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Ticks and Tick-borne Diseases Mar 2022Molecular biology has revolutionized all aspects of biological research including diagnostics, taxonomy, and systematics. Even so, the critique that molecular methods... (Review)
Review
Molecular biology has revolutionized all aspects of biological research including diagnostics, taxonomy, and systematics. Even so, the critique that molecular methods cannot truly confirm the presence of parasites, or identify new species remains prevalent and arguably relevant. The current review considers the ability of molecular diagnostic methods to detect parasites and the relevance of molecular sequences to identify species and attempt to answer the question of whether molecular data ever lie. It shows that well-validated molecular assays should be able to accurately confirm the presence of parasites in a host or vector species, while well-selected sequences should conclusively identify existing or new species. It addresses pitfalls in the use of molecular techniques and how these can be avoided. It also considers the self-correcting nature of science and the caveat that a scientist should use all tools at their disposal to uncover the mysteries of nature.
Topics: Animals; Parasites; Pathology, Molecular
PubMed: 35078135
DOI: 10.1016/j.ttbdis.2022.101907 -
The Journal of Molecular Diagnostics :... Nov 2015Next-generation sequencing (NGS) technologies are increasingly being used for diagnosis and monitoring of infectious diseases. Herein, we review the application of NGS... (Review)
Review
Next-generation sequencing (NGS) technologies are increasingly being used for diagnosis and monitoring of infectious diseases. Herein, we review the application of NGS in clinical microbiology, focusing on genotypic resistance testing, direct detection of unknown disease-associated pathogens in clinical specimens, investigation of microbial population diversity in the human host, and strain typing. We have organized the review into three main sections: i) applications in clinical virology, ii) applications in clinical bacteriology, mycobacteriology, and mycology, and iii) validation, quality control, and maintenance of proficiency. Although NGS holds enormous promise for clinical infectious disease testing, many challenges remain, including automation, standardizing technical protocols and bioinformatics pipelines, improving reference databases, establishing proficiency testing and quality control measures, and reducing cost and turnaround time, all of which would be necessary for widespread adoption of NGS in clinical microbiology laboratories.
Topics: Communicable Diseases; Computational Biology; High-Throughput Nucleotide Sequencing; Humans; Laboratory Proficiency Testing; Pathology, Molecular
PubMed: 26433313
DOI: 10.1016/j.jmoldx.2015.07.004 -
Pathology Oct 2011
Topics: Cytodiagnosis; Humans; Pathology, Clinical; Pathology, Molecular; Pathology, Surgical
PubMed: 21921731
DOI: 10.1097/PAT.0b013e32834b6aae -
American Journal of Clinical Pathology Jul 2022To overcome the challenges associated with molecular and cytogenetic (MG) education in hematopathology (HP), a monthly joint HP/MG conference with specific curricular...
OBJECTIVES
To overcome the challenges associated with molecular and cytogenetic (MG) education in hematopathology (HP), a monthly joint HP/MG conference with specific curricular goals was established and evaluated by the participants.
METHODS
All cases from the HP/MG conference over 56 months were reviewed. To assess the educational impact, a survey was distributed to current/former HP/molecular genetic pathology fellows and faculty.
RESULTS
During the study period, a total of 252 cases covering MG testing considered important for HP fellowship training were presented. The 100 most recent cases since 2018 discussed findings of diagnostic (85%), prognostic (40%), or therapeutic (10%) importance. A broad range of technologies were discussed such as karyotyping, cytogenetic fluorescence in situ hybridization studies, microarrays, polymerase chain reaction-based tests, next-generation sequencing, and Sanger sequencing. Twenty-three (95.8%) of 24 survey respondents agreed that the conference achieved all of its goals, and all agreed it was worth implementing.
CONCLUSIONS
This educationally based HP/MG conference supplements existing rotations, didactic presentations, and consensus case conferences and enhances MG education in HP without excessive time commitment or need for extensive in-house MG testing. It also contributes to enhancing HP knowledge among the MG faculty and fellows.
