Xiaotu Ma
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View article: CanID: A Robust and Accurate RNA-seq Expression-based Diagnostic Classification Scheme for Pediatric Malignancies
CanID: A Robust and Accurate RNA-seq Expression-based Diagnostic Classification Scheme for Pediatric Malignancies Open
Cancer subtype classification is critical for precision therapy and there is a growing trend of augmenting histopathology testing procedures with omics-based machine learning classifiers. However, analytical challenges remain for pediatric…
View article: Clonal Evolution of Pediatric Acute Myeloid Leukemia and Its Contribution to Disease Relapse
Clonal Evolution of Pediatric Acute Myeloid Leukemia and Its Contribution to Disease Relapse Open
Relapse remains the leading cause of mortality in pediatric acute myeloid leukemia (AML), yet the genetic changes contributing to relapse remain incompletely defined. To address this gap, we performed whole-genome sequencing and targeted-c…
View article: Precise combination therapy of radiotherapy and immunotherapy guided by joint PD-L1 imaging and T-cell imaging
Precise combination therapy of radiotherapy and immunotherapy guided by joint PD-L1 imaging and T-cell imaging Open
Background PD-1/PD-L1 blockade therapy is often used in combination with radiotherapy (RT) to enhance therapeutic efficacy in clinic. However, the effectiveness of the combination therapy is still unsatisfactory due to the blindness in the…
View article: Fast and sensitive detection of targeted gene fusions using frequency minimizers and fuzzy pattern matching with Fuzzion2
Fast and sensitive detection of targeted gene fusions using frequency minimizers and fuzzy pattern matching with Fuzzion2 Open
To enable fast and sensitive fusion detection critical for clinical oncology testing, we developed Fuzzion2, a pattern-matching program for detecting targeted gene fusions that employs an index of frequency minimizers and fuzzy matching to…
View article: Molecular Risk Markers Define Risk of Relapse in Myeloid Leukemia of Down syndrome Beyond Measurable Residual Disease
Molecular Risk Markers Define Risk of Relapse in Myeloid Leukemia of Down syndrome Beyond Measurable Residual Disease Open
Myeloid leukemia of Down syndrome (ML-DS) is a distinct form of pediatric acute myeloid leukemia (AML) that responds to reduced intensity chemotherapy as compared to non-DS AML that requires intensive chemotherapy and often stem cell trans…
View article: Seq2Karyotype (S2K): A Method for <i>in-silico</i> Karyotyping Using Single-Sample Whole-Genome Sequencing Data
Seq2Karyotype (S2K): A Method for <i>in-silico</i> Karyotyping Using Single-Sample Whole-Genome Sequencing Data Open
DNA abnormalities characterized by cytogenetic imaging at the single cell resolution, i.e. karyotyping, have long served as cancer diagnostic and prognostic biomarkers. To enable in-silico karyotyping using unpaired whole-genome sequencing…
View article: CanID: a robust and accurate RNAseq Expression-based diagnostic classification scheme for pediatric malignancies
CanID: a robust and accurate RNAseq Expression-based diagnostic classification scheme for pediatric malignancies Open
Cancer subtype classification is critical for precision therapy and there is a growing trend of augmenting histopathology testing procedures with omics-based machine learning classifiers. However, analytical challenges remain for pediatric…
View article: Germline Variant Burden Warrants Universal Genetic Testing in Pediatric Myeloid Leukemia
Germline Variant Burden Warrants Universal Genetic Testing in Pediatric Myeloid Leukemia Open
Causal germline genetic variants are frequently detected in young (under age 40) patients presenting with myelodysplastic syndromes (MDS) or bone marrow failure (BMF), where progression to acute myeloid leukemia (AML) contributes substanti…
View article: Confounding factors affecting analysis of germline structural variants in pediatric solid tumors
Confounding factors affecting analysis of germline structural variants in pediatric solid tumors Open
We provide data showing the germline predisposition structural variants (SV) involving MYCN and RAF1::TMEM40 reported by Gillani et al. (2025) in pediatric solid tumors are confounded by circulating tumor DNA (ctDNA) and enrichment for His…
