Combined diagnosis of QF‐PCR and CNV‐Seq in fetal chromosomal abnormalities: A new perspective on prenatal diagnosis

Abstract

Objective This study aimed to evaluate the effect of QF‐PCR and CNV‐seq in diagnosing prenatal fetal chromosomal aberrations, explore the advantages and necessity of multimethod joint diagnosis. Methods We chose pregnant women with the indication of fetal chromosome examination in our hospital last year, collected 657 cases of amniotic fluid for QF‐PCR and CNV‐seq analyzes. Results While detecting aneuploidy, the coincidence rate of QF‐PCR and CNV‐seq was 100% (56/56). For all 46 chromosomes, 523 cases (79.60%, 523/657) coincided precisely, 128 cases (19.48%, 128/657) showed abnormality with CNV‐seq, 8 cases (1.22%, 8/657) revealed abnormality by QF‐PCR. In serological Down's syndrome screening, 328 cases showed a high risk of trisomy 21, of which CNV‐seq and QF‐PCR were consistent in 4 cases (1.22%, 4/328), CNV‐seq found 87 cases of CNVs in 78 samples except for chromosomal aneuploidy abnormalities, among these, 18 cases (20.69%, 18/87) were polymorphic, 7 cases (8.05%, 7/87) might cause disease, 13 cases (14.94%, 13/87) caused disease explicitly, 21 cases (24.14%, 21/87) were possibly benign, 17 cases (19.54%, 17/87) were explicitly benign, and the classification of 11 cases (12.64%, 11/87) was unclear. Conclusion QF‐PCR and CNV‐seq were highly consistent in diagnosing chromosomal aneuploidy. The high risk of serological Down's screening might not only due to the aneuploidy of chromosomes 21, 18, and NTD, but also the microdeletion or microduplication of all 46 chromosomes. So using CNV‐seq combined with QF‐PCR could effectively reduce the risk of missed diagnosis.

Additional diagnostic value of CNV‐seq over conventional karyotyping in prenatal diagnosis: A systematic review and meta‐analysis

“…33 Some scholars combined CNV-seq with QF-PCR to improve the detection rate of chromosomal abnormalities in prenatal diagnosis and concluded that this combination may be considered as the first-line method of prenatal chromosomal diagnosis. 34,35 The most frequent copy number variation revealed by our meta-analysis was Xp22.31 deletion. X-linked ichthyosis, which caused by the deletion of steroid sulfatase in Xp22.31., is a common recessive genetic disease characterized by generalized dryness and scaling of the skin.…”

“…Quantitative fluorescence polymerase chain reaction (QF‐PCR) makes use of the amplification of selected short tandem repeats (STRs) sites and quantitative analysis of the allelic dosage ratios to evaluate the numbers of copies of specific chromosomes, so it could find the MCC, some euploidies, and some common aneuploidies 33 . Some scholars combined CNV‐seq with QF‐PCR to improve the detection rate of chromosomal abnormalities in prenatal diagnosis and concluded that this combination may be considered as the first‐line method of prenatal chromosomal diagnosis 34,35 …”

Prenatal Diagnosis of Apert Syndrome due to A De novo FGFR2 Mutation at the Second Trimester: a case report

“…Generally, when copy number (CN) > 2.8, duplication was de ned. Deletion was de ned when CN < 1.2 and disomy (1.8 < CN < 2.2) [15]. The sequencing reads were referred to the Genome Reference Consortium Human genome build 37 (GRCh37) or humangenome 19 (hg19).…”

Comparison of the combined use of CNV-seq and karyotyping or QF-PCR in prenatal diagnosis: a retrospective study

“…Through whole genome low-coverage sequencing, CNV-seq is able to detect genetic aberrations, including chromosome aneuploidies and CNVs larger than 100 kb 8 . Combined with the advantages of using small amounts of genomic DNA and detecting low-level mosaicism, CNV-seq has been used increasingly widely for prenatal diagnosis 9 – 12 . However, due to its low sequencing depth, CNV-seq cannot detect balanced karyotypic changes and polyploidies such as 69, XXX 8 .…”

“…Currently, CNV-seq is usually performed in combination with karyotyping or QF-PCR for prenatal diagnosis 9 , 11 , 13 . Karyotyping, the gold standard for detecting chromosome abnormalities, has been used for prenatal diagnosis since the 1960s 14 .…”