FISH for 22q11.2 deletion not cost-effective for infants with congenital heart disease with microarray.

The objective of this study is to evaluate the yield of genetic testing in infants with congenital heart disease, who undergo surgical intervention prior to one year of age, and develop a cost-effective strategy to screen infants with congenital heart disease for genetic conditions while providing standard of care. 409 charts of patients with congenital heart disease, who underwent surgical intervention prior to one year of age, were retrospectively reviewed for cytogenetic testing results. 278 patients underwent cytogenetic testing, and 89.6 % of these patients had more than one cytogenetic test completed. The most commonly encountered chromosomal anomaly within the sample was Down Syndrome (12.5 %), followed by 22q11.2 Deletion Syndrome (4.6 %). G-Banded Karyotypes were abnormal in 10.5 % of patients, fluorescence in situ hybridization (FISH) probe for 22q11.2 deletion was abnormal in 7.1 % of patients. SNP microarray testing showed the highest yield and was abnormal in 33 % of patients. Based on the data at our institution, a more directed approach of genetic screening with only microarray would have saved our institution approximately $101, 200 on the 103 patients who underwent genetic evaluation with microarray reviewed. Screening infants with congenital heart disease for 22q11.2 deletion with FISH resulted in a loss of approximately $32,000 per 100 patients at our institution. Institutions should develop microarray-based protocols for genetic screening in patients with congenital heart disease with the anticipation of adding lesion-specific single gene testing as single gene testing becomes routinely available.

The Clinical Utility of a Tiered Approach to Pediatric Glioma Molecular Characterization for Resource-Limited Settings.

PURPOSE: Molecular characterization is key to optimally diagnose and manage cancer. The complexity and cost of routine genomic analysis have unfortunately limited its use and denied many patients access to precision medicine. A possible solution is to rationalize use-creating a tiered approach to testing which uses inexpensive techniques for most patients and limits expensive testing to patients with the highest needs. Here, we tested the utility of this approach to molecularly characterize pediatric glioma in a cost- and time-sensitive manner. METHODS: We used a tiered testing pipeline of immunohistochemistry (IHC), customized fusion panels or fluorescence in situ hybridization (FISH), and targeted RNA sequencing in pediatric gliomas. Two distinct diagnostic algorithms were used for low- and high-grade gliomas (LGGs and HGGs). The percentage of driver alterations identified, associated testing costs, and turnaround time (TAT) are reported. RESULTS: The tiered approach successfully characterized 96% (95 of 99) of gliomas. For 82 LGGs, IHC, targeted fusion panel or FISH, and targeted RNA sequencing solved 35% (29 of 82), 29% (24 of 82), and 30% (25 of 82) of cases, respectively. A total of 64% (53 of 82) of samples were characterized without targeted RNA sequencing. Of 17 HGG samples, 13 were characterized by IHC and four were characterized by targeted RNA sequencing. The average cost per sample was more affordable when using the tiered approach as compared with up-front targeted RNA sequencing in LGG ($405 US dollars [USD] v $745 USD) and HGGs ($282 USD v $745 USD). The average TAT per sample was also shorter using the tiered approach (10 days for LGG, 5 days for HGG v 14 days for targeted RNA sequencing). CONCLUSION: Our tiered approach molecularly characterized 96% of samples in a cost- and time-sensitive manner. Such an approach may be feasible in neuro-oncology centers worldwide, particularly in resource-limited settings.

Assessing the potential cost-effectiveness of retesting IHC0, IHC1+, or FISH-negative early stage breast cancer patients for HER2 status.

BACKGROUND: Fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC) tests are commonly used to assess human epidermal growth factor 2 (HER2) status of tumors in patients with breast cancer. This analysis evaluates the likely cost-effectiveness of expanded retesting to assess HER2 tumor status in women with early stage breast cancer. METHODS: We developed a decision-analytic model to estimate the incremental cost-effectiveness ratio (ICER) of expanded reflex testing from a US payer perspective. Expanded reflex testing is defined as retesting tumor specimens from patients whose tumors are IHC0, IHC1+, or FISH-negative on their first test. In the base case, we assumed that 80% of patient tumors are initially IHC-tested and 20% are FISH-tested. Testing outcomes for IHC and FISH with and without retesting were based on published meta-analyses. The cost of tests and treatment and the long-term health outcomes were obtained from the literature. RESULTS: In the base case, we estimated that 2.27% of women who received expanded reflex testing would be HER2-positive and receive trastuzumab treatment: the projected ICER was $36,721 per life year or $39,745 per quality-adjusted life year (QALY). This varied between $47,100 per QALY and $35,500 per QALY if we assumed that 1%-8% of patients retested were then HER2+, respectively. The results of deterministic and probabilistic sensitivity analysis were robust. This strategy would result in 4700 (2000-17,000) patients being eligible to receive trastuzumab treatment annually. CONCLUSIONS: Retesting patients who are IHC0, IHC1+, or FISH-negative is projected to be a cost-effective clinical strategy.

