scholarly journals Natural history bycatch: a pipeline for identifying metagenomic sequences in RADseq data

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4662 ◽  
Author(s):  
Iris Holmes ◽  
Alison R. Davis Rabosky
Keyword(s):  
Restriction Site ◽  
Tissue Sample ◽  
Host Tissue ◽  
Blood Parasites ◽  
Tissue Banks ◽  
Target Tissue ◽  
Tissue Samples ◽  
Reduced Representation ◽  
Assembly Pipeline ◽  
Hind Gut

Background Reduced representation genomic datasets are increasingly becoming available from a variety of organisms. These datasets do not target specific genes, and so may contain sequences from parasites and other organisms present in the target tissue sample. In this paper, we demonstrate that (1) RADseq datasets can be used for exploratory analysis of tissue-specific metagenomes, and (2) tissue collections house complete metagenomic communities, which can be investigated and quantified by a variety of techniques. Methods We present an exploratory method for mining metagenomic “bycatch” sequences from a range of host tissue types. We use a combination of the pyRAD assembly pipeline, NCBI’s blastn software, and custom R scripts to isolate metagenomic sequences from RADseq type datasets. Results When we focus on sequences that align with existing references in NCBI’s GenBank, we find that between three and five percent of identifiable double-digest restriction site associated DNA (ddRAD) sequences from host tissue samples are from phyla to contain known blood parasites. In addition to tissue samples, we examine ddRAD sequences from metagenomic DNA extracted snake and lizard hind-gut samples. We find that the sequences recovered from these samples match with expected bacterial and eukaryotic gut microbiome phyla. Discussion Our results suggest that (1) museum tissue banks originally collected for host DNA archiving are also preserving valuable parasite and microbiome communities, (2) that publicly available RADseq datasets may include metagenomic sequences that could be explored, and (3) that restriction site approaches are a useful exploratory technique to identify microbiome lineages that could be missed by primer-based approaches.

Biomedical applications: Pitfalls in the practice

1994 ◽  
Vol 52 ◽  
pp. 378-379
Author(s):  
J. D. Shelburne ◽  
Peter Ingram ◽  
Victor L. Roggli ◽  
Ann LeFurgey
Keyword(s):  
Operating Room ◽  
Liquid Nitrogen ◽  
Lung Tissue ◽  
Biomedical Applications ◽  
Microprobe Analysis ◽  
Tissue Sample ◽  
Cellular Level ◽  
Tissue Samples ◽  
Asbestos Fibers

At present most medical microprobe analysis is conducted on insoluble particulates such as asbestos fibers in lung tissue. Cryotechniques are not necessary for this type of specimen. Insoluble particulates can be processed conventionally. Nevertheless, it is important to emphasize that conventional processing is unacceptable for specimens in which electrolyte distributions in tissues are sought. It is necessary to flash-freeze in order to preserve the integrity of electrolyte distributions at the subcellular and cellular level. Ideally, biopsies should be flash-frozen in the operating room rather than being frozen several minutes later in a histology laboratory. Electrolytes will move during such a long delay. While flammable cryogens such as propane obviously cannot be used in an operating room, liquid nitrogen-cooled slam-freezing devices or guns may be permitted, and are the best way to achieve an artifact-free, accurate tissue sample which truly reflects the in vivo state. Unfortunately, the importance of cryofixation is often not understood. Investigators bring tissue samples fixed in glutaraldehyde to a microprobe laboratory with a request for microprobe analysis for electrolytes.

scholarly journals The Dutch National TissueArchive Portal enables efficient, consistent, and transparent procurement of diagnostic tissue samples for scientific use

2021 ◽  
Author(s):  
Robin Verjans ◽  
Annette H. Bruggink ◽  
Robby Kibbelaar ◽  
Jos Bart ◽  
Aletta Debernardi ◽  
...  
Keyword(s):  
The Netherlands ◽  
Tissue Sample ◽  
Ffpe Tissue ◽  
Tissue Samples ◽  
Internet Portal ◽  
Formalin Fixed Paraffin ◽  
Practical Support ◽  
Formalin Fixed Paraffin Embedded ◽  
The Rich ◽  
Formalin Fixed

