The Evaluation of Genetic Diagnosis on High-Risk Fetal CAKUT

Abstract

Background: It is challenging to make an accurate prenatal diagnosis for congenital anomalies of the kidney and urinary tract (CAKUT) because of its pathologic diversity. This study aims to evaluate the performance of whole-exome sequencing (WES) combined with karyotype analysis and copy number variations (CNVs) in diagnosing high-risk fetal CAKUT. Methods: We conducted a retrospective study on prenatal diagnoses of CAKUT in our hospital from January 2020 to April 2021. The research studied 24 high-risk fetuses with CAKUT who were scanned by ultrasonography at the prenatal diagnosis center of Tongji Hospital affiliated to Tongji Medical College of Huazhong University of Science and Technology. The likely pathogenic gene variants were screened for the patients and their parents by multiple approaches, including karyotype analysis, CNVs and WES, and further verified with Sanger sequencing. Results: ①We detected abnormal CNVs in 20.8% (5/24) of the fetuses but only 8.3% (2/24) fetuses had abnormal karyotypes. ②Of the 15 CAKUT fetuses, positive findings (40%) were detected by WES. Of the 9 high-risk fetuses with CAKUT (negative findings in ultrasound scan but with family history), we found abnormal variants (77.8%) through WES. Conclusion: The application of CNVs and WES showed advance in prenatal diagnosis of CAKUT and the pathogenic gene variants were detectable especially for high-risk fetuses with negative ultrasound findings on CAKUT in the preliminary study. The applied strategy could be used to improve the accuracy of prenatal diagnosis for CAKUT in the future.

Keywords: (copy number variants); CAKUT; karyotype analysis; prenatal diagnosis; whole-exome sequencing.

FIGURE 1

case7: (A) Pedigree of a family with Polycystic kidney disease 1. The empty symbols indicate unaffected individuals, and the filled symbols indicate affected individuals. The black arrow points out the proband (I-2). (B) Sequencing results showed that the proband and the fetus carried the splicing c.2853+2T>C in PKDI gene which was not present in the father.

FIGURE 2

case22: (A) Pedigree of a family with congenital nephrotic syndrome. The empty symbols indicate unaffected individuals, and the filled symbols indicate affected individuals. The black arrow points out the proband (II-1). (B) Sequencing results showed that the proband, her father and the fetus carried the stopgain mutation c.3478C>T (p.R1160*) in NPHSI gene except her mother (the arrow showed the mutation site). (C) Sequencing results showed that the proband and her mother carried the frameshift insertion mutation ¢.2201_2205dup (p. V736Wfs*18) in NPHSI gene which was not present in her father and the fetus (the arrow showed the mutation site).

FIGURE 3

case 23: (A) Pedigree of a family with renal failure. The proband was diagnosed with renal failure at 12-years old. The empty symbols indicate unaffected individuals, and the filled symbols indicate affected individuals. The black arrow points out the proband (II-1). (B) Sequencing results showed that the proband carried the frameshift insertion mutation c.76dup (p. V26Gfs*28) in P4X2 gene which was not found in his parents and the fetus (the arrow showed the mutation site).

FIGURE 4

case24: (A) Pedigree of a family with von Hippel- Lindau syndrome. The empty symbols indicate unaffected individuals, and the filled symbols indicate affected out individuals. The black arrow points the proband (II-1). (B)Sequencing results showed that the proband (II-1) and the fetus (III-1) carried the stopgain mutation c.280G>T (p.E94*) in VHL gene which was not found in the mother (1-2) and the grandparents (I-1, I-2) (the arrow showed the mutation site).