The UCSC Genome Browser Database: update 2009.

The UCSC Genome Browser Database (GBD, http://genome.ucsc.edu) is a publicly available collection of genome assembly sequence data and integrated annotations for a large number of organisms, including extensive comparative-genomic resources. In the past year, 13 new genome assemblies have been added, including two important primate species, orangutan and marmoset, bringing the total to 46 assemblies for 24 different vertebrates and 39 assemblies for 22 different invertebrate animals. The GBD datasets may be viewed graphically with the UCSC Genome Browser, which uses a coordinate-based display system allowing users to juxtapose a wide variety of data. These data include all mRNAs from GenBank mapped to all organisms, RefSeq alignments, gene predictions, regulatory elements, gene expression data, repeats, SNPs and other variation data, as well as pairwise and multiple-genome alignments. A variety of other bioinformatics tools are also provided, including BLAT, the Table Browser, the Gene Sorter, the Proteome Browser, VisiGene and Genome Graphs.

The UCSC Genome Browser Database: 2008 update.

The University of California, Santa Cruz, Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes. Seventeen new assemblies have been added to the database in the past year, for a total coverage of 19 vertebrate and 21 invertebrate species as of September 2007. For each assembly, the GBD contains a collection of annotation data aligned to the genomic sequence. Highlights of this year's additions include a 28-species human-based vertebrate conservation annotation, an enhanced UCSC Genes set, and more human variation, MGC, and ENCODE data. The database is optimized for fast interactive performance with a set of web-based tools that may be used to view, manipulate, filter and download the annotation data. New toolset features include the Genome Graphs tool for displaying genome-wide data sets, session saving and sharing, better custom track management, expanded Genome Browser configuration options and a Genome Browser wiki site. The downloadable GBD data, the companion Genome Browser toolset and links to documentation and related information can be found at: http://genome.ucsc.edu/.

The UCSC genome browser database: update 2007.

The University of California, Santa Cruz Genome Browser Database contains, as of September 2006, sequence and annotation data for the genomes of 13 vertebrate and 19 invertebrate species. The Genome Browser displays a wide variety of annotations at all scales from the single nucleotide level up to a full chromosome and includes assembly data, genes and gene predictions, mRNA and EST alignments, and comparative genomics, regulation, expression and variation data. The database is optimized for fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. In the past year, 22 new assemblies and several new sets of human variation annotation have been released. New features include VisiGene, a fully integrated in situ hybridization image browser; phyloGif, for drawing evolutionary tree diagrams; a redesigned Custom Track feature; an expanded SNP annotation track; and many new display options. The Genome Browser, other tools, downloadable data files and links to documentation and other information can be found at http://genome.ucsc.edu/.

The UCSC Genome Browser Database: update 2006.

The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms. Genome annotations typically include assembly data, sequence composition, genes and gene predictions, mRNA and expressed sequence tag evidence, comparative genomics, regulation, expression and variation data. The database is optimized to support fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. The Genome Browser displays a wide variety of annotations at all scales from single nucleotide level up to a full chromosome. The Table Browser provides direct access to the database tables and sequence data, enabling complex queries on genome-wide datasets. The Proteome Browser graphically displays protein properties. The Gene Sorter allows filtering and comparison of genes by several metrics including expression data and several gene properties. BLAT and In Silico PCR search for sequences in entire genomes in seconds. These tools are highly integrated and provide many hyperlinks to other databases and websites. The GBD, browsing tools, downloadable data files and links to documentation and other information can be found at http://genome.ucsc.edu/.

Protection of coronary angioplasty-induced oxidative stress by Isovue used during angioplasty.

