scholarly journals Weakly-Supervised Tumor Purity Prediction From Frozen H&E Stained Slides

2021 ◽  
Author(s):  
Matthew Brendel ◽  
Vanesa Getseva ◽  
Majd Al Assaad ◽  
Michael Sigouros ◽  
Alexandros Sigaras ◽  
...  
Keyword(s):  
Tumor Type ◽  
Dependent Manner ◽  
Disease Outcomes ◽  
Tumor Purity ◽  
Independent Test ◽  
Hematoxylin And Eosin ◽  
Tumor Sequencing ◽  
Selection For ◽  
Weakly Supervised ◽  
Generation Sequencing

Estimating tumor purity is especially important in the age of precision medicine. Purity estimates have been shown to be critical for correction of tumor sequencing results, and higher purity samples allow for more accurate interpretations from next-generation sequencing results. In addition, tumor purity has been shown to be correlated with survival outcomes for several diseases. Molecular-based purity estimates using computational approaches require sequencing of tumors, which is both time-consuming and expensive. Here we propose an approach, weakly-supervised purity (wsPurity), which can accurately quantify tumor purity within a slide, using multiple and different types of cancer. This approach allows for a flexible analysis of tumors from whole slide imaging (WSI) of histology hematoxylin and eosin (H&E) slides. Our model predicts tumor type with high accuracy (greater than 80% on an independent test cohort), and tumor purity at a higher accuracy compared to a comparable fully-supervised approach (0.1335 MAE on an independent test cohort). In addition to tumor purity prediction, our approach can identify high resolution tumor regions within a slide, to enrich tumor cell selection for downstream analyses. This model could also be used in a clinical setting, to stratify tumors into high and low tumor purity, using different thresholds, in a cancer-dependent manner, depending on what purity levels correlate with worse disease outcomes. In addition, this approach could be used in clinical practice to select the best tissue block for sequencing. Overall, this approach can be used in several different ways to analyze WSIs of tumor H&E sections.

scholarly journals Complexities of Next-Generation Sequencing in Solid Tumors: Case Studies

2020 ◽  
Vol 18 (9) ◽  
pp. 1150-1155
Author(s):  
Alexandra O. Sokolova ◽  
Brian H. Shirts ◽  
Eric Q. Konnick ◽  
Ginger J. Tsai ◽  
Bernardo H.L. Goulart ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Case Studies ◽  
Checkpoint Inhibitors ◽  
Hereditary Cancer Syndrome ◽  
Next Generation ◽  
Cancer Syndrome ◽  
Expert Review ◽  
Tumor Boards ◽  
Tumor Sequencing ◽  
Generation Sequencing

With the promise and potential of clinical next-generation sequencing for tumor and germline testing to impact treatment and outcomes of patients with cancer, there are also risks of oversimplification, misinterpretation, and missed opportunities. These issues risk limiting clinical benefit and, at worst, perpetuating false conclusions that could lead to inappropriate treatment selection, avoidable toxicity, and harm to patients. This report presents 5 case studies illustrating challenges and opportunities in clinical next-generation sequencing interpretation and clinical application in solid tumor oncologic care. First is a case that dissects the origin of an ATM mutation as originating from a hematopoietic clone rather than the tumor. Second is a case illustrating the potential for tumor sequencing to suggest germline variants associated with a hereditary cancer syndrome. Third are 2 cases showing the potential for variant reclassification of a germline variant of uncertain significance when considered alongside family history and tumor sequencing results. Finally, we describe a case illustrating challenges with using microsatellite instability for predicting tumor response to immune checkpoint inhibitors. The common theme of the case studies is the importance of examining clinical context alongside expert review and interpretation, which together highlight an expanding role for contextual examination and multidisciplinary expert review through molecular tumor boards.

Improving cord blood typing with next-generation sequencing: impact of allele-level HLA and NIMA determination on their selection for transplantation

2020 ◽  
Vol 55 (8) ◽  
pp. 1623-1631
Author(s):  
Emma Enrich ◽  
Francisco Vidal ◽  
Irene Corrales ◽  
Eva Campos ◽  
Nina Borràs ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Cord Blood ◽  
Next Generation ◽  
Blood Typing ◽  
Selection For ◽  
Generation Sequencing

scholarly journals Oncologists’ Use of Genomic Sequencing Data to Inform Clinical Management

2018 ◽  
pp. 1-13
Author(s):  
Michele C. Gornick ◽  
Erin Cobain ◽  
Lan Q. Le ◽  
Natalie Bartnik ◽  
Elena Stoffel ◽  
...  
Keyword(s):  
Medical Record ◽  
Medical Records ◽  
Clinical Management ◽  
Response Rate ◽  
Sequencing Data ◽  
Prospective Survey ◽  
Actual Change ◽  
Tumor Sequencing ◽  
Survey Responses ◽  
Generation Sequencing

