Despite the improved outcome associated with current treatment strategies ofpediatric acute lymphoblastic leukemia (ALL), relapse still represents a major challenge. Pediatric ALL demonstrates branched evolution in response to selective pressure exerted by therapy; relapse founder clones emerge from pre-leukemic clones or minor subclones present at diagnosis. It is hence crucial to develop biomarkers capable of tracking subclones throughout therapy. Current practices for monitoring disease response in leukemia rely on the analysis of BM biopsy sample at specific time points throughout therapy. Not only the invasiveness of the BM biopsy hinders the sequential sampling, but also, the currently implied techniques are associated with a lack of sensitivity to detect subclones other than the major diagnostic clone. Somatic mutation detection in circulating-tumor DNA (Ct-DNA) offers a new venue for non-invasive studying of genetic heterogeneity and tracking clonal dynamics throughout therapy. Here, we employ targeted Next-Generation Sequencing (NGS) using a specifically designed ALL custom gene panel for Ct-DNA analysis of sequential plasma samples of 14 pediatric ALL during remission induction therapy. Utilizing 1 ml of plasma, Ct-DNA successfully captured all the clinically relevant somatic single nucleotide variants (SNVs) detected by whole exome sequencing (WES) in bone marrow (BM) biopsy samples at diagnosis. Moreover, we were able to show the ability of Ct-DNA analysis to track the change in the mutant allele fraction (MAF) across multiple time points as well as, to detect mutations in Flowcytometry (FC) MRD-negative patients. Taken together, sequential analysis of Ct-DNA in plasma demonstrates a role, as a non-invasive technique, for detecting the clonal composition as well as, tracking clonal dynamics in pediatric ALL.
","abstract_html":"<p>Despite the improved outcome associated with current treatment strategies ofpediatric acute lymphoblastic leukemia (ALL), relapse still represents a major challenge. Pediatric ALL demonstrates branched evolution in response to selective pressure exerted by therapy; relapse founder clones emerge from pre-leukemic clones or minor subclones present at diagnosis. It is hence crucial to develop biomarkers capable of tracking subclones throughout therapy. Current practices for monitoring disease response in leukemia rely on the analysis of BM biopsy sample at specific time points throughout therapy. Not only the invasiveness of the BM biopsy hinders the sequential sampling, but also, the currently implied techniques are associated with a lack of sensitivity to detect subclones other than the major diagnostic clone. Somatic mutation detection in circulating-tumor DNA (Ct-DNA) offers a new venue for non-invasive studying of genetic heterogeneity and tracking clonal dynamics throughout therapy. Here, we employ targeted Next-Generation Sequencing (NGS) using a specifically designed ALL custom gene panel for Ct-DNA analysis of sequential plasma samples of 14 pediatric ALL during remission induction therapy. Utilizing 1 ml of plasma, Ct-DNA successfully captured all the clinically relevant somatic single nucleotide variants (SNVs) detected by whole exome sequencing (WES) in bone marrow (BM) biopsy samples at diagnosis. Moreover, we were able to show the ability of Ct-DNA analysis to track the change in the mutant allele fraction (MAF) across multiple time points as well as, to detect mutations in Flowcytometry (FC) MRD-negative patients. Taken together, sequential analysis of Ct-DNA in plasma demonstrates a role, as a non-invasive technique, for detecting the clonal composition as well as, tracking clonal dynamics in pediatric ALL.</p>","abstract_has_math":false,"creators":["Youssef, Sarah Hisham Abdelaziz"],"institution":null,"degree_name":"Master of Science (MS)","degree_level":"Thesis","degree_discipline":"Pharmaceutical Sciences","degree_department":null,"school":null,"contributors":["Charles Gawad, MD, Ph.D."],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2018,"date_issued":"2018-05-01T07:00:00Z","date_published":"2018-05-01T07:00:00Z","updated_at":"2026-07-24T05:00:33Z","subjects":["Acute Lymphoblastic Leukemia","Circulating-tumor DNA (Ct-DNA)","Clonal Dynamics","Leukemia-derived Circulating DNA","Pediatrics","Somatic Mutations","Medical Genetics","Medical Molecular Biology","Medical Sciences","Medicine and Health Sciences","Pharmacy and Pharmaceutical Sciences"],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://dc.uthsc.edu/dissertations/458","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Charles Gawad, MD, Ph.D."]