FISH is not Suitable as a Standalone Test for Detecting Fetal Chromosomal Abnormalities

Abstract

Karyotyping and fluorescence in situ hybridization (FISH) detect fetal chromosome abnormalities. The choice between karyotyping and FISH is still debatable. In a developing country, parents face an emotional and economic constraint of a prenatal test. Therefore, the results of karyotyping and FISH were analyzed to determine the percentage of clinically abnormal fetuses which would be missed by using standalone FISH. Amniotic fluid samples from 9033 high-risk pregnancies were subjected to karyotyping and FISH for chromosomes 13, 18, 21, X, and Y. Karyotype and FISH were normal in 8680 (96.1 %) of these samples and 353 (3.9 %) had abnormal karyotypes: 285 (3.2 %) were aneuploidies, also detected by FISH and 68 (0.7 %) were structural chromosomal aberrations not detected by FISH. Out of these 68 structural aberrations, 40 (0.4 %) were balanced rearrangements with no apparent clinical significance and 28 (0.3 %) were unbalanced rearrangements with potential clinical significance. By standalone FISH, 0.3 % clinically-significant samples would have been missed. A 0.2 % risk of procedure-related abortion may be acceptable but a 0.3 % risk of having an abnormal child may not be acceptable to the parents. FISH may be offered as a first test, followed by karyotyping. Although, karyotyping increases the cost, it is preferable to carry this out once an invasive procedure has been opted for, with its accompanying risk of miscarriage.

Progress and Challenges in Laboratory-Based Diagnostic and Screening Approaches for Aneuploidy Detection during Pregnancy

“…24 While FISH has been a crucial technique used in aneuploidy detection, many DNA-based technologies continue to outperform this technique due to the low resolution, limits on how many chromosomes can be analyzed, and the accuracy of the technique compared with others. 25…”

Reliability of Cell-Free DNA and Targeted NGS in Predicting Chromosomal Abnormalities of Patients With Myeloid Neoplasms

“…For example, the European LeukemiaNet (ELN) recommendations for diagnosis and management of acute myeloid leukemia (AML) state conventional cytogenetic analysis remains mandatory in the evaluation of suspected AML, and these guidelines provide risk stratification recommendations based on the results of cytogenetic studies ( 5 ). However, cytogenetic analysis has considerable limitations as these studies are more costly, require fresh viable cells for culturing, need to be manually performed by an expert, and have a turnaround time of approximately two weeks for results ( 6 ). Therefore, there has been growing interest in alternative and less invasive methods to determine chromosomal variations for patients with hematologic neoplasms.…”

“…One widely accepted method as an adjunct to cytogenetic analysis is fluorescence in situ hybridization (FISH) studies, which comparatively have a shorter turnaround time to results of approximately 2 days, are more cost effective, can be prepared in formalin-fixed paraffin-embedded (FFPE) samples, and eliminates the need for tissue cultures ( 6 , 7 ). However, FISH studies can only test for predetermined chromosomal abnormalities one at a time and are unable to identify other non-targeted chromosomal variations ( 6 ). Recent advances in high-throughput genomic technologies have allowed for broader evaluation of chromosomal abnormalities using arrays.…”

Molecular characterization of supernumerary marker chromosomes found as unexpected chromosome abnormalities in nine prenatal and nine postnatal samples

“…3,5 FISH is a targeted approach and has some limitations. 6 Sometimes multiple attempts of FISH with various centromere enumerating probes or whole chromosome paint probes may be required, sequentially, even then the gene content remains undefined. The newer approach of Chromosome Microarray Analysis (CMA) offers identification of the copy number variations (CNVs) at the whole genome level along with defined breakpoints and the gene content of the involved duplication forming the SMC.…”