Purpose To determine whether oncologists intended to change treatment as a result of tumor sequencing, and subsequently, whether patients experienced an alteration of clinical management or derived clinical benefit. Patients and Methods A prospective survey of oncologists referring adult patients with rare, advanced, or refractory cancer to the Michigan Oncology Sequencing program was conducted from June 2014 to March 2015 to assess the use of and intent to disclose sequencing findings. Oncologists’ responses were compared with the referred patients’ self-reported survey responses, and a content analysis of disclosure documented in the medical record was performed. Medical records were reviewed retrospectively to determine if clinical management was informed or changed by sequencing results. Results Oncologists (response rate, 93%) referring 112 consecutive patients were surveyed. Medical records of patients were reviewed for changes in clinical management on the basis of sequencing findings. Oncologists intended to change the treatment of 22% of patients (n = 24) on the basis of sequencing findings. Of these patients, 37.5% (n = 9) had an actual change in clinical management. Thirty-four patients with postsequencing survey data reported that a results disclosure discussion did not occur, despite documentation of disclosure by the physician in the medical record. Conclusions Findings demonstrate that many oncologists view next-generation sequencing results to be potentially valuable in directing subsequent therapy for their patients; however, barriers in communicating results to patients and implementing them in clinical management remain.

Imbalance of the renin–angiotensin system may contribute to inflammation and fibrosis in IBD: a novel therapeutic target?

Gut ◽  
2019 ◽  
Vol 69 (5) ◽  
pp. 841-851 ◽  
Author(s):  
Mayur Garg ◽  
Simon G Royce ◽  
Chris Tikellis ◽  
Claire Shallue ◽  
Duygu Batu ◽  
...  
Keyword(s):  
Ace Inhibitors ◽  
Intestinal Inflammation ◽  
Angiotensin Receptor Blockers ◽  
Renin Angiotensin System ◽  
Dependent Manner ◽  
Ang Ii ◽  
Angiotensin System ◽  
Renin Angiotensin ◽  
Disease Outcomes ◽  
Collagen Secretion

ObjectiveWe evaluated the influence of the renin–angiotensin system (RAS) on intestinal inflammation and fibrosis.DesignCultured human colonic myofibroblast proliferation and collagen secretion were assessed following treatment with angiotensin (Ang) II and Ang (1–7), their receptor antagonists candesartan and A779, and the ACE inhibitor captopril. Circulating and intestinal RAS components were evaluated in patients with and without IBD. Disease outcomes in patients with IBD treated with ACE inhibitors and angiotensin receptor blockers (ARBs) were assessed in retrospective studies.ResultsHuman colonic myofibroblast proliferation was reduced by Ang (1–7) in a dose-dependent manner (p<0.05). Ang II marginally but not significantly increased proliferation, an effect reversed by candesartan (p<0.001). Colonic myofibroblast collagen secretion was reduced by Ang (1–7) (p<0.05) and captopril (p<0.001), and was increased by Ang II (p<0.001). Patients with IBD had higher circulating renin (mean 25.4 vs 18.6 mIU/L, p=0.026) and ACE2:ACE ratio (mean 0.92 vs 0.69, p=0.015) than controls without IBD. RAS gene transcripts and peptides were identified in healthy and diseased bowels. Colonic mucosal Masson’s trichrome staining correlated with Ang II (r=0.346, p=0.010) and inversely with ACE2 activity (r=−0.373, p=0.006). Patients with IBD who required surgery (1/37 vs 12/75, p=0.034) and hospitalisation (0/34 vs 8/68, p=0.049) over 2 years were less often treated with ACE inhibitors and ARBs than patients not requiring surgery or hospitalisation.ConclusionsThe RAS mediates fibrosis in human cell cultures, is expressed in the intestine and perturbed in intestinal inflammation, and agents targeting this system are associated with improved disease outcomes.

scholarly journals Putative biomarkers for predicting tumor sample purity based on gene expression data

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Yuanyuan Li ◽  
David M. Umbach ◽  
Adrienna Bingham ◽  
Qi-Jing Li ◽  
Yuan Zhuang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Data ◽  
Supervised Machine Learning ◽  
Tumor Type ◽  
Expression Data ◽  
Expression Levels ◽  
Gene Set ◽  
Tumor Purity ◽  
Tumor Types ◽  
Cancerous Cells