BACKGROUND: Oxygen free radicals (OFRs) have been implicated in ischemic-reperfusion cardiac injury. Use of percutaneous transluminal coronary angioplasty (PTCA) has created renewed interest in salvation of ischemic myocardium. The PTCA procedure is similar to the ischemia-reperfusion model. It is possible that OFRs are increased following PTCA. However, OFR-related cardiac complications are uncommon and the evidence for lipid peroxidation is conflicting. PATIENTS AND METHODS: In this study the levels of plasma malondialdehyde, OFR-producing activity of polymorphonuclear leukocytes (PMNL-CL) and blood antioxidant enzymes (superoxide dismutase, catalase and glutathione peroxidase) were measured in peripheral venous blood of 50 consecutive patients with stable angina undergoing elective PTCA. The ability of Isovue (used during PTCA) and of streptokinase (used during thrombolysis) to scavenge OH in the high performance liquid chromatography method and to reduce OH-induced lipid peroxidation were also assessed. Patients were divided into three groups: group 1, single vessel PTCA; group 2, two or more vessel PTCA; and group 3, combined single and multivessel PTCA. RESULTS: The results indicated that there was an increase in PMNL-CL (22% to 44%) and a decrease in plasma malondialdehyde (33% to 40%) at 60 mins following PTCA. The activity of antioxidant enzymes remained unaltered. Isovue scavenged OH in a concentration-dependent manner and was complete at a concentration below that used in patients. Streptokinase, on the other hand, was ineffective in scavenging OH. CONCLUSIONS: These results suggest that, in spite of increased production of OFR by polymorphonuclear leukocytes and unaltered activity of antioxidant enzymes, lipid peroxidation decreased. Lack of lipid peroxidation may have been due to the OH-scavenging property of Isovue. The observed differences in OFR-related complications between PTCA and thrombolytic therapy may have been due to the antioxidant activity of Isovue.

Differentiated thyroid cancer in children and adolescents: clinical outcome and mortality after long-term follow-up.

BACKGROUND: Children and adolescents with differentiated thyroid cancer (DTC) have a good prognosis and prolonged survival even when extensive regional disease or lung metastases are present at the diagnosis; very-long-term follow-up is needed to appreciate what, if any, impact the disease may exert on the ultimate outcome. METHODS: We retrospectively reviewed the clinical course of 112 patients with DTC who registered at M. D. Anderson Cancer Center between 1944 and 1986, were younger than 20 years old at the time of diagnosis, and were followed for at least 10 years. Surgery alone or combined with radioactive iodine or radiotherapy was used for most cases. RESULTS: At the time of most recent contact, 99 patients remained alive and 13 had died. The 99 patients had 25 +/- 0.9 years of available follow-up (mean +/- SEM) and were 41 +/- 0.9 years of age at time of last contact; one fourth had had recurrent disease at some point since diagnosis. Among the 13 patients who died, one died of complications from coexisting diabetes mellitus, and the cause of death was not clear in one other case. Two patients died of breast cancer 13 and 15 years after thyroid cancer diagnosis. In three cases, cause of death could be considered etiologically related to initial radiotherapy: one patient developed tracheal necrosis 26 years after diagnosis and died of upper airway complications, whereas another two patients developed sarcomas of the cervical region 22 and 29 years after thyroid cancer diagnosis. Lastly, six patients died of thyroid cancer 26 +/- 3.1 years after initial diagnosis (at age 40 +/- 2.1 years). Among these cases, one patient had invasive disease and lung metastases at diagnosis and died of progressive lung metastases after 36 years. The other five patients were initially seen with local/regional disease and developed lung and skeletal metastases after a 2- to 20-year disease-free interval. CONCLUSIONS: Our findings support the clinical impression that children and adolescents with DTC live for many years regardless of apparent extent of disease at diagnosis or development of recurrence. Indeed, overall survival was 100% at 10 years even in patients with distant metastases. However, attention to these patients' clinical course beyond the first decade indicates that a small minority (5% to 7%) of patients eventually succumb to progressive disease and that a similar number develop possibly treatment-related lethal complications or second neoplasms. We suggest lifelong surveillance for all such patients.

Hepatoblastoma in children: a review.

