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In the last decades, food allergy has been revealed as an important public health problem affecting the worldwide population, and in the most delicate age group such as children, can cause severe symptoms. Specifically, walnut allergens often induce anaphylactic reaction in paediatric and adult allergic patients, therefore timely and certain diagnosis is essential to avoid dangerous complications and restore patients' quality of life. Currently, the diagnostic tests for food allergy are mainly based on hydrophilic allergens, underestimating the relevance of the lipophilic component. In this work, raw and boiled walnuts proteins were differentially extracted, characterized by LDS-PAGE and the patient IgE immunoreaction vs walnut hydrophilic and hydrophobic protein extract were evaluated. By using mass spectrometry, we identified all the already known walnut allergens and four oleosins were found out in the walnuts lipophilic fraction. Our investigations suggested that boiling may slightly modify walnuts allergenicity for both hydrophilic and hydrophobic protein extracts, although this finding have to be confirmed on a larger number of patients.

A major effort has been focused on the detection of oncogenes' mutations in diverse types of clinical specimens including formalin-fixed and paraffin embedded tissues, presently the gold-standard samples, up to plasma, that constitute a noninvasive alternative source of tumor DNA. The reliable detection of mutations in circulating tumor DNA requires a high analytical sensitivity. Here, we applied three different highly sensitive methodologies (COLD-PCR, a microarray-based approach and the droplet digital PCR, ddPCR) to identify mutations in the plasma of 30 metastatic colorectal cancer patients previously genotyped on tissue biopsy. The methods showed a modest concordance rate with respect to the results obtained on tissue biopsies: 63.3% by ddPCR, 63% by microarray and 55.6% by COLD-PCR. This could be ascribed either to the different timing between tissue and liquid biopsy collection, which could reflect a different stage of disease progression or to the diverse sensitivity of the methodologies applied. Indeed, if we compare the results obtained on plasma samples, the concordance rates were higher especially by comparing ddPCR versus COLD-PCR (92.6%). Thus, we consider both methodologies as useful procedures easily transferable in a clinical setting. Notably, the ddPCR allows a quantitative assessment of the fractional abundance of the mutation.

Highlights • High sensitivity of Simplexa™ COVID-19 Direct assay. • 100 % specificity of this new assay. • “Almost perfect” agreement with Corman’s method (κ = 0.938). • High-speed detection, all-in-one reagent mix and no separate extraction required. • Promising for laboratory diagnosis of COVID-19 and field application., Background So far, one of the major drawbacks of the available molecular assays for the diagnosis of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) is the need for viral nucleic acid extraction from clinical specimens. Objective The aim of this study was to evaluate the performances of a newly designed real-time RT-PCR (Simplexa™ COVID-19 Direct assay), that is established with an all-in-one reagent mix and no separate extraction required. Results The lower limit of detection (LOD) for both target genes resulted the same: 3.2 (CI: 2.9–3.8) log10 cp/mL and 0.40 (CI: 0.2–1.5) TCID50/mL for S gene while 3.2 log10 (CI: 2.9–3.7) log10 cp/mL and 0.4 (CI: 0.2–1.3) TCID50/mL for ORF1ab. The LOD obtained with extracted viral RNA for both S gene or ORF1ab was 2.7 log10 cp/mL. Crossreactive analysis performed in 20 nasopharyngeal swabs confirmed a 100% of clinical specificity of the assay. Clinical performances of Simplexa™ COVID-19 Direct assay were assessed in 278 nasopharyngeal swabs tested in parallel with Corman's method. Concordance analysis showed an "almost perfect" agreement in SARS-CoV-2 RNA detection between the two assays, being κ = 0.938; SE = 0.021; 95% CI = 0.896-0.980. Conclusions The high sensitivity and specificity of this new assay indicate that it is promising for laboratory diagnosis, enabling highspeed detection in just over one hour, which is significantly faster than the up to five hours currently required by traditional extraction followed by amplification technologies, thus allowing prompt decision making regarding isolation of infected patients.