AbstractBiobanks play a crucial role in enabling biomedical research by facilitating scientific use of valuable human biomaterials. The PALGA foundation—a nationwide network and registry of histo- and cytopathology in the Netherlands—was established to promote the provision of data within and between pathology departments, and to make the resulting knowledge available for healthcare. Apart from the pathology data, we aimed to utilize PALGA’s nationwide network to find and access the rich wealth of Formalin-Fixed Paraffin-Embedded (FFPE) tissue samples for scientific use.  We implemented the Dutch National TissueArchive Portal (DNTP) to utilize PALGA’s nationwide network for requesting FFPE tissue samples. The DNTP consists of (1) a centrally organized internet portal to improve the assessing, processing, harmonization, and monitoring of the procurement process, while (2) dedicated HUB-employees provide practical support at peripheral pathology departments. Since incorporation of the DNTP, both the number of filed requests for FFPE tissue samples and the amount of HUB-mediated support increased 55 and 29% respectively. In line, the sample procurement duration time decreased significantly (− 47%). These findings indicate that implementation of the DNTP improved the frequency, efficiency, and transparency of FFPE tissue sample procurement for research in the Netherlands. To conclude, the need for biological resources is growing persistently to enable precision medicine. Here, we access PALGA’s national, pathology network by implementation of the DNTP to allow for efficient, consistent, and transparent exchange of FFPE tissue samples for research across the Netherlands.

A study on the genomic alterations of transformation from colorectal adenoma to colorectal cancer.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. e15607-e15607
Author(s):  
Qingjian Chen ◽  
Pan Yang ◽  
Linna Luo ◽  
Wenhua Fan ◽  
Chen Wei ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Cancer Patients ◽  
Tissue Sample ◽  
Intraepithelial Neoplasia ◽  
Stage I ◽  
Tissue Samples ◽  
Diagnostic Potential ◽  
Notch Pathways ◽  
Colorectal Cancer Patients ◽  
Villous Adenomas

e15607 Background: Colorectal cancer is one of the most common malignancies worldwide. Approximately 85% of colorectal cancers are thought to result from adenoma. However, the molecular mechanism of adenoma transformation into colorectal cancer is still unclear. Methods: Ninety-nine adenoma patients aged from 25 to 78 years old were enrolled in this study. We collected tissue sample from each patient and 77 matched blood samples. Pathological subtypes included tubular villous adenomas, villous adenomas, tubular adenomas, high-grade intraepithelial neoplasia, and polyps. Eighty-one stage I colorectal cancer patients (CRC I) were also enrolled in this study. All samples underwent Next-generation sequencing with a panel of 405 cancer related genes. Results: Mutational profiles of adenoma and CRC I patients were compared. The top 5 most frequently mutated genes in adenoma were APC (71%), KRAS (41%), ATM (33%), RIF1 (31%), SYNE1 (28%). While in CRC I patients, top 5 mutated genes were APC (78%), TP53 (57%), TTN (35%), KRAS (33%) and TCF7L2 (22%). There were significant differences between TP53 and TTN by chi-square test. The frequency, number and TMB of mutations in stage I colorectal cancer patients were significantly higher than those in various adenoma subtypes. Stage I colorectal cancer patients have more mutated genes enriched in the Wnt and Notch pathways than adenoma patients. We analyzed mutation signatures in CRC I and adenoma patients, and CRC I were more focused on mutation signatures of mismatch repair such as signature 1, signature 6, signature 10, and signature 15. A total of 391 mutations were identified in tissue samples, while 130 mutations were found in plasma cell-free DNA, with 116 mutations shared between them. The two genes with the highest consistency between tissue and blood were PAX7 and KMT2D. Conclusions: TP53 and TTN are associated with the transition from CRC I to adenoma, and Wnt and Notch pathways may also be involved. PAX7 and KMT2D mutations frequently found in adenoma tissue and blood cfDNA demonstrate the diagnostic potential of these two genes in clinic.

scholarly journals Correlation of Ki-67 indices from biopsy and resection specimens of neuroendocrine tumours