Cost-effectiveness of fluorescence in situ hybridization in patients with atypical cytology for the detection of urothelial carcinoma.

PURPOSE: Patients with atypical cytology and equivocal or negative cystoscopy pose a challenge due to uncertainty about the presence of cancer. We determined the cost-effectiveness of using fluorescence in situ hybridization assays to determine the need for biopsy in patients with atypical cytology and equivocal or negative cystoscopy. MATERIALS AND METHODS: Data from 2 large prospective studies evaluating the usefulness of fluorescence in situ hybridization in the setting of atypical cytology to detect urothelial carcinoma were combined. The data were used to calculate sensitivity and specificity for the UroVysion fluorescence in situ hybridization assay in various clinical scenarios. Cost data were obtained from our institution and Medicare reimbursement rates. Evaluations with or without bladder biopsy and with or without upper tract evaluation were considered. RESULTS: The study included 263 patients with atypical cytology and equivocal (62) or negative (201) cystoscopy. In patients with equivocal cystoscopy (assuming biopsy was performed in the operating room) biopsy based on fluorescence in situ hybridization results saved $1,740 per patient ($3,267 vs $1,527 per patient) and avoided 42 biopsies compared to biopsy in all patients. If office based biopsies were used then cost savings using fluorescence in situ hybridization results were $95 per patient. Among patients with negative cystoscopy biopsy based on fluorescence in situ hybridization resulted in costs savings of $2,241 per patient, avoiding 167 biopsies, compared to biopsy in all patients. Assuming office based biopsy, the cost savings were $216 per patient. CONCLUSIONS: The decision to perform biopsy based on fluorescence in situ hybridization assay in patients with atypical cytology and equivocal or negative cystoscopy was associated with a significant decrease in bladder cancer associated costs.

[Comparative evaluation of the predictive value of UroVysion and AURKA FISH tests of urine sediment cells for the diagnosis of bladder cancer].

Informative value of two tests based on FISH of exfoliated urothelial cells in urine sediment (AURKA and UroVysion) was compared in the group of patients (31 persons) with the history of bladder cancer. Coincidence in results of both FISH assays was found in 93.5%. These preliminary data offer the possibility of replacing the expensive UroVysion kit by the less expensive AURKA FISH probe and it could be used for monitoring of recurrence in bladder cancer patients.

The utility of end-of-treatment bone marrow aspirates in pediatric acute lymphoblastic leukemia: a quality improvement project.

We reviewed the use, results and costs of end-of-treatment bone marrow aspirates (EOTBMAs) performed locally in patients diagnosed with ALL between 2000 and 2005. Of 193 patients, 188(97%) received EOTBMAs. Though 15/188(8.0%) patients experienced relapse at a median time of 1.1 years (range 0.1-4 years), no sign of relapse was detected on any EOTBMA. After communication of results to clinical staff, only 2/17 (12%) of patients with ALL finishing treatment in the subsequent 5 months received an EOTBMA (P < 0.0001). Our results confirm the futility of EOTBMAs in a large contemporary cohort. Disseminating local results may help ensure adherence to best practices.

Absence of subtelomeric rearrangements in selected patients with mental retardation as assessed by multiprobe T FISH.

BACKGROUND: Mental retardation (MR) is a heterogeneous condition that affects 2-3% of the general population and is a public health problem in developing countries. Chromosomal abnormalities are an important cause of MR and subtelomeric rearrangements (STR) have been reported in 4-35% of individuals with idiopathic MR or an unexplained developmental delay, depending on the screening tests and patient selection criteria used. Clinical checklists such as that suggested by de Vries et al. have been used to improve the predictive value of subtelomeric screening. FINDINGS: Fifteen patients (1-20 years old; five females and ten males) with moderate to severe MR from a genetics outpatient clinic of the Gaffrée and Guinle Teaching Hospital (HUGG) of the Federal University of Rio de Janeiro State (UNIRIO) were screened with Multiprobe T FISH after normal high resolution karyotyping. No subtelomeric rearrangements were detected even though the clinical score of the patients ranged from four to seven. CONCLUSION: In developing countries, FISH-based techniques such as Multiprobe T FISH are still expensive. Although Multiprobe T FISH is a good tool for detecting STR, in this study it did not detect STR in patients with unexplained MR/developmental delay even though these patients had a marked chromosomal imbalance. Our findings also show that clinical scores are not reliable predictors of STR.

