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S A Schichman

Publications and source records attributed to S A Schichman.

At least 19 recordsLinked to original sources
PubMed2002

Comparison of short tandem repeat and variable number tandem repeat genetic markers for quantitative determination of allogeneic bone marrow transplant engraftment.

Variable number tandem repeats (VNTRs) were among the first genetic markers used to quantitate bone marrow transplant engraftment. The limitations of PCR-based VNTR markers in distinguishing some donor/recipient pairs has shown the need for additional genetic markers to analyze engraftment. Short tandem repeats (STRs) provide an excellent tool for this purpose because of their high degree of polymorphism and relatively short length. We compared STR analysis results with previous VNTR results for 16 post-transplantation samples from four allogeneic bone marrow transplant patients. Previously analyzed patient samples were chosen to cover the full range of engraftment. DNA samples from each patient were analyzed in a blinded fashion. Good quantitative correlation was found between STR and VNTR results in samples from all four patients. STR markers were informative in one patient for whom PCR-based VNTR markers were not available. Correlation of VNTR and STR methods helps to validate the use of STRs for the quantitative analysis of bone marrow transplant engraftment. This study demonstrates that STR-based human identity testing kits are well suited for engraftment analysis.

Bone Marrow Transplantation↗
PubMed2001

Chronic lymphocytic leukemia incidence is substantially higher than estimated from tumor registry data.

BACKGROUND: Although chronic lymphocytic leukemia (CLL) often is described as the most common leukemia in the U.S. and Western Europe, to the authors' knowledge the true incidence of CLL in the U.S. is unknown. CLL incidence is estimated from tumor registry reports based on tissue pathology and cancer treatment data. Tumor registry data may underestimate the incidence of CLL substantially because CLL can be diagnosed by flow cytometric analysis of peripheral blood cells, and the majority of patients do not require treatment at the time of diagnosis. METHODS: To test the hypothesis that CLL has a higher incidence than estimated from tumor registry data, the authors compared the actual and reported incidence of CLL for a 10-year interval at the Central Arkansas Veterans Healthcare System (CAVHS). The accuracy of surveillance methods for new diagnoses of CLL was confirmed by reviewing the lymphocyte counts in 45,009 CAVHS patients over a 4-year period. RESULTS: The tumor registry correctly reported 58 of 93 patients with CLL (62.4%) who were diagnosed between January 1, 1990 and December 31, 1999. The tumor registry correctly reported 100% of patients with CLL diagnosed between 1990-1991 but reported only 34.5% of patients with CLL diagnosed between 1998-1999. CONCLUSIONS: The incidence of CLL in the CAVHS was 37.6% higher than estimated from tumor registry data due to an increase in the use of peripheral blood immunophenotype as the only diagnostic test for CLL over the time period of the study. These data suggest that the true incidence of CLL may be substantially higher than estimated from tumor registry data.

Humans↗
PubMed2001

Localized herpes simplex lymphadenitis mimicking large-cell (Richter's) transformation of chronic lymphocytic leukemia/small lymphocytic lymphoma.

We report a patient with chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL) who presented with rapid enlargement of a cervical lymph node due to localized herpes simplex lymphadenitis, which was clinically indistinguishable from large cell (Richter's) transformation. The diagnosis was made by excisional lymph node biopsy, which demonstrated CLL/SLL and zonal necrosis due to herpes simplex infection. The herpetic zone was surrounded by a brisk proliferation of immunoblasts. This case demonstrates the need for excisional biopsy and histologic examination of rapidly enlarging nodes in patients with CLL/SLL. The diagnosis of herpes simplex lymphadenitis in patients with CLL/SLL is especially important because, unlike large cell transformation, the infection usually responds well to treatment.

Biopsy↗
PubMed2001

Analytic validation of a competitive polymerase chain reaction assay for measuring Epstein-Barr viral load.

