Jichun Xie

Positions:

Associate Professor of Biostatistics & Bioinformatics

Biostatistics & Bioinformatics
School of Medicine

Associate Professor of Mathematics

Mathematics
Trinity College of Arts & Sciences

Member of the Duke Cancer Institute

Duke Cancer Institute
School of Medicine

Education:

Ph.D. 2011

University of Pennsylvania

Grants:

Duke CTSA (UL1)

Administered By
Institutes and Centers
Awarded By
National Institutes of Health
Role
Biostatistician Investigator
Start Date
End Date

Bioinformatics and Computational Biology Training Program

Administered By
Basic Science Departments
Awarded By
National Institutes of Health
Role
Mentor
Start Date
End Date

A hands-on, integrative next-generation sequencing course: design, experiment, and analysis

Awarded By
National Institutes of Health
Role
Training Faculty
Start Date
End Date

Race-Related Alternative Splicing: Novel Targets in Prostate Cancer

Administered By
Medicine, Medical Oncology
Awarded By
National Institutes of Health
Role
Biostatistician
Start Date
End Date

Statistical/Computational Methods for Pharmacogenomics and Individualized Therapy

Administered By
Biostatistics & Bioinformatics
Awarded By
University of North Carolina - Chapel Hill
Role
Co Investigator
Start Date
End Date

Publications:

APOBEC mutagenesis as a driver of tumor evolution by promoting tumor recurrence and modulating tumor-immune system interactions in a syngeneic murine model of breast cancer.

Authors
DiMarco, AV; Qin, X; McKinney, B; Lupo, R; Xie, J; Owzar, K; Alvarez, J
URI
https://scholars.duke.edu/individual/pub1476151
Source
wos-lite
Published In
Cancer Immunology Research
Volume
9
Published Date

Hypercapnia in Advanced Chronic Obstructive Pulmonary Disease: A Secondary Analysis of the National Emphysema Treatment Trial.

Rationale: Hypercapnia develops in one third of patients with advanced chronic obstructive pulmonary disease (COPD) and is associated with increased morbidity and mortality. Multiple factors in COPD are thought to contribute to the development of hypercapnia including increased carbon dioxide (CO2) production, increased dead space ventilation, and the complex interactions of deranged respiratory system mechanics, inspiratory muscle overload and the ventilatory control center in the brainstem. However, these factors have not previously been systematically analyzed in a large, well-characterized population of severe COPD patients. Methods: This is a secondary analysis of the clinical, physiologic and imaging data from the National Emphysema Treatment Trial (NETT). All patients with complete baseline data for the key predictor variables were included. An inclusive list of 32 potential predictor variables were selected a priori based on consensus of the investigators and literature review. Stepwise variable selection yielded 10 statistically significant associations in multivariate regression. Results: A total of 1419 patients with severe COPD were included in the analysis; mean age 66.4 years (standard deviation 6.3), 38% females, and 422 (29.7%) had baseline hypercapnia. Key variables associated with hypercapnia were low resting partial pressure of oxygen in blood, low minute ventilation (Ve), high volume of exhaled carbon dioxide, low forced expiratory volume in 1 second, high residual volume, lower % emphysema on chest computed tomography, use of oxygen, low ventilatory reserve (high Ve/maximal voluntary ventilation), and not being at high altitude. Low diffusing capacity for carbon monoxide showed a positive association with hypercapnia in univariate analysis but a negative correlation in multivariate analysis. Measures of dyspnea and quality of life did not associate with degree of hypercapnia in multivariable analysis. Conclusion: Hypercapnia in a well-characterized cohort with severe COPD and emphysema is chiefly related to poor lung mechanics, high CO2 production, and a reduced ventilatory capability. Hypercapnia is less impacted by gas exchange abnormalities or the presence of emphysema.
Authors
Mathews, AM; Wysham, NG; Xie, J; Qin, X; Giovacchini, CX; Ekström, M; MacIntyre, NR
MLA Citation
Mathews, Anne M., et al. “Hypercapnia in Advanced Chronic Obstructive Pulmonary Disease: A Secondary Analysis of the National Emphysema Treatment Trial.Chronic Obstr Pulm Dis, vol. 7, no. 4, Oct. 2020, pp. 336–45. Pubmed, doi:10.15326/jcopdf.7.4.2020.0176.
URI
https://scholars.duke.edu/individual/pub1459480
PMID
32877962
Source
pubmed
Published In
Chronic Obstructive Pulmonary Diseases
Volume
7
Published Date
Start Page
336
End Page
345
DOI
10.15326/jcopdf.7.4.2020.0176

