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1.
Diagnostics (Basel) ; 11(8)2021 Aug 03.
Artigo em Inglês | MEDLINE | ID: mdl-34441338

RESUMO

Advanced diagnostics are enabling cancer treatments to become increasingly tailored to the individual through developments in immunotherapies and targeted therapies. However, long turnaround times and high costs of molecular testing hinder the widespread implementation of targeted cancer treatments. Meanwhile, gold-standard histopathological assessment carried out by a trained pathologist is widely regarded as routine and mandatory in most cancers. Recently, methods have been developed to mine hidden information from histopathological slides using deep learning applied to scanned and digitized slides; deep learning comprises a collection of computational methods which learn patterns in data in order to make predictions. Such methods have been reported to be successful in a variety of cancers for predicting the presence of biomarkers such as driver mutations, tumour mutational burden, and microsatellite instability. This information could prove valuable to pathologists and oncologists in clinical decision making for cancer treatment and triage for in-depth sequencing. In addition to identifying molecular features, deep learning has been applied to predict prognosis and treatment response in certain cancers. Despite reported successes, many challenges remain before the clinical implementation of such diagnostic strategies in the clinical setting is possible. This review aims to outline recent developments in the field of deep learning for predicting molecular genetics from histopathological slides, as well as to highlight limitations and pitfalls of working with histopathology slides in deep learning.

2.
J Thorac Oncol ; 16(5): 798-806, 2021 05.
Artigo em Inglês | MEDLINE | ID: mdl-33588111

RESUMO

INTRODUCTION: RET gene fusions are established oncogenic drivers in 1% of NSCLC. Accurate detection of advanced patients with RET fusions is essential to ensure optimal therapy choice. We investigated the performance of fluorescence in situ hybridization (FISH) as a diagnostic test for detecting functional RET fusions. METHODS: Between January 2016 and November 2019, a total of 4873 patients with NSCLC were routinely screened for RET fusions using either FISH (n = 2858) or targeted RNA next-generation sequencing (NGS) (n = 2015). If sufficient material was available, positive cases were analyzed by both methods (n = 39) and multiple FISH assays (n = 17). In an independent cohort of 520 patients with NSCLC, whole-genome sequencing data were investigated for disruptive structural variations and functional fusions in the RET and compared with ALK and ROS1 loci. RESULTS: FISH analysis revealed RET rearrangement in 48 of 2858 cases; of 30 rearranged cases double tested with NGS, only nine had a functional RET fusion. RNA NGS yielded RET fusions in 14 of 2015 cases; all nine cases double tested by FISH had RET locus rearrangement. Of these 18 verified RET fusion cases, 16 had a split signal and two a complex rearrangement by FISH. By whole-genome sequencing, the prevalence of functional fusions compared with all disruptive events was lower in the RET (4 of 9, 44%) than the ALK (27 of 34, 79%) and ROS1 (9 of 12, 75%) loci. CONCLUSIONS: FISH is a sensitive but unspecific technique for RET screening, always requiring a confirmation using an orthogonal technique, owing to frequently occurring RET rearrangements not resulting in functional fusions in NSCLC.


Assuntos
Neoplasias Pulmonares , Proteínas Tirosina Quinases , Quinase do Linfoma Anaplásico/genética , Detecção Precoce de Câncer , Rearranjo Gênico , Humanos , Hibridização in Situ Fluorescente , Neoplasias Pulmonares/genética , Proteínas de Fusão Oncogênica/genética , Proteínas Tirosina Quinases/genética , Proteínas Proto-Oncogênicas/genética , Proteínas Proto-Oncogênicas c-ret/genética
3.
J Mol Diagn ; 23(3): 323-340, 2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-33385586

