Li-Xuan Qin

Associate Attending Biostatistician

Li-Xuan Qin

Office Phone




University of Washington

Current Research Interests

Dr. Qin develops statistical methods for high throughput data analysis problems to address clinically important questions in cancer research. Within this framework, her current research primarily focuses on the use of statistical experimental design, exploratory data analysis, and mixture models for cancer biomarker discovery and on the genomics and translational studies of soft tissue sarcoma. She serves as the Corresponding Co-Director of the Biostatistics and Bioinformatics Core in the Soft Tissue Sarcoma Specialized Program of Research Excellence, and received an NIH R01 grant to develop efficient statistical methods for analyzing microRNA array and sequencing data.


Qin LX and Self SG. The clustering of regression models method with applications to gene expression data. Biometrics 2006, 62:526-533.

Qin LX, Zhou Q, Bogomolniy F, Villafania L, Olvera N, Cavatore M, Satagopan JM, Begg CB, Levine DA. Blocking and randomization to improve molecular biomarker discovery. Clinical Cancer Research 2014, 20:3371-3378.

Qin LX, Levine DA. Study design and data normalization to improve the discovery of prognostic molecular biomarkers. BMC Medical Genomics 2016, 9:27.

Qin LX, Huang HC, Begg CB. Cautionary note on using cross-validation for molecular classification. Journal of Clinical Oncology 2016, Epub ahead of print.

Qin LX, Tuschl T, Singer S. Empirical insights into the stochasticity of small RNA sequencing. Scientific Reports 2016, 6:24061.

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Statistics Papers

  1. Qin LX, Kerr KF, Contributing Members of the Toxicogenomics Research Consortium. Empirical evaluation of data transformations and ranking statistics for microarray analysis. Nucleic Acids Research 2004, 32:5471-5479.

  2. Bammler T, Beyer RP, Bhattacharya S, Boorman GA, Boyles A, Bradford BU, Bumgarner RE, Bushel PR, Chaturvedi K, Choi D,Cunningham ML, Deng S, Dressman HK, Fannin RD, Farin FM, Freedman JH, Fry RC, Harper A, Humble MC, Hurban P,Kavanagh TJ, Kaufmann WK, Kerr KF, Jing L, Lapidus JA, Lasarev MR, Li J, Li YJ, Lobenhofer EK, Lu X, Malek RL, Milton S,Nagalla SR, O’malley JP, Palmer VS, Pattee P, Paules RS, Perou CM, Phillips K, Qin LX, Qiu Y, Quigley SD, Rodland M, Rusyn I,Samson LD, Schwartz DA, Shi Y, Shin JL, Sieber SO, Slifer S, Speer MC, Spencer PS, Sproles DI, Swenberg JA, Suk WA, Sullivan RC, Tian R, Tennant RW, Todd SA, Tucker CJ, Van Houten B, Weis BK, Xuan S, Zarbl H; Members of the Toxicogenomics Research Consortium. Standardizing global gene expression analysis between laboratories and across platforms. Nature Methods 2005, 2:351-356.

  3. Qin LX, Beyer R, Hudson N, Linford N, Morris D, Kerr KF. Evaluation of methods for oligonucleotide array data via quantitative real-time PCR. BMC Bioinformatics 2006, 7:23.

  4. Qin LX and Self SG. The clustering of regression models method with applications to gene expression data. Biometrics 2006, 62:526-533.

  5. Qin LX. An integrative analysis of microRNA and mRNA expression – a case study. Cancer Informatics 2008, 6:369-379.

  6. Qin LX and Satagopan J. Normalization method for transcriptional studies of heterogeneous samples – simultaneous array normalization and identification of equivalent expression. Statistical Applications in Genetics and Molecular Biology 2009, 8:Article 10.

  7. Qin LX, Tuschl T, Singer S. An empirical evaluation of normalization methods for microRNA arrays in a liposarcoma study. Cancer Informatics 2013, 12:83-101.

  8. Qin LX, Breeden L, Self SG. Finding gene clusters for a replicated time course study. BMC Research Notes 2014, 7:60.

  9. Shi J, Qin LX. CORM: an R package implementing the clustering of regression models method for gene clustering. Cancer Informatics 2014, S4:11-13.

