routine and performed renal ultrasound for the babies/children and their parents. We collected blood samples from newborns/children and their parents for further chromosomal microarray analysis. After chromosomal microarray analysis (CMA) technology was induced into the hospital,22 pregnant women chose amniocentesis to undergo CMA for fetuses with MCDKs and positive results of serum screening. DNA was extracted from these 37 cases that were all prenatally diagnosed with MCDK by ultrasound. CMA was performed on the Affymetrix CytoScan HD platform. The CNV calling was conducted according to the standard procedure. Pathogenic CNVs were called and searched for their possible phenotypes. The frequencies of the detected CNVs were compared with 461 cases that underwent CMA for anomalies unrelated to CAKUT as the control group 1 or 124 healthy newborns as the control group 2. We filtered CNVs that having higher frequencies in the MCDKs group than that in the control group 1. After that we listed CNV of uncertain significance that only detected in the MCDKs group. All of the annotated CNVs and were validated by MLPA or qPCR.Results Pathogenic CNVs were detected in 13.5% (5/37) of MCDKs. Two 17q12 deletion (fetus 18:17q12(34,823,294-36,316,144)×1; fetus 21: 17ql2(34,822,465-36,404,104)×1), one untypical 22q11.2 deletion (fetus 10: 22q11.21(21,033,586-21,800,797)×1), and one 22q11.2 duplication (fetus 16: 22q11.21(18,648,855-21,800,471)x3) were detected in four cases with isolated MCDK. Duplication of 1q31.3q44 was identified in a case of non-isolated MCDK that was also diagnosed of cri-du-chat syndrome since the baby carried the 5p 15.33 deletion and many of its anomalies matched with the phenotypes that cri-du-chat syndrome could bring. The 1q31.33q44 duplication contained several genes (CCSAP、 DSTYK、REN、AGT) that were dosage-sensitive and participated in kidney development and renal diseases. We also validated eight CNVs of uncertain significance only detected in the MCDKs group and five CNVs with higher frequency in the MCDKs group. We filtered the most frequent CNV, the 14q11.2 deletions in the MCDKs group and further confirmed its higher frequency in the MCDKs group when compared with the control group 2. We suggested a possible mechanism of pathogenesis via T cell receptor genes for 14q11.2 deletions.Conclusion A substantial proportion of MCDKs were associated with pathogenic CNVs. It may be reasonable to perform CMA when MCDKs are identified prenatally. The heterogeneity and the incomplete penetrance of CNVs, and the variability of phenotypes that CNVs can bring pose challenges for genetic counseling. Further effort must be made to solve the difficulty.