Distance Assisted Recursive Testing

In many applications, a large number of features are collected with the goal to identify a few important ones. Sometimes, these features lie in a metric space with a known distance matrix, which partially reflects their co-importance pattern. Proper use of the distance matrix will boost the power of identifying important features. Hence, we develop a new multiple testing framework named the Distance Assisted Recursive Testing (DART). DART has two stages. In stage 1, we transform the distance matrix into an aggregation tree, where each node represents a set of features. In stage 2, based on the aggregation tree, we set up dynamic node hypotheses and perform multiple testing on the tree. All rejections are mapped back to the features. Under mild assumptions, the false discovery proportion of DART converges to the desired level in high probability converging to one. We illustrate by theory and simulations that DART has superior performance under various models compared to the existing methods. We applied DART to a clinical trial in the allogeneic stem cell transplantation study to identify the gut microbiota whose abundance will be impacted by the after-transplant care.
Authors
Li, X; Sung, A; Xie, J
MLA Citation
URI
https://scholars.duke.edu/individual/pub1476701
Source
arxiv

Abstract P1-06-02: Characterization of gene- and sample-level APOBEC mutagenesis enrichment with respect to intrinsic subtypes, tumor mutational burden, and immune composition in breast cancer

Authors
Force, J; Qin, X; Zhang, D; Marcom, PK; Marks, J; Taylor, ML; Anders, C; Owzar, K; Xie, J
MLA Citation
Force, Jeremy, et al. “Abstract P1-06-02: Characterization of gene- and sample-level APOBEC mutagenesis enrichment with respect to intrinsic subtypes, tumor mutational burden, and immune composition in breast cancer.” Poster Session Abstracts, American Association for Cancer Research, 2020. Crossref, doi:10.1158/1538-7445.sabcs19-p1-06-02.
URI
https://scholars.duke.edu/individual/pub1442732
Source
crossref
Published In
Poster Session Abstracts
Published Date
DOI
10.1158/1538-7445.sabcs19-p1-06-02

Microtransplantation in older patients with AML: A pilot study of safety, efficacy and immunologic effects.

Older AML patients have low remission rates and poor survival outcomes with standard chemotherapy. Microtransplantation (MST) refers to infusion of allogeneic hematopoietic stem cells without substantial engraftment. MST has been shown to improve clinical outcomes compared with chemotherapy alone. This is the first trial reporting on broad correlative studies to define immunologic mechanisms of action of MST in older AML patients. Older patients with newly diagnosed AML were eligible for enrollment, receiving induction chemotherapy with cytarabine (100 mg/m2) on days 1-7 and idarubicin (12 mg/m2) on days 1-3 (7 + 3). MST was administered 24 hours later. Patients with complete response (CR) were eligible for consolidation with high dose cytarabine (HiDAC) and a second cycle of MST. Responses were evaluated according to standard criteria per NCCN. Immune correlative studies were performed. Sixteen patients were enrolled and received 7 + 3 and MST (median age 73 years). Nine (56%) had high-risk and seven (44%) had standard-risk cytogenetics. Ten episodes of CRS were observed. No cases of GVHD or treatment-related mortality were reported. Event-free survival (EFS) was 50% at 6 months and 19% at 1 year. Overall survival (OS) was 63% at 6 months and 44% at 1 year. Donor microchimerism was not detected. Longitudinal changes were noted in NGS, TCR sequencing, and cytokine assays. Addition of MST to induction and consolidation chemotherapy was well tolerated in older AML patients. Inferior survival outcomes in our study may be attributed to a higher proportion of very elderly patients with high-risk features. Potential immunologic mechanisms of activity of MST include attenuation of inflammatory cytokines and emergence of tumor-specific T cell clones.
Authors
Sung, AD; Jauhari, S; Siamakpour-Reihani, S; Rao, AV; Staats, J; Chan, C; Meyer, E; Gadi, VK; Nixon, AB; Lyu, J; Xie, J; Bohannon, L; Li, Z; Hourigan, CS; Dillon, LW; Wong, HY; Shelby, R; Diehl, L; de Castro, C; LeBlanc, T; Brander, D; Erba, H; Galal, A; Stefanovic, A; Chao, N; Rizzieri, DA
MLA Citation
Sung, Anthony D., et al. “Microtransplantation in older patients with AML: A pilot study of safety, efficacy and immunologic effects.Am J Hematol, vol. 95, no. 6, June 2020, pp. 662–71. Pubmed, doi:10.1002/ajh.25781.
URI
https://scholars.duke.edu/individual/pub1434771
PMID
32162718
Source
pubmed
Published In
Am J Hematol
Volume
95
Published Date
Start Page
662
End Page
671
DOI
10.1002/ajh.25781