  10. Qin LX, Zhou Q, Bogomolniy F, Villafania L, Olvera N, Cavatore M, Satagopan JM, Begg CB, Levine DA. Blocking and randomization to improve molecular biomarker discovery. Clinical Cancer Research 2014, 20:3371-3378.

  11. Qin LX, Zhou Q. MicroRNA array normalization: an evaluation using a randomized dataset as the benchmark. PLOS ONE 2014, 9:e98879.

  12. Qin LX, Huang HC, Zhou Q. Preprocessing steps for Agilent microRNA arrays: does the order matter. Cancer Informatics 2015, S4:105-109.

  13. Huang HC, Niu Y, Qin LX. An overview of differential expression analysis for RNA-seq data: statistical methods and computational software. Cancer Informatics 2015, S1:57-67.

  14. Qin LX, Levine DA. Study design and data normalization to improve the discovery of prognostic molecular biomarkers. BMC Medical Genomics 2016, 9:27.

  15. Qin LX, Huang HC, Begg CB. Cautionary note on using cross-validation for molecular classification. Journal of Clinical Oncology 2016, Epub ahead of print.

  16. Qin LX, Tuschl T, Singer S. Empirical insights into the stochasticity of small RNA sequencing. Scientific Reports 2016, 6:24061.

Clinical Papers

  1. Qin L, Marrs GS, McKim R, Dailey ME. Hippocampal mossy fibers induce assembly and clustering of PSD95-containing postsynaptic densities independent of glutamate receptor activation. Journal of Comparative Neurology 2001, 440:284-298.

  2. Canter RJ, Qin LX, Downey R, Brennan MF, Singer S, Maki RG. Perioperative chemotherapy in patients undergoing pulmonary resection for metastasis soft tissue sarcoma of the extremity. Cancer 2007, 110:2050-2060.

  3. Canter RJ, Qin LX, Ferrone CR, Maki RG, Singer S, Brennan MF. Why do patients with low grade sarcoma die? Annals of Surgical Oncology 2008, 15:3550-3560.

  4. Canter RJ, Qin LX, Moraco N, Dalal KM, Maki RG, Brennan MF, Ladanyi M, Singer S. A synovial sarcoma specific preoperative nomogram supports a survival benefit to Ifosfamide-based chemotherapy and improves risk stratification for patients. Clinical Cancer Research 2008, 14:8191-8197.

  5. Al-Ahmadie HA, Alden D, Qin LX, Olgac S, Fine SW, Gopalan A, Russo P, Motzer RJ, Reuter VE, Tickoo SK. Carbonic anhydrase IX expression in clear cell renal cell carcinoma: an immunohistochemical study comparing two antibodies. American Journal of Surgical Pathology 2008, 32:377-382.

  6. The Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 2008, 455:1061-1068.

  7. Ambrosini G, Seelman SL, Qin LX, Schwartz GK. The cyclin-dependent kinase inhibitor flavopiridol potentiates the effects of topoisomerase I poisons by suppressing Rad51 expression in a p53-dependent manner. Cancer Research 2008, 68:2312-2320.

  8. Forslund A, Zeng A, Qin LX, Rosenberg S, Ndubuisi M, Pincas H, Gerald W, Notterman D, Barany F, Paty PB. MDM2 gene amplification is correlated to tumor progression but not to presence of SNP309 or TP53 mutational status in primary colorectal cancers. Molecular Cancer Research 2008, 6:205-211.

  9. Maki RG, D’Adamo DR, Keohan ML, Saulle M, Schuetze SM, Undevia SD, Livingston MB, Cooney MM, Hensley ML, Mita MM, Takimoto CH, Kraft AS, Elias AD, Brockstein B, Blachère NE, Edgar MA, Schwartz LH, Qin LX, Antonescu CR, Schwartz GK. A phase II study of sorafenib in patients with metastatic or recurrent sarcomas. Journal of Clinical Oncology 2009, 27:3133-3140.

  10. Park JO, Qin LX, Prete FP, Antonescu C, Brennan MF, Singer S. Predicting outcome by growth rate of locally recurrent retroperitoneal liposarcoma: the one centimeter per month rule. Annals of Surgery 2009, 250:977-982

  11. Kushner BH, Kramer K, Modak S, Qin LX, Yataghena K, Jhanwar SC, and Cheung NKV. Reduced risk of secondary leukemia with fewer cycles of dose-intensive induction chemotherapy in patients with neuroblastoma. Pediatric Blood & Cancer 2009, 53:17-22.

