Name: comparative lesions analysis through a targeted sequencing approach
Uploaded: 2019-11-05T13:00:00
Description: Watch this Scientific Journal Video about Comparative Lesions Analysis Through a Targeted Sequencing Approach at JoVE.com

The study was supported by the Italian Cancer Genome Project (Grant No. FIRB RBAP10AHJB), Associazione Italiana Ricerca Cancro (AIRC; Grant No. 12182 to AS and 18178 to VC), FP7 European Community Grant (Cam-Pac No 602783 to AS). The funding agencies had no role in the collection, analysis and interpretation of data or in the writing of the manuscript.

The material used in the study was collected under a specific protocol, which was approved by the local ethics committee. Written informed consent from all patients was available.
1. Histological and immunophenotypical revision of tissue specimens
NOTE: An expert pathologist is responsible for activities described hereafter.
<ol>
	<li>Histopathological revision of selected cases according to well-established diagnostic criteria.
	<ol>
		<li>Use the microtome to cu...

<ol>
	<li>Koboldt, D. C., Steinberg, K. M., Larson, D. E., Wilson, R. K., Mardis, E. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+next-generation+sequencing+revolution+and+its+impact+on+genomics.">The next-generation sequencing revolution and its impact on genomics.</a> Cell. 155 (1), 27-38 (2013).</li><li>McGranahan, N., Swanton, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Clonal+Heterogeneity+and+Tumor+Evolution:+Past,+Present,+and+the+Future.">Clonal Heterogeneity and Tumor Evolution: Past, Present, and the Future.</a> Cell. 168 (4), 613-628 (2017).</li><li>Stratton, M. R., Campbell, P. J., Futreal, P. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+cancer+genome.">The cancer genome.</a> Nature. 458 (7239), 719-724 (2009).</li><li>Makohon-Moore, A. P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Limited+heterogeneity+of+known+driver+gene+mutations+among+the+metastases+of+individual+patients+with+pancreatic+cancer.">Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer.</a> Nature Genetics. 49 (3), 358-366 (2017).</li><li>Seyfried, T. N., Huysentruyt, L. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=On+the+origin+of+cancer+metastasis.">On the origin of cancer metastasis.</a> Critical reviews in oncogenesis. 18 (1-2), 43-73 (2013).</li><li>McLaren, W., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Deriving+the+consequences+of+genomic+variants+with+the+Ensembl+API+and+SNP+Effect+Predictor.">Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor.</a> Bioinformatics. 26 (16), 2069-2070 (2010).</li><li>Robinson, J. T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Integrative+genomics+viewer.">Integrative genomics viewer.</a> Nature Biotechnology. 29 (1), 24-26 (2011).</li><li>Amato, E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+alterations+associated+with+metastases+of+solid+pseudopapillary+neoplasms+of+the+pancreas.">Molecular alterations associated with metastases of solid pseudopapillary neoplasms of the pancreas.</a> The Journal of Pathology. 247 (1), 123-134 (2019).</li><li>Mafficini, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reporting+tumor+molecular+heterogeneity+in+histopathological+diagnosis.">Reporting tumor molecular heterogeneity in histopathological diagnosis.</a> PLoS One. 9 (8), e104979 (2014).</li><li>Shi, W., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reliability+of+Whole-Exome+Sequencing+for+Assessing+Intratumor+Genetic+Heterogeneity.">Reliability of Whole-Exome Sequencing for Assessing Intratumor Genetic Heterogeneity.</a> Cell Reports. 25 (6), 1446-1457 (2018).</li><li>Simbolo, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DNA+qualification+workflow+for+next+generation+sequencing+of+histopathological+samples.">DNA qualification workflow for next generation sequencing of histopathological samples.</a> PLoS One. 8 (6), e62692 (2013).</li><li>Connor, A. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Integration+of+Genomic+and+Transcriptional+Features+in+Pancreatic+Cancer+Reveals+Increased+Cell+Cycle+Progression+in+Metastases.">Integration of Genomic and Transcriptional Features in Pancreatic Cancer Reveals Increased Cell Cycle Progression in Metastases.</a> Cancer Cell. 35 (2), 267-282 (2019).</li><li>Priestley, P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Pan-cancer+whole+genome+analyses+of+metastatic+solid+tumors.">Pan-cancer whole genome analyses of metastatic solid tumors.</a> bioRxiv. , (2018).</li></ol>

Our method enables the identification of molecular alterations involved in progression of solid tumors through integration of vertical data (i.e., morphology, DNA sequencing, and immunohistochemistry) from distinct lesions of a given patient. We demonstrated the capability of our method to detect clonal and subclonal events in a mutational silent tumor type (i.e., SPN, solid-pseudopapillary neoplasm of the pancreas) by interrogating the coding sequences of 409 cancer relevant genes8. An advantage ...

