Chromosome 5q deletion: Specific diagnoses and cytogenetic details among 358 consecutive cases from a single institution

FANCA, TP53, and del(5q)/RPS14 alterations in a patient with T-cell non-Hodgkin lymphoma and concomitant Fanconi anemia and Li-Fraumeni syndrome

We traced the neoplastic history (from 5 to 11 years of age) of a child with concomitant Fanconi anemia and Li-Fraumeni syndrome. Interestingly, the patient developed a highly malignant T-cell non-Hodgkin lymphoma (NHL), which does not represent the typical tumor type in the two aforementioned syndromes, presumably due to the underlying genomic instability. By using a combination of molecular and immunohistochemical approaches, we characterized the accumulation of multiple genetic alterations in a single patient, with both germline (parentally inherited biallelic FANCA variants and a likely de novo nonsense variant in TP53) and somatic (TP53 loss of heterozygosity and 5q interstitial deletion) contributions. Our findings support the interplay of TP53 and FANC genes in DNA damage response pathways and further highlight the genetic heterogeneity of lymphomas as well as the contribution of genomic instability to lymphomagenesis.

Genetic Alterations in Essential Thrombocythemia Progression to Acute Myeloid Leukemia: A Case Series and Review of the Literature

The genetic events associated with transformation of myeloproliferative neoplasms (MPNs) to secondary acute myeloid leukemia (sAML), particularly in the subgroup of essential thrombocythemia (ET) patients, remain incompletely understood. Deep studies using high-throughput methods might lead to a better understanding of genetic landscape of ET patients who transformed to sAML. We performed array-based comparative genomic hybridization (aCGH) and whole exome sequencing (WES) to analyze paired samples from ET and sAML phases. We investigated five patients with previous history of MPN, which four had initial diagnosis of ET (one case harboring JAK2 p.Val617Phe and the remaining three CALR type II p.Lys385fs*47), and one was diagnosed with MPN/myelodysplastic syndrome with thrombocytosis (SF3B1 p.Lys700Glu). All were homogeneously treated with hydroxyurea, but subsequently transformed to sAML (mean time of 6 years/median of 4 years to transformation). Two of them have chromosomal abnormalities, and both acquire 2p gain and 5q deletion at sAML stage. The molecular mechanisms associated with leukemic progression in MPN patients are not clear. Our WES data showed TP53 alterations recurrently observed as mutations (missense and frameshift) and monoallelic loss. On the other hand, aCGH showed novel chromosome abnormalities (+2p and del5q) potentially associated with disease progression. The results reported here add valuable information to the still fragmented molecular basis of ET to sAML evolution. Further studies are necessary to identify minimal deleted/amplified region and genes relevant to sAML transformation.

Chromosome 5q deletion is extremely rare in patients with myelofibrosis

Chromosome 5q deletion can be found in rare cases of myelofibrosis (MF) but the incidence, clinical significance and response to therapies are not well studied. We retrospectively reviewed charts of 939 patients with MF and identified 8 patients [0.8%] who carried 5q deletion. Of the 8, seven had complex cytogenetic abnormalities and one had additional clone with different cytogenetic abnormality. All 8 had significant three-lineage pancytopenia. Three patients took lenalidomide and one (patient with 5q-clone) achieved long-lasting hematologic response. Two patients responded to JAK2 inhibitor therapy. MF patients with 5q deletion often have complex karyotype and poor outcome.

Bone marrow morphology predicts additional chromosomal abnormalities in patients with myelodysplastic syndrome with del(5q)

The current World Health Organization classification considers myelodysplastic syndrome with isolated del(5q) a distinct entity owing to its characteristic clinical and pathologic features. Recently, several studies have examined survival, leukemic transformation, and various prognostic factors in these patients. However, there is a lack of detailed comparative pathologic analysis of myelodysplastic syndrome cases in which del(5q) is present in association with additional cytogenetic abnormalities. We studied 26 cases of myelodysplastic syndrome at initial diagnosis with 5q- alone, 5q- plus 1 additional abnormality, and 5q- as part of a complex karyotype. Four of 17 patients had evidence of JAK2 V617F mutation. In contrast to cases of myelodysplastic syndrome with isolated 5q-, patients with additional abnormalities had normal mean corpuscular volume and decreased platelet counts (P < .001). Based on bone marrow examination, they were significantly more likely to have increased cellularity, trilineage dysplasia, lower proportion of small hypolobated megakaryocytes, higher number of blasts, and fibrosis. The presence of these morphologic features can be used to distinguish these more aggressive cases from those with myelodysplastic syndrome with isolated 5q- and a more benign clinical course.