  12. Jhawer M, Coit D, Brennan M, Qin LX, Gonen M, Klimstra D, Tang L, Kelsen DP, Shah MA. Perineural invasion following preoperative chemotherapy predicts poor survival in patients with locally advanced gastric cancer: gene expression analysis with pathologic validation. American Journal of Clinical Oncology 2009, 32:356-362.

  13. Antonescu CR, Yoshida A, Guo T, Chang NE, Zhang L, Agaram NP, Qin LX, Brennan  MF, Singer S, Maki RG. KDR activating mutations in human angiosarcomas are sensitive to specific kinase inhibitors. Cancer Research. 2009, 69:7175-7179.

  14. Meng RD, Shelton CC, Li YM, Qin LX,  Notterman D, Paty PB, Schwartz GK. Gamma-secretase inhibitors abrogate Oxaliplatin-induced activation of the Notch-1 signaling pathway in colon cancer cells resulting in enhanced chemosensitivity. Cancer Research 2009, 69:573-582.

  15. Korkola JE, Houldsworth J, Feldman DR, Olshen AB, Qin LX, Patil S, Reuter VE,  Bosl GJ, Chaganti RS. Identification and validation of a gene expression signature that predicts outcome in adult men with germ cell tumors. Journal of Clinical Oncology 2009, 27:5240-5247.

  16. Gershon TR, Shirazi A, Qin LX, Gerald WL, Kenney AM, Cheung NK. Enteric neural crest differentiation in ganglioneuromas implicates Hedgehog signaling in peripheral neuroblastic tumor pathogenesis. PLOS ONE 2009, 4:e7491.

  17. Allen PJ, Qin LX, Tang L, Klimstra D, Brennan MF, Lokshin A. Pancreatic cyst fluid protein expression profiling for discriminating between serous cystadenoma and intraductal papillary mucinous neoplasm. Annals of Surgery 2009, 250:754-760.

  18. Li L, Lu Y, Qin LX, Bar-Joseph Z, Werner-Washburne M, Breeden LL. Budding yeast SSD1-V regulates transcript levels of many longevity genes and extends chronological life span in purified quiescent cells. Molecular Biology of the Cell 2009, 20:3851-3864.

  19. Gladdy RA, Qin LX, Moraco N, Edgar MA, Antonescu CR, Alektiar KM, Brennan MF, Singer S. Do radiation-associated soft tissue sarcomas have the same prognosis as sporadic soft tissue sarcomas? Journal of Clinical Oncology 2010, 28:2064-2069.

  20. Kushner BH, Kramer K, Modak S, Qin LX, Cheung NK. Differential impact of high-dose cyclophosphamide, topotecan, and vincristine in clinical subsets of patients with chemoresistant neuroblastoma. Cancer 2010, 116:3054-3060.

  21. Esemuede I, Forslund A, Khan SA, Qin LX, Gimbel MI, Nash GM, Zeng Z, Rosenberg S, Shia J, Barany F, Paty PB. Improved testing for microsatellite instability in colorectal cancer using a simplified 3-marker assay. Annals of Surgical Oncology 2010, 17:3370-3378.

  22. Fields RC, Hameed M, Qin LX, Moraco N, Jia X, Maki RG, Singer S, Brennan MF. Dermatofibrosarcoma protuberans (DFSP): Predictors of recurrence and the use of systemic therapy. Annals of Surgical Oncology 2011, 18:328-336.

  23. Gobble RM, Qin LX, Brill ER, Angeles CV, Ugras S, O’Connor RB, Moraco NH, Decarolis PL, Antonescu CR, Singer S. Expression profiling of liposarcoma yields a multigene predictor of patient outcome and identifies genes that contribute to liposarcomagenesis. Cancer Research 2011, 71:2697-2705.

  24. Maker AV, Katabi N, Qin LX, Klimstra DS, Schattner M, Brennan MF, Jarnagin WR, Allen PJ. Cyst fluid interleukin-1b levels predict the risk of carcinoma in intraductal papillary mucinous neoplasms of the pancreas. Clinical Cancer Research 2011, 17:1502-1508.