The advent of next generation sequencing (NGS) has revolutionized the way cancers are diagnosed and treated1. NGS coupled to multiregional sequencing have exposed a high degree of intra-tumoral heterogeneity (ITH) in solid tumors2, which explains in part the failure of targeted therapy due to the presence of subclones with differing drug sensitivity2. An important challenge posed by genome-wide sequencing studies is the necessity to distinguish between passenger (i.e., neutral) and driver mutations in individual cancers3. Several studies have indeed shown that, in certain tumors, passenger mutations account for the majority of ITH, while driver alterations tend to be conserved among lesions of the same individual4. It is also important to note that large mutational burden (as seen in lung cancers and melanoma) does not necessarily imply a large subclonal mutational burden2. Therefore, a high degree of ITH can be found in tumors with low mutational burden.
Metastases are responsible for more than 90% of cancer-related death worldwide5; therefore, capturing the mutational heterogeneity of driver genes among primary and metastatic lesions is critical to the design of effective therapies for advanced-stage diseases. Clinical sequencing is generally performed on nucleic acids from fixed tissues, which renders genome-wide exploration difficult because of poor DNA quality. On the other hand, the intent of clinical sequencing is to identify actionable mutations and/or mutations that might predict responsiveness/unresponsiveness to a given therapeutic regimen. As it stands, sequencing can be restricted to a smaller fraction of the genome for timely extraction of clinically relevant information. The transition from low-throughput DNA profiling (e.g., Sanger Sequencing) to NGS has rendered it possible to analyze hundreds of cancer-relevant genes at a high depth of coverage, which allows for the detection of subclonal events. Here, we report a method for comparative lesions analysis that allows for the identification of clonal and subclonal populations among different specimens from the same individual. The method described here integrates three well-established approaches (histological analysis, high-coverage multi-lesion sequencing, and immunophenotypic analyses) to predict functional consequences of the variations identified. The approach is schematically described in Figure 1 and has been applied to the study of 5 metastatic cases of solid pseudopapillary neoplasms (SPNs) of the pancreas. While we describe processing and analysis of formalin-fixed paraffin-embedded (FFPE) tissue specimens, the same procedure can be applied to genetic material from fresh-frozen tissue.