Topics: Curriculum; Education, Medical, Graduate; Fellowships and Scholarships; Humans; In Situ Hybridization, Fluorescence; Pathology, Molecular
PubMed: 35142790
DOI: 10.1093/ajcp/aqac011 -
Clinics in Laboratory Medicine Sep 2022
Topics: Humans; Medical Oncology; Neoplasms; Pathology, Molecular
PubMed: 36150827
DOI: 10.1016/j.cll.2022.06.001 -
Annales de Pathologie Apr 2010
Topics: Biomarkers, Tumor; Female; Histocytological Preparation Techniques; Humans; Male; Neoplasms; Pathology, Clinical; Pathology, Molecular; Specimen Handling
PubMed: 20451061
DOI: 10.1016/j.annpat.2010.03.014 -
The Lancet. Respiratory Medicine Jan 2020
Topics: Cystic Fibrosis; Humans; Pathology, Molecular
PubMed: 31570319
DOI: 10.1016/S2213-2600(19)30333-9 -
Seminars in Cancer Biology Oct 2011Genetically engineered mouse models (GEMM) have made major contributions to a molecular understanding of several adult cancers and these results are increasingly being... (Review)
Review
Genetically engineered mouse models (GEMM) have made major contributions to a molecular understanding of several adult cancers and these results are increasingly being translated into the pre-clinical setting where GEMM will very likely make a major impact on the development of targeted therapeutics in the near future. The relationship of pediatric cancers to altered developmental programs, and their genetic simplicity relative to adult cancers provides unique opportunities for the application of new advances in GEMM technology. In neuroblastoma the well-characterized TH-MYCN GEMM is increasingly used for a variety of molecular-genetic, developmental and pre-clinical therapeutics applications. We discuss: the present and historical application of GEMM to neuroblastoma research, future opportunities, and relevant targets suitable for new GEMM strategies in neuroblastoma. We review the potential of these models to contribute both to an understanding of the developmental nature of neuroblastoma and to improved therapy for this disease.
Topics: Animals; Child; Disease Models, Animal; Genetic Engineering; Humans; Mice; Neuroblastoma; Pathology, Molecular
PubMed: 21958944
DOI: 10.1016/j.semcancer.2011.09.011 -
Virchows Archiv : An International... Jan 2016The aim of accreditation of a pathology laboratory is to control and optimize, in a permanent manner, good professional practice in clinical and molecular pathology, as... (Review)
Review
The aim of accreditation of a pathology laboratory is to control and optimize, in a permanent manner, good professional practice in clinical and molecular pathology, as defined by internationally established standards. Accreditation of a pathology laboratory is a key element in fine in increasing recognition of the quality of the analyses performed by a laboratory and in improving the care it provides to patients. One of the accreditation standards applied to clinical chemistry and pathology laboratories in the European Union is the ISO 15189 norm. Continued functioning of a pathology laboratory might in time be determined by whether or not it has succeeded the accreditation process. Necessary requirements for accreditation, according to the ISO 15189 norm, include an operational quality management system and continuous control of the methods used for diagnostic purposes. Given these goals, one would expect that all pathologists would agree on the positive effects of accreditation. Yet, some of the requirements stipulated in the accreditation standards, coming from the bodies that accredit pathology laboratories, and certain normative issues are perceived as arduous and sometimes not adapted to or even useless in daily pathology practice. The aim of this review is to elaborate why it is necessary to obtain accreditation but also why certain requirements for accreditation might be experienced as inappropriate.
Topics: Accreditation; European Union; Humans; Laboratories; Pathology, Clinical; Pathology, Molecular
PubMed: 26334197
DOI: 10.1007/s00428-015-1837-1 -
Cancer Research Aug 2016The Cancer Genome Atlas (TCGA) project has generated abundant genomic data for human cancers of various histopathology types and enabled exploring cancer molecular...
The Cancer Genome Atlas (TCGA) project has generated abundant genomic data for human cancers of various histopathology types and enabled exploring cancer molecular pathology per big data approach. We developed a new algorithm based on most differentially expressed genes (DEG) per pairwise comparisons to calculate correlation coefficients to be used to quantify similarity within and between cancer types. We systematically compared TCGA cancers, demonstrating high correlation within types and low correlation between types, thus establishing molecular specificity of cancer types and an alternative diagnostic method largely equivalent to histopathology. Different coefficients for different cancers in study may reveal that the degree of the within-type homogeneity varies by cancer types. We also performed the same calculation using the TCGA-derived DEGs on patient-derived xenografts (PDX) of different histopathology types corresponding to the TCGA types, as well as on cancer cell lines. We, for the first time, demonstrated highly similar patterns for within- and between-type correlation between PDXs and patient samples in a systematic study, confirming the high relevance of PDXs as surrogate experimental models for human diseases. In contrast, cancer cell lines have drastically reduced expression similarity to both PDXs and patient samples. The studies also revealed high similarity between some types, for example, LUSC and HNSCC, but low similarity between certain subtypes, for example, LUAD and LUSC. Our newly developed algorithm seems to be a practical diagnostic method to classify and reclassify a disease, either human or xenograft, with better accuracy than traditional histopathology. Cancer Res; 76(16); 4619-26. ©2016 AACR.
Topics: Algorithms; Animals; Cell Line, Tumor; Computational Biology; Gene Expression Profiling; Heterografts; Humans; Mice; Neoplasms; Oligonucleotide Array Sequence Analysis; Pathology, Molecular; Transcriptome
PubMed: 27325646
DOI: 10.1158/0008-5472.CAN-15-3245