Epstein-Barr virus (EBV) is associated with several benign and malignant diseases, and blood tests for EBV viral load show promise as markers of disease burden in affected patients. A commercial quantitative PCR method (BioSource International) was recently introduced to facilitate measuring viral load. It relies on coamplification of EBV DNA and a spiked competitor in plasma or serum, followed by semiautomated product detection on enzyme-linked immunosorbent assay (ELISA) plates. In the current study, analytic performance characteristics were assessed, and the authors describe several methodologic improvements to facilitate laboratory implementation. Rapid DNA extraction was accomplished using commercial silica spin columns, heat-labile uracil-N-glycosylase was used to inhibit amplicon contamination, and inexpensive agarose gels were used to screen for polymerase chain reaction products requiring ELISA plate quantitation. Accuracy and precision were verified using EBV DNA standards derived from two cell lines and plasmid containing viral sequences. The assay was sensitive to as few as five template copies per polymerase chain reaction and was linear across four orders of magnitude (correlation coefficient 0.995). When applied to matched plasma and serum samples from 15 patients with nasopharyngeal carcinoma, both sample types yielded similar viral load results. This commercial EBV viral load assay provides sensitive and quantitative detection of EBV DNA using equipment already available in many molecular diagnostic laboratories.

DNA, Viral↗
PubMed2000

Use of HFE mutation analysis for hereditary hemochromatosis: the need for physician education in the translation of basic science to clinical practice.

BACKGROUND: Hereditary hemochromatosis (HH) is a common hereditary disorder of iron metabolism causing iron overload, organ failure, and malignancy. Preclinical diagnosis using HFE gene analysis followed by prophylactic phlebotomy can completely prevent the disease. METHODS: We conducted a mail survey of all registered primary care physicians, gastroenterologists, and hematologists in Arkansas (n = 860) to determine utilization of HFE mutation analysis in clinical medicine a year after the new molecular test first became available. RESULTS: Of 346 responding physicians (40%), 71 (21%) were aware of the test, 36 (10%) knew that the test was available in Arkansas, and 10 (3%) had used the test. One physician had used the test to screen first-degree relatives of a homozygous HH proband. CONCLUSIONS: Because of poor utilization of the test, the discovery of the role of HFE mutations in HH has had minimal impact on clinical care in Arkansas.

Arkansas↗
PubMed1999

An automated method for the analysis of T-cell receptor repertoires. Rapid RT-PCR fragment length analysis of the T-cell receptor beta chain complementarity-determining region 3.

The examination of T-cell receptor (TCR) repertoires has an important role in the study of lymphoproliferative disorders and autoimmune diseases. Analysis of the complementarity-determining region 3 (CDR3) of the TCR beta chain is used to assess the clonality of T-cell populations. We developed a rapid fluorescence-based method for CDR3 length analysis of expressed TCR gene families. TCR beta chain complementary DNA is amplified by a nested polymerase chain reaction with V beta family-specific oligonucleotide primers and a fluorochrome-labeled C beta primer. The polymerase chain reaction products were analyzed on a compact automated DNA sequencing system (OpenGene system, Visible Genetics, Toronto, Ontario). To demonstrate the usefulness of our technique, we examined the CDR3 length distribution of peripheral blood T cells from a healthy subject, intestinal T cells from a patient with ulcerative colitis, and the T-cell leukemia cell line Jurkat. The analysis revealed polyclonal, oligoclonal, and monoclonal CDR3 distributions, respectively, for the 3 T-cell populations. Our new method shows virtually identical CDR3 length patterns compared with the traditional radioisotope-based method. The new technique offers the convenience of rapid throughput, nonradioactive labeling, and quality data analysis.

Automation↗
PubMed1996

Complete exon structure of the ALL1 gene.