The past 25 years have seen a dramatic improvement in results of treatment of children with HBL; formerly, < 25% were cured, and today, 65 to 75% may be cured. New, active agents are still needed, and the late effects of therapy, especially on the heart and kidneys, remain a concern. Nevertheless, it is clear that treatment of HBL is indeed "a bit of a success story" (42).

Profiling primary care physicians for a new managed care network.

We developed methods for comparing physicians who would be selected to participate in a major employer's self-insurance program. These methods used insurance claims data to identify and profile physicians according to deviations from prevailing practice and outcome patterns, after considering differences in case-mix and severity of illness among the patients treated by those providers. The discussion notes the usefulness and limitations of claims data for this and other purposes. We also comment on policy implications and the relationships between our methods and health care reform strategies designed to influence overall health care costs.

Fibromyxoid sarcoma in a four-year-old child: case report and review of the literature.

We present a child with a rare and chemotherapy-resistant form of soft-tissue cancer, low-grade fibromyxoid sarcoma, first noted when he was 4 years old. He is the youngest patient reported to date. An 11-year-old white male presented to. The University of Texas M.D. Anderson Cancer Center's Department of Pediatrics with a 7-year history of right thigh mass and pulmonary nodules, confirmed on examination. He had undergone extensive prior chemotherapy and surgery. He received chemotherapy with high-dose cyclophosphamide (7 g/m2) and later etoposide (150 mg/m2/day x 5), with only slight shrinkage of the thigh mass and none in the lungs. Subsequently the tumor in his proximal thigh and his lung metastases were resected, and radiation therapy was administered to the thigh. His disease remained stable for 12 months, but he then developed a pleural-based metastasis on the left side and new bilateral lung metastases also. The tumors on the left side were removed; residual disease is stable after treatment for 6 months with subcutaneous alpha-interferon-2b. Low-grade fibromyxoid sarcoma is very uncommon in children. It grows slowly and metastasizes to distant organs, chiefly to the lungs. It is resistant to conventional chemotherapy, and thus far only surgery seems to have a life-prolonging effect. Newer chemotherapeutic and possibly biologic agents should be tried in future patients, in order to find an effective way to control the disease.

Evaluation of hydroxyl radical-scavenging property of garlic.

Garlic has been reported to provide protection against hypercholesterolemic atherosclerosis and ischemia-reperfusion-induced arrhythmias and infarction. Oxygen free radicals (OFRs) have been implicated as causative factors in these diseases and antioxidants have been shown to be effective against these conditions. The effectiveness of garlic in these disease states could be due to its ability to scavenge OFRs. However, the OFR-scavenging activity of garlic is not known. Also it is not known if its activity is affected by cooking. We therefore investigated, using high pressure liquid chromatography, the ability of garlic extract (heated or unheated) to scavenge exogenously generated hydroxyl radical (.OH). .OH was generated by photolysis of H2O2 (1.2-10 mumoles/ml) with ultraviolet (UV) light and was trapped with salicylic acid (500 nmoles/ml). H2O2 produced .OH in a concentration-dependent manner as estimated by .OH adduct products 2,3-dihydroxybenzoic acid (DHBA) and 2,5-DHBA. Garlic extract (5-100 microliters/ml) produced an inhibition (30-100%) of 2,3-DHBA and 2,5-DHBA generated by photolysis of H2O2 (5.00 pmoles/ml) in a concentration-dependent manner. Its activity is reduced by 10% approximately when heated to 100 degrees C for 20, 40 or 60 min. The extent of reduction in activity was similar for the three heating periods. Garlic extract prevented the .OH-induced formation of malondialdehyde in the rabbit liver homogenate in a concentration-dependent manner. It alone did not affect the MDA levels in the absence of .OH. These results indicate that garlic extract is a powerful scavenger of .OH and that heating reduces its activity slightly.

Antioxidant activity of allicin, an active principle in garlic.

