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Background: CD49d is emerging as a powerful adverse prognostic marker in chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL). However, flow cytometric testing for CD49d has not yet been widely adopted in the United States, in part due to the lack of establishment of its performance characteristics in the clinical setting, especially in comparison with the more common CLL/SLL prognostic markers CD38 and ZAP-70., Methods: CD49d expression levels in 124 CLL/SLL cases were assessed among peripheral blood (PB), bone marrow (BM), and lymph node (LN) specimens and correlated with available CD38 and ZAP-70 expression and cytogenetic findings. For 10 PB/BM specimens, the stability of CD49d, CD38, and ZAP-70 expression was assessed at <24 hours, 48 hours, 72 hours, and 96 hours., Results: 39% (28 of 71) PB, 56% (18 of 32) BM, and 71% (15 of 21) LN involved by CLL/SLL were CD49d+, using a ≥30% threshold. The mean for the CD49d+ cases was 2.8 standard deviations (SD) above the cutoff for positivity, compared with 1.7 SD for CD38 and 1.1 SD for ZAP-70. CD49d demonstrated the lowest mean SD (0.91) and coefficient of variation (CV) (8.0%) compared with CD38 (SD = 2.1, CV = 10.4%) and ZAP-70 (SD = 9.8, CV = 40.5%) in stability studies over a 96-hours time period. CD49d+ CLL/SLL correlated with trisomy 12 (P = 0.025) and lack of isolated deletion (13q) (P = 0.005). CD38+ CLL/SLL correlated with deletion (11q) (P = 0.025). ZAP-70 did not correlate with any underlying cytogenetic abnormality., Conclusions: CD49d is a robust adverse prognostic marker in CLL/SLL with superior performance characteristics. © 2016 International Clinical Cytometry Society., (© 2016 International Clinical Cytometry Society.)

Background: Altered neutrophil maturation patterns have been reported useful for identification of myelodysplastic syndromes (MDS)., Methods: Neutrophil maturation patterns based on CD11b, CD13, and CD16 were visually and numerically evaluated in 19 control, 23 MDS, 37 nondiagnostic for MDS (NDM) specimens, and 19 also processed 1 and 2 days subsequently., Results: In contrast to maturation patterns illustrated previously by others as "normal," 84% of controls displayed diminished acquisition of CD16, imparting a contracted appearance. Such divergence from published "normal" patterns was usually mild-moderate, considered nonspecific, and associated with delayed processing: longer intervals between collection and processing (median 20.5 vs. 5.2 h), and following 1 and 2 days delay. Findings restricted to nonspecific contraction were found in 56% MDS and 78% NDM specimens. Evaluation for aberrant patterns was still performed with mild-moderate contraction present, but concern for over interpretation led to use of an equivocal-aberrant category. Nine cases had aberrant or equivocal-aberrant patterns (seven MDS, two NDM) with distinct visual alterations that differed from nonspecific contraction and had numerical evidence for a left shift: myeloblasts increased (67%) and least mature neutrophils (CD11b-/low, CD16-/low) increased (78%). Although evidence for a left shift was associated with MDS, it was also seen in NDM specimens with a synchronous left shift., Conclusions: Neutrophil maturation patterns that diverge from previously illustrated "normal" patterns, not specific for MDS, may be common in some settings. Laboratories seeking to implement FC evaluation for MDS must determine which findings have sufficient specificity for MDS within their own practice and patient population., (Copyright © 2012 International Clinical Cytometry Society.)

SOX5 encodes a transcription factor involved in the regulation of chondrogenesis and the development of the nervous system. Despite its important developmental roles, SOX5 disruption has yet to be associated with human disease. We report one individual with a reciprocal translocation breakpoint within SOX5, eight individuals with intragenic SOX5 deletions (four are apparently de novo and one inherited from an affected parent), and seven individuals with larger 12p12 deletions encompassing SOX5. Common features in these subjects include prominent speech delay, intellectual disability, behavior abnormalities, and dysmorphic features. The phenotypic impact of the deletions may depend on the location of the deletion and, consequently, which of the three major SOX5 protein isoforms are affected. One intragenic deletion, involving only untranslated exons, was present in a more mildly affected subject, was inherited from a healthy parent and grandparent, and is similar to a deletion found in a control cohort. Therefore, some intragenic SOX5 deletions may have minimal phenotypic effect. Based on the location of the deletions in the subjects compared to the controls, the de novo nature of most of these deletions, and the phenotypic similarities among cases, SOX5 appears to be a dosage-sensitive, developmentally important gene., (© 2012 Wiley Periodicals, Inc.)

