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Chakravarti A, Desilvio M, Zhang M, Grignon D, Rosenthal S, Asbell S, Hanks G, Sandler H, Pollack A, Zhai G, Shipley W. The Prognostic Value of p16 Expression in Locally Advanced Prostate Cancer: A Study Based on RTOG 92-02. Int J Radiat Oncol Biol Phys 2005. [DOI: 10.1016/j.ijrobp.2005.07.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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152
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Zhai G, Ho A, Hammond E, Fontanesi J, Rotman M, Pilepich M, Shipley W, Sandler H, Pollack A, Zhang M, Chakravarti A. Phospho-AKT Expression and Prognosis of Locally Advanced Prostate Cancer: A Study Based on RTOG 8610. Int J Radiat Oncol Biol Phys 2005. [DOI: 10.1016/j.ijrobp.2005.07.546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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153
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Chakravarti A, Verma V. Prevalence of hepatitis C and B viral markers in patients with chronic liver disease: a study from Northern India. Indian J Med Microbiol 2005; 23:273-4. [PMID: 16327131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
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154
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Abstract
OBJECTIVE This study was carried out to evaluate the adequacy of seroconversion when Hepatitis B vaccine is given along with other vaccines at 0, 6 weeks (along with DPT and OPV) and at 9 months (along with measles). METHODS 725 infants born to apparently healthy mothers were enrolled to receive the hepatitis B vaccine at 0, 6 weeks and 9 months (Group A) or at 0, 1 and 6 months as per WHO schedule--(Group B). Baseline HbsAg testing was carried out and the babies were immunized with the first dose of hepatitis B vaccine within 48 hours of birth. BCG and the other EPI vaccines were given as per schedule. Serum samples were collected 4 weeks after the second and the third immunizations. 604 infants (83.3%) completed the study. The testing for HbsAg and Anti Hbs titers were conducted in the Department of Microbiology, Maulana Azad Medical College, New Delhi utilizing standard ELISA kits. RESULTS The seroconversion rates 4 weeks after the second dose of the vaccine were 90.89% (GMT = 48.23) and 91.82% (GMT = 43.95) (P=0.8) in Group A and Group B respectively. After 4 weeks of the third dose the seroconversion rates were 98.99 (GMT = 161.12) and 98.45 (GMT = 150.12) (p=0.17) in Group A and Group B respectively. The two schedules were comparable on using the Kruskal-Wallis H method for analysis. CONCLUSION The schedule of hepatitis B vaccination at 0, 6 weeks and 9 months has the same seroefficacy as the currently recommended schedule of 0, 1 and 6 months.
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155
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Walston J, Arking DE, Fallin D, Li T, Beamer B, Xue Q, Ferrucci L, Fried LP, Chakravarti A. IL-6 gene variation is not associated with increased serum levels of IL-6, muscle, weakness, or frailty in older women. Exp Gerontol 2005; 40:344-52. [PMID: 15820616 DOI: 10.1016/j.exger.2005.01.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2004] [Revised: 12/28/2004] [Accepted: 01/28/2005] [Indexed: 10/25/2022]
Abstract
Elevated levels of the inflammatory cytokine IL-6 are associated with the development of disability, frailty, and mortality in older adults. These outcomes are likely mediated through inflammatory activity that alters hormones, skeletal muscle, and the immune system. Polymorphic variants in the IL-6 gene influence IL-6 expression. We hypothesized that IL-6 alleles associate with increased serum of IL-6, decreased muscle strength, and frailty, and tested this in the Women's Health and Aging cohorts. We genotyped 463 participants age 70-79, and identified three common IL-6 haplotype blocks for the Caucasian (n=363) and African American (n=100) subsets. Using linear and logistic regression, and adjusting for age, BMI, race, and osteoarthritis, we identified no significant or clinically meaningful relationship between any single IL-6 single nucleotide polymorphism (SNP) or any IL-6 haplotype and serum IL-6 level, grip, knee, or hip strength, or frailty. Given that the promoter SNP (rs1800795) has been reported to influence IL-6 levels and health outcomes, we performed a similar association study in the In Chianti population (n=266) and confirmed lack of association. These results suggest that IL-6 gene variation may not be an important factor in the determination of elevated IL-6 levels and related phenotypes found in older women.