View article: Hematopoietic Stem Cell Transplantation Outcomes for High-Risk AML: A Report From the Children's Oncology Group
Hematopoietic Stem Cell Transplantation Outcomes for High-Risk AML: A Report From the Children's Oncology Group Open
PURPOSE Hematopoietic stem cell transplantation (HSCT) is used as consolidation for pediatric patients with high-risk AML in first complete remission (CR1). The definition of high-risk AML has evolved considerably over the past two decades…
View article: The landscape of structural variation in pediatric cancer
The landscape of structural variation in pediatric cancer Open
Structural variants (SVs) account for over 60% of the driver variants in pediatric cancer, and in many cases act as the cancer initiating event. To study SVs from a pan-cancer perspective, we analyzed 1,616 pediatric cancer genomes in 16 m…
View article: <i>TP53</i> Inactivation Confers Resistance to the Menin Inhibitor Revumenib in Acute Myeloid Leukemia
<i>TP53</i> Inactivation Confers Resistance to the Menin Inhibitor Revumenib in Acute Myeloid Leukemia Open
Acute myeloid leukemia (AML) is a heterogeneous cancer that is associated with poor outcomes. Revumenib and other menin inhibitors have shown promising activity against AMLs with KMT2A -rearrangements or NPM1 mutations. However, mechanisms…
View article: Supplementary Table S1 from Conditional Activation of c-MYC in Distinct Catecholaminergic Cells Drives Development of Neuroblastoma or Somatostatinoma
Supplementary Table S1 from Conditional Activation of c-MYC in Distinct Catecholaminergic Cells Drives Development of Neuroblastoma or Somatostatinoma Open
CSTN tumor metadata
View article: Supplementary Table S4 from Conditional Activation of c-MYC in Distinct Catecholaminergic Cells Drives Development of Neuroblastoma or Somatostatinoma
Supplementary Table S4 from Conditional Activation of c-MYC in Distinct Catecholaminergic Cells Drives Development of Neuroblastoma or Somatostatinoma Open
Differentially expressed genes in c-MYC PNET and c-MYC neuroblastoma
View article: Supplementary Table S5 from Conditional Activation of c-MYC in Distinct Catecholaminergic Cells Drives Development of Neuroblastoma or Somatostatinoma
Supplementary Table S5 from Conditional Activation of c-MYC in Distinct Catecholaminergic Cells Drives Development of Neuroblastoma or Somatostatinoma Open
GSEA results for c-MYC PNET and c-MYC neuroblastoma
View article: Supplementary Data from Conditional Activation of c-MYC in Distinct Catecholaminergic Cells Drives Development of Neuroblastoma or Somatostatinoma
Supplementary Data from Conditional Activation of c-MYC in Distinct Catecholaminergic Cells Drives Development of Neuroblastoma or Somatostatinoma Open
Supplementary Data including 12 figures and table S1
View article: Data from Conditional Activation of c-MYC in Distinct Catecholaminergic Cells Drives Development of Neuroblastoma or Somatostatinoma
Data from Conditional Activation of c-MYC in Distinct Catecholaminergic Cells Drives Development of Neuroblastoma or Somatostatinoma Open
c-MYC is an important driver of high-risk neuroblastoma. A lack of c-MYC–driven genetically engineered mouse models (GEMM) has hampered the ability to better understand mechanisms of neuroblastoma oncogenesis and to develop effective thera…
View article: Supplementary Table S3 from Conditional Activation of c-MYC in Distinct Catecholaminergic Cells Drives Development of Neuroblastoma or Somatostatinoma
Supplementary Table S3 from Conditional Activation of c-MYC in Distinct Catecholaminergic Cells Drives Development of Neuroblastoma or Somatostatinoma Open
Differentially expressed genes in c-MYC- and MYCN-driven neuroblastomas
View article: Strategies and Mechanisms of Radiosensitization in Cancer Therapy
Strategies and Mechanisms of Radiosensitization in Cancer Therapy Open
View article: Analysis of Error Profiles of Indels and Structural Variants in Deep Sequencing Data
Analysis of Error Profiles of Indels and Structural Variants in Deep Sequencing Data Open
View article: <i>bamSliceR</i> : a Bioconductor package for rapid, cross-cohort variant and allelic bias analysis
<i>bamSliceR</i> : a Bioconductor package for rapid, cross-cohort variant and allelic bias analysis Open