2017 ◽  
Vol 99 (3) ◽  
pp. 193-197 ◽  
Author(s):  
J Barnes ◽  
SJ Johnson ◽  
JJ French
Keyword(s):  
Neuroendocrine Tumours ◽  
Tissue Sample ◽  
Cohort Analysis ◽  
Tumour Grade ◽  
Tertiary Referral Centre ◽  
Ki 67 ◽  
Tissue Samples ◽  
Tumour Grading ◽  
Retrospective Cohort Analysis ◽  
Resection Specimen

INTRODUCTION Neuroendocrine tumours (NETs) are a heterogeneous group of tumours with a highly variable presentation and prognosis. Management decisions are complex. Ki-67 levels in tissue samples are a key indicator used to grade tumours and guide treatment. This study assessed whether the Ki-67 index and tumour grade generated from tissue samples correlated with that assessed in resection specimens. METHODS This was a retrospective cohort analysis of all patients who had both a tissue sample and a resection specimen analysed in our trust, a tertiary referral centre, during 2012 and 2013. RESULTS Data from 36 patients were reviewed. Ki-67 indices from tissue samples and resection specimens showed strong correlation (r=0.95, p<0.001). Tumour grading was the same in the tissue sample and resection specimens for 22 patients (61.1%). In four patients (11.1%), the tissue sample overestimated the grade while in ten (27.8%), the sample underestimated the grade. CONCLUSIONS In most cases, the Ki-67 index and tumour grade from the tissue sample matched that of the resection specimen. However, in nearly 40% of cases, the tissue sample grading did not match the resection tumour grading. In the majority of these, the tissue sample underestimated disease activity. A low Ki-67 index in a tissue sample should therefore be taken as provisional and should not, in isolation, persuade clinicians to choose a more conservative treatment approach if there is clinical, biochemical or radiological evidence suggestive of a more aggressive disease pathology.

Application of Restriction Site-Associated DNA Sequencing (RAD-Seq) for Copy Number Variation and Triploidy Detection in Human

2021 ◽  
pp. 1-8
Author(s):  
Jian-Chun He ◽  
Shao-Ying Li ◽  
Wen-Zhi He ◽  
Jia-Jia Xian ◽  
Xiao-Yan Ma ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Cell Lines ◽  
Genome Sequencing ◽  
Copy Number ◽  
Restriction Site ◽  
Chromosomal Abnormalities ◽  
Copy Number Variations ◽  
Str Analysis ◽  
Tissue Samples ◽  
Low Pass

At present, low-pass whole-genome sequencing (WGS) is frequently used in clinical research and in the screening of copy number variations (CNVs). However, there are still some challenges in the detection of triploids. Restriction site-associated DNA sequencing (RAD-Seq) technology is a reduced-representation genome sequencing technology developed based on next-generation sequencing. Here, we verified whether RAD-Seq could be employed to detect CNVs and triploids. In this study, genomic DNA of 11 samples was extracted employing a routine method and used to build libraries. Five cell lines of known karyotypes and 6 triploid abortion tissue samples were included for RAD-Seq testing. The triploid samples were confirmed by STR analysis and also tested by low-pass WGS. The accuracy and efficiency of detecting CNVs and triploids by RAD-Seq were then assessed, compared with low-pass WGS. In our results, RAD-Seq detected 11 out of 11 (100%) chromosomal abnormalities, including 4 deletions and 1 aneuploidy in the purchased cell lines and all triploid samples. By contrast, these triploids were missed by low-pass WGS. Furthermore, RAD-Seq showed a higher resolution and more accurate allele frequency in the detection of triploids than low-pass WGS. Our study shows that, compared with low-pass WGS, RAD-Seq has relatively higher accuracy in CNV detection at a similar cost and is capable of identifying triploids. Therefore, the application of this technique in medical genetics has a significant potential value.