Garlic has been claimed to be effective against diseases, in the pathophysiology of which oxygen free radicals (OFRs) have been implicated. Effectiveness of garlic could be due to its ability to scavenge OFRs. However, its antioxidant activity is not known. We investigated the ability of allicin (active ingredient of garlic) contained in the commercial preparation Garlicin to scavenge hydroxyl radicals (.OH) using high pressure liquid chromatographic (HPLC) method. .OH was generated by photolysis of H2O2 (1.25-10 mumoles/ml) with ultraviolet light and was trapped with salicylic acid which is hydroxylated to produce .OH adduct products 2,3- and 2,5-dihydroxybenzoic acid (DHBA). H2O2 produced a concentration-dependent .OH as estimated by .OH adduct products 2,3-DHBA and 2,5-DHBA. Allicin equivalent in Garlicin (1.8, 3.6, 7.2, 14.4, 21.6, 28.8 and 36 micrograms) produced concentration-dependent decreases in the formation of 2,3-DHBA and 2,5-DHBA. The inhibition of formation of 2,3-DHBA and 2,5-DHBA with 1.8 micrograms/ml was 32.36% and 43.2% respectively while with 36.0 micrograms/ml the inhibition was approximately 94.0% and 90.0% respectively. The decrease in .OH adduct products was due to scavenging of .OH and not by scavenging of formed .OH adduct products. Allicin prevented the lipid peroxidation of liver homogenate in a concentration-dependent manner. These results suggest that allicin scavenges .OH and Garlicin has antioxidant activity.

Renal toxicity of ifosfamide in pilot regimens of the intergroup rhabdomyosarcoma study for patients with gross residual tumor.

PURPOSE: The purpose of this review is to characterize the nephrotoxicity noted in newly diagnosed patients under 21 years of age after treatment with ifosfamide-containing chemotherapy regimens and local irradiation for localized gross residual rhabdomyosarcoma or undifferentiated sarcoma. PATIENTS AND METHODS: From 1987 to 1991, 194 previously untreated patients received vincristine and ifosfamide plus dactinomycin or etoposide for 1-2 years. Ifosfamide was given at 1.8 g/m2/day for 5 days with sodium mercaptoethane sulfonate, or 9 g/m2 of ifosfamide per course. The three-drug regimen was repeated every 3-4 weeks. RESULTS: Twenty-eight patients (14%) developed renal toxicity: 19 had renal tubular dysfunction (RTD) characterized by low serum phosphate (< or = 3 mg/dl) or bicarbonate (< 20 or = mEq/L) levels, five had decreased glomerular function (DGF), and four had both RTD and DGF. When nine or more courses of ifosfamide (> 72 g/m2) were given, children < 3 years of age had a higher incidence of RTD than did children > or = 3 years of age (34% versus 6%; p < 0.001). A similar age difference was observed even when eight or fewer courses (< or = 72 g/m2) were given (p = 0.03). A matched case-control comparison showed that renal abnormalities at diagnosis, chiefly hydronephrosis, also increased the risk of renal tubular injury by ifosfamide by a factor of 13 (p < 0.001). Patients with DGF tended to be older than those with RTD, and all but one received > 72 g/m2 of ifosfamide. CONCLUSIONS: Patients who are < 3 years of age who receive more than eight courses (> 72 g/m2) of ifosfamide and who have a preexisting renal abnormality have an increased risk of RTD and DGF. The renal function of patients being considered for ifosfamide treatment must be carefully monitored. Ifosfamide should be avoided in patients with renal abnormalities at diagnosis unless the potential benefit clearly exceeds the risk of further renal impairment.

Metastatic intracranial chordoma in a child with massive pulmonary tumor emboli.

