Adam C. Smith
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View article: What the VAF? A guide to the interpretation of variant allele fraction, percent mosaicism, and copy number in cancer
What the VAF? A guide to the interpretation of variant allele fraction, percent mosaicism, and copy number in cancer Open
The evolution of techniques used to identify structural variants (SVs) and copy number variants (CNVs) in genomes have seen significant development in the last decade. With the growing use of more technologies including chromosomal microar…
View article: A Single‐Center Study on Frontline Treatment for Multiple Myeloma Patients With 1q Abnormalities
A Single‐Center Study on Frontline Treatment for Multiple Myeloma Patients With 1q Abnormalities Open
Introduction Chromosome 1q copy gains (with‐1q‐gain) is a frequently observed genetic abnormality in multiple myeloma (MM) patients. Recent research has demonstrated that 1q gain is a prognostic factor, linked to poorer clinical outcomes. …
View article: Integrative cytogenetic and molecular studies unmask “chromosomal mimicry” in hematologic malignancies
Integrative cytogenetic and molecular studies unmask “chromosomal mimicry” in hematologic malignancies Open
The detection of structural variants (SVs) represents a critical component in the diagnostic evaluation and treatment of many hematologic malignancies. Although clinical SV testing mainly consists of traditional cytogenetic methodologies, …
View article: Membrane Stabilization of Helical Previtamin D Conformers as Possible Enhancement of Vitamin D Photoproduction
Membrane Stabilization of Helical Previtamin D Conformers as Possible Enhancement of Vitamin D Photoproduction Open
Photoinduced vitamin D formation occurs 10-15-fold faster in phospholipid bilayers (PLB) than in isotropic solution. It has been hypothesized that amphipatic interactions of the PLB with the rotationally flexible previtamin D (Pre) stabili…
View article: Diagnosis of systemic mastocytosis with cryptic deletion of <scp>TET2</scp> and <scp>DNMT3A</scp> resulting from unbalanced translocation
Diagnosis of systemic mastocytosis with cryptic deletion of <span>TET2</span> and <span>DNMT3A</span> resulting from unbalanced translocation Open
Summary Systemic mastocytosis (SM) is a rare haematological neoplasm associated with the gain of function mutation KIT D816V in 90% of adult patients. Classically, cytogenetic aberrations are not common except in cases of SM associated wit…
View article: Genomic Characterization of Partial Tandem Duplication Involving the KMT2A Gene in Adult Acute Myeloid Leukemia
Genomic Characterization of Partial Tandem Duplication Involving the KMT2A Gene in Adult Acute Myeloid Leukemia Open
Background: Gene rearrangements affecting KMT2A are frequent in acute myeloid leukemia (AML) and are often associated with a poor prognosis. KMT2A gene fusions are often detected by chromosome banding analysis and confirmed by fluorescence…
View article: Genomic Characterization of Partial Tandem Duplication Involving the KMT2A Gene in Adult Acute Myeloid Leukemia
Genomic Characterization of Partial Tandem Duplication Involving the KMT2A Gene in Adult Acute Myeloid Leukemia Open
Background. Gene rearrangements affecting KMT2A are frequent in acute myeloid leukemia (AML) and are often associated with a poor prognosis. KMT2A gene fusions are often detected by chromosome banding analysis and confirmed by fluorescence…
View article: A framework for the clinical implementation of optical genome mapping in hematologic malignancies
A framework for the clinical implementation of optical genome mapping in hematologic malignancies Open
Optical Genome Mapping (OGM) is rapidly emerging as an exciting cytogenomic technology both for research and clinical purposes. In the last 2 years alone, multiple studies have demonstrated that OGM not only matches the diagnostic scope of…
View article: Cytogenetics Is a Science, Not a Technique! Why Optical Genome Mapping Is So Important to Clinical Genetic Laboratories
Cytogenetics Is a Science, Not a Technique! Why Optical Genome Mapping Is So Important to Clinical Genetic Laboratories Open
Karyotyping is a technique that has been used in clinical cytogenetic laboratories for more than 40 years [...]
