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Introduction: MET amplification (METamp) can be a de novo or acquired resistance driver; however, the definition of METamp that best captures patients who may respond to targeted therapy remains debated. We explored the genomic landscape of METamp NSCLC including degree of amplification, co-drivers, amplicon size, and outcomes to MET inhibitors., Methods: Hybrid-capture NGS-based genomic profiling from 88,547 tissue and 12,428 liquid NSCLC samples were queried for METamp (copy number (CN) ≥ ploidy + 4, or amplification ratio (AmpRatio; [CN/sample ploidy] ≥ 3). A nationwide de-identified real-world (rw) clinico-genomic database (CGDB) of NGS results linked to deidentified, electronic health record-derived clinical data was used to assess treatment and outcomes., Results: Among 10,760 evaluable patients in CGDB, 362 (3.4%) had a METamp. In targeted therapy-naïve cases, MET AmpRatio negatively correlated with non-METex14 co-drivers (median 4.1 vs 2.9, p < 0.0001). MET AmpRatio was not significantly correlated with tumor mutational burden (p = 0.79) but was inversely correlated with amplicon size (p < 0.001). Among paired METamp tissue samples, 8/30 had METamp detected in liquid; higher tumor fraction and AmpRatio were associated with liquid detection. Among 39 METamp patients receiving MET inhibitors, longer median real-world progression free survival was observed with MET AmpRatio ≥ 3 vs < 3 (4.9 vs. 1.7mos, HR 0.53 [95 %CI:0.21-1.3])., Conclusions: MET AmpRatio positively correlated with focal amplification and absence of co-drivers and trended with increased benefit from MET inhibitors. Further studies evaluatingcombinatorial data including MET AmpRatio, amplicon size and presence of other potential drivers, as predictive biomarkers for therapies targeting MET amplification in NSCLC are warranted., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: DCCT: none. JKL, CFT, JH, BF, BD, GMF, and ABS are employees of Foundation Medicine, Inc., a wholly-owned subsidiary of Roche, with Roche stock ownership. DRC: consulting or advisory role with Inivata Ltd, Regeneron Pharmaceuticals Inc, AbbVie Inc and EMD Serono Inc., (Copyright © 2025 Foundation Medicine, Inc. Published by Elsevier B.V. All rights reserved.)

Background: The amounts of circulating cell-free DNA (cfDNA) and circulating-tumor DNA (ctDNA) present in peripheral blood liquid biopsies can vary due to preanalytic/analytic variables. In this study, we examined the impact of patient age, sex, stage, and tumor type on cfDNA yield, ctDNA fraction, and estimated ctDNA quantity from a large cohort of clinical liquid biopsy samples., Methods: We performed a retrospective analysis of 12 139 consecutive samples received for liquid biopsy (FoundationOne® Liquid) clinical testing., Results: Significant differences in both cfDNA yield and estimated ctDNA quantity were observed based on the underlying tumor type that initiated the liquid biopsy analysis and the stage of the patient (P < 0.001). In addition, significant differences in ctDNA quantity were present based in both the patient age and sex (P < 0.001). Importantly, we saw a significantly higher success rate of issuing a clinically useful report in patients with higher levels of cfDNA yield and ctDNA quantity (P < 0.001)., Conclusions: In this study, we show that ctDNA quantity varied significantly based on patient age, sex, stage, and tumor type, which could offer an explanation as to why certain liquid biopsy specimens are more likely to fail sequencing or provide clinically meaningful results. In addition, this could affect future clinical decisions on the blood sample volumes required to allow successful liquid biopsy testing., (© American Association for Clinical Chemistry 2021. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Genomic profiling of circulating tumor DNA derived from cell-free DNA (cfDNA) in blood can provide a noninvasive method for detecting genomic biomarkers to guide clinical decision making for cancer patients. We developed a hybrid capture-based next-generation sequencing assay for genomic profiling of circulating tumor DNA from blood (FoundationACT). High-sequencing coverage and molecular barcode-based error detection enabled accurate detection of genomic alterations, including short variants (base substitutions, short insertions/deletions) and genomic re-arrangements at low allele frequencies (AFs), and copy number amplifications. Analytical validation was performed on 2666 reference alterations. The assay achieved >99% overall sensitivity (95% CI, 99.1%-99.4%) for short variants at AF >0.5%, >95% sensitivity (95% CI, 94.2%-95.7%) for AF 0.25% to 0.5%, and 70% sensitivity (95% CI, 68.2%-71.5%) for AF 0.125% to 0.25%. No false positives were detected in 62 samples from healthy volunteers. Genomic alterations detected by FoundationACT demonstrated high concordance with orthogonal assays run on the same clinical cfDNA samples. In 860 routine clinical FoundationACT cases, genomic alterations were detected in cfDNA at comparable frequencies to tissue; for the subset of cases with temporally matched tissue and blood samples, 75% of genomic alterations and 83% of short variant mutations detected in tissue were also detected in cfDNA. On the basis of analytical validation results, FoundationACT has been approved for use in our Clinical Laboratory Improvement Amendments-certified/College of American Pathologists-accredited/New York State-approved laboratory., (Copyright © 2018 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.)

