HIGH THROUGHPUT SEQUENCING AS A MEASURE OF EARLY RESPONSE TO THERAPY IN CHILDHOOD ALL
(Abstract release date: 05/19/16)
EHA Library. Kirsch I. 06/11/16; 135252; S496
Dr. Ilan Kirsch
Contributions
Contributions
Abstract
Abstract: S496
Type: Oral Presentation
Presentation during EHA21: On Saturday, June 11, 2016 from 16:00 - 16:15
Location: Auditorium 2
Background
Early response to induction chemotherapy has been demonstrated to be a highly significant prognostic factor in the outcome of children with acute lymphoblastic leukemia. Multiparametric flow cytometry (mpFC) has been the routinely used methodology in the US for determination of this response. New high throughput sequencing (HTS) technologies of rearranged immune receptor (TCR and Ig) genes have raised the possibility of a more accurate, sensitive, and standardizable approach to determination of early response to therapy in ALL patients.
Aims
In this study, we investigated whether the Adaptive Biotechnologies assay of IgH and TCRG would be able to quantify residual disease at the end of induction therapy for children with ALL and be of prognostic value with regard to outcome (event free survival) in these patients.
Methods
The first study involved a total of 480 patients enrolled on Children’s Oncology Group (COG) clinical trials AALL0331 and AALL0232 for whom mpFC measurement of residual disease and outcome data are available. A second study involved samples from 73 patients enrolled in a former Pediatric Oncology Group trial, POG 9905, who were mpFC negative at d29. For increased statistical power the patients in POG 9905 were selected for analysis so that ~50% had relapsed disease determined in follow-up monitoring.MpFC was performed at COG reference laboratories the University of Washington or Johns Hopkins Hospital as part of the evaluation for MRD. Genomic DNA was extracted from frozen bone marrow specimens collected at diagnosis and at day 29 post the start of induction therapy. High throughput sequencing of CDR3 regions of IGH and TCRG was performed on all samples, with the testing laboratory blinded to patient outcome. Diagnostic and d29 matched samples from a given patient were sequenced and dominant clonal CDR3 sequences from diagnosis were searched for in the corresponding d29 sample. Both the presence and the frequency of the MRD clone relative to the total IGH repertoire and total nucleated cell population were determined.
Results
The assays defined the dominant clonal sequences in 93% of the patients. 70% of this subgroup was found to have residual disease present at d29. Clones from some of the patients demonstrated a single “trackable” sequence while clones from other patients demonstrated multiple trackable sequences either within or between the two immune receptor loci being assessed. 60 % of the residual disease detected by HTS was previously reported as MRD negative by mpFC. For “standard risk” patients, 53% were positive for MRD by HTS and negative by mpFC. With the combined COG data, using a MRD cutoff of 10-4, HTS was able to define a correlation with event-free survival (p=0.0003). Furthermore, for the “standard risk” patients, being MRD positive or negative as determined by the more sensitive HTS assay was also correlated with outcome (p=0.02). In addition, a correlation was noted between poorer outcome and a “germline” or TCRG only (i.e. IgH loci retained in the germline configuration) genotype (p=0.04). In the second study of patients enrolled in the POG 9905 trial, the more sensitive HTS cut-off of 10-5 was correlated with outcome (p=0.0228).
Conclusion
This is the largest patient cohort studied to date for which mpFC, HTS, and outcome data are available. This work suggests that HTS is an accurate and standardized assay whose increased sensitivity compared to mpFC is relevant to determination of patient outcome.
Session topic: Acute lymphoblastic leukemia - Clinical
Keyword(s): Acute lymphoblastic leukemia, Ig and TCR gene rearrangement, Prognosis
Type: Oral Presentation
Presentation during EHA21: On Saturday, June 11, 2016 from 16:00 - 16:15
Location: Auditorium 2
Background
Early response to induction chemotherapy has been demonstrated to be a highly significant prognostic factor in the outcome of children with acute lymphoblastic leukemia. Multiparametric flow cytometry (mpFC) has been the routinely used methodology in the US for determination of this response. New high throughput sequencing (HTS) technologies of rearranged immune receptor (TCR and Ig) genes have raised the possibility of a more accurate, sensitive, and standardizable approach to determination of early response to therapy in ALL patients.
Aims
In this study, we investigated whether the Adaptive Biotechnologies assay of IgH and TCRG would be able to quantify residual disease at the end of induction therapy for children with ALL and be of prognostic value with regard to outcome (event free survival) in these patients.