The ALL1 gene is found rearranged in approximately 10% of acute lymphoblastic leukemias and in over 5% of acute myeloid leukemias. The gene undergoes fusion with either a variety of partner genes located on different chromosomes or with itself. To further characterize the role of the ALL1 gene in the leukemogenic process, and possibly in solid malignancies, we defined its complete genomic structure. The gene, which spans a region on chromosome band 11q23 approximately 90 kb in length, consists of 36 exons, ranging in size from 65 bp to 4249 bp. The determination of intronic sequences flanking the exon boundaries will allow the determination of whether point mutations may be responsible for inactivation of the gene in solid tumors showing loss of heterozygosity at region 11q23.

Base Sequence↗
PubMed1996

Partial tandem duplication of ALL1 as a recurrent molecular defect in acute myeloid leukemia with trisomy 11.

Gains of a single chromosome are frequent cytogenic findings in human cancer, but no molecular rearrangement has been consistently associated with any trisomy. In acute myeloid leukemia (AML), trisomy 11 (+11) occurring as a sole abnormality is the third most common trisomy. We have shown that the ALL1 gene, located at 11q23, can be rearranged as a result of a partial tandem duplication in two such cases of AML. To test the hypothesis that the partial tandem duplication of ALL1 is the recurrent molecular defect in cases of AML presenting with +11 as a sole cytogenic abnormality, we performed Southern analysis and PCR for defects of ALL1 in 17 cases of AML and one case of myelodysplastic syndrome with +11 or +11q but without cytogenic evidence of a structural abnormality involving 11q23. Twelve cases (67%) had rearrangement of ALL1, including 10 of 11 patients (91%) with +11 as a sole abnormality and 2 of 7 cases (29%) with +11 and other aberrations; all were classified as FAB M1 or M2. In 10 of the 12 cases, material was available for additional characterization; a partial tandem duplication of ALL1 was detected in each of these 10 cases (100%). Four cases demonstrated previously unreported duplications, two of which were detectable only by reverse transcription-PCR. Four patients with the ALL1 duplication also displayed a loss of material from 7q, suggesting an association between these two findings. We conclude that the partial tandem duplication of ALL1 is present in most, if not all, cases of AML with +11 as a sole abnormality, and can be found in cases of AML with +11 or +11q accompanied by other cytogenic abnormalities. The duplication is more prevalent in AML than was recognized previously in part because its size and location vary considerably, requiring a variety of molecular probes for detection. Our finding of the ALL1 duplication as a consistent defect in patients with +11 represents the first identification of a specific gene rearrangement associated with recurrent trisomy in human cancer.

Acute Disease↗
PubMed1996

Molecular diagnosis of lymphoma.

The biologic and clinical heterogeneity of lymphomas represents the major obstacle to their diagnosis. Because histologic analysis, which is the initial diagnostic approach, has been demonstrated to be insufficient in the definition of certain types of lymphomas, molecular and immunologic techniques have been increasingly applied to obtain a precise diagnosis and to establish a correct treatment. Fluorescence in situ hybridization, in particular, is a powerful technique with many applications to the study of chromosomal rearrangements. In addition, because of their specificity and sensitivity, molecular techniques provide an important tool in assessing response to treatment, in detecting minimal residual disease, and in understanding the clinical and prognostic significance of the disease.

Blotting, Southern↗
PubMed1995

Involvement of the ALL-1 gene in a solid tumor.

Translocations involving chromosome band 11q23, found in 5-10% of human acute leukemias, disrupt the ALL-1 gene. This gene is fused by reciprocal translocation with a variety of other genes in acute lymphoblastic and myelogenous leukemias, and it undergoes self-fusion in acute myeloid leukemias with normal karyotype or trisomy 11. Here we report an alteration of the ALL-1 gene in a gastric carcinoma cell line (Mgc80-3). Characterization of this rearrangement revealed a three-way complex translocation, involving chromosomes 1 and 11, resulting in a partial duplication of the ALL-1 gene. Sequencing of reverse transcription-PCR products and Northern blot analysis showed that only the partially duplicated ALL-1 gene was transcribed, producing an mRNA with exon 8 fused to exon 2. This report of ALL-1 gene rearrangement in a solid tumor suggests that ALL-1 plays a role in the pathogenesis of some solid malignancies. The absence of the normal transcript in this cell line, in association with the loss-of-heterozygosity studies on chromosome 11q23 seen in solid tumors, suggests that ALL-1 is involved in tumorigenesis by a loss-of-function mechanism.

