Dataset Information

Genomic prediction of relapse in recipients of allogeneic haematopoietic stem cell transplantation.

ABSTRACT: Allogeneic haematopoietic stem cell transplantation currently represents the primary potentially curative treatment for cancers of the blood and bone marrow. While relapse occurs in approximately 30% of patients, few risk-modifying genetic variants have been identified. The present study evaluates the predictive potential of patient genetics on relapse risk in a genome-wide manner. We studied 151 graft recipients with HLA-matched sibling donors by sequencing the whole-exome, active immunoregulatory regions, and the full MHC region. To assess the predictive capability and contributions of SNPs and INDELs, we employed machine learning and a feature selection approach in a cross-validation framework to discover the most informative variants while controlling against overfitting. Our results show that germline genetic polymorphisms in patients entail a significant contribution to relapse risk, as judged by the predictive performance of the model (AUC?=?0.72 [95% CI: 0.63-0.81]). Furthermore, the top contributing variants were predictive in two independent replication cohorts (n?=?258 and n?=?125) from the same population. The results can help elucidate relapse mechanisms and suggest novel therapeutic targets. A computational genomic model could provide a step toward individualized prognostic risk assessment, particularly when accompanied by other data modalities.

SUBMITTER: Ritari J

PROVIDER: S-EPMC6326954 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Genomic prediction of relapse in recipients of allogeneic haematopoietic stem cell transplantation.

Ritari J J Hyvärinen K K Koskela S S Itälä-Remes M M Niittyvuopio R R Nihtinen A A Salmenniemi U U Putkonen M M Volin L L Kwan T T Pastinen T T Partanen J J

Leukemia 20180808 1

Allogeneic haematopoietic stem cell transplantation currently represents the primary potentially curative treatment for cancers of the blood and bone marrow. While relapse occurs in approximately 30% of patients, few risk-modifying genetic variants have been identified. The present study evaluates the predictive potential of patient genetics on relapse risk in a genome-wide manner. We studied 151 graft recipients with HLA-matched sibling donors by sequencing the whole-exome, active immunoregulat ...[more]

PMID: 30089915

Similar Datasets

Project description:Haematopoietic stem cell transplantation has been proposed as treatment for mitochondrial neurogastrointestinal encephalomyopathy, a rare fatal autosomal recessive disease due to TYMP mutations that result in thymidine phosphorylase deficiency. We conducted a retrospective analysis of all known patients suffering from mitochondrial neurogastrointestinal encephalomyopathy who underwent allogeneic haematopoietic stem cell transplantation between 2005 and 2011. Twenty-four patients, 11 males and 13 females, median age 25 years (range 10-41 years) treated with haematopoietic stem cell transplantation from related (n = 9) or unrelated donors (n = 15) in 15 institutions worldwide were analysed for outcome and its associated factors. Overall, 9 of 24 patients (37.5%) were alive at last follow-up with a median follow-up of these surviving patients of 1430 days. Deaths were attributed to transplant in nine (including two after a second transplant due to graft failure), and to mitochondrial neurogastrointestinal encephalomyopathy in six patients. Thymidine phosphorylase activity rose from undetectable to normal levels (median 697 nmol/h/mg protein, range 262-1285) in all survivors. Seven patients (29%) who were engrafted and living more than 2 years after transplantation, showed improvement of body mass index, gastrointestinal manifestations, and peripheral neuropathy. Univariate statistical analysis demonstrated that survival was associated with two defined pre-transplant characteristics: human leukocyte antigen match (10/10 versus <10/10) and disease characteristics (liver disease, history of gastrointestinal pseudo-obstruction or both). Allogeneic haematopoietic stem cell transplantation can restore thymidine phosphorylase enzyme function in patients with mitochondrial neurogastrointestinal encephalomyopathy and improve clinical manifestations of mitochondrial neurogastrointestinal encephalomyopathy in the long term. Allogeneic haematopoietic stem cell transplantation should be considered for selected patients with an optimal donor.