A 27-month-old boy of Hispanic background developed multiple cranial nerve palsies, difficulty swallowing, bloody nasal discharge, and irritability. Radiographic evaluations showed extensive destruction of the clivus by a large tumor that invaded the sphenoid bone, left cavernous sinus, ethmoid sinus, nasal cavity, and left orbit. Multiple pulmonary nodules were also noted. The bone marrow and spinal fluid showed no evident tumor cells. Transnasal biopsy revealed a chordoma. Treatment was initiated with a combination of ifosfamide, mesna, and etoposide along with radiation therapy to the cranial tumor. Shifting pulmonary densities were noted on serial films. Despite some clinical improvement, the child developed rapidly progressive hypoxemia 3 weeks after admission and died. Autopsy showed persistent viable tumor in the primary site and massive pulmonary arteriolar tumor emboli, infarcts, and widespread lung parenchymal metastases. No other sites of tumor involvement were discovered. This is the second child reported with intracranial chordoma, pulmonary metastases at diagnosis, and early death attributed to pulmonary tumor emboli.

Using claims data to select primary care physicians for a managed care network.

An insurance claims databased profiling system was developed to help select new primary care physicians (PCPs) for a managed care network. PCPs (family practitioners, internists, and pediatricians) were ranked based on how closely their actual use of outpatient services conformed to the predictions of a mathematical model that adjusted for differences in age, sex, and case mix.

Sequelae of treatment in 109 patients followed for 5 to 15 years after diagnosis of sarcoma of the bladder and prostate. A report from the Intergroup Rhabdomyosarcoma Study Committee.

BACKGROUND: As increasing numbers of young patients with cancer survive, interest in the late effects of therapy is rising. METHODS: The sequelae of treatment were reviewed after a minimum of 5 years of observation in 109 surviving patients with sarcoma of the bladder or prostate who were enrolled in the Intergroup Rhabdomyosarcoma Studies I and II (1972-1984). The 82 male and 27 female patients were 3 weeks to 19 years of age when the diagnosis was made (median, 2 years) and were 5-29 years of age at last contact (median, 11 years). Treatment consisted of chemotherapy with vincristine, dactinomycin, and cyclophosphamide and bladder irradiation in nearly all patients. RESULTS: Fifty-four patients underwent total cystectomy, and 10 had a partial cystectomy. Of the 55 patients with bladder preservation, 1 had a urinary conduit with a nonfunctioning bladder. Thus, 54 bladders (50% of the total) remained in place as part of the urinary tract. There was no information regarding bladder function in two patients. Satisfactory bladder function was found in 38 patients (73%), 9 were incontinent, and 5 had urinary frequency with or without nocturia. Posttherapy hematuria was detected in 29% of patients. Nine of the 31 patients (29%) with follow-up renal imaging studies had a structural abnormality, chiefly hydronephrosis, which was more frequent in those with urinary diversion. Positive urine cultures were found mainly among those with enteric urinary conduits, but only two cases of pyelonephritis were documented. Abnormalities of irradiated bone and bowel were observed infrequently. Only one patient had a significantly elevated blood urea nitrogen or serum creatinine value, and only one patient was hypertensive. Most patients were still prepubertal at last follow-up. Of 24 patients who were intrapubertal or postpubertal, 7 (29%) were receiving sex hormone replacement because of delayed pubertal development. Height was decreased by 25% or more in 11 patients, as confirmed by growth chart analysis. Secondary surgical procedures other than repeat biopsy or cystectomy consisted primarily of urinary conduit revisions and repair of bowel adhesions or fistulous tracts. Information about psychosocial status was limited. CONCLUSIONS: Overall, 50% of the patients retained their bladders, and 73% of them had satisfactory bladder function. Renal function was preserved in nearly every patient.

Ascending myelitis after intensive chemotherapy and radiation therapy in children with cranial parameningeal sarcoma.