Isolated del(5q) in myeloid malignancies: clinicopathologic and molecular features in 143 consecutive patients

World Health Organization (WHO) criteria were used to identify 143 consecutive patients (median age 73 years; 90 females) with myeloid neoplasms and isolated del(5q) seen between 1989 and 2009. We have previously reported on 88 (61%) of these patients who met criteria for WHO defined "myelodysplastic syndromes (MDS) with isolated del(5q)." The remaining 55 patients were classified as having "other" MDS variants (n = 29; 20%), acute myeloid leukemia (AML; n = 14; 10%), or myeloproliferative neoplasms (MPN; n = 12; 8%). DNA was available in 138 patients and mutation screening revealed 20 cases with JAK2, 6 with IDH, and 3 with MPL mutations; JAK2 and MPL mutations were seen mostly in MPN or "MDS with isolated del(5q)" whereas IDH mutations were frequent in other MDS variants. Overall median survival for the 143 patient cohort was 35 months and leukemic transformation (LT) was documented in 19 (~13%) cases. "MDS with isolated del(5q)" had the best prognosis with median survival of 66 months and LT rate of ~6%. Survival was poor among the other myeloid neoplasm subgroups regardless of specific morphologic diagnosis. Multivariable analysis identified higher leukocyte count and percentage of bone marrow and circulating blasts as independent predictors of shortened survival. The first two parameters and the presence of IDH mutations predicted inferior leukemia-free survival. The current study validates the prognostic relevance of considering "MDS with isolated del(5q)" as a separate WHO subcategory and identifies leukocytosis, higher blast count, and IDH mutations as being prognostically detrimental, in myeloid neoplasms associated with isolated del(5q).

WHO-defined 'myelodysplastic syndrome with isolated del(5q)' in 88 consecutive patients: survival data, leukemic transformation rates and prevalence of JAK2, MPL and IDH mutations

The 2008 World Health Organization (WHO) criteria were used to identify 88 consecutive Mayo Clinic patients with ‘myelodysplastic syndrome with isolated del(5q)' (median age 74 years; 60 females). In all, 60 (68%) patients were followed up to the time of their death. Overall median survival was 66 months; leukemic transformation was documented in five (5.7%) cases. Multivariable analysis identified age ⩾70 years (P=0.01), transfusion need at diagnosis (P=0.04) and dysgranulopoiesis (P=0.02) as independent predictors of shortened survival; the presence of zero (low risk), one (intermediate risk) or ⩾2 (high risk) risk factors corresponded to median survivals of 102, 52 and 27 months, respectively. Janus kinase 2 (JAK2), thrombopoietin receptor (MPL), isocitrate dehydrogenase 1 (IDH1) and IDH2 mutational analysis was performed on archived bone marrows in 78 patients; JAK2V617F and MPLW515L mutations were shown in five (6.4%) and three (3.8%) patients, respectively, and did not seem to affect phenotype or prognosis. IDH mutations were not detected. Survival was not affected by serum ferritin and there were no instances of death directly related to iron overload. The current study is unique in its strict adherence to WHO criteria for selecting study patients and providing information on long-term survival, practical prognostic factors, baseline risk of leukemic transformation and the prevalence of JAK2, MPL and IDH mutations.

Myelodysplastic syndromes associated with interstitial deletion of chromosome 5q: clinicopathologic correlations and new insights from the pre-lenalidomide era

To better estimate prognosis for patients with myelodysplastic syndromes (MDS) associated with clonal interstitial deletions of the long arm of chromosome 5 (del(5q)), we reviewed the medical records of 130 adults with del(5q) MDS seen at our institution over a 15-year period. Overall median survival of this cohort was 9.5 months, shorter than reported in earlier series. The least favorable outcomes are associated with complex cytogenetics, lack of any normal metaphases, normocytic rather than macrocytic erythrocyte indices, and low baseline lymphocyte counts. Lymphopenia but not neutropenia at the time of diagnosis appears to be a new adverse prognostic indicator. Cytogenetic breakpoints defined by G-banded karyotyping correlate poorly with particular disease features. Surprisingly, survival of patients with treatment-related MDS was equivalent to that of de novo MDS with del(5q) in this series. Morphologic features associated with del(5q) are diverse. Most patients with del(5q) MDS do not meet criteria for WHO-defined 5q-syndrome, and the presence of del(5q) does not appear to modify the clinical phenotype otherwise risk-stratified by the International Prognostic Scoring System (IPSS). Additional important prognostic factors not taken into account by the IPSS include the baseline erythrocyte indices, lymphocyte count, and clonal burden.

Whole-genome scanning by array comparative genomic hybridization as a clinical tool for risk assessment in chronic lymphocytic leukemia

Array-based comparative genomic hybridization (array CGH) provides a powerful method for simultaneous genome-wide scanning and prognostic marker assessment in chronic lymphocytic leukemia (CLL). In the current study, commercially available bacterial artificial chromosome and oligonucleotide array CGH platforms were used to identify chromosomal alterations of prognostic significance in 174 CLL cases. Tumor genomes were initially analyzed by bacterial artificial chromosome array CGH followed by confirmation and breakpoint mapping using oligonucleotide arrays. Genomic changes involving loci currently interrogated by fluorescence in situ hybridization (FISH) panels were detected in 155 cases (89%) at expected frequencies: 13q14 loss (47%), trisomy 12 (13%), 11q loss (11%), 6q loss (7.5%), and 17p loss (4.6%). Genomic instability was the second most commonly identified alteration of prognostic significance with three or more alterations involving loci not interrogated by FISH panels identified in 37 CLL cases (21%). A subset of 48 CLL cases analyzed by six-probe FISH panels (288 total hybridizations) was concordant with array CGH results for 275 hybridizations (95.5%); 13 hybridizations (4.5%) were discordant because of clonal populations that comprised less than 30% of the sample. Array CGH is a powerful, cost-effective tool for genome-wide risk assessment in the clinical evaluation of CLL.