Background: Flow cytometric immunophenotyping has an established role in the diagnosis and monitoring of B-lymphoblastic leukemia (B-LL). However, the search continues for an optimal reagent set that can identify leukemic blasts with specificity, reproducibility, and sensitivity, at any point during the course of the disease and in every specimen type., Methods: This study evaluated the diagnostic utility of detecting the intracytoplasmic antigens zeta-associated protein (ZAP-70) and Bcl-2 in the distinction between the leukemic blasts of B-LL and hematogones., Results: In comparison with hematogones in reference specimens, significantly higher levels of Bcl-2 were identified in 21 of 23 (91%) B-LL. In particular, Bcl-2 expression was consistently higher in leukemic blasts with bright intensity CD10 expression than the equivalent most immature (CD10 bright intensity) hematogones. As previously reported, Bcl-2 expression was lower in B-LL with BCR-ABL1 gene rearrangement, but the fluorescence intensity of this group of specimens was still significantly higher than that seen for hematogones. In contrast, ZAP-70 was expressed at significantly higher levels in only 7 of 23 (30%) B-LL and demonstrated other findings that might limit clinical utility, including differences in the level of ZAP-70 expression during therapy and between blasts in the peripheral blood and bone marrow., Conclusions: Bcl-2 over-expression provides a useful tool for the distinction between B-LL and hematogones. In contrast, although further optimization of the ZAP-70 assay might increase the sensitivity of detection, over-expression of ZAP-70 was identified in only a minority of B-LL., (Copyright © 2011 International Clinical Cytometry Society.)

The molecular hallmark of angiomatoid fibrous histiocytoma (AFH) is not well defined, with only six cases with specific gene fusions reported to date, consisting of either FUS-ATF1 or EWSR1-ATF1. To address this, we investigated the presence of FUS-ATF1, EWSR1-ATF1, and the highly related EWSR1-CREB1 fusion in a group of nine AFHs. All cases were subjected to RT-PCR for EWSR1-ATF1 and EWSR1-CREB1. FISH for EWSR1 and FUS rearrangements was performed in most cases. Transcriptional profiling was performed in three tumors and their gene expression was compared to five clear cell sarcomas expressing either the EWSR1-ATF1 or EWSR1-CREB1 fusion. By RT-PCR, eight out of nine tumors showed the presence of the EWSR1-CREB1 fusion, while one had an EWSR1-ATF1 transcript. FISH showed evidence of EWSR1 rearrangement in seven out of eight cases. Karyotypic analysis performed in one tumor showed a t(2;22)(q33;q12). High transcript levels were noted for TFE3 in AFH tumors, while overexpression of genes involved in melanogenesis, such as MITF, GP100, and MET was noted in somatic clear cell sarcomas. We report for the first time the presence of EWSR1-CREB1 in AFH, which now appears to be the most frequent gene fusion in this tumor. EWSR1-CREB1 is a novel translocation recently described in clear cell sarcoma of the GI tract. EWSR1-ATF1, identified in some AFH cases, is the most common genetic abnormality in soft tissue clear cell sarcoma. Thus, identical fusions involving ATF1 and CREB1 are found in two distinct sarcomas, which may be able to transform two different types of mesenchymal precursor cells, unlike most other sarcoma gene fusions., ((c) 2007 Wiley-Liss, Inc.)

We report three cases of tetrasomy 9p, two of which were confirmed prenatally. All three had characteristic findings on ultrasound and at birth. We also present a review of the literature, which suggests that a recognizable phenotype for this condition is emerging. Common findings on prenatal ultrasound include intrauterine growth restriction, ventriculomegaly, cleft lip or palate, and renal anomalies. These findings can provide a clue toward the prenatal diagnosis of this condition. There is also a clearly recognizable phenotype at birth. Facial characteristics include hypertelorism, broad nasal bridge/bulbous or beaked nose, cleft lip/palate, ear anomalies, and micrognathia. The exact extent of the isochromosome does not seem to predict severity, but mosaic cases are less severe, or at least have a greater probability of survival., (Copyright 2002 Wiley-Liss, Inc.)

We describe a girl who had been followed since birth for apparent Shprintzen-Goldberg syndrome (SGS), with macrosomia, long fingers and toes, and craniosynostosis, and presented at 4 years of age with bilateral Wilms tumors (also called nephroblastoma). Cytogenetic analysis of her peripheral blood revealed a de novo supernumerary marker chromosome. This stable marker chromosome is present in 19 of 20 lymphocytes analyzed, as well as in all 40 tumor cells (20 from each tumor) studied. Classical and molecular cytogenetic studies indicate that the marker is derived from an inverted duplication of chromosome 15q25.3 --> qter and contains a neocentromere. The presence of this marker chromosome in our patient results in tetrasomy 15q25.3 --> qter. The relationship between her genotype and phenotype are discussed in light of genes, including IGF1R and FES, mapped to the aneusomic segment., (Copyright 2002 Wiley-Liss, Inc.)