Fish-on-a-chip: a sensitive detection microfluidic system for Alzheimer's disease.

Microfluidics has become an important tool in diagnosing many diseases, including neurological and genetic disorders. Alzheimer's disease (AD) is a neurodegenerative disease that irreversibly and progressively destroys memory, language ability, and thinking skills. Commonly, detection of AD is expensive and complex. Fluorescence in situ hybridization (FISH)-based microfluidic chip platform is capable of diagnosing AD at an early stage and they are effective tools for the diagnosis with low cost, high speed, and high sensitivity. In this review, we tried to provide basic information on the diagnosis of AD via FISH-based microfluidics. Different sample preparations using a microfluidic chip for diagnosis of AD are highlighted. Moreover, rapid innovations in nanotechnology for diagnosis are explained. This review will provide information on dynamic quantification methods for the diagnosis and treatment of AD. The knowledge provided in this review will help develop new integration diagnostic techniques based on FISH and microfluidics.

Next-Generation Sequencing Panel for 1p/19q Codeletion and IDH1-IDH2 Mutational Analysis Uncovers Mistaken Overdiagnoses of 1p/19q Codeletion by FISH.

The 1p/19q codeletion is the result of a translocation between chromosome 1 (Chr1p) and chromosome 19 (Chr19q) with the loss of derivative (1;19)(p10;q10) chromosome. The 1p/19q codeletion has predictive and prognostic significance, and it is essential for the classification of gliomas. In routine practice, the fluorescence in situ hybridization (FISH) diagnosis of 1p/19q codeletion is sometimes unexpected. This study aimed to develop a next-generation sequencing panel for the concurrent definition of the 1p/19q codeletion and IDH1/IDH2 mutation status to resolve these equivocal cases. A total of 65 glioma samples were investigated using a 1p/19q-single-nucleotide polymorphism (SNP)-IDH panel. The panel consists of 192 amplicons, including SNPs mapping to Chr1 and Chr19 and amplicons for IDH1/IDH2 analysis. The 1p/19q SNP-IDH panel consistently identified IDH1/IDH2 mutations. In 49 of 60 cases (81.7%), it provided the same 1p/19q results obtained by FISH. In the remaining 11 cases, the 1p/19q SNP-IDH panel uncovered partial chromosome imbalances as a result of interstitial amplification or deletion of the regions where the FISH probes map, leading to a mistaken overdiagnosis of 1p/19q codeletion by FISH. The 1p/19q SNP-IDH next-generation sequencing panel allows reliable analysis of the 1p/19q codeletion and IDH1/IDH2 mutation at the same time. The panel not only allows resolution of difficult cases but also represents a cost-effective alternative to standard molecular diagnostics procedures.

Human epidermal growth factor receptor 2 expression in early breast cancer patients: a Swiss cost-effectiveness analysis of different predictive assay strategies.

Trastuzumab has conferred significant clinical benefits in HER-2-positive breast carcinomas. HER-2 status is determined by immunohistochemistry (IHC) and/or fluorescence in situ hybridisation (FISH), but appropriate assessment of HER2 status remains subject to considerable debate. Data on the health economic impact of HER-2 test strategies are limited. A life-long Markov state transition model was used to assess costs and effectiveness of HER-2 assay strategies (based on IHC, FISH, both combined or FISH confirmation of IHC2+) for a hypothetical cohort of early breast cancer patients from the perspective of the Swiss health system. We compared clinically relevant strategies of predictive testing and subsequent trastuzumab treatment of HER-2-positive patients only. FISH testing was the most cost-effective strategy with an incremental cost-effectiveness ratio of €12,245 per additional quality-adjusted life-year (QALY) gained, compared to no trastuzumab treatment. The next best strategy was parallel IHC and FISH, with costs of €400,154/QALY gained compared to FISH alone. FISH as primary HER-2 testing modality remained the preferred option in deterministic and probabilistic sensitivity analysis. Predictive testing to identify adjuvant breast cancer patients who benefit from trastuzumab treatment is a clinical and economic necessity. Our model identifies FISH as the most cost-effective approach.