<table>
	<tbody>
		<tr>
			<td>2100 Bioanalyzer Instrument</td>
			<td>Agilent Technologies</td>
			<td>G2939BA</td>
			<td>&#160;Automated electrophoresis tool</td>
		</tr>
		<tr>
			<td>Agencourt AMPure XP Kit</td>
			<td>Fisher Scientific</td>
			<td>NC9959336</td>
			<td>Beads technology for the purification of PCR products; beads-based purification reagent</td>
		</tr>
		<tr>
			<td>Agilent High Sensitivity DNA Kit</td>
			<td>Agilent Technologies</td>
			<td>5067-4627</td>
			<td>Library quantification</td>
		</tr>
		<tr>
			<td>Anti-BAP1</td>
			<td>Santa Cruz Biotechnology</td>
			<td>sc-28383</td>
			<td>Antibody</td>
		</tr>
		<tr>
			<td>Anti-GLUT1</td>
			<td>Thermo Scientific</td>
			<td>RB-9052</td>
			<td>Antibody</td>
		</tr>
		<tr>
			<td>Anti-KDM6A</td>
			<td>Cell Signaling</td>
			<td>#33510</td>
			<td>Antibody</td>
		</tr>
		<tr>
			<td>Anti-p53</td>
			<td>Novocastra</td>
			<td>NCL-L-p53-DO7</td>
			<td>Antibody</td>
		</tr>
		<tr>
			<td>Anti-&#946;catenin</td>
			<td>Sigma-Aldrich</td>
			<td>C7207</td>
			<td>Antibody</td>
		</tr>
		<tr>
			<td>Blocking Solution</td>
			<td>home made</td>
			<td>-</td>
			<td>5 % Bovine serum albumin (BSA) in TBST</td>
		</tr>
		<tr>
			<td>Endogenous peroxidases inactivation solution</td>
			<td>home made</td>
			<td>-</td>
			<td>3% H2O2 in Tris-buffered saline (TBS) 1x</td>
		</tr>
		<tr>
			<td>Leica CV ultra</td>
			<td>Leica</td>
			<td>70937891</td>
			<td>Entellan mountin media</td>
		</tr>
		<tr>
			<td>Epitope Retrieval Solution 1</td>
			<td>Leica Biosystems</td>
			<td>AR9961</td>
			<td>Citrate based pH 6.0 epitope retrieval solution</td>
		</tr>
		<tr>
			<td>Epitope Retrieval Solution 2</td>
			<td>Leica Biosystems</td>
			<td>AR9640</td>
			<td>EDTA based pH 9.0 epitope retrieval solution</td>
		</tr>
		<tr>
			<td>Eppendorf 0.2 ml PCR Tubes, clear</td>
			<td>Eppendorf</td>
			<td>951010006</td>
			<td>Tubes</td>
		</tr>
		<tr>
			<td>Eppendorf DNA LoBind Tubes, 1.5 mL</td>
			<td>Eppendorf</td>
			<td>22431021</td>
			<td>Tubes</td>
		</tr>
		<tr>
			<td>Ethanol</td>
			<td>DIAPATH</td>
			<td>A0123</td>
			<td>IHC deparaffinization reagent</td>
		</tr>
		<tr>
			<td>ImmEdge Pen&#160;Hydrophobic&#160;Barrier&#160;Pen</td>
			<td>Vector Laboratories</td>
			<td>H&#173;4000</td>
			<td>Hydrophobic Pen</td>
		</tr>
		<tr>
			<td>ImmPACT DAB&#160;Peroxidase</td>
			<td>Vector Laboratories</td>
			<td>SK&#173;4105</td>
			<td>HRP substrate</td>
		</tr>
		<tr>
			<td>ImmPRESS Anti&#173;Rabbit&#160;Ig&#160;Reagent&#160;Peroxidase</td>
			<td>Vector Laboratories</td>
			<td>MP&#173;7401&#173;50</td>
			<td>Secondary antibody</td>
		</tr>
		<tr>
			<td>ImmPRESS Anti&#173;Mouse&#160;Ig&#160;Reagent&#160;Peroxidase</td>
			<td>Vector Laboratories</td>
			<td>MP&#173;7402&#173;50</td>
			<td>Secondary antibody</td>
		</tr>
		<tr>
			<td>Integrative Genomics Viewer (IGV)</td>
			<td>Broad Institute</td>
			<td>-</td>
			<td>https://software.broadinstitute.org/software/igv/home</td>
		</tr>
		<tr>
			<td>Ion AmpliSeq Comprehensive Cancer Panel</td>
			<td>Thermofisher Scientific</td>
			<td>4477685</td>
			<td>Multiplexed target selection of 409 cancer related gene. https://assets.thermofisher.com/TFS-Assets/CSD/Reference-Materials/ion-ampliseq-cancer-panel-gene-list.pdf</td>
		</tr>
		<tr>
			<td>Ion AmpliSeq Library Kit 2.0</td>
			<td>Thermofisher Scientific</td>
			<td>4480441</td>
			<td>Preparation of amplicon libraries using Ion AmpliSeq panels</td>
		</tr>
		<tr>
			<td>Ion Chef Instrument</td>
			<td>Thermofisher Scientific</td>
			<td>4484177</td>
			<td>Automated library preparation, template preparation and chip loading</td>
		</tr>
		<tr>
			<td>Ion PI Chip Kit v3 or Ion 540 Chip</td>
			<td>Thermofisher Scientific</td>
			<td>A26771 or A27766</td>
			<td>Barcoded chips for sequencing</td>
		</tr>
		<tr>
			<td>Ion PI Hi-Q Chef Kit or Ion 540 Kit-Chef</td>
			<td>Thermofisher Scientific</td>
			<td>A27198 or A30011</td>
			<td>Template preparation</td>
		</tr>
		<tr>
			<td>Ion PI Hi-Q Sequencing 200 Kit or Ion S5 Sequencing Kit</td>
			<td>Thermofisher Scientific</td>
			<td>A26433 or A30011</td>
			<td>Sequencing</td>
		</tr>
		<tr>
			<td>Ion Proton or Ion GeneStudio S5 System</td>
			<td>Thermofisher Scientific</td>
			<td>4476610 or A38196</td>
			<td>Sequencing system</td>
		</tr>
		<tr>
			<td>Ion Reporter Software - AmpliSeq Comprehensive Cancer Panel tumour-normal pair</td>
			<td>Thermofisher Scientific</td>
			<td>4487118</td>
			<td>Workflow</td>
		</tr>
		<tr>
			<td>Ion Reporter Software - uploader plugin</td>
			<td>Thermofisher Scientific</td>
			<td>4487118</td>
			<td>Data analysis tool</td>
		</tr>
		<tr>
			<td>Ion Torrent Suite Software - Coverege Analysis plugin</td>
			<td>Thermofisher Scientific</td>
			<td>4483643</td>
			<td>Plugin that describe the level of sequance coverage produced</td>
		</tr>
		<tr>
			<td>Ion Torrent Suite Software - Variant Caller plugin</td>
			<td>Thermofisher Scientific</td>
			<td>4483643</td>
			<td>Plugin able to identify single-nucleotide polymorphisms (SNPs), insertions and deletions in a sample across a reference</td>
		</tr>
		<tr>
			<td>Ion Xpress Barcode Adapters 1-96 Kit</td>
			<td>Thermofisher Scientific</td>
			<td>4474517</td>
			<td>Unique barcode adapters</td>
		</tr>
		<tr>
			<td>NanoDrop 2000/2000c Spectrophotometers</td>
			<td>Thermofisher Scientific</td>
			<td>ND-2000</td>
			<td>DNA purity detection</td>
		</tr>
		<tr>
			<td>NCBI reference sequence (RefSeq) database</td>
			<td>NCBI</td>
			<td>-</td>
			<td>https://www.ncbi.nlm.nih.gov/refseq/</td>
		</tr>
		<tr>
			<td>Platinum PCR SuperMix High Fidelity</td>
			<td>Fisher Scientific</td>
			<td>12532-016 or 12532-024</td>
			<td>SuperMix for PCR amplification; high-fidelity PCR mix</td>
		</tr>
		<tr>
			<td>QIAamp DNA Blood Mini Kit</td>
			<td>Quiagen</td>
			<td>51106 0r 51104</td>
			<td>DNA blood extraction kit</td>
		</tr>
		<tr>
			<td>QIAamp DNA FFPE Tissue</td>
			<td>Quiagen</td>
			<td>56404</td>
			<td>DNA FFPE tissue extraction kit</td>
		</tr>
		<tr>
			<td>Qubit 2.0 Fluorometer</td>
			<td>Thermofisher Scientific</td>
			<td>Q32866</td>
			<td>DNA quantification</td>
		</tr>
		<tr>
			<td>Qubit dsDNA BR Assay Kit</td>
			<td>Thermofisher Scientific</td>
			<td>Q32850</td>
			<td>Kit for DNA quantification on Qubit 2.0 Fluorometer</td>
		</tr>
		<tr>
			<td>TBST</td>
			<td>home made</td>
			<td>-</td>
			<td>Tris-buffered saline (TBS) and 0.1% of Tween 20</td>
		</tr>
		<tr>
			<td>Tissue-Tek Prisma Plus &#38; Tissue-Tek Film</td>
			<td>Sakura Europe</td>
			<td>6172</td>
			<td>Automated tissue slide stainer instrument</td>
		</tr>
		<tr>
			<td>Variant Effect Predictor (VEP) software</td>
			<td>EMBI-EBI</td>
			<td>-</td>
			<td>http://grch37.ensembl.org/Homo_sapiens /Tools/VEP</td>
		</tr>
		<tr>
			<td>Xilene, mix of isomeres</td>
			<td>Carlo Erba</td>
			<td>492306</td>
			<td>IHC deparaffinization reagent</td>
		</tr>
	</tbody>
</table>