RESUMO

Diffuse large B-cell lymphoma (DLBCL) is a heterogeneous disease. Cell-of-origin classification in DLBCL has identified activated B cell (ABC) and germinal center B cell (GCB) as two major subtypes. Patients with the ABC subtype show reduced overall survival with standard therapies. Development of a quantitative RT-PCR-based lymphoma cell-of-origin (LCOO) assay to determine ABC, GCB, and unclassifiable subtypes in formalin-fixed, paraffin-embedded tissue (FFPET) DLBCL samples is reported. The LCOO classifier was trained on two DLBCL cohorts with validation performed by using an analytical grade assay in an independent cohort of 60 FFPET DLBCL samples. In the validation cohort, LCOO classification was 88.1%, 84.7%, and 84.7% concordant with microarray, immunohistochemistry (Hans classification), and Lymphoma Subtyping Test, respectively. Importantly, LCOO and Lymphoma Subtyping Test assays commonly assigned subtypes in 17 (94.4%) of 18 ABC samples and 34 (89.5%) of 38 GCB DLBCL samples from this cohort. Progression-free survival and overall survival of ABC and GCB subtypes, as classified by all platforms, were not significantly different in the validation cohort. LCOO classification using publicly available microarray gene expression from two independent data sets (414 fresh frozen and 474 FFPET DLBCL biopsies) revealed a significantly worse outcome for the ABC subtype compared with that of the GCB subtype. Thus, a sensitive, reproducible, LCOO assay developed on an easy to standardize quantitative RT-PCR platform may be an important clinical tool for DLBCL cell-of-origin classification.

4.
Case Rep Hematol ; 2020: 8375986, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32637179

RESUMO

Acquired, activating mutations of MPL W515 are recognised driver mutations of the myeloproliferative neoplasms (MPN), namely, essential thrombocythemia and primary myelofibrosis. The most common mutation at this codon is W515L with several other mutations also described at a lower frequency. Of these less common mutations, MPL W515S has only been reported sporadically with limited information on clinicopathological associations. We describe the case of an elderly man with persistent thrombocytosis presenting with an ischemic cerebral event. Bone marrow biopsy showed evidence of prefibrotic myelofibrosis with targeted sequencing demonstrating the presence of the rare MPL W515S mutation. Thrombolytic and cytoreductive therapies resulted in a favorable outcome and follow-up. This case provides additional, necessary, and phenotypic data for the rare MPN-associated MPL W515S mutation.

5.
Breast Cancer Res Treat ; 181(3): 571-580, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32378053

RESUMO

PURPOSE: The association between pathological complete response (pCR) in patients receiving neoadjuvant chemotherapy (NAC) for breast cancer and Circulating Tumour Cells (CTCs) is not clear. The aim of this study was to assess whether CTC enumeration could be used to predict pathological response to NAC in breast cancer as measured by the Miller-Payne grading system. METHODS: Twenty-six patients were recruited, and blood samples were taken pre- and post-NAC. CTCs were isolated using the ScreenCell device and stained using a modified Giemsa stain. CTCs were enumerated by 2 pathologists and classified as single CTCs, doublets, clusters/microemboli and correlated with the pathological response as measured by the Miller-Payne grading system. χ2 or ANOVA was performed in SPSS 24.0 statistics software for associations. RESULTS: 89% of patients had invasive ductal carcinoma (IDC) and 11% invasive lobular carcinoma (ILC). At baseline 85% of patients had CTCs present, median 7 (0-161) CTCs per 3 ml of whole blood. Post-chemotherapy, 58% had an increase in CTCs. This did not correlate with the Miller-Payne grade of response. No significant association was identified between the number of CTCs and clinical characteristics; however, we did observe a correlation between pre-treatment CTC counts and body mass index, p < 0.05. CONCLUSIONS: Patients with a complete response to NAC still had CTCs present, suggesting enumeration is not sufficient to aid surgery stratification. Additional characterisation and larger studies are needed to further characterise CTCs isolated pre- and post-chemotherapy. Long-term follow-up of these patients will determine the significance of CTCs in NAC breast cancer patients.


