Discussions
CNV-seq and karyotyping have the same effectiveness in aneuploidy detection, as shown in table 1. However, the abnormal detection rate of CNV-seq was higher than that of karyotyping[7] in mosaic aneuploidy and imbalanced chromosome abnormalities. In addition, it has a higher detection success rate. Huilin Wang et al[8] showed that CNV-seq needs lesser DNA and lower detection cost than CMA technology. We can identify additional and clinically significant CNVs with enhanced resolution and increased sensitivity of detecting mosaicism. The reason is that CMA has limited the coverage area of probe and cannot detect low proportion of mosaic. Compared with CMA, CNV-seq cannot detect the absence of heterozygosity (AOH). The absence of triploidy and polyploidy can be detected by CMA and karyotyping, but not by CNV-seq. Compared with karyotyping, CNV-seq cannot detect the absence of balanced rearrangement, such as reciprocal translocation, Robertsonian translocation, inversion, etc. In fact, most bases are in the state of AOH. Therefore, AOH is not pathogenic, unless there is a recessive homozygous mutation behind it, or a uniparental disomy with imprinted genes[9] . In addition, triploidy, polyploidy and ”truly” balanced chromosomal rearrangements do not lead to birth defects (triploid and polyploid fetuses generally die in early pregnancy). It still requires further examination by CNV-seq for the cases with suspicious chromosome change, and the cases that have not been identified by karyotyping. Therefore, CNV-seq can completely replace the karyotyping in prenatal diagnosis for fetal chromosome analysis alone, as shown in figure 1.
With the improvement of the resolution by CNV-seq, some CNVs with variants of uncertain significance (VOUS), and even the unprecedented CNVs identified by CNV-seq will cause problems to clinicians’ genetic counseling and pregnant women. This can cause unnecessary pregnancy termination. In this study, cases 63~92 of CNVs classified as VOUS (case 63 classified as pCNVs) were reclassified as bCNVs, as shown in table S2. The reason is that these CNVs in fetuses were found to be inherited from one parent after parental verification. Thus, this technology can help us to avoid this trouble. The pathogenicity of some VOUS can be determined in the future with extensive application of CNV-seq and accumulation of databases, thus more pCNVs can be diagnosed in the future. CNV-seq is beneficial to the clinic with its extensive application.
In this study, abnormal results on Down’s Syndrome Screening were the most cause of indications for amniocentesis, followed by abnormal fetal ultrasound, abnormal result on noninvasive prenatal diagnosis, then advanced maternal age, adverse pregnancy history, abnormal parental chromosomes, and voluntary testing. In fig.1, the abnormal rate of chromosome abnormality on the noninvasive prenatal screening group is the highest, followed by abnormal fetal ultrasound group and abnormal parental chromosomes group, then advanced maternal age group. In addition, the abnormal result on Down’s Syndrome Screening group, adverse pregnancy history group and voluntary testing group are the lowest. In fig.1, abnormal detection rate of CNV-seq was higher than that of karyotyping, either in all cases or in each clinical indication groups. This value is especially high in the abnormal parental chromosomes group. Parental chromosome abnormalities are mainly the balanced rearrangement. Almost all the fetuses that can survive to the amniocentesis period were the same balanced rearrangement with their parents or normal karyotype. In addition, “true” balanced chromosome rearrangement do not cause fetal birth defects[10] . Some apparently balanced chromosome rearrangement may be accompanied by microdeletion/microduplication. This can be identified by CNV-seq (case 45~46 in table S1 and case 96~108 in table S2), even some of them were pCNVs (case 45~46 in table S1). In this study, 1.44% of fetal chromosome abnormalities identified by CNV-seq in abnormal parental chromosomes group were all pCNVs. This may be missed by karyotying. Therefore, CNV-seq can be used for prenatal diagnosis in group of abnormal parental chromosomes. An inherited balanced rearrangement will have no consequences for the pregnancy, but is relevant to future reproductive counseling[11] . Therefore, peripheral blood karyotyping should be performed after birth on fetuses. Their parental balanced rearrangement will cause abnormal fetal chromosome for future fertility guidance.