comparative lesions analysis through a targeted sequencing approach

Assessing intra-tumoral heterogeneity (ITH) is of paramount importance to anticipate failure of targeted therapies and design accordingly effective anti-tumor strategies. Although concerns are frequently raised due to differences in sample processing and depth of coverage, next-generation sequencing of solid tumors have unraveled a highly variable degree of ITH across tumor types. Capturing the genetic relatedness between primary and metastatic lesions through the identification of clonal and subclonal populations is critical to the design of therapies for advance-stage diseases. Here, we report a method for comparative lesions analysis that allows for the identification of clonal and subclonal populations among different specimens from the same patient. The experimental approach described here integrates three well-established approaches: histological analysis, high-coverage multi-lesion sequencing, and immunophenotypic analyses. In order to minimize the effects on the detection of subclonal events by inappropriate sample processing, we subjected tissues to careful pathological examination and neoplastic cell enrichment. Quality controlled DNA from neoplastic lesions and normal tissues was then subjected to high coverage sequencing, targeting the coding regions of 409 relevant cancer genes. While only looking at a limited genomic space, our approach enables evaluating the extent of heterogeneity among somatic alterations (single-nucleotide mutations and copy-number variations) in distinct lesions from a given patient. Through comparative analysis of sequencing data, we were able to distinguish clonal vs. subclonal alterations. The majority of ITH is often ascribed to passenger mutations; therefore, we also used immunohistochemistry to predict functional consequences of mutations. While this protocol has been applied to a specific tumor type, we anticipate that the methodology described here is broadly applicable to other solid tumor types.

The study workflow is illustrated in Figure 1. Multi-lesions (n = 13) sequencing of 5 SPN cases targeting the coding sequences of 409 cancer related genes identified a total of 27 somatic mutations in 8 genes (CTNNB1, KDM6A, BAP1, TET1, SMAD4, TP53, FLT1, and FGFR3). Mutations were defined as founder/clonal when shared among all lesions of a given patient, and progressor/subclonal when detected in some but not all lesion...

Watch this Scientific Journal Video about Comparative Lesions Analysis Through a Targeted Sequencing Approach at JoVE.com

Comparative Lesions Analysis Through a Targeted Sequencing Approach

This article describes a method to identify clonal and subclonal alterations among different specimens from a given patient. Although the experiments described here focus on a specific tumor type, the approach is broadly applicable to other solid tumors.

Assessing intra-tumoral heterogeneity (ITH) is of paramount importance to anticipate failure of targeted therapies and design accordingly effective ...