Genomic alterations were analyzed in 21 uterine leiomyosarcomas (ULMSs) by comparative genomic hybridization. DNA copy number changes were detected in all 21 tumors. The most frequent losses were 13q (16/21 = 76%), 10q (13/21 = 62%), 16q (8/21 = 38%), 12p (7/21 = 33%), and 2p (9/21 = 43%). The most common gains were 17p (8/21 = 38%), Xp (7/21 = 33%), and 1q (7/21 = 33%). High-copy-number gains (ratio > 1.5) were identified in Xp, 1q, and 17p. Loss of 13q was identified in both low-grade and high-grade tumors. Inactivation of a tumor suppressor gene in 13q may be an early event in the development of leiomyosarcomas. Loss of 10q, 2p, and 12p and gains of 1q as well as 17p were frequently found in high-grade tumors and recurrent tumors. Inactivation of tumor suppressor genes and activation of oncogenes in these regions may be associated with a more aggressive behavior of ULMS. Patients with only loss of 13q and without the other alterations listed above had longer survival times. Gains of Xp, 17p, and 1q and losses of 13q, 10q, 16q, 12p, and 2p have been reported in extra-uterine leiomyosarcomas. Our findings indicate that the pathogenesis of uterine leiomyosarcomas and extra-uterine leiomyosarcomas follows the same genetic pathways., (Copyright 2001 Wiley-Liss, Inc.)

Coffin-Siris syndrome is a multiple anomaly/mental retardation syndrome characterized by "coarse" facial appearance, hypoplastic or absent nails on the fifth digits, generalized hirsutism with sparse scalp hair, hypotonia, and developmental delay. Due to several reports of affected sibs with or without a mildly affected parent, both autosomal recessive and autosomal dominant inheritance have been suggested. All previous patients with well-documented Coffin-Siris syndrome are chromosomally normal, and the gene has not been mapped. We report on an infant with typical findings of Coffin-Siris syndrome who also has a de novo apparently balanced translocation of chromosomes 1 and 7, karyotype 46,XY,t(1;7)(q21.3;q34). The parental chromosomes are normal and none of the relatives have signs of Coffin-Siris syndrome. The breakpoints 1q21.3 and 7q34 are suggested as possible locations for a Coffin-Siris gene.

This study further defines the region of consistent deletion of chromosome 7 in uterine leiomyomas. We have examined 74 leiomyomas for allelic loss of markers spanning the 7q22 region defined by markers D7S518 and D7S471. Forty tumors with cytogenetically defined 7q deletions, twenty-nine tumors without cytogenetically visible 7q deletions, and five tumors with no cytogenetic information were examined for allelic loss of D7S518, D7S666, D7S515, D7S658, D7S496, D7S692, and D7S471. Loss of heterozygosity for one or more of these loci was observed in twenty-eight leiomyomas with cytogenetically defined 7q deletions and in three leiomyomas with a normal karyotype. Allelic loss of D7S666 was common and was observed in all twenty-three informative tumors with 7q deletions and in two tumors with normal karyotypes. This study indicates the presence of a tumor suppressor gene in close proximity to the D7S666 locus. Eight tumors followed an unusual pattern of allelic loss. These tumors showed retention of heterozygosity for at least one locus flanked by deleted loci. These results suggest the possibility that two discrete regions of deletion at 7q22 are involved in the development of a subset of leiomyomas.

We report on our findings of 4 patients with mosaicism for a deletion of chromosome 15, most commonly associated with Prader-Willi syndrome (PWS). We examined a series of typical and atypical PWS patients in order to identify cytogenetically undetected deletions, using fluorescence in situ hybridization. In 4 of the patients analyzed we detected a deletion in 14-60% of peripheral blood leukocytes, using four commercially available probes. Our results indicate that mosaicism may play a role in the etiology of some PWS cases. These findings may be especially useful in patients who display discrepancies between clinical phenotype and established diagnostic criteria. Methylation and microsatellite polymorphism analyses of 2 patients with low-level mosaicism failed to identify the deletion. We propose that fluorescence in situ hybridization is the most effective method for detecting somatic mosaicism, since a large number of cells can be individually examined for the presence or absence of a specific deletion.

