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.