Improved detection of aneuploid blastocysts using a new 12-chromosome FISH test.

Fluorescence in-situ hybridization (FISH) has been the principal method used for the identification and preferential transfer of chromosomally normal embryos, in the context of both preimplantation genetic diagnosis (PGD) and screening (PGS). Generally, the probe combinations used during PGS have focused on chromosomes frequently identified as abnormal in prenatal samples or material derived from first-trimester spontaneous abortions. Recent data, however, obtained with the use of comparative genomic hybridization (CGH), have suggested that commonly used PGS strategies may fail to detect a large number of aneuploidies affecting preimplantation embryos. Some chromosomes, which have been relatively neglected in PGS protocols thus far, display a disproportionate contribution to embryo aneuploidy and should be prioritized for screening. Using CGH data, it is possible to design new probe combinations that examine between 10 and 12 chromosomes and are capable of accurately diagnosing 89-91% of anomalies seen in embryos. At present, 24-chromosome tests, such as CGH, array CGH or single nucleotide polymorphism arrays, remain relatively costly and, in some cases, are yet to be fully validated. For these reasons, a cost-effective method, capable of accurately detecting almost all aneuploid embryos, represents an attractive alternative to comprehensive chromosome screening approaches.

Prenatal diagnosis of BACs-on-Beads assay in 1520 cases from Fujian Province, China.

BACKGROUND: The aim of this study was to evaluate the application of BACs-on-Beads (BoBs™) assay for rapid detection of chromosomal abnormalities for prenatal diagnosis (PND). METHODS: A total of 1520 samples, including seven chorionic villi biopsy samples, 1328 amniotic fluid samples, and 185 umbilical cord samples from pregnant women were collected to detect the chromosomal abnormalities using BoBs™ assay and karyotyping. Furthermore, abnormal specimens were verified by chromosome microarray analysis (CMA) and fluorescence in situ hybridization (FISH). RESULTS: The results demonstrated that the success rate of karyotyping and BoBs™ assay in PND was 98.09% and 100%, respectively. BoBs™ assay was concordant with karyotyping for Trisomy 21, Trisomy 18, and Trisomy 13, sex chromosomal aneuploidy, Wolf-Hirschhorn syndrome, and mosaicism. BoBs™ assay also detected Smith-Magenis syndrome, Williams-Beuren syndrome, DiGeorge syndrome, Miller-Dieker syndrome, Prader-Willi syndrome, Xp22.31 microdeletions, 22q11.2, and 17p11.2 microduplications. However, karyotyping failed to show these chromosomal abnormalities. A case of 8q21.2q23.3 duplication which was found by karyotyping was not detected by BoBs™ assay. Furthermore, all these chromosomal abnormalities were consistent with CMA and FISH verifications. According to the reports, we estimated that the detection rates of karyotyping, BoBs™, and CMA in the present study were 4.28%, 4.93%, and 5%, respectively, which is consistent with the results of a previous study. The respective costs for the three methods were about $135-145, $270-290, and $540-580. CONCLUSION: BoBs™ assay is considered a reliable, rapid test for use in PND. A variety of comprehensive technological applications can complement each other in PND, in order to maximize the diagnosis rate and reduce the occurrence of birth defects.

Rapid screening of tissue microarrays for Her-2 fluorescence in situ hybridization testing is an accurate, efficient and economic method of providing an entirely in situ hybridization-based Her-2 testing service.

AIMS: Fluorescence in situ hybridization (FISH) testing is the 'gold standard' method for Her-2 status assessment in breast cancer patients, yet is only employed in about 30% of tests carried out because of cost and labour considerations. We have previously described tissue microarray (TMA)-based testing to eliminate cost constraints, and now describe a rapid screening approach to reduce time spent testing. METHODS AND RESULTS: We examined 88 cases of invasive breast cancer on TMAs comparing formal FISH scoring with a rapid screening technique. Each core was screened by two observers and results recorded as positive, equivocal or negative. Each approach was timed. Data were analysed by comparing the rapid screening results with formal counts. Using rapid screening, two-thirds of negative and half the positive cases could be eliminated with 100% accuracy. It took 2 min per observer per case to rapid screen six TMA cores at x100 magnification. The remaining cases required formal counting, which took no longer than with whole-section techniques. CONCLUSION: Rapid screening of TMAs for routine Her-2 FISH testing is safe, economical and time efficient. The technique ensures that all patients receive 'gold standard' testing.

