Clinical and Prognostic Impact of Copy Number Alterations and Associated Risk Profiles in a Cohort of Pediatric B-cell Precursor Acute Lymphoblastic Leukemia Cases Treated Under ICiCLe Protocol.

Copy number alteration (CNA) status and CNA risk profiles of IKZF1 plus , UK-ALL CNA risk groups and MRplus scores, were evaluated for clinical and prognostic impact in a cohort of 493 B-cell acute lymphoblastic leukemia cases diagnosed and treated under the Indian Collaborative Childhood Leukemia group (ICiCLe) protocol trial. Overall CNA frequency was 59% with 60% of cases showing 2-loci deletion. CDKN2A/B deletion was most common CNA (36.3%), while IKZF1 deletion and IKZF1 plus profile were noted in 19.5% and 13.4% of cases, respectively. IKZF1 deletions and other CNA risk profiles were significantly associated with poor (PR)/high risk (HR) clinical and genetic profile parameters (P < 0.001). In addition, the 3-year OS, event-free survival (EFS) was significantly poor with high relapse rate (RR) of 38.6%, 46.5%, and 35.2% for IKZF1 deletions, IKZF1 plus profiles, and UK-ALL CNA-intermediate risk (IR)+PR risk groups, respectively (P < 0.001). Integrated evaluation of UK-ALL CNA risk profile with ICiCLe trial risk stratification groups revealed a worse overall survival, EFS, and RR of 63.3%, 43.2%, and 35.2% for CNA-IR+PR profile compared to CNA-good risk profile (81.3%, 65.0%, and 21.0%; P < 0.001). Hence, routine CNA testing in our setting is must to identify standard risk and IR cases likely to benefit from HR treatment.

Cell-free EBV DNA as a biomarker during clinical management of nasopharyngeal carcinoma in a nonendemic region.

Nasopharyngeal carcinoma (NPC) is the most common malignant tumor of the nasopharynx. Although NPC is not endemic in India, higher incidences were observed in its North-Eastern regions particularly Sikkim, Nagaland, Manipur, and Mizoram. Early detection of NPC is difficult because the nasopharynx is not readily amenable to clinical examination and symptoms of NPC are nonspecific. The development of suitable biomarkers for early diagnosis of NPC as well as accurate monitoring of treatment response is needed urgently. In this exploratory pilot study, we have investigated the clinical significance of assessing plasma Epstein-Barr virus (EBV) DNA load at diagnosis and during treatment. We found that EBV DNA is detectable at diagnosis in the majority of patients with nonendemic NPC and the absolute copy number of circulating EBV DNA per milliliter increases progressively with the stage of the disease. The viral load declined significantly with induction chemotherapy and definitive chemoradiation but showed a sharp rise at relapse. Patients with EBV DNA levels ≥1500 copies/ml had a higher risk of disease progression or relapse when compared with patients who had EBV DNA <1500 copies/ml at baseline. Estimation of plasma EBV DNA may serve as an excellent noninvasive tool to monitor disease extent, response to therapy, and for better prediction of future relapse or progression-free survival in a nonendemic NPC patient population.

Proposal and clinical application of molecular genetic risk scoring system, "MRplus", for BCR-ABL1 negative pediatric B-cell acute lymphoblastic leukemia- report from a single centre.

INTRODUCTION: We propose "MRplus", a molecular genetic risk score and check its clinical application in the risk-stratification of pediatric B-ALL. METHODS: The genomic DNA of untreated pediatricBCR-ABL1 negative B-ALL patients was analyzed for deletions of IKZF1, PAX5, CDKN2A/B, BTG1, RB1, ETV6, EBF1, ERG, pseudoautosomal region(PAR) genes using multiplex ligation-dependent probe amplification, along with the routine genetic work-up. The patients were assigned an 'M'score- 0 (M0) for low and 1 (M1) for high genetic-risk as per the criteria by Moorman et al., and another score "IKplus"-1 (IKplus1) for IKZF1plus as per the criteria by Stanulla et al., and 0 (IKplus0) for other patients. The final "MRplus" risk-score of 0 (MRplus0), 1 (MRplus1) or 2 (MRplus2) was obtained by adding both these scores. The association of risk scores with overall survival (OS) and event free survival(EFS) was seen using Cox proportion hazard model. The overall goodness of fit of the model was done using Cox-Snell residuals. RESULTS: The median age of 320 patients was 6 years (1-18 years). The patients with score M1 were 139 (43.4 %), M0-181 (56.6 %); IKplus1-32 (10 %) and IKplus0-288 (90 %). The final "MRplus" score of 0,1,or 2 was obtained in 181(56.6 %), 107(33.4 %) and 32(10 %) patients respectively. The post-induction remission rate was 90.7 %, 77.8 %, 73.9 % (p = 0.004); 4-year OS 67 %, 48 %, 27 % (p < 0.001); and 4-year EFS 56 %, 34 %, 19 %(p < 0.001) in patients with "MRplus" score 0,1,and 2 respectively. CONCLUSIONS: The proposed "MRplus" scoring at baseline could identify three distinct risk groups-good (MRplus0), intermediate (MRplus1) and poor (MRplus2), with different outcomes; in pediatricBCR-ABL1 negative B-ALL. This may help in better risk-stratification and selection of patients for alternative treatment approaches.

IKZF1 Deletion Subtyping and Outcome Analysis in BCR-ABL1-Negative Pediatric B-Cell Acute Lymphoblastic Leukemia: A Single-Institution Experience from North India.

BACKGROUND: IKZF1 deletions are associated with adverse outcomes in B-cell acute lymphoblastic leukemia (B-ALL). We assessed the prevalence and clinical impact of functional subtypes of IKZF1 deletions in pediatric BCR-ABL1-negative B-ALL. PATIENTS AND METHODS: This retrospective study of IKZF1 deletions was done in cases of pediatric BCR-ABL1-negative B-ALL. The genomic DNA of cases, over a 53-month period, was analyzed using multiplex ligation-dependent probe amplification and multiplex fluorescent polymerase chain reaction. The deletions were divided into functional subgroups: (1) loss-of-function/haploinsufficiency, (2) dominant-negative, and (3) a combination of both types of deletion. The post-induction remission status, event-free survival (EFS), and overall survival (OS) were noted. RESULTS: Out of 320 cases, 47 (14.7%) had IKZF1 deletions. Thirty-six of the 47 (77%) had loss-of-function deletions, 10 (21%) had dominant-negative deletions, and one (2%) had a combination of both types. The post-induction remission rates in cases with loss-of-function deletions (22/30, 73%; P = .060) and dominant-negative deletions (4/5, 80%; P = .517) were lower compared with those without deletions (215/248, 86.7%). These cases also had worse median EFS: 21.1 months (P = .006) for loss-of-function and 15.4 months (P = .156) for dominant-negative deletions, compared with 46.4 months in cases without IKZF1 deletions. They also had worse median OS: 23.4 months (P = .012) for loss-of-function deletions and 15.7 months (P = .233) for dominant-negative deletions, compared with median not reached in cases without IKZF1 deletions. CONCLUSION: The IKZF1 deletions were seen in 14.7% of BCR-ABL1-negative pediatric B-ALL. Most of these deletions (77%) were loss-of-function type. The cases with loss-of-function deletions had lower remission rates and poor EFS and OS compared with cases without IKZF1 deletions. A similar trend of poor outcome was seen in the few cases with dominant-negative IKZF1 deletions.