  25. Shih KK, Qin LX, Tanner EJ, Zhou Q, Bisogna M, Dao F, Olvera N, Viale A, Barakat RR, Levine DA. A microRNA survival signature (MiSS) for advanced ovarian cancer. Gynecological Oncology 2011, 121:444-450.

  26. Cahlon O, Brennan MF, Jia X, Qin LX, Singer S, Alektiar KM. A postoperative nomogram for local recurrence risk in extremity soft tissue sarcomas after limb-sparing surgery without adjuvant radiation. Annals of Surgery 2012, 255:343-347.

  27. Chen J, Guo T, Zhang L, Qin LX, Singer S, Maki RG, Taguchi T, Dematteo R, Besmer P, Antonescu CR. CD133 and CD44 are universally overexpressed in GIST and do not represent cancer stem cell markers. Genes Chromosomes & Cancer 2012, 51:186-195.

  28. Crago AM, Socci ND, Decarolis P, O’Connor R, Taylor BS, Qin LX, Antonescu CR, Singer S. Copy number losses define subgroups of dedifferentiated liposarcoma with poor prognosis and genomic instability. Clinical Cancer Research 2012, 18:1334-1340.

  29. Ambrosini G, Pratilas CA, Qin LX, Tadi M, Surriga O, Carvajal RD, Schwartz GK. Identification of unique MEK-dependent genes in GNAQ mutant uveal melanoma involved in cell growth, tumor cell invasion, and MEK-resistance. Clinical Cancer Research 2012, 18:3552-3561.

  30. Winter JM, Tang LH, Klimstra DS, Brennan MF, Brody JR, Rocha FG, Jia X, Qin LX, D’Angelica MI, DeMatteo RP, Fong Y, Jarnagin WR, O’Reilly EM, Allen PJ. A novel survival-based tissue microarray of pancreatic cancer validates MUC1 and mesothelin as biomarkers. PLOS ONE 2012, 7:e40157.

  31. Morrogh M, Andrade VP, Patil AJ, Qin LX, Mo Q, Sakr R, Arroyo CD, Brogi E, Morrow M, King TA. Differentially expressed genes in window trials are influenced by the wound-healing process: lessons learned from a pilot study with Anastrozole. Journal of Surgical Research 2012, 176:121-132.

  32. Morrogh M, Andrade VP, Giri D, Sakr RA, Paik W, Qin LX, Arroyo CD, Brogi E, Morrow M, King TA. Cadherin-catenin complex dissociation in lobular neoplasia of the breast. Breast Cancer Research and Treatment 2012, 132:641-52.

  33. Schwartz GK, Tap WD, Qin LX, Livingston MB, Undevia SD, Chmielowski B, Agulnik M, Schuetze SM, Reed DR, Okuno SH, Ludwig JA, Keedy V, Rietschel P, Kraft AS, Adkins D, Van Tine BA, Brockstein B, Yim V, Bitas C, Abdullah A, Antonescu CR, Condy M, Dickson MA, Vasudeva SD, Ho AL, Doyle LA, Chen HX, Maki RG. IGF-1R Inhibitor cixutumumab (IMC-A12) and the mTOR inhibitor temsirolimus in patients with bone and soft tissue sarcoma: a multicenter, open-label phase 2 trial. Lancet Oncology 2013, 14:371-382.

  34. Dickson MA, Tap WD, Keohan ML, D’Angelo SP, Gounder MM, Antonescu CR, Landa J, Qin LX, Rathbone DD, Condy MM, Ustoyev Y, Crago AM, Singer S, Schwartz GK. Phase II trial of the CDK4 inhibitor PD0332991 in patients with advanced CDK4-amplified well-differentiated or dedifferentiated liposarcoma. Journal of Clinical Oncology 2013, 31:2024-2028.

  35. Lafemina J, Qin LX, Moraco NH, Antonescu CR, Fields RC, Crago AM, Brennan MF, Singer S. Oncologic outcomes of sporadic, neurofibromatosis-associated, and radiation-induced malignant peripheral nerve sheath tumors. Annals of Surgical Oncology 2013, 1:66-72.