Motivation The National Cancer Institute Genomic Data Commons (GDC) provides controlled access to sequencing data from thousands of subjects, enabling large-scale study of impactful genetic alterations such as simple and complex germline a…
View article: Conditional Activation of c-MYC in Distinct Catecholaminergic Cells Drives Development of Neuroblastoma or Somatostatinoma
Conditional Activation of c-MYC in Distinct Catecholaminergic Cells Drives Development of Neuroblastoma or Somatostatinoma Open
c-MYC is an important driver of high-risk neuroblastoma. A lack of c-MYC–driven genetically engineered mouse models (GEMM) has hampered the ability to better understand mechanisms of neuroblastoma oncogenesis and to develop effective thera…
View article: Supplementary Note from Mutational Landscape and Patterns of Clonal Evolution in Relapsed Pediatric Acute Lymphoblastic Leukemia
Supplementary Note from Mutational Landscape and Patterns of Clonal Evolution in Relapsed Pediatric Acute Lymphoblastic Leukemia Open
Supplementary results, figures, and table notes
View article: SJPedPanel: A Pan-Cancer Gene Panel for Childhood Malignancies to Enhance Cancer Monitoring and Early Detection
SJPedPanel: A Pan-Cancer Gene Panel for Childhood Malignancies to Enhance Cancer Monitoring and Early Detection Open
Purpose: The purpose of the study was to design a pan-cancer gene panel for childhood malignancies and validate it using clinically characterized patient samples. Experimental Design: In addition to 5,275 coding exons, SJPedPanel also cove…
View article: Conditional c-MYC activation in catecholaminergic cells drives distinct neuroendocrine tumors: neuroblastoma vs somatostatinoma
Conditional c-MYC activation in catecholaminergic cells drives distinct neuroendocrine tumors: neuroblastoma vs somatostatinoma Open
The MYC proto-oncogenes (c-MYC, MYCN , MYCL ) are among the most deregulated oncogenic drivers in human malignancies including high-risk neuroblastoma, 50% of which are MYCN -amplified. Genetically engineered mouse models (GEMMs) based on …
View article: <i>UBTF</i> tandem duplications in pediatric myelodysplastic syndrome and acute myeloid leukemia: implications for clinical screening and diagnosis
<i>UBTF</i> tandem duplications in pediatric myelodysplastic syndrome and acute myeloid leukemia: implications for clinical screening and diagnosis Open
Recent genomic studies in adult and pediatric acute myeloid leukemia (AML) demonstrated recurrent in-frame tandem duplications (TD) in exon 13 of upstream binding transcription factor (UBTF). These alterations, which account for ~4.3% of A…
View article: A new genomic framework to categorize pediatric acute myeloid leukemia
A new genomic framework to categorize pediatric acute myeloid leukemia Open
Recent studies on pediatric acute myeloid leukemia (pAML) have revealed pediatric-specific driver alterations, many of which are underrepresented in the current classification schemas. To comprehensively define the genomic landscape of pAM…
View article: SJPedPanel: A pan-cancer gene panel for childhood malignancies
SJPedPanel: A pan-cancer gene panel for childhood malignancies Open
Background Large scale genomics projects have identified driver alterations for most childhood cancers that provide reliable biomarkers for clinical diagnosis and disease monitoring using targeted sequencing. However, there is lack of a co…
View article: A longitudinal single-cell atlas of treatment response in pediatric AML
A longitudinal single-cell atlas of treatment response in pediatric AML Open
Pediatric acute myeloid leukemia (pAML) is characterized by heterogeneous cellular composition, driver alterations and prognosis. Characterization of this heterogeneity and how it affects treatment response remains understudied in pediatri…
View article: <i>UBTF</i>Tandem Duplications in Pediatric MDS and AML: Implications for Clinical Screening and Diagnosis
<i>UBTF</i>Tandem Duplications in Pediatric MDS and AML: Implications for Clinical Screening and Diagnosis Open
Recent genomic studies in adult and pediatric acute myeloid leukemia (AML) demonstrated recurrent in-frame tandem duplications (TD) in exon 13 of upstream binding transcription factor ( UBTF ). These alterations, which account for ~4.3% of…