Quality control in FISH as part of a laboratory's quality management system

Improving RNA fusion call confidence and reliability in molecular diagnostic testing

Next-generation sequencing (NGS) is a superior method for detecting known and novel RNA fusions in formalin-fixed paraffin-embedded tissue over FISH and RT-PCR. However, confidence in fusion calling and true negatives may be compromised by poor RNA quality. Using a commercial panel of 507 genes and the recommended 3 million read threshold to accept results, two cases yielded false negatives while exceeding this recommendation during clinical validation. To develop a reliable quality control metric that better reflects internal sample quality and improve call confidence, gene expression across 361 patient tumor samples was evaluated to derive a set of 15 genes to serve as a proxy quality control (pQC). These 15 genes were assessed for their normalized expression using the sequencing data from each case and selected for robustness. A threshold of 11 pQC genes produced a 4.71% fail rate, selected for stringency as an acceptable level of repeat testing in the clinical setting, minimizing false negative calls. To increase the chance that low-quality samples pass pQC, a revision to the library preparation methodology was also tested, with 75% of previously failed samples passing pQC upon re-sequencing by increasing cDNA input. Taken together, an NGS analysis quality control tool is presented that serves as a surrogate for housekeeping genes and improves confidence in fusion calls.

European guidelines for constitutional cytogenomic analysis

With advancing technology and the consequent shift towards an increasing application of molecular genetic techniques (e.g., microarrays, next-generation sequencing) with the potential for higher resolution in specific contexts, as well as the application of combined testing strategies for the diagnosis of chromosomal disorders, it is crucial that cytogenetic/cytogenomic services keep up to date with technology and have documents that provide guidance in this constantly evolving scenario. These new guidelines therefore aim to provide an updated, practical and easily available document that will enable genetic laboratories to operate within acceptable standards and to maintain a quality service.

Desirable quality-control materials for the establishment of qualified external quality assessment on prenatal diagnosis of chromosomal aneuploidies

OBJECTIVE

To prepare desirable quality-control materials for the establishement of qualified external quality assessment on fluorescence in situ hybridization (FISH)-detected prenatal diagnosis of chromosomal aneuploidies.

METHODS

Four types of amniotic fluid cell suspensions (13-trisomy, 18-trisomy, 21-trisomy and 47,XXY) were mixed together by ratio to produce mosaicism with the percentages of each aneuploidy as 10%, 20%, 30% and 40%, respectively. After being stored in liquid nitrogen of -196 °C for six months, randomly selected samples were incubated in 37 °C water, followed by cultivation, hypo-osmosis and fixation. Finally, FISH detetion was applied on them before and after external laboratory mailing, in step with detection on conventional case samples.

RESULTS

Before mailing, the positive rates of each aneuploidy described above were 12.8%, 23.6%, 33.8%, 44.0%, while 12.6%, 23.8%, 34.0%, 43.5% after mailing. t-test, criteria for stability assessment of quality-control materials in CANS-GL03:2006, showed no significant effect of external mailing on mosaicism since corresponding t values are lower than threshold with significance level α as 0.05 and degree of freedom as 10.

CONCLUSION

As FISH detection showed, the mosaic cell strains prepared in current study exhibited excellent stabilities after cryopreservation in -196 °C, subculture, hypo-osmosis, fixation and external laboratory mailing, demonstrating them as reliable and promising quality-control materials for the establishment of a qualified external quality assessment on prenatal diagnosis of chromosomal aneuploidies.

Spatial Genome Organization and Its Emerging Role as a Potential Diagnosis Tool

In eukaryotic cells the genome is highly spatially organized. Functional relevance of higher order genome organization is implied by the fact that specific genes, and even whole chromosomes, alter spatial position in concert with functional changes within the nucleus, for example with modifications to chromatin or transcription. The exact molecular pathways that regulate spatial genome organization and the full implication to the cell of such an organization remain to be determined. However, there is a growing realization that the spatial organization of the genome can be used as a marker of disease. While global genome organization patterns remain largely conserved in disease, some genes and chromosomes occupy distinct nuclear positions in diseased cells compared to their normal counterparts, with the patterns of reorganization differing between diseases. Importantly, mapping the spatial positioning patterns of specific genomic loci can distinguish cancerous tissue from benign with high accuracy. Genome positioning is an attractive novel biomarker since additional quantitative biomarkers are urgently required in many cancer types. Current diagnostic techniques are often subjective and generally lack the ability to identify aggressive cancer from indolent, which can lead to over- or under-treatment of patients. Proof-of-principle for the use of genome positioning as a diagnostic tool has been provided based on small scale retrospective studies. Future large-scale studies are required to assess the feasibility of bringing spatial genome organization-based diagnostics to the clinical setting and to determine if the positioning patterns of specific loci can be useful biomarkers for cancer prognosis. Since spatial reorganization of the genome has been identified in multiple human diseases, it is likely that spatial genome positioning patterns as a diagnostic biomarker may be applied to many diseases.

An external quality assessment scheme for prenatal detection of rare chromosomal abnormalities

OBJECTIVE

To improve the accuracy of prenatal cytogenetic diagnosis by establishing an external quality assessment (EQA) scheme for rare, or subtle, structural chromosomal abnormalities.

METHOD

Typical metaphase images of rare chromosomal abnormalities along with an anonymized clinical history were sent to 35 prenatal diagnosis laboratories. The laboratories were required to provide independent reports using current nomenclature. Evaluation of reports was based on established criteria for quality assessment of karyotype analysis.

RESULTS

Totally 6 kinds of typical rare chromosomal abnormalities were collected. 35 laboratories were enrolled with a response rate of 94.29%. The overall analytical accuracy is 82.20%. This is comparable with our former EQA scheme using established lymphocyte cell lines with rare abnormal chromosome karyotypes (χ²=0.065, P=0.799).

CONCLUSION

Introduction of efficient EQA for prenatal genetic diagnosis is currently imperative, due to the limited performances of karyotype analysis of rare chromosomal abnormalities. Metaphase images could be used as a simple and effective material for EQA and to improve the quality of prenatal genetic diagnosis.