Pancreatic islets exhibit bursting oscillations in response to elevated blood glucose. These oscillations are accompanied by oscillations in the free cytosolic Ca 2+ concentration ( Ca c ), which drives pulses of insulin secretion. Both islet Ca 2+ and metabolism oscillate, but there is some debate about their interrelationship. Recent experimental data show that metabolic oscillations in some cases persist after the addition of diazoxide (Dz), which opens K(ATP) channels, hyperpolarizing β -cells and preventing Ca 2+ entry and Ca 2+ oscillations. Further, in some islets in which metabolic oscillations were eliminated with Dz, increasing the cytosolic Ca 2+ concentration by the addition of KCl could restart the metabolic oscillations. Here we address why metabolic oscillations persist in some islets but not others, and why raising Ca c restarts oscillations in some islets but not others. We answer these questions using the dual oscillator model (DOM) for pancreatic islets. The DOM can reproduce the experimental data and shows that the model supports two different mechanisms for slow metabolic oscillations, one that requires calcium oscillations and one that does not.

Background: The evolutionary pressures that underlie the large-scale functional organization of the genome are not well understood in eukaryotes. Recent evidence suggests that functionally similar genes may colocalize (cluster) in the eukaryotic genome, suggesting the role of chromatin-level gene regulation in shaping the physical distribution of coordinated genes. However, few of the bioinformatic tools currently available allow for a systematic study of gene colocalization across several, evolutionarily distant species. Furthermore, most tools require the user to input manually curated lists of gene position information, DNA sequence or gene homology relations between species. With the growing number of sequenced genomes, there is a need to provide new comparative genomics tools that can address the analysis of multi-species gene colocalization., Results: Kerfuffle is a web tool designed to help discover, visualize, and quantify the physical organization of genomes by identifying significant gene colocalization and conservation across the assembled genomes of available species (currently up to 47, from humans to worms). Kerfuffle only requires the user to specify a list of human genes and the names of other species of interest. Without further input from the user, the software queries the e!Ensembl BioMart server to obtain positional information and discovers homology relations in all genes and species specified. Using this information, Kerfuffle performs a multi-species clustering analysis, presents downloadable lists of clustered genes, performs Monte Carlo statistical significance calculations, estimates how conserved gene clusters are across species, plots histograms and interactive graphs, allows users to save their queries, and generates a downloadable visualization of the clusters using the Circos software. These analyses may be used to further explore the functional roles of gene clusters by interrogating the enriched molecular pathways associated with each cluster., Conclusions: Kerfuffle is a new, easy-to-use and publicly available tool to aid our understanding of functional genomics and comparative genomics. This software allows for flexibility and quick investigations of a user-defined set of genes, and the results may be saved online for further analysis. Kerfuffle is freely available at http://atwallab.org/kerfuffle, is implemented in JavaScript (using jQuery and jsCharts libraries) and PHP 5.2, runs on an Apache server, and stores data in flat files and an SQLite database.