Animals↗
PubMed1995

Partial duplication of HRX in acute leukemia with trisomy 11.

The HRX gene has recently been shown to be involved in most of the chromosomal abnormalities of band 11q23 frequently present in human hematological malignancies. Rearrangements are strikingly diverse, but most affect a restricted area of the HRX gene and lead to gene fusion between HRX and a gene located on the partner chromosome. Another kind of HRX alteration seen in human acute leukemia is a partial duplication of the NH2 part of the HRX locus. We have characterized two cases of partial HRX duplication in acute leukemias bearing trisomy 11 as the sole chromosomal abnormality. In one patient analyzed at the genomic level, an Alu repeat was involved within exon 6 but not within intron 1. Splicing of exon 6 to exon 2 was observed in this patient while splicing of exon 8 to exon 2 was observed in the other. Our data indicated that HRX duplication is highly similar to the translocation affecting the HRX locus both in the restricted diversity of the fusion points and the involvement of Alu repeats within the breakpoint cluster region (exon 5 to 10).

Acute Disease↗
PubMed1994

ALL-1 tandem duplication in acute myeloid leukemia with a normal karyotype involves homologous recombination between Alu elements.

Rearrangements of the ALL-1 gene by reciprocal translocations involving chromosome band 11q23 are frequently associated with human acute leukemia. We have previously reported the detection of ALL-1 gene rearrangements in adult patients with acute myeloid leukemia lacking cytogenetic evidence of 11q23 translocations. These included 2 of 19 patients with normal karyotypes as well as 3 of 4 patients with trisomy 11 as a sole cytogenetic abnormality. Rearrangement of the ALL-1 genes in two of the patients with trisomy 11 was shown to result from a direct tandem duplication of a portion of the gene spanning exons 2-6. Here we report the characterization of the ALL-1 gene rearrangement in one of the previously reported acute myeloid leukemia patients with a normal karyotype. ALL-1 rearrangement in this patient results from a direct tandem duplication of a portion of the gene spanning exons 2-8. RNA polymerase chain reaction and DNA sequence analysis show that the partially duplicated ALL-1 gene is transcribed into mRNA capable of encoding a partially duplicated protein. Sequence analysis of the genomic fusion region provides evidence for Alu-mediated homologous recombination as a mechanism for partial duplication of the ALL-1 gene.

Acute Disease↗
PubMed1994

ALL-1 partial duplication in acute leukemia.

The ALL-1 gene, located on chromosome band 11q23, is fused to a variety of other genes by reciprocal chromosomal translocations present in 5-10% of human acute leukemias. We have recently reported the detection by Southern blot of ALL-1 gene rearrangements in adult patients with acute myeloid leukemia lacking cytogenetic evidence of 11q23 translocations. These include 2 of 19 patients with normal karyotypes as well as 3 of 4 patients with trisomy 11. To characterize the abnormal ALL-1 genes, we cloned the ALL-1 rearrangements from two patients with trisomy 11. Characterization of the clones, together with Southern blot analysis, indicates that the ALL-1 rearrangement in both patients is the result of a direct tandem duplication of a portion of the ALL-1 gene spanning exons 2-6. The partial ALL-1 duplication is also detected by Southern blot analysis in a patient with a normal karyotype. RNA PCR and DNA sequence analysis show that the partially duplicated ALL-1 gene is transcribed into mRNA capable of encoding a partially duplicated protein. Partial duplication of ALL-1, in which a portion of a putative protooncogene is fused with itself, represents an additional genetic mechanism for leukemogenesis. Our findings suggest that the presence of trisomy in malignancy may sometimes indicate the partial duplication of a cellular protooncogene.