The selective use of rapid aneuploidy screening in prenatal diagnosis.

AIMS: To evaluate the diagnostic utility and costing of the selective use of rapid aneuploidy screening (RAS) for chorion villus sampling (CVS) and amniocentesis specimens. METHODS: CVS and amniocenteses performed between 2000 and 2006 were identified. Cases were subdivided into two groups: (i) RAS in addition to long-term culture and (ii) long-term chromosome culture alone. The frequency of RAS, the proportion of abnormal results and the cytogenetic costings were reviewed. RESULTS: A total of 3315 procedures were performed: 730 CVS and 2585 amniocenteses. An abnormal karyotype culture was present in 366 of 3315 (11%). For CVS an abnormal culture was present in 164 (22.5%). RAS (short-term culture/direct preparation) was selectively used in 399 cases (54.6%) with an abnormal result in 128 (32% of RAS). For amniocentesis, 206 chromosome abnormalities were present (8.0% of specimens). RAS (interphase FISH) was selectively used in 580 amniocenteses (22.4%). FISH was requested in 95 (66.4%) of the 143 abnormal cases potentially detectable with standard probes. There was a progressive increase in utilisation of RAS for amniocentesis (8.9% in 2000 to 43.3% of cases in 2006, P < 0.001). CVS RAS was stable. This liberalisation resulted in a fourfold increase in expenditure for FISH and cost/abnormality detected ($A970 per abnormal result in 2000 to $A4015 per abnormal result in 2006). CONCLUSION: The selective use of prenatal RAS results in a reasonably high detection rate for chromosomal anomalies. Liberalisation of RAS, however, is an expensive cytogenetic model. An approach based on some predictive level of risk combined with resource funding levels may be a more pragmatic approach.

Cost-effectiveness of HER2 testing and 1-year adjuvant trastuzumab therapy for early breast cancer.

BACKGROUND: Clinical studies have demonstrated statistically significant reduction of breast cancer relapse and improved overall survival by adding trastuzumab for 1 year after adjuvant chemotherapy in human epidermal growth factor receptor-2 protein (HER2)/neu-positive breast cancer. The aim of this study was to analyze the cost-effectiveness of HER2/neu testing and the addition of 1-year adjuvant trastuzumab after adjuvant chemotherapy from a societal perspective in a Swedish setting. MATERIAL AND METHODS: We used a Markov state transition model to simulate HER2/neu testing and adjuvant trastuzumab treatment in a hypothetical cohort of early breast cancer patients. RESULTS: The cost per quality adjusted life year (QALY) gained for immunohistochemical (IHC) testing for all patients with FISH confirmation of IHC 2+ and 3+ and 1-year adjuvant trastuzumab for FISH-positive patients was estimated to 36,000 euros. The strategy of FISH testing for all patients, with 1-year adjuvant trastuzumab for FISH-positive patients was associated with the longest quality adjusted survival of all evaluated treatment strategies and the cost per QALY gained was estimated to 41,500 euros. The remaining testing and treatment strategies were dominated. CONCLUSION: FISH testing for all patients with 1-year adjuvant trastuzumab for FISH+ patients is a cost-effective treatment option from a societal perspective.

Quantitative PCR and HER2 testing in breast cancer: a technical and cost-effectiveness analysis.

We performed a technical and cost-effectiveness analysis of quantitative reverse transcription-polymerase chain reaction (Q-RT-PCR) for the assessment of HER2 in breast cancer. We evaluated 44 frozen and 55 formalin-fixed paraffin-embedded (FFPE) breast carcinoma specimens by Q-RT-PCR, immunohistochemical analysis, and fluorescent in situ hybridization (FISH). Immunohistochemical and FISH analyses were performed on individual slides and on tissue microarray. Costs of techniques were calculated to study 1 case and 10 or 40 cases. Q-RT-PCR provided reliable data in frozen and FFPE specimens, which were significantly correlated. HER2 messenger RNA levels were significantly stratified in agreement with immunohistochemical data (P < .05). There was complete concordance between Q-RT-PCR and immunohistochemical results for negative and strongly positive (3+) cases. The intermediate immunohistochemical group (2+), including FISH+ and FISH- cancers, could also be stratified by Q-RT-PCR. Cost analysis documented the advantage of Q-RT-PCR in all US Food and Drug Administration-approved assays. Our data support the use of Q-RT-PCR for testing breast cancer specimens to select patients for HER2 inhibitory therapy.