When growth regulatory genes are damaged in a cell, it may become cancerous. Current technological advances in the last decade have allowed the characterization of the whole genome of these cells by directly or indirectly measuring DNA changes. Complementary analyses were developed to make sense of the massive amounts of data generated. A large majority of these analyses were developed to construct interaction networks between genes from, primarily, expression array data. We review the current technologies and analyses that have developed in the last decade. We further argue that as cancer genomics evolves from single gene validations to gene network inferences, new analyses must be developed for the different technological platforms.

Plasma insulin is pulsatile and reflects oscillatory insulin secretion from pancreatic islets. Although both islet Ca(2+) and metabolism oscillate, there is disagreement over their interrelationship, and whether they can be dissociated. In some models of islet oscillations, Ca(2+) must oscillate for metabolic oscillations to occur, whereas in others metabolic oscillations can occur without Ca(2+) oscillations. We used NAD(P)H fluorescence to assay oscillatory metabolism in mouse islets stimulated by 11.1 mM glucose. After abolishing Ca(2+) oscillations with 200 microM diazoxide, we observed that oscillations in NAD(P)H persisted in 34% of islets (n = 101). In the remainder of the islets (66%) both Ca(2+) and NAD(P)H oscillations were eliminated by diazoxide. However, in most of these islets NAD(P)H oscillations could be restored and amplified by raising extracellular KCl, which elevated the intracellular Ca(2+) level but did not restore Ca(2+) oscillations. Comparatively, we examined islets from ATP-sensitive K(+) (K(ATP)) channel-deficient SUR1(-/-) mice. Again NAD(P)H oscillations were evident even though Ca(2+) and membrane potential oscillations were abolished. These observations are predicted by the dual oscillator model, in which intrinsic metabolic oscillations and Ca(2+) feedback both contribute to the oscillatory islet behavior, but argue against other models that depend on Ca(2+) oscillations for metabolic oscillations to occur., (Copyright 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.)

Individual mouse pancreatic islets exhibit oscillations in [Ca(2+)](i) and insulin secretion in response to glucose in vitro, but how the oscillations of a million islets are coordinated within the human pancreas in vivo is unclear. Islet to islet synchronization is necessary, however, for the pancreas to produce regular pulses of insulin. To determine whether neurohormone release within the pancreas might play a role in coordinating islet activity, [Ca(2+)](i) changes in 4-6 isolated mouse islets were simultaneously monitored before and after a transient pulse of a putative synchronizing agent. The degree of synchronicity was quantified using a novel analytical approach that yields a parameter that we call the "Synchronization Index". Individual islets exhibited [Ca(2+)](i) oscillations with periods of 3-6 min, but were not synchronized under control conditions. However, raising islet [Ca(2+)](i) with a brief application of the cholinergic agonist carbachol (25 microM) or elevated KCl in glucose-containing saline rapidly synchronized islet [Ca(2+)](i) oscillations for >/=30 min, long after the synchronizing agent was removed. In contrast, the adrenergic agonists clonidine or norepinephrine, and the K(ATP) channel inhibitor tolbutamide, failed to synchronize islets. Partial synchronization was observed, however, with the K(ATP) channel opener diazoxide. The synchronizing action of carbachol depended on the glucose concentration used, suggesting that glucose metabolism was necessary for synchronization to occur. To understand how transiently perturbing islet [Ca(2+)](i) produced sustained synchronization, we used a mathematical model of islet oscillations in which complex oscillatory behavior results from the interaction between a fast electrical subsystem and a slower metabolic oscillator. Transient synchronization simulated by the model was mediated by resetting of the islet oscillators to a similar initial phase followed by transient "ringing" behavior, during which the model islets oscillated with a similar frequency. These results suggest that neurohormone release from intrapancreatic neurons could help synchronize islets in situ. Defects in this coordinating mechanism could contribute to the disrupted insulin secretion observed in Type 2 diabetes.