Assuntos
Protocolos de Quimioterapia Combinada Antineoplásica/uso terapêutico , Neoplasias da Mama/patologia , Carcinoma Ductal de Mama/patologia , Carcinoma Lobular/patologia , Terapia Neoadjuvante/mortalidade , Células Neoplásicas Circulantes/patologia , Adulto , Idoso , Neoplasias da Mama/tratamento farmacológico , Neoplasias da Mama/metabolismo , Carcinoma Ductal de Mama/tratamento farmacológico , Carcinoma Ductal de Mama/metabolismo , Carcinoma Lobular/tratamento farmacológico , Carcinoma Lobular/metabolismo , Estudos de Coortes , Feminino , Seguimentos , Humanos , Pessoa de Meia-Idade , Gradação de Tumores , Células Neoplásicas Circulantes/efeitos dos fármacos , Receptor ErbB-2/metabolismo , Receptores de Estrogênio/metabolismo , Receptores de Progesterona/metabolismo , Taxa de Sobrevida
6.
Diagnostics (Basel) ; 9(1)2019 Jan 18.
Artigo em Inglês | MEDLINE | ID: mdl-30669306

RESUMO

MET is a receptor tyrosine kinase (RTK) that plays important roles in carcinogenesis. Despite being frequently overexpressed in cancer, clinical responses to targeting this receptor have been limited. Recently novel splicing mutations involving the loss of exon 14 (called METex14 skipping) have emerged as potential biomarkers to predict for responsiveness to targeted therapies with Met inhibitors in non-small cell lung cancer (NSCLC). Currently, the diverse genomic alterations responsible for METex14 skipping pose a challenge for routine clinical diagnostic testing. In this report, we examine three different methodologies to detect METex14 and assess their potential utility for use as a diagnostic assay for both the identification of METex14 and intra-tumoural distribution in NSCLC.

7.
Ir J Med Sci ; 188(2): 405-408, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-30030673

RESUMO

BACKGROUND: De novo epidermal growth factor receptor (EGFR) resistance mutations in tyrosine kinase inhibitor-naïve patients are rare when assessed by standard genotyping methods. METHODS: Patients with EGFR mutations were identified using PCR-based fragment length analysis, mass spectrometry-based genotyping (Sequenom), and Sanger sequencing. RESULTS: From 2008 to 2015, we observed de novo EGFR resistance mutations in 12.8 patients who received an EGFR TKI with an overall response rate of 25%, median PFS 24 months, and median OS 34 months. Five patients (63%) received erlotinib in the first-line setting with a 60% disease control rate (DCR) and a median duration of response of 6 months (range 4-45 months). Three (37%) received cytotoxic chemotherapy in the first-line setting with 67% DCR and a median duration of response of 11 months (range 10-12 months). In patients with de novo EGFR T790M mutations, 50% (2/4) had stable disease with one patient having an ongoing response to erlotinib of over 96 months. In patients with de novo EGFR S768I mutations who received erlotinib, 50% (2/4) have ongoing partial responses at 30 and 6 months. CONCLUSION: This is the largest Irish review of de novo synchronous EGFR mutations. The incidence of co-occurring EGFR mutations in our cohort of non-small cell lung carcinoma (NSCLCA) is 1% on routine assays. Erlotinib appears to have activity in this cohort in both in the first- and second-line setting. De novo S768I and T790M represent distinct clinical entities. For de novo T790M mutations cytotoxic chemotherapy may still be considered first line. For de novo S768I mutations, erlotinib appears to be a reasonable therapeutic option.