Our protocol allows the capture of the genetic relatedness between primary and metastatic lesions through the identification of molecular alterations involved in disease progression. Our method provides the opportunity to explore genetic relatedness in clinical specimen with high sensitivity and specificity. This is due to the integration of molecular and histopathological analysis.The assessment of intratumor heterogeneity in the cancer research field is of paramount importance in designing effective anti-tumor strategies and our method is broadly applicable to many solid tumor types. After preparing and quantifying the libraries of interest, dilute each library to a 100 picomolar concentration in nuclease-free water and combine 10 microliters of each diluted library for a single run in a single tube. Then mix the pooled libraries by pipetting.To initiate a sequencing run, first open the Torrent browser on a computer connected to the sequencing system. Plan a new run using the generic template for the selected application and under the kits tab select Ion Proton system or Ion Gene Studio S5 system. Select the appropriate chip from the chip type dropdown menu and select Ion AmpliSeq 2.0 Library Kit from the library kit dropdown list.Select the Ion Chef button for the template kit and select the appropriate Chef Kit from the template kit dropdown list. Select the appropriate sequencing kit from the sequencing kit dropdown menu and select Ion Express from the barcode set dropdown list. Under the plugin tab, select the coverage analysis plugin.Under the plan tab, select the GRCH37HG19 genome from the reference library dropdown list. From the target regions dropdown list, select the appropriate panel to be sequenced. Then set the number of barcodes to be sequenced and set the barcode name and sample name for each library.For a pooled libraries dilution, dilute the stock library with nuclease-free water to a 25 picomolar concentration for an ion proton chip and pipette 50 microliters of each diluted library to the bottom of the appropriate library sample tube. Load sample tubes containing the pooled diluted libraries onto the library preparation system and start the clonal amplification. For next generation sequencing, follow the on-screen instructions to initialize the instrument.When the clonal amplification is finished, open the Ion Chef instrument door, then open the lid of the chip loading centrifuge and remove the two chips from the library preparation system. Place the chips into separate chip storage containers and load one of the chips into the chip compartment in the instrument. Then close the chip compartment lid and start the sequencing.For mutation analysis, open the coverage analysis plugin and use the coverage analysis output to verify the depth of coverage and uniformity. Use the Torrent Variant Caller plugin to perform the variant calling selecting the germ line or somatic workflow as appropriate. Then download filtered variants variant call format files and use the variant effect predictor software in the NCBI RefSeq database to annotate the variants.To estimate the copy-number variations, use the ion reporter uploader plugin to load the sequencing data into the ion reporter software and use the comprehensive cancer panel tumor normal pair workflow to analyze the data. Manually filter the mutations and copy-number variations based on the scores assigned by the software and verify the variations visually with the Integrative Genomics Viewer. Then visually inspect the alignment for unusual reads that may generate artifactual calls and inspect the normalized coverage for all of the amplicons across a given gene against the normalized coverage of the baseline to verify the copy-number variations.For each case, index the mutation calls from the sequencing of normal tissue or blood or primary tumor or metastasis. Flag as germ line and discard calls that are also evident from the sequencing data of germ line DNA. Flag as clonal or founder the mutations that are shared among all lesions of a given patient.Then flag as subclonal or progressor the mutations that are detected in some but not all of the lesions of a given patient. In this representative experiment, multi-lesion sequencing of five solid pseudopapillary neoplasm cases targeting the coding sequences of 409 cancer-related genes identified a total of 27 somatic mutations in eight genes. Mutations were defined as founder or clonal when shared among all of the lesions of a given patient and progressor or subclonal when detected in some but not all of the lesions of a given patient.Consistently, immunohistochemical staining for beta-catenin and KMD6A was homogenous among the diverse lesions of cases with mutations of the corresponding genes. The moderate staining for KMD6A in mutated specimens suggest that genetic alteration is likely to alter the function rather than the expression of the protein. KMD6A loss of function in pancreatic tumors is associated with up regulation of the hypoxia marker GLUT-1.And accordingly, GLUT-1 was over expressed in cases bearing KMD6A mutations. Immunohistochemistry for BAP1 and TP53 confirmed that mutations in those genes were subclonal. In this virtual karyotype of a representative case showing the location, proximity, and copy-number status of altered genes, the copy-number variation analysis using sequencing data revealed alterations in all of the specimens analyzed.And in contrast to point mutations, the majority of copy-number variation alterations were subclonal. Validation and indexing of mutations and copy-number variation and using the tumor normal DNA comparison are important for avoiding the generation of artifactual calls that could invalidate the results. This procedure could also be applied to whole genome sequencing studies aimed at interrogating the entire genome for the identification of mutation between lesion of different solid tumor types.In the cancer research field, these techniques are critical tools for understanding the biology of diseases with important clinical implications aimed at designing personalized and effective targeted therapies.

comparative-lesions-analysis-through-a-targeted-sequencing-approach

Research

JoVE Journal

Behavior

Contextual and Cued Fear Conditioning Test Using a Video Analyzing System in Mice