Our knowledge of the genetic basis of myelodysplastic syndromes (MDS) and myelodysplastic/myeloproliferative neoplasms (MDS/MPN) has considerably improved. To define genotype/phenotype relationships of clinical relevance, we studied 308 patients with MDS, MDS/MPN, or acute myeloid leukemia evolving from MDS. Unsupervised statistical analysis, including the World Health Organization classification criteria and somatic mutations, showed that MDS associated with SF3B1-mutation (51 of 245 patients, 20.8%) is a distinct nosologic entity irrespective of current morphologic classification criteria. Conversely, MDS with ring sideroblasts with nonmutated SF3B1 segregated in different clusters with other MDS subtypes. Mutations of genes involved in DNA methylation, splicing factors other than SF3B1, and genes of the RAS pathway and cohesin complex were independently associated with multilineage dysplasia and identified a distinct subset (51 of 245 patients, 20.8%). No recurrent mutation pattern correlated with unilineage dysplasia without ring sideroblasts. Irrespective of driver somatic mutations, a threshold of 5% bone marrow blasts retained a significant discriminant value for identifying cases with clonal evolution. Comutation of TET2 and SRSF2 was highly predictive of a myeloid neoplasm characterized by myelodysplasia and monocytosis, including but not limited to, chronic myelomonocytic leukemia. These results serve as a proof of concept that a molecular classification of myeloid neoplasms is feasible.

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 (coamplification 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.

We searched for JAK2 exon 12 mutations in patients with JAK2 (V617F)-negative myeloproliferative disorders. Seventeen patients with polycythemia vera (PV), including 15 sporadic cases and 2 familial cases, carried deletions or duplications of exon 12 in circulating granulocytes but not in T lymphocytes. Two of the 8 mutations detected were novel, and the most frequent ones were N542-E543del and E543-D544del. Most patients with PV carrying an exon 12 mutation had isolated erythrocytosis at clinical onset, unlike patients with JAK2 (V617F)-positive PV, most of whom had also elevations in white blood cell and/or platelet counts. Both patients with familial PV carrying an exon 12 mutation had an affected sibling with JAK2 (V617F)-positive PV. Thus, several somatic mutations of JAK2 exon 12 can be found in a myeloproliferative disorder that is mainly characterized by erythrocytosis. Moreover, a genetic predisposition to acquisition of different JAK2 mutations is inherited in families with myeloproliferative disorders.

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.

To the Editor: After the discovery of fetal DNA in maternal plasma, investigators reported different strategies for the noninvasive prenatal diagnosis of genetic diseases (1). Despite the advances in improving the analytical sensitivity of methods, distinguishing between fetal and maternal sequences remains very challenging, and the field of noninvasive prenatal diagnosis of genetic diseases has yet to attain a routine application in clinical diagnostics. An innovative strategy that has been reported is based on COLD-PCR (coamplification at a lower denaturation temperature PCR),1 which exploits melting temperature ( T m) differences between variant or mismatched sequences and wild-type sequences. This approach uses a critical denaturation temperature ( T c) lower than the T m to selectively amplify minority mutated alleles (2). We have developed assays for the identification of fetal paternally inherited mutations in maternal plasma. These assays use full COLD-PCR for the detection of IVSI.110 (G>A) and Cd39 (C>T) HBB (globin, beta) gene mutations that cause β-thalassemia. Full COLD-PCR is based on the generation of heteroduplexes between mutant and wild-type sequences. These heteroduplexes melt at lower temperatures than the wild-type homoduplexes. They are selectively denatured at the T c and then subsequently amplified. Given that both the fetal and maternal DNA content in maternal plasma has been demonstrated to vary from pregnancy to …

Somatic mutations of MPL exon 10, mainly involving a W515 substitution, have been described in JAK2 (V617F)-negative patients with essential thrombocythemia and primary myelofibrosis. We used direct sequencing and high-resolution melt analysis to identify mutations of MPL exon 10 in 570 patients with myeloproliferative neoplasms, and allele specific PCR and deep sequencing to further characterize a subset of mutated patients. Somatic mutations were detected in 33 of 221 patients (15%) with JAK2 (V617F)-negative essential thrombocythemia or primary myelofibrosis. Only one patient with essential thrombocythemia carried both JAK2 (V617F) and MPL (W515L). High-resolution melt analysis identified abnormal patterns in all the MPL mutated cases, while direct sequencing did not detect the mutant MPL in one fifth of them. In 3 cases carrying double MPL mutations, deep sequencing analysis showed identical load and location in cis of the paired lesions, indicating their simultaneous occurrence on the same chromosome.