Pitt-Rogers-Danks syndrome (PRDS) is a rare, presumed autosomal recessive, syndrome with pre- and postnatal growth retardation, microcephaly, characteristic facial appearance, seizures, unusual palmar creases and developmental delay. Since the first description in 1984, only 7 cases have been reported. We report the identification of a 4p microdeletion in 2 new patients, who were previously diagnosed with PRDS, as well as the sibs in Pitt et al. [1984]. PRDS can no longer be considered autosomal recessive. Although our cases are attributable to a microdeletion in 4p16, it is uncertain if the critical region involves a single locus or multiple loci or to what extent this region overlaps with the critical region for Wolf-Hirschhorn syndrome.

In order to further our understanding of the epigenetic modifications of DNA and its role in imprinting, we examined DNA methylation patterns of human tissues of uniparental origin. We used complete hydatidiform moles (CHM), which are totally androgenetic conceptions, to examine the paternal methylation pattern in the absence of a maternal contribution and we used ovarian teratomas to represent the maternal counterpart. We carried out an analysis of DNA methylation of a gene which has been shown to contain sites which are differentially methylated in a parent-specific fashion. The gene, ZNF127, is located on chromosome 15q11-q13 in the region associated with Prader-Willi and Angelman syndromes. The parent-of-origin DNA methylation has been postulated to reflect the presence of an imprint and recent studies have confirmed that ZNF127 is differentially expressed only from the paternal chromosome. We identified a unique pattern of hyper- and hypomethylated sites in androgenetic conceptions which was nearly identical to the paternal pattern found in sperm. This may represent the paternal germ-line methylation imprint. We also studied partial hydatidiform moles, non-molar triploid conceptions, normal chorionic villi, and somatic tissue. These all demonstrated a modified DNA methylation pattern characteristic of normal chorionic villi with only limited findings of the imprint. Our results suggest that human androgenetic conceptions may provide an excellent model to analyze epigenetic DNA modifications, such as methylation, in imprinted genes. The paternal allele-specific methylation imprint will also be useful clinically to confirm the androgenetic nature of suspected molar conceptions in which parental blood samples may not be available.

Uterine leiomyomas are benign tumors that arise clonally from smooth muscle cells of the myometrium. Cytogenetic studies of uterine leiomyomas have shown that about 40% have chromosome abnormalities and that deletion of 7q is a common finding. The observations suggest the possible location of a growth-suppressor gene within the 7q21-q22 region. Molecular genetic analysis of cytogenetically normal tumors has frequently shown somatic loss of specific tumor suppressor genes detected by loss of heterozygosity in the critical region. To test the hypothesis that chromosome region 7q21-q22 contains a growth-suppressor gene involved in the development of leiomyomas, we examined 92 leiomyomas for allelic loss of 7q markers spanning the cytogenetically defined critical region. Forty tumors with cytogenetically defined 7q deletion, 45 tumors without cytogenetically visible 7q deletion, and seven tumors with no cytogenetic information were examined for allelic loss of loci D7S489, D7S440, D7S492, D7S518, D7S471, D7S466, and D7S530. Loss of heterozygosity for one or more of these loci was observed in 23 of 40 (57.5%) of the tumors with deletion of 7q and in 2 of 45 cases without a cytogenetically visible deletion. The tumors with cytogenetic deletion of 7q, but no loss of 7q21-q22 markers, were mosaics, with only a minority of cells containing the cytogenetic deletion. The critical region of loss is defined by the markers D7S518 and D7S471, each showing loss in approximately 50% of informative cases.(ABSTRACT TRUNCATED AT 250 WORDS)

Paracentric inversions, involving a rearrangement within one chromosome arm, are rare. Although carriers of balanced paracentric inversions should theoretically not be at risk for abnormal offspring, such cases have been reported. We report on 2 unrelated cases of inherited paracentric inversions of 1p with breakpoints at p32 and p36.1 and p32.3 and p36.22 in individuals with abnormal phenotypes. Another case of 2 abnormal monozygotic twins with a de novo paracentric inversion of 1p with breakpoints at p22 and p34 is presented as well.

We present the necropsy findings of a 21-week-gestation male fetus with deletion of the terminal portion of long arm of chromosome 6 [46,XY,del(6)(q23----qter)]. Major anomalies include intrauterine growth retardation, facial anomalies, nuchal cyst, scoliosis, bilateral diaphragmatic hernias, persistent common atrioventricular canal, absent olfactory bulbs and agenesis of corpus callosum. In aberrations of chromosome 6q, patients usually have psychomotor retardation, somatic growth failure, and facial anomalies; nuchal cyst and bilateral diaphragmatic hernias have not yet been described.