The contextual and cued fear conditioning test is one of the behavioral tests that assesses the ability of mice to learn and remember an association between environmental cues and aversive experiences. In this test, mice are placed into a conditioning chamber and are given parings of a conditioned stimulus (an auditory cue) and an aversive unconditioned stimulus (an electric footshock). After a delay time, the mice are exposed to the same conditioning chamber and a differently shaped chamber with presentation of the auditory cue. Freezing behavior during the test is measured as an index of fear memory. To analyze the behavior automatically, we have developed a video analyzing system using the ImageFZ application software program, which is available as a free download at http://www.mouse-phenotype.org/. Here, to show the details of our protocol, we demonstrate our procedure for the contextual and cued fear conditioning test in C57BL/6J mice using the ImageFZ system. In addition, we validated our protocol and the video analyzing system performance by comparing freezing time measured by the ImageFZ system or a photobeam-based computer measurement system with that scored by a human observer. As shown in our representative results, the data obtained by ImageFZ were similar to those analyzed by a human observer, indicating that the behavioral analysis using the ImageFZ system is highly reliable. The present movie article provides detailed information regarding the test procedures and will promote understanding of the experimental situation.

This article presents a protocol for a contextual and cued fear conditioning test using a video analyzing system to assess fear learning and memory in mice.

The contextual and cued fear conditioning test is one of the behavioral tests that assesses the ability of mice to learn and remember an association ...

Measurement of Fronto-limbic Activity Using an Emotional Oddball Task in Children with Familial High Risk for Schizophrenia

Adolescence is a critical developmental period where the early symptoms of schizophrenia frequently emerge. First-degree relatives of people with schizophrenia who are at familial high risk (FHR) may show similar cognitive and emotional changes. However, the neurological changes underlying the emergence of these symptoms remain unclear. This study sought to identify differences in frontal, striatal, and limbic regions in children and adolescents with FHR using functional magnetic resonance imaging. Groups of 21 children and adolescents at FHR and 21 healthy controls completed an emotional oddball task that relied on selective attention and the suppression of task-irrelevant emotional information. The standard oddball task was modified to include aversive and neutral distractors in order to examine potential group differences in both emotional and executive processing. This task was designed specifically to allow for children and adolescents to complete by keeping the difficulty and emotional image content age-appropriate. Furthermore, we demonstrate a technique for suitable fMRI registration for children and adolescent participants. This paradigm may also be applied in future studies to measure changes in neural activity in other populations with hypothesized developmental changes in executive and emotional processing.

This paper describes how to use the emotional oddball task and fMRI to measure brain activation in children and adolescents at familial high risk for schizophrenia (FHR).&#160;FMRI was used to measure differences in fronto-striato-limbic regions during an emotional oddball task. Children with FHR exhibited abnormal functional activation during adolescence.

Adolescence is a critical developmental period where the early symptoms of schizophrenia frequently emerge. First-degree relatives of people with ...

Experimental Assessment of Mouse Sociability Using an Automated Image Processing Approach

Mouse is the preferred model organism for testing drugs designed to increase sociability. We present a method to quantify mouse sociability in which the test mouse is placed in a standardized apparatus and relevant behaviors are assessed in three different sessions (called session I, II, and III).
The apparatus has three compartments (see Figure 1), the left and right compartments contain an inverted cup which can house a mouse (called &#34;stimulus mouse&#34;).
In session I, the test mouse is placed in the cage and its mobility is characterized by the number of transitions made between compartments. In session II, a stimulus mouse is placed under one of the inverted cups and the sociability of the test mouse is quantified by the amounts of time it spends near the cup containing the enclosed stimulus mouse vs. the empty inverted cup. In session III, the inverted cups are removed and both mice interact freely. The sociability of the test mouse in session III is quantified by the number of social approaches it makes toward the stimulus mouse and by the number of times it avoids a social approach by the stimulus mouse.
The automated evaluation of the movie detects the nose of the test mouse, which allows the determination of all described sociability measures in session I and II (in session III, approaches are identified automatically but classified manually). To find the nose, the image of an empty cage is digitally subtracted from each frame of the movie and the resulting image is binarized to identify the mouse pixels. The mouse tail is automatically removed and the two most distant points of the remaining mouse are determined; these are close to nose and base of tail. By analyzing the motion of the mouse and using continuity arguments, the nose is identified.
<img alt="Figure 1" src="/files/ftp_upload/52508/52508fig1.jpg" /> 
Figure 1. Assessment of Sociability During 3 sessions. Session I (top): Acclimation of test mouse to the cage. Session II (middle): Test mouse moving freely in the cage while the stimulus mouse is enclosed in an inverted cup. Session III (bottom): Both test mouse and stimulus mouse are allowed to move freely and interact with each other.

This protocol describes a method to quantify mouse sociability. Mice are videotaped as they move and interact in a special cage. Movie processing allows for the automated quantification of sociability with excellent accuracy and reliability.

Mouse is the preferred model organism for testing drugs designed to increase sociability. We present a method to quantify mouse sociability in which the ...