View article: Frontmatter
Frontmatter Open
Scottish philosophy through the agesThis series covers the full range of Scottish philosophy over five centuries -from the medieval period through the Reformation and Enlightenment periods, to the nineteenth and early twentieth centuries.T…
View article: Molecular dynamics simulation of apolipoprotein E3 lipid nanodiscs
Molecular dynamics simulation of apolipoprotein E3 lipid nanodiscs Open
View article: Molecular Dynamics Simulation of Apolipoprotein E3 Lipid Nanodiscs
Molecular Dynamics Simulation of Apolipoprotein E3 Lipid Nanodiscs Open
Nanodiscs are binary discoidal complexes of a phospholipid bilayer circumscribed by belt-like helical scaffold proteins. Using coarse-grained and all-atom molecular dynamics simulations, we explore the stability, size, and structure of nan…
View article: Molecular characterization and clonal evolution in Richter transformation: Insights from a case of plasmablastic lymphoma (RT‐PBL) arising from chronic lymphocytic leukaemia (CLL) and review of the literature
Molecular characterization and clonal evolution in Richter transformation: Insights from a case of plasmablastic lymphoma (RT‐PBL) arising from chronic lymphocytic leukaemia (CLL) and review of the literature Open
Richter transformation (RT) represents a high-grade transformation observed in chronic lymphocytic leukaemia (CLL)/small lymphocytic lymphoma, leading to increased aggressiveness and unfavourable outcomes. Among the variants of RT, diffuse…
View article: Biallelic disruption of DDX41 activity is associated with distinct genomic and immunophenotypic hallmarks in acute leukemia
Biallelic disruption of DDX41 activity is associated with distinct genomic and immunophenotypic hallmarks in acute leukemia Open
Introduction Inherited DDX41 mutations cause familial predisposition to hematologic malignancies including acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS), with the majority of DDX41 mutated MDS/AMLs described to date harb…
View article: Upfront Next Generation Sequencing in Non-Small Cell Lung Cancer
Upfront Next Generation Sequencing in Non-Small Cell Lung Cancer Open
In advanced non-small cell lung cancer (NSCLC), patients with actionable genomic alterations may derive additional clinical benefit from targeted treatment compared to cytotoxic chemotherapy. Current guidelines recommend extensive testing …
View article: Severe small intestinal bacterial overgrowth syndrome after jejunal feeding requiring surgical intervention: a case report and review of the literature
Severe small intestinal bacterial overgrowth syndrome after jejunal feeding requiring surgical intervention: a case report and review of the literature Open
View article: LB-2 | Distal versus Proximal Radial Artery Access for Cardiac Catheterization and Intervention: 30-day Outcomes of The DIPRA Study
LB-2 | Distal versus Proximal Radial Artery Access for Cardiac Catheterization and Intervention: 30-day Outcomes of The DIPRA Study Open
BackgroundProximal radial artery (PRA) access for cardiac catheterization has been shown to be safe and with a mortality benefit compared to femoral access.However, it can jeopardize subsequent use of the artery due to occlusion. Distal ra…
View article: Single cell proteogenomic sequencing identifies a relapse‐fated AML subclone carrying <i>FLT3</i>‐ITD with CN‐LOH at chr13q
Single cell proteogenomic sequencing identifies a relapse‐fated AML subclone carrying <i>FLT3</i>‐ITD with CN‐LOH at chr13q Open
Internal tandem duplication of the Feline McDonough Sarcoma (FMS)‐like tyrosine kinase 3 ( FLT3 ‐ITD) is one of the most clinically relevant mutations in acute myeloid leukemia (AML), with a high FLT3 ‐ITD allelic ratio (AR) (≥0.5) being s…
View article: Guiding the global evolution of cytogenetic testing for hematologic malignancies
Guiding the global evolution of cytogenetic testing for hematologic malignancies Open
Cytogenetics has long represented a critical component in the clinical evaluation of hematologic malignancies. Chromosome banding studies provide a simultaneous snapshot of genome-wide copy number and structural variation, which have been …
View article: Correction to: Inflammatory breast cancer defined: proposed common diagnostic criteria to guide treatment and research
Correction to: Inflammatory breast cancer defined: proposed common diagnostic criteria to guide treatment and research Open