Abstract Background Tumor purity is the percent of cancer cells present in a sample of tumor tissue. The non-cancerous cells (immune cells, fibroblasts, etc.) have an important role in tumor biology. The ability to determine tumor purity is important to understand the roles of cancerous and non-cancerous cells in a tumor. Methods We applied a supervised machine learning method, XGBoost, to data from 33 TCGA tumor types to predict tumor purity using RNA-seq gene expression data. Results Across the 33 tumor types, the median correlation between observed and predicted tumor-purity ranged from 0.75 to 0.87 with small root mean square errors, suggesting that tumor purity can be accurately predicted υσινγ expression data. We further confirmed that expression levels of a ten-gene set (CSF2RB, RHOH, C1S, CCDC69, CCL22, CYTIP, POU2AF1, FGR, CCL21, and IL7R) were predictive of tumor purity regardless of tumor type. We tested whether our set of ten genes could accurately predict tumor purity of a TCGA-independent data set. We showed that expression levels from our set of ten genes were highly correlated (ρ = 0.88) with the actual observed tumor purity. Conclusions Our analyses suggested that the ten-gene set may serve as a biomarker for tumor purity prediction using gene expression data.

Performance of next-generation sequencing for detection of clinically actionable genetic variants in cancer.

2013 ◽  
Vol 31 (15_suppl) ◽  
pp. 11099-11099
Author(s):  
Mohammed Omar Hussaini ◽  
Ian S. Hagemann ◽  
Teresa Mary Cox ◽  
Christina Lockwood ◽  
Karen Seibert ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genetic Variants ◽  
Simultaneous Detection ◽  
Genetic Alterations ◽  
Sequence Variants ◽  
Tumor Type ◽  
Cancer Genes ◽  
Next Generation ◽  
Therapeutic Implications ◽  
Generation Sequencing

11099 Background: Next-generation sequencing (NGS) allows for simultaneous detection of numerous actionable somatic variants in cancer. We have implemented a clinical NGS panel to detect genetic alterations in 25 genes with established roles in cancer and report here the frequency of clinically actionable genetic variants in a variety of cancer types. Methods: NGS testing was performed in a CAP-certified, CLIA-licensed environment on DNA extracted from FFPE tissue in 209 cases spanning 41 histologic tumor types. DNA was enriched by hybrid capture and sequenced to >1,000x average coverage on Illumina sequencers with 2x101bp or 2x150bp reads. Variants were called using clinically validated parameters using the Genome Analysis Toolkit, Pindel, and the custom-written Clinical Genomicist Workstation. Results: Non-small cell lung cancer (45%), pancreatic cancer (10%), and colorectal cancer (8%) were the most common tumors sent for NGS analysis. An average of 3 (range 1- 16) non-synonymous, non-SNP sequence variants per case (SNVs and indels) were detected in the 130kb exonic target. Variants were most commonly seen in TP53, KRAS, and EGFR. 27% of cases (56/209) had one or more variants with therapeutic implications for the tumor type tested (e.g., EGFR mutation in NSCLC). 15% of cases (32/209) showed actionable variants not generally associated with the malignancy tested (e.g., detection of an activating KITvariant in thymic carcinoma). 10% of cases (21/209) had variants that were prognostically significant but not directly targetable. Some cases (9%) had variants that were prognostic/diagnostic and targetable. In 117 cases (56% of total), no therapeutically or prognostically significant variants were identified. Overall, in 92 cases (44%), NGS testing yielded information with therapeutic (majority), prognostic, or diagnostic ramifications. Conclusions: We found that 44% of unselected cancer cases have clinically relevant sequence variants in a set of 25 commonly mutated cancer genes. Our data suggest that clinical NGS testing may serve as an integral tool in realizing the potential of precision medicine in oncology.

scholarly journals High-throughput single-cell DNA sequencing of AML tumors with droplet microfluidics

2017 ◽  
Author(s):  
Maurizio Pellegrino ◽  
Adam Sciambi ◽  
Sebastian Treusch ◽  
Robert Durruthy-Durruthy ◽  
Kaustubh Gokhale ◽  
...  
Keyword(s):  
Single Cell ◽  
Clonal Evolution ◽  
Droplet Microfluidics ◽  
Next Generation Sequencing Data ◽  
Sequencing Data ◽  
Single Cell Sequencing ◽  
Selection For ◽  
Genetic Profiles ◽  
Generation Sequencing