A Microdissection and Molecular Genotyping Assay to Confirm the Identity of Tissue Floaters in Paraffin-Embedded Tissue Blocks

2003 ◽  
Vol 127 (2) ◽  
pp. 213-217 ◽  
Author(s):  
Jennifer L. Hunt ◽  
Patricia Swalsky ◽  
E. Sasatomi ◽  
Laura Niehouse ◽  
Anke Bakker ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Tissue Sample ◽  
Small Samples ◽  
Allelic Loss ◽  
Chain Reaction ◽  
Neoplastic Tissue ◽  
Tissue Samples ◽  
Genotyping Assay ◽  
Tissue Identification ◽  
Polymerase Chain

Abstract Context.—A recurring problem in surgical pathology practice is specimen mix-up and floater contamination. While many cases can be resolved histologically, a significant number remain unclear and may have serious clinical and medicolegal implications. Objectives.—To design a microdissection and genotyping assay to identify contaminating floater tissues in paraffin-embedded tissues that is optimized for small samples, and to use the assay to resolve a series of clinical cases with floater tissues. Materials and Methods.—Twenty-one cases of possible tissue floater contamination in paraffin-embedded tissue blocks were included. Using 4 unstained, 4-μm-thick histologic sections, multiple sites were microdissected under direct visualization either by hand or by laser capture microdissection. Nonneoplastic and neoplastic tissues were sampled. Polymerase chain reaction was performed for a panel of 10 polymorphic microsatellite markers at 1p34, 3p26, 5q21, 9p21, 10q23, and 17p13. Allele size and content were analyzed semiquantitatively by fluorescent capillary electrophoresis, and the genotypes for the tissues in the paraffin-embedded tissue blocks were compared for identity. Results.—Tissue identification was successful in all cases, despite small tissue sample size and fixation effects. Comparative analysis of neoplastic tissue floaters and the presumptive source tumor was performed when possible to control for possible allelic loss or microsatellite instability. Conclusions.—Microdissection and genotyping are effective and reliable means to objectively resolve problems of possible floater contamination. Even minute tissue samples provide sufficient DNA template for polymerase chain reaction microsatellite analysis. Because of the potential clinical implications of floaters, we recommend that all suspected floaters that would change a diagnosis from benign to malignant be subjected to genotyping assay to confirm the identity of the floater tissue.

Tissue engineering

2013 ◽  
pp. 664-668
Author(s):  
Andrew McCaskie ◽  
Paul Genever ◽  
Cosimo De Bari
Keyword(s):  
Tissue Engineering ◽  
Host Tissue ◽  
Target Tissue ◽  
Cell Therapies ◽  
Cell Matrix ◽  
Wide Range ◽  
Regenerative Approach ◽  
Great Relevance ◽  
Functional Interface

The field of tissue engineering has developed rapidly over the last few decades and is of great relevance to musculoskeletal therapy and intervention. Tissue engineering strategies are often considered in a simplified form in terms of cells, scaffolds, and additional factors, although it should be noted that successful translation of such a strategy is more complex. There are many variations of usage and combination and it is not necessary for all three to be provided by the proposed treatment. However, the regenerative approach must produce both the quantity and quality of target tissue at the level of the cell, matrix, and environment. Moreover, the regenerated tissue must interact with the host tissue with a seamless biological and functional interface. Tissue engineering, regenerative medicine, and cell therapies have developed significantly over the last few decades and are applicable to a wide range of musculoskeletal applications. Many strategies have been identified that would potentially benefit patients but the future will require successful translation from the laboratory into clinical practice. It is important to identify clinical targets where there is both clinical need and an informed view that the approach is likely to be successful.

Gas-Liquid Chromatographic Determination of Sodium Fluoroacetate (Compound 1080)

1980 ◽  
Vol 63 (1) ◽  
pp. 49-55
Author(s):  
Iwao Okuno ◽  
Dennis L Meeker
Keyword(s):  
Liquid Chromatography ◽  
Tissue Sample ◽  
Chromatographic Determination ◽  
Gas Liquid Chromatography ◽  
Tissue Samples ◽  
Fluoroacetic Acid ◽  
Pentafluorobenzyl Bromide ◽  
Liquid Chromatographic Determination ◽  
Liquid Chromatographic

