Non-inferior long-term outcomes of adults with Philadelphia chromosome-like acute lymphoblastic leukemia.

Philadelphia chromosome-like acute lymphoblastic leukemia (Ph-like ALL) is associated with inferior outcomes in the chemotherapy setting. We hypothesized that allogeneic hematopoietic cell transplantation (allo-HCT)-based post-remission therapy would improve outcomes of this entity. We examined the frequency and long-term outcomes of adults with Ph-like ALL, particularly focusing on allo-HCT outcomes for Ph-like ALL versus non-Ph-like ALL. Ph-like ALL was determined by anchored multiplex PCR-based targeted next-generation sequencing. Of the 344 patients, 57 (16.6%) had Ph-like ALL, 197 (57.3%) had Ph-positive ALL, and 90 (26.1%) had B-other ALL. To further evaluate the prognosis of Ph-like ALL, outcome analyses were restricted to 147 patients, excluding Ph-positive ALL. The actual allo-HCT rates in complete remission were 87.7% for Ph-like ALL, 71.4% for B-other standard-risk ALL, and 70.4% for B-other poor-risk ALL. Patients with Ph-like ALL had a higher 5-year overall survival (60.6% vs 27.1%; P = 0.008) than B-other poor-risk ALL subgroup, while no difference was observed compared with B-other standard-risk ALL subgroup. Similar results were noted in a separate analysis for patients receiving allo-HCT in complete remission. In multivariate analyses, B-other poor-risk ALL was associated with poorer outcomes. Our data showed that allo-HCT-based post-remission therapy may have contributed to non-inferior outcomes of adult Ph-like ALL.

KRAS, NRAS, and BRAF mutations in plasma cell myeloma at a single Korean institute.

BACKGROUND: Plasma cell myeloma (PCM) is a genetically heterogeneous disease. The genetic spectrum of PCM has been expanded to mutations such as KRAS, NRAS, and BRAF genes in the RAS-RAF-MAPK pathway. In this study, we have evaluated the frequency of these mutations and their significance, including baseline characteristics and clinical outcomes. METHODS: We explored 50 patients who were newly diagnosed with PCM between 2009 and 2012 at a single Korean institute. Clinical and laboratory parameters were gathered through careful review of medical records. Mutation analysis was carried out using DNA from the bone marrow at the time of diagnosis. Pyrosequencing was performed to detect KRAS G12V, KRAS G13D, and NRAS G61R. BRAF V600E was analyzed by allele-specific real- time PCR. Comparison of clinical and laboratory parameters was carried out according to those mutations. RESULTS: We identified 14 patients (28%) with activating mutations in the RAS-RAF-MAPK pathway (RAS/RAF mutations): KRAS (N=3), NRAS (N=4), BRAF (N=7), and both KRAS and BRAF (N=1). RAS/RAF mutations were more frequently observed in patients with complex karyotypes and showed poorer progression free survival (PFS). Specifically, the BRAF V600E mutation had a significantly negative impact on median PFS. CONCLUSION: We first showed the frequency of RAS/RAF mutations in Korean patients with PCM. Screening of these mutations could be considered as a routine clinical test at the time of diagnosis and follow-up due to their influence on clinical outcome, as well as its potential as a therapeutic target.

Analytical and Potential Clinical Performance of Oncomine Myeloid Research Assay for Myeloid Neoplasms.

INTRODUCTION: Next-generation sequencing (NGS) panels have recently been introduced to efficiently detect genetic variations in hematologic malignancies. OBJECTIVES: Our aim was to evaluate the performance of the commercialized Oncomine™ myeloid research assay (OMA) for myeloid neoplasms. METHODS: Certified reference materials and clinical research samples were used, including 60 genomic DNA and 56 RNA samples. NGS was performed using OMA, which enables the interrogation of 40 target genes, 29 gene fusions, and five expression target genes with five expression control genes by the Ion S5 XL Sequencer. The analyzed data were compared with clinical data using karyotyping, reverse transcription polymerase chain reaction (PCR), fluorescence in situ hybridization, Sanger sequencing, customized NGS panel, and fragment analysis. RESULTS: All targets of reference materials were detected except three (two ASXL1 and one CEBPA) mutations, which we had not expected OMA to detect. In clinical search samples, OMA satisfactorily identified DNA variants, including 90 single nucleotide variants (SNVs), 48 small insertions and deletions (indels), and eight FLT3 internal tandem duplications (ITDs) (Kappa agreement 0.938). The variant allele frequencies of SNVs and indels measured by OMA correlated well with clinical data, whereas those of FLT3-ITDs were significantly lower than with fragment analysis (P = 0.008). Together, OMA showed strong ability to identify RNA gene fusions (Kappa agreement 0.961), except one RUNX1-MECOM. The MECOM gene was highly expressed in all five samples with MECOM-associated rearrangements, including inv(3), t(3;3), and t(3;21). CONCLUSION: OMA revealed excellent analytical and potential clinical performance and could be a good replacement for conventional molecular tests.