ABSTRACTTo enable the characterization of genetic heterogeneity in tumor cell populations, we developed a novel microfluidic approach that barcodes amplified genomic DNA from thousands of individual cancer cells confined to droplets. The barcodes are then used to reassemble the genetic profiles of cells from next generation sequencing data. Using this approach, we sequenced longitudinally collected AML tumor populations from two patients and genotyped up to 62 disease relevant loci across more than 16,000 individual cells. Targeted single-cell sequencing was able to sensitively identify tumor cells during complete remission and uncovered complex clonal evolution within AML tumors that was not observable with bulk sequencing. We anticipate that this approach will make feasible the routine analysis of heterogeneity in AML leading to improved stratification and therapy selection for the disease.

scholarly journals The NSL complex mediated nucleosome landscape is required to maintain transcription fidelity and suppression of transcription noise

2018 ◽  
Author(s):  
Kin Chung Lam ◽  
Ho-Ryun Chung ◽  
Giuseppe Semplicio ◽  
Vivek Bhardwaj ◽  
Shantanu S. Iyer ◽  
...  
Keyword(s):  
Transcription Initiation ◽  
Dependent Manner ◽  
Gene Promoters ◽  
Transcription Start ◽  
Transcription Start Sites ◽  
Chromatin Remodeling Complex ◽  
Selection For ◽  
Necessary And Sufficient ◽  
Target Promoters ◽  
Active Genes

AbstractNucleosomal organization at gene promoters is critical for transcription, with a nucleosome-depleted region (NDR) at transcription start sites (TSSs) being required for transcription initiation. How NDR and the precise positioning of the +1 nucleosome is maintained on active genes remains unclear. Here, we report that the Drosophila Non-Specific Lethal (NSL) complex is necessary to maintain this stereotypical nucleosomal organization at promoters. Upon NSL1 depletion, nucleosomes invade the NDRs at TSSs of NSL-bound genes. NSL complex member NSL3 binds to TATA-less promoters in a sequence-dependent manner. The NSL complex interacts with the NURF chromatin remodeling complex and is necessary and sufficient to recruit NURF to target promoters. The NSL complex is not only essential for transcription but is required for accurate TSS selection for genes with multiple TSSs. Further, loss of NSL complex leads to an increase in transcriptional noise. Thus, the NSL complex establishes a canonical nucleosomal organization that enables transcription and determines TSS fidelity.

scholarly journals Selective Isolation of Multidrug-Resistant Pedobacter spp., Producers of Novel Antibacterial Peptides

2021 ◽  
Vol 12 ◽  
Author(s):  
Joakim Bjerketorp ◽  
Jolanta J. Levenfors ◽  
Christina Nord ◽  
Bengt Guss ◽  
Bo Öberg ◽  
...  
Keyword(s):  
Sequence Variation ◽  
Hierarchical Cluster ◽  
Multidrug Resistant ◽  
Next Generation Sequencing Data ◽  
Antibacterial Peptides ◽  
Sequencing Data ◽  
Bacterial Strains ◽  
Separate Branch ◽  
Selection For ◽  
Generation Sequencing

Twenty-eight multidrug-resistant bacterial strains closely related or identical to Pedobacter cryoconitis, Pedobacter lusitanus and Pedobacter steynii were isolated from soil samples by selection for multidrug-resistance. Approximately 3–30% of the selected isolates were identified as Pedobacter, whereas isolation without antibiotics did not yield any isolates of this genus. Next generation sequencing data showed Pedobacter to be on 69th place among the bacterial genera (0.32% of bacterial sequences). The Pedobacter isolates produced a wide array of novel compounds when screened by UHPLC-MS/MSMS, and hierarchical cluster analysis resulted in several distinct clusters of compounds produced by specific isolates of Pedobacter, and most of these compounds were found to be peptides. The Pedobacter strain UP508 produced isopedopeptins, whereas another set of strains produced pedopeptins, which both are known cyclic lipodepsipeptides produced by Pedobacter sp. Other Pedobacter strains produced analogous peptides with a sequence variation. Further strains of Pedobacter produced additional novel antibacterial cyclic lipopeptides (ca 800 or 1400 Da in size) and/or linear lipopeptides (ca 700–960 Da in size). A 16S rRNA phylogenetic tree for the Pedobacter isolates revealed several distinct clades and subclades of isolates. One of the subclades comprised isolates producing isopedopeptin analogs, but the isopedopeptin producing isolate UP508 was clearly placed on a separate branch. We suggest that the non-ribosomal peptide synthases producing pedopeptins, isopedopeptins, and the analogous peptides, may derive from a common ancestral non-ribosomal peptide synthase gene cluster, which may have been subjected to a mutation leading to changed specificity in one of the modules and then to a modular rearrangement leading to the changed sequence found in the isopedopeptins produced by isolate UP508.

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