Assuntos
Carcinoma Pulmonar de Células não Pequenas/genética , Neoplasias Pulmonares/genética , Idoso , Carcinoma Pulmonar de Células não Pequenas/metabolismo , Carcinoma Pulmonar de Células não Pequenas/patologia , Receptores ErbB/genética , Receptores ErbB/metabolismo , Feminino , Humanos , Neoplasias Pulmonares/metabolismo , Neoplasias Pulmonares/patologia , Masculino , Pessoa de Meia-Idade , Mutação , Estudos Retrospectivos
8.
J Anat ; 234(2): 165-178, 2019 02.
Artigo em Inglês | MEDLINE | ID: mdl-30426493

RESUMO

The precise cause of the bands of Fontana, striations on peripheral nerves visible to the naked eye, has been the subject of debate for hundreds of years. Some researchers have described them as reflecting the sinuous course of nerve fibres passing through nerves, and others have proposed that endoneurial collagen and sheaths surrounding nerves play a role in their appearance. We hypothesised that the bands are caused exclusively by reflection of light from the surfaces of nerve fibres travelling in phase in sinusoidal waveforms through peripheral nerves. We aligned images of obliquely illuminated nerves with confocal images of axons in those nerves, and the numbers and positions of the bands precisely matched the axonal waves. We also developed three-dimensional models of nerves with representations of the sinusoidal path of axons at their surface. We observed patterns resembling the bands of Fontana when these models were obliquely illuminated. This provides evidence that the bands of Fontana can be caused by light reflected sinusoidal path of axons alone. We subsequently describe a mechanism of band production based on our observations of both nerves and models. We report that smaller diameter nerves such as phrenic nerves and distal branches of sciatic nerves have shorter band intervals than larger nerves, such as proximal trunks of sciatic nerves, and that shorter band intervals correlate with longer axons per unit length of nerve, which suggests a greater tolerance to stretch. Inspection of banding patterns on peripheral nerves may permit prediction of axon length within nerves, and assist in the interpretation of nerve conduction data, especially in diseases where axon path has become altered.


Assuntos
Axônios/fisiologia , Nervo Frênico/citologia , Nervo Isquiático/citologia , Animais , Camundongos Endogâmicos C57BL , Ratos Wistar
9.
Genet Test Mol Biomarkers ; 22(2): 98-103, 2018 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-29323541

RESUMO

BACKGROUND: The classical Philadelphia chromosome-negative myeloproliferative neoplasms (MPNs), consisting of polycythemia vera, essential thrombocythemia, and primary myelofibrosis, are a heterogeneous group of neoplasms that harbor driver mutations in the JAK2, CALR, and MPL genes. The detection of mutations in these genes has been incorporated into the recent World Health Organization (WHO) diagnostic criteria for MPN. Given a pressing clinical need to screen for mutations in these genes in a routine diagnostic setting, a targeted next-generation sequencing (NGS) assay for the detection of MPN-associated mutations located in JAK2 exon 14, JAK2 exon 12, CALR exon 9, and MPL exon 10 was developed to provide a single platform alternative to reflexive, stepwise diagnostic algorithms. METHODS: Polymerase chain reaction (PCR) primers were designed to target mutation hotspots in JAK2 exon 14, JAK2 exon 12, MPL exon 10, and CALR exon 9. Multiplexed PCR conditions were optimized by using qualitative PCR followed by NGS. Diagnostic genomic DNA from 35 MPN patients, known to harbor driver mutations in one of the target genes, was used to validate the assay. RESULTS: One hundred percent concordance was observed between the previously-identified mutations and those detected by NGS, with no false positives, nor any known mutations missed (specificity = 100%, CI = 0.96, sensitivity = 100%, CI = 0.89). Improved resolution of mutation sequences was also revealed by NGS analysis. CONCLUSION: Detection of diagnostically relevant driver mutations of MPN is enhanced by employing a targeted multiplex NGS approach. This assay presents a robust solution to classical MPN mutation screening, providing an alternative to time-consuming sequential analyses.


Assuntos
Calreticulina/genética , Análise Mutacional de DNA/métodos , Janus Quinase 2/genética , Transtornos Mieloproliferativos/genética , Receptores de Trombopoetina/genética , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Reação em Cadeia da Polimerase
10.
J Thorac Oncol ; 13(3): 413-425, 2018 03.
Artigo em Inglês | MEDLINE | ID: mdl-29191776

RESUMO

INTRODUCTION: The reported prevalence of ALK receptor tyrosine kinase gene (ALK) rearrangement in NSCLC ranges from 2% to 7%. The primary standard diagnostic method is fluorescence in situ hybridization (FISH). Recently, immunohistochemistry (IHC) has also proved to be a reproducible and sensitive technique. Reverse-transcriptase polymerase chain reaction (RT-PCR) has also been advocated, and most recently, the advent of targeted next-generation sequencing (NGS) for ALK and other fusions has become possible. This study compares anaplastic lymphoma kinase (ALK) evaluation with all four techniques in resected NSCLC from the large European Thoracic Oncology Platform Lungscape cohort. METHODS: A total of 96 cases from the European Thoracic Oncology Platform Lungscape iBiobank, with any ALK immunoreactivity were examined by FISH, central RT-PCR, and NGS. An H-score higher than 120 defines IHC positivity. RNA was extracted from the same formalin-fixed, paraffin-embedded tissues. For RT-PCR, primers covered the most frequent ALK translocations. For NGS, the Oncomine Solid Tumour Fusion Transcript Kit (Thermo Fisher Scientific, Waltham, MA) was used. The concordance was assessed using the Cohen κ coefficient (two-sided α ≤ 5%). RESULTS: NGS provided results for 77 of the 95 cases tested (81.1%), whereas RT-PCR provided results for 77 of 96 (80.2%). Concordance occurred in 55 cases of the 60 cases tested with all four methods (43 ALK negative and 12 ALK positive). Using ALK copositivity for IHC and FISH as the criterion standard, we derived a sensitivity for RT-PCR/NGS of 70.0%/85.0%, with a specificity of 87.1%/79.0%. When either RT-PCR or NGS was combined with IHC, the sensitivity remained the same, whereas the specificity increased to 88.7% and 83.9% respectively. CONCLUSION: NGS evaluation with the Oncomine Solid Tumour Fusion transcript kit and RT-PCR proved to have high sensitivity and specificity, advocating their use in routine practice. For maximal sensitivity and specificity, ALK status should be assessed by using two techniques and a third one in discordant cases. We therefore propose a customizable testing algorithm. These findings significantly influence existing testing paradigms and have clear clinical and economic impact.


Assuntos
Quinase do Linfoma Anaplásico/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Reação em Cadeia da Polimerase Via Transcriptase Reversa/métodos , Neoplasias Torácicas/genética , Carcinoma Pulmonar de Células não Pequenas/patologia , Estudos de Coortes , Europa (Continente) , Feminino , Humanos , Neoplasias Pulmonares/patologia , Masculino , Neoplasias Torácicas/patologia
11.
BJR Case Rep ; 3(3): 20160110, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-30363209

RESUMO

We present a rare case of bilateral Morgagni hernias in an elderly female patient. She initially presented with coffee-ground vomiting and underwent an OGD from which she was given a diagnosis of oesophagitis. On her second presentation (a year later), CT was performed after OGD to evaluate what was thought to be a complex hiatus hernia causing haematemesis, at which point a diagnosis of bilateral Morgagni hernias was made. Surgical management with laparoscopic mesh repair was performed and she made an uneventful recovery.

12.
J Am Soc Nephrol ; 27(9): 2906-16, 2016 09.
Artigo em Inglês | MEDLINE | ID: mdl-26940094

RESUMO

A specific biomarker that can separate active renal vasculitis from other causes of renal dysfunction is lacking, with a kidney biopsy often being required. Soluble CD163 (sCD163), shed by monocytes and macrophages, has been reported as a potential biomarker in diseases associated with excessive macrophage activation. Thus, we hypothesized that urinary sCD163 shed by crescent macrophages correlates with active glomerular inflammation. We detected sCD163 in rat urine early in the disease course of experimental vasculitis. Moreover, microdissected glomeruli from patients with small vessel vasculitis (SVV) had markedly higher levels of CD163 mRNA than did those from patients with lupus nephritis, diabetic nephropathy, or nephrotic syndrome. Both glomeruli and interstitium of patients with SVV strongly expressed CD163 protein. In 479 individuals, including patients with SVV, disease controls, and healthy controls, serum levels of sCD163 did not differ between the groups. However, in an inception cohort, including 177 patients with SVV, patients with active renal vasculitis had markedly higher urinary sCD163 levels than did patients in remission, disease controls, or healthy controls. Analyses in both internal and external validation cohorts confirmed these results. Setting a derived optimum cutoff for urinary sCD163 of 0.3 ng/mmol creatinine for detection of active renal vasculitis resulted in a sensitivity of 83%, specificity of 96%, and a positive likelihood ratio of 20.8. These data indicate that urinary sCD163 level associates very tightly with active renal vasculitis, and assessing this level may be a noninvasive method for diagnosing renal flare in the setting of a known diagnosis of SVV.


Assuntos
Antígenos CD/urina , Antígenos de Diferenciação Mielomonocítica/urina , Nefropatias/urina , Rim/irrigação sanguínea , Vasculite/urina , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Biomarcadores/urina , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Receptores de Superfície Celular , Adulto Jovem
13.
Methods Mol Biol ; 1326: 193-201, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26498622

RESUMO

Investigation of the chemistry of the gliadin proteins has played an important role in our comprehension of how celiac disease (CoD) develops and progresses as a response to challenge with this immune stimulus. Studies in this area have implicated gut enzymes, tissue transglutaminase-mediated deamidation, and peptide binding affinity for the HLA-DQ2 and DQ8 molecules in disease pathogenesis. As the number and availability of prolamin sequences increases, the complexity and cost of laboratory analysis will similarly increase. Freely available tools to bioinformatically analyze candidate protein sequences can be employed as a low-cost, high-return preliminary mechanism to focus one's laboratory analyses on the most rewarding sequences. This chapter describes the use of antigen prediction, deamidation prediction, and protease cleavage prediction as may be applied to CoD research.


Assuntos
Doença Celíaca/metabolismo , Biologia Computacional , Antígenos HLA-DQ/imunologia , Doença Celíaca/imunologia , Humanos
14.
Melanoma Res ; 25(3): 189-99, 2015 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-25746038

RESUMO

Because of advances in targeted therapies, the clinical evaluation of cutaneous melanoma is increasingly based on a combination of traditional histopathology and molecular pathology. Therefore, it is necessary to expand our knowledge of the molecular events that accompany the development and progression of melanoma to optimize clinical management. The central objective of this study was to increase our knowledge of the mutational events that complement melanoma progression. High-throughput genotyping was adapted to query 159 known single nucleotide mutations in 33 cancer-related genes across two melanoma cohorts from Ireland (n=94) and Belgium (n=60). Results were correlated with various clinicopathological characteristics. A total of 23 mutations in 12 genes were identified, that is--BRAF, NRAS, MET, PHLPP2, PIK3R1, IDH1, KIT, STK11, CTNNB1, JAK2, ALK, and GNAS. Unexpectedly, we discovered significant differences in BRAF, MET, and PIK3R1 mutations between the cohorts. That is, cases from Ireland showed significantly lower (P<0.001) BRAF(V600E) mutation rates (19%) compared with the mutation frequency observed in Belgian patients (43%). Moreover, MET mutations were detected in 12% of Irish cases, whereas none of the Belgian patients harbored these mutations, and Irish patients significantly more often (P=0.027) had PIK3R1-mutant (33%) melanoma versus 17% of Belgian cases. The low incidence of BRAF(V600E)(-) mutant melanoma among Irish patients was confirmed in five independent Irish cohorts, and in total, only 165 of 689 (24%) Irish cases carried mutant BRAF(V600E). Together, our data show that melanoma-driving mutations vary by demographic area, which has important implications for the clinical management of this disease.