Identification of small marker chromosomes using microarray comparative genomic hybridization and multicolor fluorescent in situ hybridization.

BACKGROUND: Marker chromosomes are small supernumerary chromosomes that cannot be unambiguously identified by chromosome banding techniques alone. However, the precise characterization of marker chromosomes is important for prenatal diagnosis and proper genetic counseling. In this study, we evaluated the chromosomal origin of marker chromosomes using a combination of banding cytogenetics and molecular cytogenetic techniques including diverse fluorescence in situ hybridization (FISH) assays and array comparative genomic hybridization (array CGH). RESULTS: In a series of 2871 patients for whom cytogenetic analysis was requested, 14 cases with small supernumerary marker chromosomes (sSMCs) were identified. Nine sSMCs were mosaic, and five nonmosaic. Of the nine cases with known parental origins, four were identified as de novo, and four and one were maternally and paternally inherited, respectively. Six sSMCs were identified by FISH using centromeric probes; three sSMCs were derived from chromosome 15, including two heterochromatic sSMC(15)s and a large sSMC(15) spanning 15q11.1q13.1, and three sSMCs originated from chromosome 14 or 22. Array CGH revealed two cases with derivatives of chromosome 2 and whole chromosome painting multicolor-FISH (M-FISH) identified three cases with derivatives of chromosome 6, 16, and 19, respectively. One maker chromosome in Turner syndrome was characterized as sSMC(X) by preferential application of a centromeric probe for X-chromosome. In addition, one sSMC composed of genomic materials from chromosomes 12 and 18 was identified in parallel with parental karyotype analysis that revealed the reciprocal balanced translocation. CONCLUSIONS: This report is the largest study on sSMCs in Korea and expands the spectrum of sSMCs that are molecularly characterized.

Chromosome abnormalities in T-cell acute lymphoblastic leukemia in Korea.

The aim of the present study was to analyze chromosome abnormalities in Korean patients with T-cell acute lymphoblastic leukemia (T-ALL). A total of 65 patients with newly diagnosed T-ALL were enrolled in the study from December 2004 to December 2011. Chromosome analysis was performed at diagnosis on short-term cultures of bone marrow specimens. Of these 65 patients, abnormal karyotypes were found in 50 (77 %). Numerical and structural chromosome abnormalities were identified in 16 (25 %) and 47 (72 %) patients, respectively. Deletion was the most common structural abnormality (48 %), followed by translocation (29 %). Overall survival (OS) and relapse-free survival (RFS) outcome were unaffected by the number and/or type of chromosome abnormalities in both childhood and adult T-ALL; however, the OS interval was longer for childhood patients than for adult patients in the entire cohort (P = 0.0003). Similarly, patients with first complete remission (CR) showed a better OS than those who failed to achieve first CR (P < 0.0001). There was a negative clinical impact in adult patients and patients without first CR according to multivariate analysis. This study helps to fill the gap regarding chromosome findings in T-ALL and may lead to identification of the molecular background behind phenotypic differences.

Genotype-phenotype correlation of a 5q22.3 deletion associated with craniofacial and limb defects.

We describe here a newborn with a de novo 22.6Mb interstitial deletion of chromosome 5q22.3. The clinical findings included brachycephaly, a high forehead, hypertelorism with prominent eyes, low-set ears, clenched hands, club feet, a prominent coccyx with hair, ambiguous genitalia, inguinal hernia, heart defect and severe failure to thrive. This case had a more severe phenotype, compared with the previous reports of interstitial 5q syndrome. High resolution multicolor banding and array comparative genomic hybridization (array CGH) analysis delineated the breakpoints at 5q22.3 and 5q31.2. There were no obvious candidate genes for the specific correlation with the phenotypes except a PITX1 gene associated with the phenotype of club feet. Further cumulative data based on the molecular approach are needed to establish the genotype-phenotype correlation and to understand the role and influence of the genes in the interstitial 5q syndrome.