View article: Integrating comprehensive genomic sequencing of non-small cell lung cancer into a public healthcare system
Integrating comprehensive genomic sequencing of non-small cell lung cancer into a public healthcare system Open
CGP identifies additional actionable targets beyond single gene tests with a direct impact on patient treatment and increased clinical trial eligibility. These benefits highlight the value of CGP in patients with NSCLC in public health sys…
View article: Inflammatory breast cancer defined: proposed common diagnostic criteria to guide treatment and research
Inflammatory breast cancer defined: proposed common diagnostic criteria to guide treatment and research Open
View article: Reflex ROS1 IHC Screening with FISH Confirmation for Advanced Non-Small Cell Lung Cancer—A Cost-Efficient Strategy in a Public Healthcare System
Reflex ROS1 IHC Screening with FISH Confirmation for Advanced Non-Small Cell Lung Cancer—A Cost-Efficient Strategy in a Public Healthcare System Open
ROS1 rearrangements are identified in 1–2% of lung adenocarcinoma cases, and reflex testing is guideline-recommended. We developed a decision model for population-based ROS1 testing from a Canadian public healthcare perspective to determin…
View article: MDS/MPN-Unclassifiable with t(X;17)(q28;q21) and <b><i>KANSL1-MTCP1/CMC4</i></b> Fusion Gene
MDS/MPN-Unclassifiable with t(X;17)(q28;q21) and <b><i>KANSL1-MTCP1/CMC4</i></b> Fusion Gene Open
Myelodysplastic/myeloproliferative neoplasm, unclassifiable (MDS/MPN-U) is a poorly characterized entity among overlap myeloid syndromes. Recent studies have shown heterogeneous mutational profiles in this group being able to subclassify t…
View article: Fusion of Large Polypeptides to Human Adenovirus Type 5 Capsid Protein IX Can Compromise Virion Stability and DNA Packaging Capacity
Fusion of Large Polypeptides to Human Adenovirus Type 5 Capsid Protein IX Can Compromise Virion Stability and DNA Packaging Capacity Open
Human adenovirus capsid protein IX (pIX) is involved in stabilizing the virion but has also been developed as a platform for presentation of various polypeptides on the surface of the virion. Whether such modifications affect the ability o…
View article: Centromeric cohesion failure invokes a conserved choreography of chromosomal mis-segregations in pancreatic neuroendocrine tumor
Centromeric cohesion failure invokes a conserved choreography of chromosomal mis-segregations in pancreatic neuroendocrine tumor Open
Background Pancreatic neuroendocrine tumors (PANETs) are rare, slow growing cancers that often present with local and distant metastasis upon detection. PANETS contain distinct karyotypes, epigenetic dysregulation, and recurrent mutations …
View article: Additional file 5 of Centromeric cohesion failure invokes a conserved choreography of chromosomal mis-segregations in pancreatic neuroendocrine tumor
Additional file 5 of Centromeric cohesion failure invokes a conserved choreography of chromosomal mis-segregations in pancreatic neuroendocrine tumor Open
Additional file 5. Somatic mutation calls from the exome and whole-genome cohort analyzed in this study.
View article: Additional file 1 of Centromeric cohesion failure invokes a conserved choreography of chromosomal mis-segregations in pancreatic neuroendocrine tumor
Additional file 1 of Centromeric cohesion failure invokes a conserved choreography of chromosomal mis-segregations in pancreatic neuroendocrine tumor Open
Additional file 1. Details of CGH datasets, listing chromosome gains and losses as reported in the paper of origin.
View article: Additional file 4 of Centromeric cohesion failure invokes a conserved choreography of chromosomal mis-segregations in pancreatic neuroendocrine tumor
Additional file 4 of Centromeric cohesion failure invokes a conserved choreography of chromosomal mis-segregations in pancreatic neuroendocrine tumor Open
Additional file 4. Supplementary tables for the manuscript.
View article: Additional file 6 of Centromeric cohesion failure invokes a conserved choreography of chromosomal mis-segregations in pancreatic neuroendocrine tumor
Additional file 6 of Centromeric cohesion failure invokes a conserved choreography of chromosomal mis-segregations in pancreatic neuroendocrine tumor Open
Additional file 6. Cellular fraction estimates of SNVs from 43 samples from the AACR GENIE v1.0 cohort as well as the exome and whole-genome datasets generated in this study.