Assuntos
Melanoma/genética , Mutação , Fosfatidilinositol 3-Quinases/genética , Proteínas Proto-Oncogênicas B-raf/genética , Proteínas Proto-Oncogênicas c-met/genética , Neoplasias Cutâneas/genética , Adulto , Idoso , Substituição de Aminoácidos , Bélgica , Classe Ia de Fosfatidilinositol 3-Quinase , Estudos de Coortes , Feminino , Estudos de Associação Genética , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Irlanda , Masculino , Melanoma/metabolismo , Pessoa de Meia-Idade , Análise de Sequência com Séries de Oligonucleotídeos , Fosfatidilinositol 3-Quinases/metabolismo , Mutação Puntual , Polimorfismo de Nucleotídeo Único , Proteínas Proto-Oncogênicas B-raf/metabolismo , Proteínas Proto-Oncogênicas c-met/metabolismo , Neoplasias Cutâneas/metabolismo
15.
Lung Cancer ; 83(3): 309-15, 2014 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-24472389

RESUMO

Recent advances in the understanding of the molecular basis of cancer and the development of molecular diagnostics based on this knowledge have done much to progress the fields of oncology and pathology. Technological developments such as Next Generation Sequencing (NGS) and multiplex assays have made feasible the widespread adoption of molecular diagnostics for clinical use. While these developments and advances carry much promise, there are pitfalls to implementing this testing. Choosing appropriate biomarkers is a vital first step for clinical use and being able to understand the complex relationship between predictive and prognostic biomarkers is a crucial component of this. Testing for standard of care biomarkers is not straightforward, one must choose carefully between clinical trial assays, assays that analyse the same biological phenomenon or surrogate biomarkers. Sample heterogeneity and population specific difference is assays may skew results and must be controlled for at the assay design stage. At a technical level, NGS has the potential to revolutionise laboratory practice and approaches to cancer treatment. However, use of this technology requires careful planning and implementation if one is to avoid technical and ethical quagmires. Finally, with FDA regulation of companion diagnostics one may be limited to therapy specific assays.


Assuntos
Oncologia/métodos , Técnicas de Diagnóstico Molecular , Neoplasias/diagnóstico , Animais , Biomarcadores Tumorais/metabolismo , Regulamentação Governamental , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Oncologia/tendências , Neoplasias/genética , Estados Unidos , United States Food and Drug Administration
16.
Front Mol Biosci ; 1: 18, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-25988159

RESUMO

Modern pathology laboratories and in particular high throughput laboratories such as clinical chemistry have developed a reliable system for statistical process control (SPC). Such a system is absent from the majority of molecular laboratories and where present is confined to quantitative assays. As the inability to apply SPC to an assay is an obvious disadvantage this study aimed to solve this problem by using a frequency estimate coupled with a confidence interval calculation to detect deviations from an expected mutation frequency. The results of this study demonstrate the strengths and weaknesses of this approach and highlight minimum sample number requirements. Notably, assays with low mutation frequencies and detection of small deviations from an expected value require greater sample numbers to mitigate a protracted time to detection. Modeled laboratory data was also used to highlight how this approach might be applied in a routine molecular laboratory. This article is the first to describe the application of SPC to qualitative laboratory data.