We searched for JAK2 exon 12 mutations in patients with JAK2 (V617F)-negative myeloproliferative disorders. Seventeen patients with polycythemia vera (PV), including 15 sporadic cases and 2 familial cases, carried deletions or duplications of exon 12 in circulating granulocytes but not in T lymphocytes. Two of the 8 mutations detected were novel, and the most frequent ones were N542-E543del and E543-D544del. Most patients with PV carrying an exon 12 mutation had isolated erythrocytosis at clinical onset, unlike patients with JAK2 (V617F)-positive PV, most of whom had also elevations in white blood cell and/or platelet counts. Both patients with familial PV carrying an exon 12 mutation had an affected sibling with JAK2 (V617F)-positive PV. Thus, several somatic mutations of JAK2 exon 12 can be found in a myeloproliferative disorder that is mainly characterized by erythrocytosis. Moreover, a genetic predisposition to acquisition of different JAK2 mutations is inherited in families with myeloproliferative disorders.

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 with MPN that had previously been analyzed by high-resolution melting (HRM), direct sequencing, and the TaqMan allelic-discrimination 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.

Molecular remission after allo-SCT in a patient with post-essential thrombocythemia myelofibrosis carrying the MPL (W515A) mutation

We studied patients with myeloid neoplasm associated with ringed sideroblasts and/or thrombocytosis. The combination of ringed sideroblasts 15% or greater and platelet count of 450 × 109/L or greater was found in 19 subjects fulfilling the diagnostic criteria for refractory anemia with ringed sideroblasts (RARS) associated with marked thrombocytosis (RARS-T), and in 3 patients with primary myelofibrosis. JAK2 and MPL mutations were detected in circulating granulocytes and bone marrow CD34+ cells, but not in T lymphocytes, from 11 of 19 patients with RARS-T. Three patients with RARS, who initially had low to normal platelet counts, progressed to RARS-T, and 2 of them acquired JAK2 (V617F) at this time. In female patients with RARS-T, granulocytes carrying JAK2 (V617F) represented only a fraction of clonal granulocytes as determined by X-chromosome inactivation patterns. RARS and RARS-T patient groups both consistently showed up-regulation of ALAS2 and down-regulation of ABCB7 in CD34+ cells, but several other genes were differentially expressed, including PSIP1 (LEDGF), CXCR4, and CDC2L5. These observations suggest that RARS-T is indeed a myeloid neoplasm with both myelodysplastic and myeloproliferative features at the molecular and clinical levels and that it may develop from RARS through the acquisition of somatic mutations of JAK2, MPL, or other as-yet-unknown genes.