  36. Gladdy RA, Qin LX, Moraco N, Agaram NP, Brennan MF, Singer S. Predictors of survival and recurrence in primary leiomyosarcoma. Annals of Surgical Oncology 2013, 20:1851-1857.

  37. D’Angelo SP, Antonescu CR, Kuk D, Qin LX, Moraco N, Carvajal RD, Chi P, Dickson MA, Gounder M, Keohan ML, Singer S, Schwartz GK, Tap WD. High-risk features in radiation-associated breast angiosarcomas. British Journal of Cancer 2013, 109: 2340-2346.

  38. Ito H, Mo Q, Qin LX, Viale A, Maithel SK, Maker AV, Shia J, Kingham P, Allen P, Dematteo RP, Fong Y, Jarnagin WR, D’Angelica M. Gene expression profiles accurately predict outcome following liver resection in patients with metastatic colorectal cancer. PLOS ONE 2013, 8:e81680.

  39. Kohsaka S, Shukla N, Ameur N, Ito T, Ng CK, Wang L, Lim D, Marchetti A, Viale A, Pirun M, Socci ND, Qin LX, Sciot R, Bridge J, Singer S, Meyers P, Wexler LH, Barr FG, Dogan S, Fletcher JA, Reis-Filho JS, Ladanyi M. A recurrent neomorphic mutation in MYOD1 defines a clinically aggressive subset of embryonal rhabdomyosarcoma associated with PI3K-AKT pathway mutations. Nature Genetics 2014, 46:595-600.

  40. Lee W, Teckie S, Wiesner T, Ran L, Prieto Granada CN, Lin M, Zhu S, Cao Z, Liang Y, Sboner A, Tap WD, Fletcher JA, Huberman KH, Qin LX, Viale A, Singer S, Zheng D, Berger MF, Chen Y, Antonescu CR, Chi P. PRC2 is recurrently inactivated through EED or SUZ12 loss in malignant peripheral nerve sheath tumors. Nature Genetics 2014, 46:1227-1232.

  41. Folkert MR, Singer S, Brennan MF, Kuk D, Qin LX, Kobayashi WK, Crago AM, Alektiar KM. Comparison of local recurrence with conventional and intensity-modulated radiation therapy for primary soft-tissue sarcomas of the extremity. Journal of Clinical Oncology 2014, 32:3236-3241.

  42. Dickson MA, D’Adamo DR, Keohan ML, D’Angelo SP, Carvajal RD, Gounder MM, Maki RG, Qin LX, Lefkowitz RA, McKennon OR, Hirst CM, Schwartz GK, Tap WD. Phase II Trial of Gemcitabine and Docetaxel with Bevacizumab in Soft Tissue Sarcoma. Sarcoma 2015, 532478.

  43. Munhoz RR, D’Angelo SP, Gounder MM, Keohan ML, Chi P, Carvajal RD, Singer S, Crago AM, Landa J, Healey JH, Qin LX, Hameed M, Ezeoke MO, Singh AS, Agulnik M, Chmielowski B, Luke JJ, Van Tine BA, Schwartz GK, Tap WD, Dickson MA. A Phase Ib/II Study of Gemcitabine and Docetaxel in Combination with Pazopanib for the Neoadjuvant Treatment of Soft Tissue Sarcomas. Oncologist 2015, 20:1245-1246.

  44. D’Angelo SP, Shoushtari AN, Agaram NP, Kuk D, Qin LX, Carvajal RD, Dickson MA, Gounder M, Keohan ML, Schwartz GK, Tap WD. Prevalence of tumor infiltrating lymphocytes and PD-L1 expression in the soft tissue sarcoma microenvironment. Human Pathology 2015, 46:357-365.

  45. Gounder M, Desai V, Kuk D, Agaram N, Arcila M, Durham B, Keohan ML, Dickson MA, D’Angelo SP, Shukla N, Moskowitz C, Noy A, Maki RG, Herrera DA, Sanchez A, Krishnan A, Pourmoussa A, Qin LX, Tap WD. Impact of surgery, radiation and systemic therapy on the outcomes of patients with dendritic cell and histiocytic sarcomas. European Journal of Cancer 2015, 51:2413-2422.