Abstract An analytical method is described for the determination of Compound 1080 (sodium fluoroacetate) residues in 1–10 g tissue. Sample extracts of tissues are cleaned up with silica gel, and Compound 1080 (as fluoroacetic acid) is separated by a micro-distillation procedure. The fluoroacetic acid in the distillate is derivatized with pentafluorobenzyl bromide to form pentafluorobenzyl fluoroacetate which is measured by electron capture gas-liquid chromatography. Recoveries of sodium fluoroacetate from fortified tissue samples averaged about 25%. Despite the limited recoveries, results were quite reproducible, and levels as low at 2 ppm were determined in fortified 1 g samples, and 0.2 ppm in 10 g samples. The method is relatively simple and has been used routinely in our laboratory for the analysis of various types of samples such as grain, and tissues from birds, rodents, and larger animals.

scholarly journals 1450-1545 Young Investigator Awards & Presentations Basic/Translational Exploring cellular subpopulations in glioblastoma and matched organoids using single-cell RNA-seq 52

2018 ◽  
Vol 45 (S3) ◽  
pp. S13-S14
Author(s):  
VG LeBlanc ◽  
D Trinh ◽  
M Hughes ◽  
I Luthra ◽  
D Livingstone ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Tissue Sample ◽  
Expression Patterns ◽  
Model Systems ◽  
Sequencing Data ◽  
Tissue Samples ◽  
Original Tumour ◽  
Current Therapies ◽  
Intratumoural Heterogeneity

Glioblastomas (GBMs) account for nearly half of all primary malignant brain tumours, and current therapies are often only marginally effective. Our understanding of the underlying biology of these tumours and the development of new therapies have been complicated in part by widespread inter- and intratumoural heterogeneity. To characterize this heterogeneity, we performed regional subsampling of primary glioblastomas and derived organoids from these tissue samples. We then performed single-cell RNA-sequencing (scRNA-seq) on these primary regional subsamples and 1-3 matched organoids per sample. We have profiled samples from six tumour sets to date and have obtained sequencing data for 21,234 primary tissue cells and 14,742 organoid cells. While the most apparent differences in gene expression appear to be between individual tumours, we were also able to identify similar cellular subpopulations across tissue samples and across organoids. Importantly, organoids derived from the same tissue sample appeared to be composed of similar cellular subpopulations and were highly comparable to each other, indicating that replicate organoids faithfully represent the original tumour tissue. Overall, our scRNA-seq approach will help evaluate the utility of tumour-derived organoids as model systems for GBM and will aid in identifying cellular subpopulations defined by gene expression patterns, both in primary GBM regional subsamples and their associated organoids. These analyses will allow for the characterization of clonal or subclonal populations that are likely to respond to different therapeutic approaches and may also uncover novel therapeutic targets previously unrevealed through bulk analyses.

scholarly journals Heart and Brain Tissue Banks for Research on Co-Occurring Cardiovascular and Neurological/Psychiatric Disorders

2009 ◽  
Vol 2009 ◽  
pp. 1-3 ◽  
Author(s):  
Milos D. Ikonomovic
Keyword(s):  
Brain Tissue ◽  
Neurological Disorders ◽  
Epidemiological Studies ◽  
Biological Research ◽  
Tissue Banks ◽  
Practical Reasons ◽  
Tissue Storage ◽  
Tissue Samples ◽  
Organ Systems ◽  
Clinical Records

Epidemiological studies point to a strong and possibly causal association of psychiatric and neurological disorders with cardiovascular disease (CVD). Mechanistic links between these co-occurring illnesses are not well understood. Better insight into their relationship could help identify novel diagnostic markers and therapeutic targets. For successful translation of basic biomedical research into clinical practice, analyses of postmortem human tissues are essential. However, current tissue banks dedicated to psychiatric and neurological research collect only brain tissue samples deemed most important to the institution's participating investigators. While this practice is often dictated by budget constraints, restricted tissue storage space and other practical reasons, it limits the ability of the biological research community to access and study multiple organ systems relevant to cardiovascular and neuronal systems dysfunction. This problem is worsened when clinical records pertaining to coexistent systemic pathology are not available. To promote further understanding of co-occurring CVD and psychiatric/neurological disorders, efforts should be made to support tissue banks that harvest heart, coronary arteries, and aorta samples as well as brain tissue, from the same subjects.

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