Abstract 1862 Refractory anemia with ring sideroblasts (RARS) is a myelodysplastic syndrome (MDS) characterized by isolated anemia, erythroid dysplasia only, less than 5% blasts and 15% or more ring sideroblasts in the bone marrow (2008 WHO Classification of Tumors of Hematopoietic and Lymphoid Tissues). The natural history of RARS is characterized by an initial phase of erythroid hyperplasia and ineffective erythropoiesis, which is usually stable for many years but in a proportion of patients may be followed by a phase of marrow failure, with or without the later emergence of leukemic blasts. Overall, RARS is a benign condition with a median survival of about 9 years (J Clin Oncol. 2005;23:7594-603). Since the vast majority of these patients have no cytogenetic abnormalities, the clonal nature of RARS has been questioned. However, a few studies of X-chromosome inactivation patterns performed in female patients have suggested that RARS derives from clonal proliferation of a multipotent hematopoietic stem cell with the potential for myeloid and lymphoid differentiation. Somatic mutations of TET2 have been recently found in myeloid neoplasms including MDS, where they appear occur early during disease evolution (Nat Genet. 2009;41:838-42), and are currently considered as a reliable clonal marker of these disorders. In this study, we therefore performed a mutation analysis of TET2 in patients with myeloid neoplasms associated with ring sideroblasts. Using direct sequencing, we studied 33 patients with RARS and 28 patients with refractory cytopenia with multilineage dysplasia (RCMD) having 15% or more ring sideroblasts in the bone marrow. Somatic mutations of TET2 were detected in circulating granulocytes from 10 out of 33 (30%) patients with RARS and 10 out of 28 (36%) patients with RCMD and ring sideroblasts. Most of these mutations were novel at the time of this writing. Fourteen patients had a single somatic mutation, and the mutation burden ranged from 10 to 80%. In 9 of these 14 cases, the mutation burden was approximately 50%, consistent with a fully clonal hematopoiesis characterized a single dominant clone that was heterozygous for the mutation. In a female patient with 10% mutant alleles, however, granulocytes carrying mutant TET2 represented only one tenth of clonal granulocytes as determined by X-chromosome inactivation patterns, suggesting the existence of alternative genetic events preceding the TET2 mutation and sustaining clonal dominance. Six patients had multiple somatic mutations of TET2: two mutations in 3 cases, three mutations in 2 cases, and four mutations in the last case. Quantitative evaluation of mutation burden showed concordant values (about 50%) for the multiple mutations in two patients (one with 4 and the other one with 3 somatic mutations of TET2), indicating the existence of a single dominant clone with multiple mutations. In the remaining 4 patients, discordant mutation loads were detected: the dominant mutation was present in about 50% alleles, while the remaining one(s) involved a lower proportion (10-35%) of alleles. These findings are consistent with the initial emergence of a clone of hematopoietic cells carrying a single mutation of TET2 and the subsequent development of subclones that carry additional TET2 mutations and become dominant with time. We also compared gene expression profiles of CD34-positive cells from patients with and without somatic mutations of TET2. While these 2 patient groups both had up-regulation of ALAS2 and down-regulation of ABCB7, distinctive “sideroblastic” features at the molecular level (Blood. 2006;108:337-45), no differentially expressed gene was identified between the 2 groups. These data indicate that somatic mutations of TET2 are unlikely to have a major impact on metabolic pathways at the CD34-positive cell level, and are more consistent with an epigenetic regulation function of TET2. In summary, this study shows that about one third of patients with RARS carry somatic mutations of TET2 in circulating granulocytes, clearly indicating that RARS is a true clonal disorder of hematopoiesis despite it presents as a benign erythroid disorder. In most cases, TET2 mutations appear to cause clonal dominance of hematopoietic stem cells, thus initiating the myelodysplastic process. During the clinical course of the disease subclonal evolution may occur through the acquisition of additional somatic mutations of TET2. Disclosures: No relevant conflicts of interest to declare.

The JAK2 (V617F) mutation is found in 95% of patients with polycythemia vera (PV) and in about 60% of those with essential thrombocythemia (ET) or primary myelofibrosis (PMF). In a portion of PV patients, the occurrence of a mitotic recombination of chromosome 9p in a hematopoietic cell that is heterozygous for the mutation generates a subclone of cells that are homozygous for JAK2 (V617F) [N Engl J Med. 2005 Apr 28;352(17):1779–90]. We have previously shown that the vast majority of patients with post-PV myelofibrosis (MF) have high percentages of granulocyte JAK2 (V617F) mutant alleles [Blood. 2008 Apr 1;111(7):3383–7], suggesting that transition from heterozygosity to homozygosity for JAK2 (V617F) is associated with progression to myelofibrosis in PV. Activating mutations of MPL, mainly involving a W515 substitution, have been detected in JAK2 (V617F)-negative patients with ET and PMF. MPL maps on chromosome 1p34, and whether a mitotic recombination of this chromosome occurs and involves a transition from heterozygosity to homozygosity for MPL mutations is currently unclear. At variance with post-PV MF, post-ET MF occurs rarely, with an estimated risk of about 6% at 15 years. We studied 315 patients with myeloproliferative disorders followed at the Department of Hematology Oncology, University of Pavia and Fondazione IRCCS Policlinico San Matteo, Pavia, Italy. This study was approved by the local Ethics Committee. The revised World Health Organization (WHO) criteria were employed for the diagnosis of PV, ET and PMF, whereas the criteria of the International Working Group for Myelofibrosis Research and Treatment (IWG-MRT) were employed for the diagnosis of post-PV MF and post- ET MF. We developed a high-resolution melting-curve (HRM) assay for detecting MPL mutations in granulocyte and T lymphocyte gDNA. The study population included 205 patients with ET [58% of whom carried JAK2 (V617F)], 91 patients with PMF [62% of whom carried JAK2 (V617F)], and 19 patients with post-ET MF [42% of whom carried JAK2 (V617F)]. By means of HRM analysis and direct sequencing, we detected the following MPL mutations in circulating granulocytes but not in T lymphocytes: W515L, W515K, W515A, S505C, and V501A – these latter two being novel mutations. Two patients carried two different MPL mutations concurrently in circulating granulocytes, while another patient carried both JAK2 (V617F) and a MPL mutation. Based on the detection of abnormal melting curve profiles in granulocytes, the prevalence of MPL mutations was found to be 5.4% in all patients with ET [12.6% in JAK2 (V617)-negative subjects], 5.5% in those with PMF [14.3% in JAK2 (V617)-negative subjects], and 21.1% in patients with post-ET MF [36.4% in JAK2 (V617)-negative subjects]. The prevalence of MPL mutations was therefore significantly higher in post-ET MF than in ET (P