In 1977, a program of early, wide-field radiation therapy (RT) to the central nervous system and repeated lumbar intrathecal (IT) medications along with systemic chemotherapy was begun by the Intergroup Rhabdomyosarcoma Study (IRS) for patients younger than 21 years of age with cranial parameningeal sarcoma and a high risk of meningeal extension. From 1977 until 1987, 149 eligible patients with high-risk cranial parameningeal sarcoma were enrolled in IRS trials. None had evidence of lower extremity or sphincter impairment at diagnosis. Five of the 149 (3.4%) had ascending myelitis at 5.5 to 9 months after the initiation of therapy, with loss of sphincter control and inability to walk; this progressed to severe flaccid quadriparesis and necessitated long-term ventilatory support in 4. All five had received vincristine, dactinomycin, cyclophosphamide, and doxorubicin; four also had received cisplatin and three also had received etoposide. All patients received 4770 to 5500 cGy to the primary tumor, and four patients received 3000 cGy of cranial RT. Three patients received cervical RT and two received spinal RT. The patients also received four to seven courses of IT methotrexate, hydrocortisone, and cytosine arabinoside. Three patients died: one after local tumor recurrence with central nervous system extension and two without known recurrence. In one of the latter patients, the results of an autopsy showed necrosis of the cervical spinal cord and caudal medulla. Although the exact cause of this complication is unclear, no additional cases have been reported to the IRS since the protocol was revised in 1987 to reduce the doses of the IT drugs and to limit them to four courses each.

The role of the American Association for Cancer Education in pediatric oncology: results of a survey.

We designed a questionnaire to elucidate the reasons for decreased participation in activities of the American Association for Cancer Education (AACE) by 34 members who listed pediatric oncology as their primary or secondary medical interest. Nineteen members from 16 institutions, 14 of them university hospitals, returned the form. These institutions treated an average of 89 new childhood cancer patients per year and educated an average of 89 trainees per year in aspects of pediatric oncology. All respondents believed that the AACE should meet in tandem with another national convocation, and most thought that the AACE meeting was reasonably priced but expensive of time. Many indicated that they would participate more actively in the AACE if they, or their institution, had an active R25 Cancer Education Grant from the National Cancer Institute. The majority believed that the AACE should be more active in educational efforts about childhood cancer (71%), should conduct a manpower survey to ascertain the need for training fellows in pediatric oncology (77%), and should prepare educational materials on childhood cancer (65%). However, less than one-half (41%) believed that the AACE has a readily identified role in pediatric oncology education. Greater communication between the AACE and the pediatric oncology community is needed, especially in coordinating and evaluating pediatric oncology education in the United States.

Neurologic complications in children with soft tissue and osseous sarcoma.

From 1980 to 1987, 162 consecutive children with soft tissue and osseous sarcoma were reviewed to determine the frequency and types of neurologic complications seen. Neurologic complications occurred in 43 of 162 (26.5%) patients. Children with poorly differentiated sarcomas and rhabdomyosarcoma were more likely to have neurologic complications, which occurred in 39% of patients at risk. The types of complications seen included: metastatic spinal cord compression (11%); symptomatic peripheral neuropathy (10%); intracranial metastatic disease (7.5%); seizures (6%); and acute and chronic methotrexate-related neurologic dysfunction (2.5%). Spinal cord compression frequently occurred early in disease whereas brain metastases was almost always a late finding. Symptomatic peripheral neuropathy occurred primarily in children with rhabdomyosarcoma and Ewing's sarcoma. The advent of increasingly successful therapies for children with sarcoma and the frequency of severe neurologic complications indicate that a heightened level of surveillance for neurologic compromise is required.

Transient myeloproliferative disorder. In a neonate with Down syndrome. Immunophenotypic studies.

This report describes the results of bone marrow leukocyte immunophenotypic studies, DNA index measurement, and chromosome analysis in a newborn with Down syndrome and transient myeloproliferative disorder. The infant's initial leukocytosis with immature cells in the peripheral blood and thrombocytopenia resolved without treatment by 6 months of age, and he was well at 2 years of age. The lack of specific reactivity between the patient's morphologically immature cells and multiple monoclonal antibodies directed against lymphoid and myeloid leukemia cells may be characteristic of this disorder. Other cases should be examined for immunophenotype to correlate the results with chromosomal analysis and to provide a basis for comparison in those who subsequently develop true acute leukemia.