  46. Kelly KJ, Yoon SS, Kuk D, Qin LX, Dukleska K, Chang KK, Chen YL, Delaney TF, Brennan MF, Singer S. Comparison of perioperative radiation therapy and surgery versus surgery alone in 204 patients with primary retroperitoneal sarcoma: a retrospective two-institution study. Annals of Surgery 2015, 262:156-162.

  47. Crago AM, Chmielecki J, Rosenberg M, O’Connor R, Byrne C, Wilder FG, Thorn K, Agius P, Kuk D, Socci ND, Qin LX, Meyerson M, Hameed M, Singer S. Near universal detection of alterations in CTNNB1 and Wnt pathway regulators in desmoid-type fibromatosis by whole-exome sequencing and genomic analysis. Genes Chromosomes Cancer 2015, 54:606-615.

  48. Andrade VP*, Morrogh M*, Qin LX*, Olvera N, Giri D, Muhsen S, Sakr RA, Schizas M, Ng CK, Arroyo CD, Brogi E, Viale A, Morrow M, Reis-Filho JS, King TA. Gene expression profiling of lobular carcinoma in situ reveals candidate precursor genes for invasion. Molecular Oncology 2015, 9:772-782. [*Equal Contribution]

  49. Barlin JN, Zhou Q, Leitao MM, Bisogna M, Olvera N, Shih KK, Jacobsen A, Schultz N, Tap WD, Hensley ML, Schwartz GK, Boyd J, Qin LX, Levine DA. Molecular subtypes of uterine leiomyosarcoma and correlation with clinical outcome. Neoplasia 2015, 17:183-189.

  50. Maker AV, Ito H, Mo Q, Weisenberg E, Qin LX, Turcotte S, Maithel S, Shia J, Blumgart L, Fong Y, Jarnagin WR, DeMatteo RP, D’Angelica1 MI. Genetic evidence that intratumoral T-cell proliferation and activation is associated with recurrence and survival in patients with resected colorectal liver metastases. Cancer Immunology Research 2015, 3:380-388.

  51. Tan MCB, Brennan MF, Kuk D, Shurell E, Agaram NP, Antonescu C, Qin LX, Moraco N, Eilber FC, Crago A, Singer S. Histology-specific nomograms for patients with primary retroperitoneal soft tissue sarcoma. Annals of Surgery 2016, 263:593-600.

  52. Lee AY, Agaram NP, Qin LX, Kuk D, Curtin C, Brennan MF, Singer S. Optimal percent myxoid component to predict outcome in high-grade myxofibrosarcoma and undifferentiated pleomorphic sarcoma. Annals of Surgical Oncology 2016, 23:818-825.

  53. Agaram NP, Zhang L, LeLoarer F, Silk T, Sung YS, Scott SN, Kuk D, Qin LX, Berger MF, Antonescu CR, Singer S. Targeted exome sequencing profiles genetic alterations in leiomyosarcoma. Genes Chromosomes Cancer 2016, 55:124-130.

  54. Dickson MA, Schwartz GK, Keohan ML, D’Angelo SP, Gounder MM, Chi P, Antonescu CR, Landa J, Qin LX, Crago AM, Singer S, Koff A, Tap WD. Progression-Free Survival Among Patients With Well-Differentiated or Dedifferentiated Liposarcoma Treated With CDK4 Inhibitor Palbociclib: A Phase 2 Clinical Trial. JAMA Oncology 2016, 2:937-940.

  55. Okada T, Lee AY, Qin LX, Agaram N, Mimae T, Shen Y, O’Connor R, López-Lago MA, Craig A, Miller ML, Agius P, Molinelli E, Socci ND, Crago AM, Shima F, Sander C, Singer S. Integrin-α10 dependency identifies RAC and RICTOR as therapeutic targets in high-grade myxofibrosarcoma. Cancer Discovery 2016, Epub ahead of print.

Editorials and Book Chapters (Non-Peer-Reviewed)

  1. Qin LX, Ma S, Huang YT, Zhang H, Cao H. Introductory Editorial: Array Platform Modeling and Analysis (A). Cancer Informatics 2014, S4: 91-93.

  2. Qin LX, Huang YT. Introductory Editorial: Sequencing Platform Modeling and Analysis (A). Cancer Informatics 2015, S1:55-56.