Detection of partial deletion and mosaicism using quantitative fluorescent polymerase chain reaction: Case reports and a review of the literature

Abstract

Background Aneuploidy of chromosomes 13, 18, 21, X, and Y can be detected by the quantitative fluorescence polymerase chain reaction (QF‐PCR) performed with short tandem repeat (STR) markers. Although QF‐PCR is designed to detect whole chromosome trisomy, the partial deletion or mosaic of chromosomes may also be detected. Methods Partial deletion or mosaic of chromosomes in three cases was detected by QF‐PCR. Karyotyping and chromosome microarray analysis(CMA) were performed. We further reviewed the clinical utility of QF‐PCR in detecting mosaicisms and deletions/duplications. Results QF‐PCR demonstrated structurally abnormal 21, X, and Y chromosomes in primary amniotic cells. QF‐PCR results in these three cases showed abnormal peak height/peak area, which could not be interpreted according to the kit instructions. QF‐PCR results suggested that there were partial deletions or mosaicism, which were confirmed by karyotyping and CMA. Conclusion In addition to detecting trisomies of whole chromosomes, QF‐PCR can also detect deletion and mosaicism of chromosomes 13, 18, 21, X, and Y, which could suggest the presence of copy number variants (CNVs). Additional testing with genetic technologies, such as karyotyping or microarrays, is recommended when an uninformative pattern is suspected.

Confusing finding of quantitative fluorescent polymerase chain reaction analysis in invasive prenatal genetic diagnosis: A case report

“…However, QF-PCR cannot detect inversions or translocations. The deletion or duplication region outside the STR loci will also be missed[ 10 , 11 ]. Consequently, QF-PCR may overlook structural chromosomal abnormalities.…”

“…This is the first case of Yp11.2 duplication that we have found among more than 3000 patients who have undergone QF-PCR in our laboratory. Previous studies have reported the function of QF-PCR in detecting mosaicism, deletions, or duplications[ 11 - 13 ]. These cases had deletion or duplication regions within the STR marker range designed in the QF-PCR kit.…”

“…Therefore, QF-PCR cannot be used as a routine method for detecting chromosomal deletions or duplications. It can only be used as a supplementary method to discover deletions or duplications in the detection of 13/18/21/X/Y chromosome aneuploidy[ 11 , 14 ]. To compensate for the shortcomings of QF-PCR, karyotyping and CNV-seq have been used in prenatal diagnosis.…”