Acute Disease↗
PubMed1994

Sequence analysis of the breakpoint cluster region in the ALL-1 gene involved in acute leukemia.

DNA rearrangements caused by chromosome translocations between band 11q23 and various chromosomes can be detected by a single probe, B859, an 859-base pair complementary DNA fragment derived from the human ALL-1 gene. To try to understand why band 11q23 becomes a frequent target of the translocations, we have sequenced the entire breakpoint cluster region, a 8342-base pair BamHI genomic fragment delineated by B859. We found eight Alu repeats located within this region in the same orientation as the ALL-1 gene. We have also analyzed the sequences of the breakpoints in 10 patients with 6 different types of 11q23 aberration. In five patients the breaks coincided with Alu sequences on chromosome 11, but not on the partner chromosomes. Also, seven of the breaks occurred in the region delineated by exons 6 and 7, which is composed mainly of Alu sequences. In three patients topoisomerase II recognition site-like sequences, at different stringency levels, were identified at the breakpoints on chromosome 11. We conclude that while there is no specific sequence element present at all the breakpoints, the high density of Alu sequences in the breakpoint cluster region possibly makes the latter more prone to recombination events.

Acute Disease↗
PubMed1994

Molecular rearrangement of the ALL-1 gene in acute myeloid leukemia without cytogenetic evidence of 11q23 chromosomal translocations.

Translocations which involve chromosome band 11q23 are frequently found in infants and adults with acute myeloid leukemia (AML) or acute lymphoblastic leukemia. We previously cloned a gene called ALL-1 which spans the 11q23 breakpoint and is rearranged in most cases of leukemia with 11q23 abnormalities. In the present report, we have investigated the occurrence of ALL-1 rearrangement in cases of AML without cytogenetic evidence of 11q23 abnormalities. We detected molecular rearrangements of the ALL-1 gene in 3 of 4 patients with de novo AML and trisomy 11 as a sole chromosomal abnormality. Furthermore, we found DNA rearrangements of ALL-1 in 2 of 19 patients with de novo AML and normal cytogenetics. We conclude that molecular rearrangement of ALL-1 often can be detected in de novo AML, despite the absence of cytogenetic abnormalities involving 11q23.

Acute Disease↗
PubMed1994

Rodent L1 evolution has been driven by a single dominant lineage that has repeatedly acquired new transcriptional regulatory sequences.

All mammalian genomes contain approximately 100,000 copies of the transposable element LINES-1 (L1). Phylogenetic analysis indicates that the L1 progenitor predates the mammalian radiation; since that time, the open reading frames encoded in L1 have evolved under selection. The least conserved regions within L1 are the 5'-terminal transcriptional regulatory sequences. In rodents, four types of L1 elements (A, F, and V from mouse and R from rat) have been defined according to the type of apparently nonhomologous promoter sequence present at the 5' end. In this study, we investigate the relationships between these four types of promoters. DNA sequence was determined from approximately 1.5-kb regions from the 5' ends of seven F- and three V-type L1 elements. These sequences were aligned with 29 previously reported L1 elements. Phylogenetic analysis was then performed on the homologous regions of the alignment. The results indicate that in mouse all of the A-, F-, and V-type elements belong to a single dominant lineage but were inserted into the genome during different time periods; V-type elements are the oldest, while A-type elements are the most recently inserted. V-type elements also appear ancestral to the R-type elements found in rat and therefore were replicatively competent prior to the divergence of rat and mouse. Analysis of sequence identity indicates that the different 5' promoters did not derive from a common ancestor. Therefore, the dominant L1 lineage appears to have acquired novel promoter sequences from non-L1 sources. Transposable elements from a wide range of species show similar structural rearrangements, suggesting that acquisition of new sequences may be a common theme in their evolution.

Animals↗