Protocol for Data Collection and Analysis Applied to Automated Facial Expression Analysis Technology and Temporal Analysis for Sensory Evaluation

We demonstrate a method for capturing emotional response to beverages and liquefied foods in a sensory evaluation laboratory using automated facial expression analysis (AFEA) software. Additionally, we demonstrate a method for extracting relevant emotional data output and plotting the emotional response of a population over a specified time frame. By time pairing each participant's treatment response to a control stimulus (baseline), the overall emotional response over time and across multiple participants can be quantified. AFEA is a prospective analytical tool for assessing unbiased response to food and beverages. At present, most research has mainly focused on beverages. Methodologies and analyses have not yet been standardized for the application of AFEA to beverages and foods; however, a consistent standard methodology is needed. Optimizing video capture procedures and resulting video quality aids in a successful collection of emotional response to foods. Furthermore, the methodology of data analysis is novel for extracting the pertinent data relevant to the emotional response. The combinations of video capture optimization and data analysis will aid in standardizing the protocol for automated facial expression analysis and interpretation of emotional response data.

A protocol for capturing and statistically analyzing emotional response of a population to beverages and liquefied foods in a sensory evaluation laboratory using automated facial expression analysis software is described.

We demonstrate a method for capturing emotional response to beverages and liquefied foods in a sensory evaluation laboratory using automated facial ...

Behavioral Disturbances: An Innovative Approach to Monitor the Modulatory Effects of a Nutraceutical Diet

In dogs, diets are often used to modulate behavioral disturbances related to chronic anxiety and stress caused by intense and restless activity. However, the traditional ways to monitor behavioral changes in dogs are complicated and not efficient. In the current clinical evaluation, a new, simple monitoring system was used to assess the effectiveness of a specific diet in positively modulating the intense and restless activity of 24 dogs of different ages and breeds. This protocol describes how to easily and rapidly evaluate improvement in a set of symptoms related to generalized anxiety by using a specific sensor, a mobile phone app, a wireless router, and a computer. The results showed that dogs treated with specific diets showed significant improvement in the times spent active and at rest after 10 days (p &lt; 0.01 and p &lt; 0.05, respectively). These dogs also showed an overall significant improvement in clinical and behavioral symptoms. A specific sensor, along with its related hardware, was demonstrated to successfully monitor behavioral changes relating to movement in dogs.

We report a simple approach to evaluate the effectiveness of a specific diet in positively modulating the daily activity and clinical and behavioral symptoms of dogs with evident behavioral disturbances.

In dogs, diets are often used to modulate behavioral disturbances related to chronic anxiety and stress caused by intense and restless activity. However, ...

Treatment of Ankle Osteoarthritis with Total Ankle Replacement Through a Lateral Transfibular Approach

Total ankle replacement (TAR) is a valid option for the treatment of ankle osteoarthritis. The traditional surgical approach for TAR is the anterior approach. Recently, the lateral transfibular approach to the ankle has gained popularity since a new TAR implant was designed to be performed via this approach that results in an ideal visualization of the center of rotation of the ankle and curved resections that allow for sparing bone cuts. The aim of the present paper is to present our preoperative, operative, and postoperative protocols for the treatment of the osteoarthritis of the ankle with TAR via lateral approach. We present our preoperative clinical and radiographic protocol. In addition, we describe our surgical technique with some technical tips. Finally, we report our follow-up schedule that includes the collection of clinical, functional, and radiographic data. The results of this procedure are encouraging: TAR through a lateral transfibular approach provides reliable pain relief and improvements in functional outcomes in patients with ankle osteoarthritis.

We present our preoperative, operative, and postoperative protocols for the treatment of osteoarthritis of the ankle with total ankle replacement via lateral transfibular approach.

Total ankle replacement (TAR) is a valid option for the treatment of ankle osteoarthritis. The traditional surgical approach for TAR is the anterior ...

Use of a Wireless Video-EEG System to Monitor Epileptiform Discharges Following Lateral Fluid-Percussion Induced Traumatic Brain Injury

The lateral fluid percussion injury (FPI) model is well established and has been used to study TBI and post-traumatic epilepsy (PTE). However, considerable variability has been reported for the specific parameters used in different studies that have employed this model, making it difficult to harmonize and interpret the results between laboratories. For example, variability has been reported regarding the size and location of the craniectomy, how the Luer lock hub is placed relative to the craniectomy, the atmospheric pressure applied to the dura and the duration of the pressure pulse. Each of these parameters can impact injury severity, which directly correlates with the incidence of PTE. This has been manifested as a wide range of mortality rates, righting reflex times and incidence of convulsive seizures reported. Here we provide a detailed protocol for the method we have used to help facilitate harmonization between studies. We used FPI in combination with a wireless EEG telemetry system to continuously monitor for electrographic changes and detect seizure activity.&#160; FPI is induced by creating a 5 mm craniectomy over the left hemisphere, between the Bregma and Lambda and adjacent to the lateral ridge. A Luer lock hub is secured onto the skull over the craniectomy. This hub is connected to the FPI device, and a 20-millisecond pressure pulse is delivered directly to the intact dura through pressure tubing connected to the hub via a twist lock connector. Following recovery, rats are re-anesthetized to remove the hub. Five 0.5 mm, stainless steel EEG electrode screws are placed in contact with the dura through the skull and serve as four recording electrodes and one reference electrode. The electrode wires are collected into a pedestal connector which is secured into place with bone cement. Continuous video/EEG recordings are collected for up to 4 weeks post TBI.