About 95% of patients with polycythemia vera (PV) carry the unique V617F mutation in JAK2 exon 14, which encodes a portion of the JH2 auto-inhibitory domain of the Jak2 kinase. Mutations in exon 12 have been recently reported in JAK2 (V617F)-negative patients with PV or idiopathic erythrocytosis. We searched for exon 12 mutations in 168 patients with JAK2 (V617F)-negative myeloproliferative disorders. The 2001 WHO criteria were employed for diagnosis. Of the 168 patients studied, 47 had sporadic PV, 11 had familial PV, 75 had essential thrombocythemia (ET), and 35 had primary myelofibrosis (PM). Seventeen patients with PV, including 15/47 sporadic cases and 2/11 familial cases, were found to carry deletions (n=15) or duplications (n=2) of exon 12 in circulating granulocytes but not in T-lymphocytes. None of the 110 patients with ET or PM was found to be positive. Mutations were detected by sequencing, and were then confirmed by sub-cloning in bacteria in 7/17 cases. Four of the 8 mutations detected were novel, while the most frequent ones were N542–E543del and E543–D544del. Mutations spanned from base 1606 to 1640, and the two duplications modified the rest of the sequence by adding 33 bp. In terms of protein, deletions predicted aminoacid changes spanning from phenylalanine 537 to aspartic acid 544, while duplications predicted changes from phenylalanine 547 onwards within the JH2 pseudokinase domain. Three categories of molecular lesions were identified: those involving a K539L substitution; those involving the E543del; and aminoacid duplications involving a substitution of phenylalanine 547. At clinical onset, 16/17 (94%) patients carrying a JAK2 exon 12 mutation had low serum erythropoietin (Epo) levels, indicating a combination of absolute erythrocytosis and suppressed endogenous Epo production. Moreover, 12/17 patients had erythrocytosis associated with normal white blood cell and platelet counts, i.e., isolated erythrocytosis. This frequency (71%) was significantly higher than that observed in 92 patients diagnosed with JAK2 (V617F)-positive PV at the Department of Hematology, IRCCS Policlinico San Matteo, Pavia, Italy (P12 x 109/L) and/or thrombocytosis (PLT>400 x 109/L), and only 22% of them had isolated erythrocytosis. Both patients with familial PV carrying an exon 12 mutation had an affected sibling with JAK2 (V617F)-positive PV. While the former showed isolated erythrocytosis, their JAK2 (V617F)-positive siblings had also thrombocytosis. In conclusion: several somatic mutations of JAK2 exon 12 - mostly 6 bp deletions - can be found in patients with a myeloproliferative disorder that is mainly characterized by erythrocytosis associated with low serum Epo levels; a genetic predisposition to acquisition of different JAK2 mutations is inherited in families with myeloproliferative disorders, and the mutation type (exon 12 vs exon 14) contributes to determining their variable clinical phenotype.