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156
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Abstract
Although only a small proportion of common cancers show familial aggregation, studying such families can elucidate the roles of shared environment and genes in the development of neoplasia. We report an analysis of nine colon cancer pedigrees using new nonparametric objective methods to measure familial aggregation as a means of determining the existence of heterogeneity in the data. Each family was selected through a proband with nonpolyposis colon cancer who had a first-degree relative with documented colon cancer. To assess the aggregation of different cancers in these families we employ a method which evaluates both excess number of cases as well as distribution by risk in family members. We find that eight of the nine families exhibit significant aggregation of colon cancer: endometrial cancer aggregates in three families, breast in none, kidney in one, and all sites in eight. In this way, we show that two families fit the criteria for Cancer Family Syndrome, and that one is not a high-risk cancer family.
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157
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Coen J, Bermudez S, Suzuki Y, Wu CL, Zhang M, Zietman A, Shipley W, Chakravarti A. VEGF-D expression predicts biochemical outcome in localized prostate cancer treated with external radiation: A ten-year cohort analysis. J Clin Oncol 2005. [DOI: 10.1200/jco.2005.23.16_suppl.9660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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158
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Cardinale R, Won M, Choucair A, Gillin M, Chakravarti A, Schultz C, Souhami L, Chen A, Pham H, Mehta M. A phase II trial of accelerated radiotherapy using weekly stereotactic conformal boosts for supratentorial glioblastoma multiforme. RTOG-0023. J Clin Oncol 2005. [DOI: 10.1200/jco.2005.23.16_suppl.1511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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159
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Chakravarti A, Mukherjee N, Mukherjee S, Zhai G, Robe P, Carroll R, Loeffler JS, Black PM. Novel gene expression patterns associated with progression and adverse outcome in high-grade gliomas. J Clin Oncol 2005. [DOI: 10.1200/jco.2005.23.16_suppl.1562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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160
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Knisely JPS, Berkey BA, Chakravarti A, Yung WKA, Curran WJ, Robins HI, Movsas B, Brachman DG, Henderson RH, Mehta MP. RTOG 0118: A phase III study of conventional radiation therapy alone vs. conventional radiation therapy plus thalidomide for multiple brain metastases. J Clin Oncol 2005. [DOI: 10.1200/jco.2005.23.16_suppl.1500] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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161
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Mulle JG, McDonough JA, Chowdari KV, Nimgaonkar V, Chakravarti A. Evidence for linkage to chromosome 13q32 in an independent sample of schizophrenia families. Mol Psychiatry 2005; 10:429-31. [PMID: 15738936 DOI: 10.1038/sj.mp.4001639] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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162
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Mulle JG, Chowdari KV, Nimgaonkar V, Chakravarti A. No evidence for association to the G72/G30 locus in an independent sample of schizophrenia families. Mol Psychiatry 2005; 10:431-3. [PMID: 15753958 DOI: 10.1038/sj.mp.4001619] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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163
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Chakravarti A, Rawat D, Jain M. A STUDY ON THE PERINATAL TRANSMISSION OF THE HEPATITIS B VIRUS. Indian J Med Microbiol 2005. [DOI: 10.1016/s0255-0857(21)02654-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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164
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Chakravarti A, Verma V, Kumaria R, Dubey AP. Anti-HCV seropositivity among multiple transfused patients with beta thalassaemia. JOURNAL OF THE INDIAN MEDICAL ASSOCIATION 2005; 103:64-6. [PMID: 16008315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Hepatitis C virus is considered to be the main aetiological agent responsible for the occurrence of post-transfusion hepatitis. Patients with thalassaemia acquire hepatitis most often from viruses contracted through blood transfusions. The present study was undertaken to evaluate the prevalence of hepatitis C virus (HCV) in thalassaemic patients with multiple blood transfusions. The association of HCV seropositivity with number of blood transfusions and liver enzyme profile was also analysed. The study group consisted of fifty patients (40 males and 10 females) attending the thalassaemic unit of Lok Nayak Hospital, a tertiary care hospital at Delhi, within the age group of 1-25 years. Thirty patients (60%) were found to be seropositive for HCV antibodies while one patient (2%) was co-infected with HCV antibodies and hepatitis B surface antigen. Study of liver enzyme profile showed aspartate aminotransferase levels to be significantly higher, although the level of serum alanine aminotransferase, alkaline phosphatase, total protein, bilirubin and albumin were not significantly altered in these patients. It is inferred from this study that 60% of the thalassaemics were infected with HCV and this was directly related to the number of blood transfusions received by them. The regularised national blood policy followed by blood banks for providing safe blood along with better screening method of donated blood in blood banks would bring down the incidence of hepatitis C in such high risk group.