Here we present a protocol to induce severe TBI with the lateral fluid percussion injury (FPI) model in adult, male Wistar rats. We also demonstrate the use of a wireless telemetry system to collect continuous video-EEG recordings and monitor for epileptiform discharges consistent with post-traumatic epileptogenesis.&#160;

The lateral fluid percussion injury (FPI) model is well established and has been used to study TBI and post-traumatic epilepsy (PTE). However, ...

A Machine Learning Approach to Design an Efficient Selective Screening of Mild Cognitive Impairment

Mild cognitive impairment (MCI) is the first sign of dementia among elderly populations and its early detection is crucial in our aging societies. Common MCI tests are time-consuming such that indiscriminate massive screening would not be cost-effective. Here, we describe a protocol that uses machine learning techniques to rapidly select candidates for further screening via a question-based MCI test. This minimizes the number of resources required for screening because only patients who are potentially MCI positive are tested further.
This methodology was applied in an initial MCI research study that formed the starting point for the design of a selective screening decision tree. The initial study collected many demographic and lifestyle variables as well as details about patient medications. The Short Portable Mental Status Questionnaire (SPMSQ) and the Mini-Mental State Examination (MMSE) were used to detect possible cases of MCI. Finally, we used this method to design an efficient process for classifying individuals at risk of MCI. This work also provides insights into lifestyle-related factors associated with MCI that could be leveraged in the prevention and early detection of MCI among elderly populations.

This methodology produces decision trees that target population groups more prone to suffering from mild cognitive impairment and are useful for cost-effective selective screening of the disease.

Mild cognitive impairment (MCI) is the first sign of dementia among elderly populations and its early detection is crucial in our aging societies. Common ...

Evaluating Skilled Prehension in Mice Using an Auto-Trainer

We describe a method to introduce na&#239;ve mice to a novel prehension (reach-to-grasp) task. Mice are housed singly in cages with a frontal slot that permits the mouse to reach out of its cage and retrieve food pellets. Minimal food restriction is employed to encourage the mice to perform the food retrieval from the slot. As the mice begin to associate coming to the slot for food, the pellets are manually pulled away to stimulate extension and pronation of their paw to grasp and retrieve the pellet through the frontal slot. When the mice begin to reach for the pellets as they arrive at the slot, the behavioral assay can be performed by measuring the rate at which they successfully grasp and retrieve the desired pellet. They are then introduced to an auto-trainer that automates both the process of providing food pellets for the mouse to grasp, and the recording of successful and failed reaching and grasping attempts. This allows for the collection of reaching data for multiple mice with minimal effort, to be used in experimental analysis as appropriate.

Method to assess the impact of training on motor skills is a useful tool. Unfortunately, most behavioral assessments can be labor intensive and/or expensive.We describe here a robotic method of assessing prehension (reach-to-grasp) skill in mice.

We describe a method to introduce na&#239;ve mice to a novel prehension (reach-to-grasp) task. Mice are housed singly in cages with a frontal slot that ...

Two Different Real-Time Place Preference Paradigms Using Optogenetics within the Ventral Tegmental Area of the Mouse

Understanding how neuronal activation leads to specific behavioral output is fundamental for modern neuroscience. Combining optogenetics in rodents with behavioral testing in validated paradigms allows the measurement of behavioral consequences upon stimulation of distinct neurons in real-time with high spatial and temporal selectivity, and thus the establishment of causal relationships between neuronal activation and behavior. Here, we describe a step-by-step protocol for a real-time place preference (RT-PP) paradigm, a modified version of the classical conditioned place preference (CPP) test. The RT-PP is performed in a three-compartment apparatus and can be utilized to answer if optogenetic stimulation of a specific neuronal population is rewarding or aversive. We also describe an alternative version of the RT-PP protocol, the so-called neutral compartment preference (NCP) protocol, which can be used to confirm aversion. The two approaches are based on extensions of classical methodology originating from behavioral pharmacology and recent implementation of optogenetics within the neuroscience field. Apart from measuring place preference in real time, these setups can also give information regarding conditioned behavior. We provide easy-to-follow step-by-step protocols alongside examples of our own data and discuss important aspects to consider when applying these types of experiments.

Here we present two easy-to-follow step-by-step protocols for place preference paradigms using optogenetics in mice. Using these two different setups, preference and avoidance behaviors can be solidly assessed within the same apparatus with high spatial and temporal selectivity, and in a straightforward manner.

Understanding how neuronal activation leads to specific behavioral output is fundamental for modern neuroscience. Combining optogenetics in rodents with ...