Project description:BACKGROUND:There are very few studies investigating metabolic biomarkers to predict acute graft-versus-host disease (aGVHD) after allogeneic hematopoietic stem cell transplantation (HSCT). Metabolic models can provide a framework for analyzing the information-rich omics data sets in this setting. METHODS:Four hundred and fifty-six samples from one hundred and fourteen consecutive patients who underwent HSCT from January 2012 to May 2014 were collected for this study. The changes in serum metabolite levels were investigated using a gas chromatography-mass spectrometry-based metabolomics approach and underwent statistical analysis. RESULTS:Significant metabolic changes were observed on day 7. The stearic acid/palmitic acid (SA/PA) ratio was effective in the diagnosis of grade II-IV aGVHD. Multivariate analysis showed that patients with high SA/PA ratios on day 7 after HSCT were less likely to develop II-IV aGVHD than patients with low SA/PA ratios (odds ratio [OR] = 0.06, 95% CI 0.02-0.18, P < 0.001). After the adjustment for clinical characteristics, the SA/PA ratio had no significant effect on overall survival (hazard ratio [HR] = 1.95, 95% CI 0.92-4.14, P = 0.08), and patients in the high SA/PA ratio group were significantly more likely to relapse than those in the low ratio group (HR = 2.26, 95% CI 1.04-4.91, P = 0.04). CONCLUSION:Our findings suggest that the SA/PA ratio on day 7 after HSCT is an excellent biomarker to predict both aGVHD and relapse. The serum SA/PA ratio measured on day 7 after transplantation may improve risk stratification for aGVHD and relapse after allogeneic stem cell transplantation. FUNDING:National Natural Science Foundation of China (81470346, 81773361), Priority Academic Program Development of Jiangsu Higher Education Institutions, Jiangsu Natural Science Foundation (BK20161204), Innovation Capability Development Project of Jiangsu Province (BM2015004), Jiangsu Medical Junior Talent Person award (QNRC2016707), and NIH (AI129582 and NS106170).

Project description:IntroductionPatients receiving a haematopoietic stem cell transplant (HSCT) are subjected to complex oral medications based on prophylactic and immunosuppressive treatments. Adherence to medication plays a role in survival, and medication non-adherence (MNA) is closely associated with graft-versus-host disease and other complications. The aim of this systematic review is to summarise the available evidence regarding prevalence rates of medication adherence, the risk factors of MNA, the effectiveness of interventions to increase medication adherence and the outcomes associated with MNA.Methods and analysisWe designed a systematic review according to the Joanna Briggs Institute methodology. We will search the Cochrane Library and the CINAHL, EMBASE, MEDLINE via PubMed, PsycINFO and Scopus databases. We will include published and unpublished primary studies: (a) on humans, from inception until 10 May 2022; (b) written in any language; (c) experimental (randomised and non-randomised), observational (prospective, retrospective cohort and case-control), correlational, cross-sectional and longitudinal; and (d) with a low risk of bias, according to the quality assessment we perform. We will exclude secondary and qualitative studies, protocols, publications without original data, including paediatrics or related to autologous HSCT. The primary outcome will be the prevalence of oral medication adherence; the secondary outcomes will be the risk factors of MNA, the interventions aimed at increasing medication adherence and the outcomes of MNA. Two researchers will independently screen the eligible studies, then extract and describe the data. Disagreements will be resolved by a third researcher. We will provide a qualitative narrative synthesis of the findings.Ethics and disseminationEthical approval is not required given that previously published studies will be used. We will disseminate the findings through conference presentations and publications in international peer-reviewed scientific journals.Prospero registration numberCRD42022315298.

Dataset Information

Genomic prediction of relapse in recipients of allogeneic haematopoietic stem cell transplantation.

Publications

Genomic prediction of relapse in recipients of allogeneic haematopoietic stem cell transplantation.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets