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Galbiati S.,San Raffaele Scientific Institute | Brisci A.,San Raffaele Scientific Institute | Damin F.,CNR Institute of Chemistry of Molecular Recognition | Gentilin B.,UO Dipartimentale di Genetica Medica | And 6 more authors.
Expert Opinion on Biological Therapy | Year: 2012

Introduction: In pregnancy, the discovery of fetal DNA in maternal blood outlined new scenarios for noninvasive prenatal diagnosis of numerous fetal pathological conditions based on a new source of fetal genetic material. Tests on fetal DNA circulating in maternal plasma are expected to replace or reduce invasive procedures, such as chorionic villi sampling and amniocentesis, that are typically carried out late in pregnancy and pose a risk of miscarriage. Areas covered: Nevertheless, at present, no accurate and simple methods for noninvasive prenatal diagnosis of genetic diseases are available, thus preventing a widespread clinical application. Expert opinion: Two highly different sensitive methodologies are reported both allowing the identification of fetal paternally inherited mutations in maternal plasma DNA during the first trimester of pregnancy in a clinically relevant genetic disease. The first one includes mutant enrichment amplification protocols either based on the use of PNA (peptide nucleic acids) or on CO-amplification at Lower Denaturation temperature-PCR (COLD-PCR). In the second approach, an extremely sensitive microarray substrates are exploited which allows the detection of fetal mutated alleles even without the need of any enrichment strategy. Beta-thalassemia has been chosen as a model of clinically relevant genetic disease. © 2012 Informa UK, Ltd. Source

Pighin S.,University of Trento | Savadori L.,University of Trento | Barilli E.,University of Trento | Rumiati R.,University of Padua | And 5 more authors.
Medical Decision Making | Year: 2013

The present research provides empirical evidence of whether communicating the prenatal risk of chromosomal anomalies using comparison scenarios influences women's ability to distinguish between different risk levels. In 2 experiments, participants read a description of a hypothetical woman who was learning of the risk of chromosomal anomaly as a result of a prenatal screening test. Both experiments used a 3 (risk level) × 3 (scenario) full between-subjects design. In accordance with the experimental condition, participants were presented with a low (e.g., 1 in 5390), a medium (e.g., 1 in 770), or a high risk value (e.g., 1 in 110). Such risk values were presented either on their own or along with additional information illustrating a comparison scenario that provided 2 numerical comparison points. Participants were asked to evaluate the risk of chromosomal anomaly. In Experiment 2, participants' numeracy skills were also assessed. Results showed that the use of comparison scenarios results in significant differences in perceived risk across risk levels whereas such differences are not significant without the comparison scenario, but such a technique has differential effects according to participants' capacity to deal with numbers. Although the technique is beneficial for high-numerate participants, it has no effect on low-numerate participants. Source

Castellanos-Rizaldos E.,Dana-Farber Cancer Institute | Liu P.,Dana-Farber Cancer Institute | Milbury C.A.,Dana-Farber Cancer Institute | Guha M.,Dana-Farber Cancer Institute | And 8 more authors.
Clinical Chemistry | Year: 2012

BACKGROUND: Low-level mutations in clinical tumor samples often reside below mutation detection limits, thus leading to false negatives that may impact clinical diagnosis and patient management. COLD-PCR (co-amplification at lower denaturation temperature PCR) is a technology that magnifies unknown mutations during PCR, thus enabling downstream mutation detection. However, a practical difficulty in applying COLD-PCR has been the requirement for strict control of the denaturation temperature for a given sequence, to within ±0.3°C. This requirement precludes simultaneous mutation enrichment in sequences of substantially different melting temperature (Tm) and limits the technique to a single sequence at a time. We present a temperature-tolerant (TT) approach (TT-COLD-PCR) that reduces this obstacle. METHODS: We describe thermocycling programs featuring a gradual increase of the denaturation temperature during COLD-PCR. This approach enabled enrichment of mutations when the cycling achieves the appropriate critical denaturation temperature of each DNA amplicon that is being amplified. Validation was provided for KRAS (v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog) and TP53 (tumor protein p53) exons 6-9 by use of dilutions of mutated DNA, clinical cancer samples, and plasma-circulating DNA. RESULTS: A single thermocycling program with a denaturation-temperature window of 2.5-3.0°C enriches mutations in all DNA amplicons simultaneously, despite their different Tms. Mutation enrichments of 6-9-fold were obtained with TT-full-COLD-PCR. Higher mutation enrichments were obtained for the other 2 forms of COLD-PCR, fast-COLD-PCR, and ice-COLD-PCR. CONCLUSIONS: Low-level mutations in diverse amplicons with different Tms can be mutation enriched via TT-COLD-PCR provided that their Tms fall within the denaturation-temperature window applied during amplification. This approach enables simultaneous enrichment of mutations in several amplicons and increases significantly the versatility of COLD-PCR. © 2012 American Association for Clinical Chemistry. Source

Brisci A.,San Raffaele Scientific Institute | Damin F.,CNR Institute of Chemistry of Molecular Recognition | Pietra D.,University of Pavia | Galbiati S.,San Raffaele Scientific Institute | And 9 more authors.
Clinical Chemistry | Year: 2012

BACKGROUND: Myeloproliferative neoplasms (MPNs) include polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF). Somatic mutations in exon 10 of the MPL (myeloproliferative leukemia virus oncogene) gene, mainly substitutions encoding W515 variants, have recently been described in a minority of patients with ET or PMF. We optimized analytically sensitive methods for detecting and genotyping MPL variants. METHODS: We used DNA previously isolated from circulating granulocytes of 60 patients withMPNthat had previously been analyzed by high-resolution melting (HRM), direct sequencing, and the TaqMan allelicdiscrimination assay. We developed conditions for enriching tumor mutant alleles with COLD-PCR (coamplification at lower denaturation temperature PCR) and coupled it with direct sequencing. Assays were designed for identifying MPL W515 substitutions with full COLD-PCR protocols. In parallel, we used innovative microarray substrates to develop assays for evaluating the mutant burden in granulocyte cells. RESULTS: Mutations that were present at very low levels in patients who had previously been scored as having an MPL variant by HRM and as wild type by direct sequencing were successfully identified in granulocyte DNA. Notably, the microarray approach displayed analytical sensitivities of 0.1% to 5% mutant allele, depending on the particular mutation. This analytical sensitivity is similar to that obtained with COLD-PCR. The assay requires no enrichment strategy and allows both the characterization of each variant allele and the evaluation of its proportion in every patient. CONCLUSIONS: These procedures, which are transferable to clinical diagnostic laboratories, can be used for detecting very low proportions of minority mutant alleles that cannot be identified by other, conventional methods. © 2012 American Association for Clinical Chemistry. Source

Galbiati S.,San Raffaele Scientific Institute | Damin F.,CNR Institute of Chemistry of Molecular Recognition | Pinzani P.,University of Florence | Mancini I.,University of Florence | And 7 more authors.
PLoS ONE | Year: 2013

Molecular diagnostics of human cancers may increase accuracy in prognosis, facilitate the selection of the optimal therapeutic regimen, improve patient outcome, reduce costs of treatment and favour development of personalized approaches to patient care. Moreover sensitivity and specificity are fundamental characteristics of any diagnostic method. We developed a highly sensitive microarray for the detection of common KRAS and BRAF oncogenic mutations. In colorectal cancer, KRAS and BRAF mutations have been shown to identify a cluster of patients that does not respond to anti-EGFR therapies; the identification of these mutations is therefore clinically extremely important. To verify the technical characteristics of the microarray system for the correct identification of the KRAS mutational status at the two hotspot codons 12 and 13 and of the BRAFV600E mutation in colorectal tumor, we selected 75 samples previously characterized by conventional and CO-amplification at Lower Denaturation temperature-PCR (COLD-PCR) followed by High Resolution Melting analysis and direct sequencing. Among these samples, 60 were collected during surgery and immediately steeped in RNAlater while the 15 remainders were formalin-fixed and paraffin-embedded (FFPE) tissues. The detection limit of the proposed method was different for the 7 KRAS mutations tested and for the V600E BRAF mutation. In particular, the microarray system has been able to detect a minimum of about 0.01% of mutated alleles in a background of wild-type DNA. A blind validation displayed complete concordance of results. The excellent agreement of the results showed that the new microarray substrate is highly specific in assigning the correct genotype without any enrichment strategy. © 2013 Galbiati et al. Source

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