},{"key":"dc:creator","label":"Author","values":["Youssef, Sarah Hisham Abdelaziz"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.available","label":"Dc Date Available","values":["2018-07-09T07:00:00Z"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Pharmaceutical Sciences"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Thesis"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Master of Science (MS)"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Acute Lymphoblastic Leukemia","Circulating-tumor DNA (Ct-DNA)","Clonal Dynamics","Leukemia-derived Circulating DNA","Pediatrics","Somatic Mutations","Medical Genetics","Medical Molecular Biology","Medical Sciences","Medicine and Health Sciences","Pharmacy and Pharmaceutical Sciences"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://dc.uthsc.edu/dissertations/458"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Despite the improved outcome associated with current treatment strategies ofpediatric acute lymphoblastic leukemia (ALL), relapse still represents a major challenge. Pediatric ALL demonstrates branched evolution in response to selective pressure exerted by therapy; relapse founder clones emerge from pre-leukemic clones or minor subclones present at diagnosis. It is hence crucial to develop biomarkers capable of tracking subclones throughout therapy. Current practices for monitoring disease response in leukemia rely on the analysis of BM biopsy sample at specific time points throughout therapy. Not only the invasiveness of the BM biopsy hinders the sequential sampling, but also, the currently implied techniques are associated with a lack of sensitivity to detect subclones other than the major diagnostic clone. Somatic mutation detection in circulating-tumor DNA (Ct-DNA) offers a new venue for non-invasive studying of genetic heterogeneity and tracking clonal dynamics throughout therapy. Here, we employ targeted Next-Generation Sequencing (NGS) using a specifically designed ALL custom gene panel for Ct-DNA analysis of sequential plasma samples of 14 pediatric ALL during remission induction therapy. Utilizing 1 ml of plasma, Ct-DNA successfully captured all the clinically relevant somatic single nucleotide variants (SNVs) detected by whole exome sequencing (WES) in bone marrow (BM) biopsy samples at diagnosis. Moreover, we were able to show the ability of Ct-DNA analysis to track the change in the mutant allele fraction (MAF) across multiple time points as well as, to detect mutations in Flowcytometry (FC) MRD-negative patients. Taken together, sequential analysis of Ct-DNA in plasma demonstrates a role, as a non-invasive technique, for detecting the clonal composition as well as, tracking clonal dynamics in pediatric ALL.
"]},{"key":"dc:title","label":"Title","values":["Somatic Mutation Detection in Leukemia-Derived Circulating DNA: Utility in Monitoring Clonal Dynamics and Disease Response in Pediatric Acute Lymphoblastic Leukemia"]}]}],"canonical_facts":{"dc:contributor":["Charles Gawad, MD, Ph.D."],"dc:creator":["Youssef, Sarah Hisham Abdelaziz"],"dc:date.available":["2018-07-09T07:00:00Z"],"dc:description.abstract":["Despite the improved outcome associated with current treatment strategies ofpediatric acute lymphoblastic leukemia (ALL), relapse still represents a major challenge. Pediatric ALL demonstrates branched evolution in response to selective pressure exerted by therapy; relapse founder clones emerge from pre-leukemic clones or minor subclones present at diagnosis. It is hence crucial to develop biomarkers capable of tracking subclones throughout therapy. Current practices for monitoring disease response in leukemia rely on the analysis of BM biopsy sample at specific time points throughout therapy. Not only the invasiveness of the BM biopsy hinders the sequential sampling, but also, the currently implied techniques are associated with a lack of sensitivity to detect subclones other than the major diagnostic clone. Somatic mutation detection in circulating-tumor DNA (Ct-DNA) offers a new venue for non-invasive studying of genetic heterogeneity and tracking clonal dynamics throughout therapy. Here, we employ targeted Next-Generation Sequencing (NGS) using a specifically designed ALL custom gene panel for Ct-DNA analysis of sequential plasma samples of 14 pediatric ALL during remission induction therapy. Utilizing 1 ml of plasma, Ct-DNA successfully captured all the clinically relevant somatic single nucleotide variants (SNVs) detected by whole exome sequencing (WES) in bone marrow (BM) biopsy samples at diagnosis. Moreover, we were able to show the ability of Ct-DNA analysis to track the change in the mutant allele fraction (MAF) across multiple time points as well as, to detect mutations in Flowcytometry (FC) MRD-negative patients. Taken together, sequential analysis of Ct-DNA in plasma demonstrates a role, as a non-invasive technique, for detecting the clonal composition as well as, tracking clonal dynamics in pediatric ALL.
"],"dc:identifier":["https://dc.uthsc.edu/dissertations/458"],"dc:subject":["Acute Lymphoblastic Leukemia","Circulating-tumor DNA (Ct-DNA)","Clonal Dynamics","Leukemia-derived Circulating DNA","Pediatrics","Somatic Mutations","Medical Genetics","Medical Molecular Biology","Medical Sciences","Medicine and Health Sciences","Pharmacy and Pharmaceutical Sciences"],"dc:title":["Somatic Mutation Detection in Leukemia-Derived Circulating DNA: Utility in Monitoring Clonal Dynamics and Disease Response in Pediatric Acute Lymphoblastic Leukemia"],"thesis:degree_discipline":["Pharmaceutical Sciences"],"thesis:degree_level":["Thesis"],"thesis:degree_name":["Master of Science (MS)"]},"updated_at":"2026-07-24T05:00:33Z"}