Methods
The first study involved a total of 480 patients enrolled on Children’s Oncology Group (COG) clinical trials AALL0331 and AALL0232 for whom mpFC measurement of residual disease and outcome data are available. A second study involved samples from 73 patients enrolled in a former Pediatric Oncology Group trial, POG 9905, who were mpFC negative at d29. For increased statistical power the patients in POG 9905 were selected for analysis so that ~50% had relapsed disease determined in follow-up monitoring.MpFC was performed at COG reference laboratories the University of Washington or Johns Hopkins Hospital as part of the evaluation for MRD. Genomic DNA was extracted from frozen bone marrow specimens collected at diagnosis and at day 29 post the start of induction therapy. High throughput sequencing of CDR3 regions of IGH and TCRG was performed on all samples, with the testing laboratory blinded to patient outcome. Diagnostic and d29 matched samples from a given patient were sequenced and dominant clonal CDR3 sequences from diagnosis were searched for in the corresponding d29 sample. Both the presence and the frequency of the MRD clone relative to the total IGH repertoire and total nucleated cell population were determined.
Results
The assays defined the dominant clonal sequences in 93% of the patients. 70% of this subgroup was found to have residual disease present at d29. Clones from some of the patients demonstrated a single “trackable” sequence while clones from other patients demonstrated multiple trackable sequences either within or between the two immune receptor loci being assessed. 60 % of the residual disease detected by HTS was previously reported as MRD negative by mpFC. For “standard risk” patients, 53% were positive for MRD by HTS and negative by mpFC. With the combined COG data, using a MRD cutoff of 10-4, HTS was able to define a correlation with event-free survival (p=0.0003). Furthermore, for the “standard risk” patients, being MRD positive or negative as determined by the more sensitive HTS assay was also correlated with outcome (p=0.02). In addition, a correlation was noted between poorer outcome and a “germline” or TCRG only (i.e. IgH loci retained in the germline configuration) genotype (p=0.04). In the second study of patients enrolled in the POG 9905 trial, the more sensitive HTS cut-off of 10-5 was correlated with outcome (p=0.0228).
Conclusion
This is the largest patient cohort studied to date for which mpFC, HTS, and outcome data are available. This work suggests that HTS is an accurate and standardized assay whose increased sensitivity compared to mpFC is relevant to determination of patient outcome.
Session topic: Acute lymphoblastic leukemia - Clinical
Keyword(s): Acute lymphoblastic leukemia, Ig and TCR gene rearrangement, Prognosis
Abstract: S496
Type: Oral Presentation
Presentation during EHA21: On Saturday, June 11, 2016 from 16:00 - 16:15
Location: Auditorium 2
Background
Early response to induction chemotherapy has been demonstrated to be a highly significant prognostic factor in the outcome of children with acute lymphoblastic leukemia. Multiparametric flow cytometry (mpFC) has been the routinely used methodology in the US for determination of this response. New high throughput sequencing (HTS) technologies of rearranged immune receptor (TCR and Ig) genes have raised the possibility of a more accurate, sensitive, and standardizable approach to determination of early response to therapy in ALL patients.
Aims
In this study, we investigated whether the Adaptive Biotechnologies assay of IgH and TCRG would be able to quantify residual disease at the end of induction therapy for children with ALL and be of prognostic value with regard to outcome (event free survival) in these patients.
Methods
The first study involved a total of 480 patients enrolled on Children’s Oncology Group (COG) clinical trials AALL0331 and AALL0232 for whom mpFC measurement of residual disease and outcome data are available. A second study involved samples from 73 patients enrolled in a former Pediatric Oncology Group trial, POG 9905, who were mpFC negative at d29. For increased statistical power the patients in POG 9905 were selected for analysis so that ~50% had relapsed disease determined in follow-up monitoring.MpFC was performed at COG reference laboratories the University of Washington or Johns Hopkins Hospital as part of the evaluation for MRD. Genomic DNA was extracted from frozen bone marrow specimens collected at diagnosis and at day 29 post the start of induction therapy. High throughput sequencing of CDR3 regions of IGH and TCRG was performed on all samples, with the testing laboratory blinded to patient outcome. Diagnostic and d29 matched samples from a given patient were sequenced and dominant clonal CDR3 sequences from diagnosis were searched for in the corresponding d29 sample. Both the presence and the frequency of the MRD clone relative to the total IGH repertoire and total nucleated cell population were determined.
Results
The assays defined the dominant clonal sequences in 93% of the patients. 70% of this subgroup was found to have residual disease present at d29. Clones from some of the patients demonstrated a single “trackable” sequence while clones from other patients demonstrated multiple trackable sequences either within or between the two immune receptor loci being assessed. 60 % of the residual disease detected by HTS was previously reported as MRD negative by mpFC. For “standard risk” patients, 53% were positive for MRD by HTS and negative by mpFC. With the combined COG data, using a MRD cutoff of 10-4, HTS was able to define a correlation with event-free survival (p=0.0003). Furthermore, for the “standard risk” patients, being MRD positive or negative as determined by the more sensitive HTS assay was also correlated with outcome (p=0.02). In addition, a correlation was noted between poorer outcome and a “germline” or TCRG only (i.e. IgH loci retained in the germline configuration) genotype (p=0.04). In the second study of patients enrolled in the POG 9905 trial, the more sensitive HTS cut-off of 10-5 was correlated with outcome (p=0.0228).
Conclusion
This is the largest patient cohort studied to date for which mpFC, HTS, and outcome data are available. This work suggests that HTS is an accurate and standardized assay whose increased sensitivity compared to mpFC is relevant to determination of patient outcome.
Session topic: Acute lymphoblastic leukemia - Clinical
Keyword(s): Acute lymphoblastic leukemia, Ig and TCR gene rearrangement, Prognosis
Type: Oral Presentation
Presentation during EHA21: On Saturday, June 11, 2016 from 16:00 - 16:15
Location: Auditorium 2
Background
Early response to induction chemotherapy has been demonstrated to be a highly significant prognostic factor in the outcome of children with acute lymphoblastic leukemia. Multiparametric flow cytometry (mpFC) has been the routinely used methodology in the US for determination of this response. New high throughput sequencing (HTS) technologies of rearranged immune receptor (TCR and Ig) genes have raised the possibility of a more accurate, sensitive, and standardizable approach to determination of early response to therapy in ALL patients.
Aims
In this study, we investigated whether the Adaptive Biotechnologies assay of IgH and TCRG would be able to quantify residual disease at the end of induction therapy for children with ALL and be of prognostic value with regard to outcome (event free survival) in these patients.
Methods
The first study involved a total of 480 patients enrolled on Children’s Oncology Group (COG) clinical trials AALL0331 and AALL0232 for whom mpFC measurement of residual disease and outcome data are available. A second study involved samples from 73 patients enrolled in a former Pediatric Oncology Group trial, POG 9905, who were mpFC negative at d29. For increased statistical power the patients in POG 9905 were selected for analysis so that ~50% had relapsed disease determined in follow-up monitoring.MpFC was performed at COG reference laboratories the University of Washington or Johns Hopkins Hospital as part of the evaluation for MRD. Genomic DNA was extracted from frozen bone marrow specimens collected at diagnosis and at day 29 post the start of induction therapy. High throughput sequencing of CDR3 regions of IGH and TCRG was performed on all samples, with the testing laboratory blinded to patient outcome. Diagnostic and d29 matched samples from a given patient were sequenced and dominant clonal CDR3 sequences from diagnosis were searched for in the corresponding d29 sample. Both the presence and the frequency of the MRD clone relative to the total IGH repertoire and total nucleated cell population were determined.
Results
The assays defined the dominant clonal sequences in 93% of the patients. 70% of this subgroup was found to have residual disease present at d29. Clones from some of the patients demonstrated a single “trackable” sequence while clones from other patients demonstrated multiple trackable sequences either within or between the two immune receptor loci being assessed. 60 % of the residual disease detected by HTS was previously reported as MRD negative by mpFC. For “standard risk” patients, 53% were positive for MRD by HTS and negative by mpFC. With the combined COG data, using a MRD cutoff of 10-4, HTS was able to define a correlation with event-free survival (p=0.0003). Furthermore, for the “standard risk” patients, being MRD positive or negative as determined by the more sensitive HTS assay was also correlated with outcome (p=0.02). In addition, a correlation was noted between poorer outcome and a “germline” or TCRG only (i.e. IgH loci retained in the germline configuration) genotype (p=0.04). In the second study of patients enrolled in the POG 9905 trial, the more sensitive HTS cut-off of 10-5 was correlated with outcome (p=0.0228).
Conclusion
This is the largest patient cohort studied to date for which mpFC, HTS, and outcome data are available. This work suggests that HTS is an accurate and standardized assay whose increased sensitivity compared to mpFC is relevant to determination of patient outcome.
Session topic: Acute lymphoblastic leukemia - Clinical
Keyword(s): Acute lymphoblastic leukemia, Ig and TCR gene rearrangement, Prognosis
{{ help_message }}
{{filter}}