17.
Eur Arch Otorhinolaryngol ; 271(8): 2253-9, 2014 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-24121822

RESUMO

Radiotherapy combined with three weekly 100 mg/m2 of cisplatin is the accepted standard of care in head and neck squamous cell carcinoma. However, this regimen is associated with severe toxicities with devastating effects on patients. Alternative protocols like weekly 40 mg/m2 have been used in an attempt to reduce toxicities. The main objective of the present study is to identify the dose intensities and toxicities of weekly cisplatin in patients treated in a tertiary centre over a 12 month period. Included patients had squamous cell carcinoma arising in the oral cavity, oropharynx, larynx, or hypopharynx. Patients were excluded if they had nasopharyngeal squamous cell carcinoma, distant metastasis or if they had prior treatment for head and neck cancer excluding neck dissection. During the study period, 52 patients met the inclusion criteria and their data were retrospectively obtained from the patients' database of St James hospital, Dublin. The median age of the study cohort was 54 years (range 33-73). Of the patients, 40 (76.9 %) were male and 12 (20.1 %) were female. The primary tumour sites were as follows: oral cavity and oropharynx in 38 (73 %), larynx in 10 (19 %), and hypopharynx in 4 (8 %). In total, 33 (63.5 %) patients had stage IV disease, while 19 (36.5 %) had stage III disease. Treatment was definitive in 35 (67 %) patients and adjuvant in 17 (35 %). Full-dose radiotherapy was achieved in 50 (96 %) patients. Only 22 (42.3 %) patients completed the intended six cycles of chemotherapy. Cumulative dose of 200 mg/m2 or more was reached in 37 (71 %) patients. The acute adverse effects included grades 3 and 4 mucositis, which occurred in 22 (43.3 %) and 6 patients (12 %), respectively. Grade 3 and 4 neutropenia occurred in six (11.5 %) and three (5.7 %) patients, respectively. The only other haematological toxicity was grade 3 anaemia in 20 (38.4 %) patients. There was no grade 3 or 4 renal toxicity among the study cohort, although grade 2 was observed in six (11.5 %) patients. Death occurred in one patient due to neutropenic septicaemia. In conclusion, weekly cisplatin is associated with moderate to severe toxicities and might lead to suboptimal chemotherapy delivery. More prospective clinical studies are required to determine the optimal chemoradiation regimen in head and neck squamous cell carcinoma.


Assuntos
Carcinoma de Células Escamosas/radioterapia , Cisplatino/administração & dosagem , Neoplasias de Cabeça e Pescoço/radioterapia , Centros de Atenção Terciária , Adulto , Idoso , Antineoplásicos/administração & dosagem , Carcinoma de Células Escamosas/tratamento farmacológico , Quimiorradioterapia , Esquema de Medicação , Feminino , Neoplasias de Cabeça e Pescoço/tratamento farmacológico , Humanos , Masculino , Pessoa de Meia-Idade , Estudos Retrospectivos , Carcinoma de Células Escamosas de Cabeça e Pescoço
19.
Immunome Res ; 4: 6, 2008 Nov 26.
Artigo em Inglês | MEDLINE | ID: mdl-19036163

RESUMO

BACKGROUND: Class II Major Histocompatibility Complex (MHC) molecules have an open-ended binding groove which can accommodate peptides of varying lengths. Several studies have demonstrated that peptide flanking residues (PFRs) which lie outside the core binding groove can influence peptide binding and T cell recognition. By using data from the AntiJen database we were able to characterise systematically the influence of PFRs on peptide affinity for MHC class II molecules. RESULTS: By analysing 1279 peptide elongation events covering 19 distinct HLA alleles it was observed that, in general, peptide elongation resulted in increased MHC class II molecule affinity. It was also possible to determine an optimal peptide length for MHC class II affinity of approximately 18-20 amino acids; elongation of peptides beyond this length resulted in a null or negative effect on affinity. CONCLUSION: The observed relationship between peptide length and MHC class II affinity has significant implications for the design of vaccines and the study of the epitopic basis of immunological disease.

20.
Proc Nutr Soc ; 67(4): 395-403, 2008 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-18847516

RESUMO

The Human Genome Project and rapid advances in high-throughput molecular technologies are providing an unprecedented opportunity to advance the understanding of the common polygenic diet-related diseases, including obesity, the metabolic syndrome, type 2 diabetes mellitus, CVD and some cancers. In particular, transcriptomic approaches that allow multiple simultaneous gene-expression profiles facilitate the characterisation of metabolic perturbations that underlie diet-related pathologies. The present paper will focus on 'transcriptomic signatures' to characterise and understand the molecular mechanisms that accurately reflect 'metabolic health'.


Assuntos
Síndrome Metabólica/genética , Nutrigenômica/métodos , Biologia Computacional , Gorduras na Dieta/administração & dosagem , Humanos , Síndrome Metabólica/metabolismo , Transcrição Genética
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