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165
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McCallion AS, Emison ES, Kashuk CS, Bush RT, Kenton M, Carrasquillo MM, Jones KW, Kennedy GC, Portnoy ME, Green ED, Chakravarti A. Genomic variation in multigenic traits: Hirschsprung disease. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2004; 68:373-81. [PMID: 15338639 DOI: 10.1101/sqb.2003.68.373] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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166
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Chakravarti A, Seiferheld W, Robins HI, Guha A, Brachman D, Curran W, Choucair A, Mehta M. An update of phase I data from RTOG 0211: A phase I/II clinical study of gefitinib+ radiation for newly-diagnosed glioblastoma (GBM) patients. J Clin Oncol 2004. [DOI: 10.1200/jco.2004.22.90140.1571] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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167
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Chakravarti A, Rawat D, Yadav S. Whole blood samples as an alternative to serum for detection of immunity to measles virus by ELISA. Diagn Microbiol Infect Dis 2003; 47:563-7. [PMID: 14711476 DOI: 10.1016/s0732-8893(03)00166-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The aim of this study was to evaluate enzyme linked immunosorbent assay (ELISA) as a testing strategy for detection of antibodies against measles virus from microquantities of blood soaked onto filter paper. We studied 165 healthy children in the age group of 1 to 2 years, attending the outpatient department of pediatrics. Two sets of samples were collected from each child. One by venipuncture and the other on Whatman filter paper-3 discs of 20 mm size by finger or heel prick so that each strip is completely soaked with blood on both sides. These were tested for measles virus antibodies by ELISA using Melotest measles IgG commercial ELISA kit manufactured by Melotec S. A. (Barcelona, Spain). The resulting sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of the filter paper (FP) ELISA compared to serum ELISA was 100, 90, 97.8, and 100%, respectively. The correlation coefficient r = 0.93% (p < 0.001) and the agreement between the two techniques was 98% as calculated by the Kappa statistical method. The present study has found filter paper testing by ELISA to be a promising qualitative technique for detection of immunity against measles.
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168
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Chakravarti A, Heydon K, Wu CL, Hammond E, Pollack A, Roach M, Wolkov H, Okunieff P, Cox J, Fontanesi J, Abrams R, Pilepich M, Shipley W. Loss of p16 expression is of prognostic significance in locally advanced prostate cancer: an analysis from the Radiation Therapy Oncology Group protocol 86-10. J Clin Oncol 2003; 21:3328-34. [PMID: 12947069 DOI: 10.1200/jco.2003.12.151] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE The retinoblastoma (RB) cell cycle regulatory pathway is known to be deregulated in virtually all known human tumors. The protein product of the RB gene, pRB, and its upstream regulator, p16, are among the most commonly affected members of this pathway. We investigated the prognostic significance of both pRB and p16 expression in locally advanced prostate cancers, from patients treated on the Radiation Therapy Oncology Group (RTOG) protocol 86-10. MATERIALS AND METHODS Sixty-seven cases from RTOG 86-10 had immunohistochemically stained slides, judged interpretable for both p16 and pRB, available for analysis. Median follow-up was 8.9 years (range, 6.0 to 11.8 years) for surviving patients. Staining for each marker was then correlated with overall survival, local progression, distant metastasis, and disease-specific survival. RESULTS Loss of p16 expression, as defined by expression was significantly associated with reduced overall survival (P =.039), disease-specific survival (P =.006), and higher risk of local progression (P =.0007) and distant metastasis (P =.026) in the univariate analysis. In the multivariate analysis, loss of p16 was significantly associated with reduced disease-specific survival (P =.0078) and increased risk of local failure (P =.0035) and distant metastasis (P =.026). A borderline association with reduced overall survival (P =.07) was also evident. Loss of pRB was associated with improved disease-specific survival on univariate (P =.028) and multivariate analysis (P =.043), but carried no other significant outcome associations. CONCLUSION Loss of p16 is significantly associated with adverse clinical outcome in cases of locally advanced prostate cancer.
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169
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Thomas JW, Touchman JW, Blakesley RW, Bouffard GG, Beckstrom-Sternberg SM, Margulies EH, Blanchette M, Siepel AC, Thomas PJ, McDowell JC, Maskeri B, Hansen NF, Schwartz MS, Weber RJ, Kent WJ, Karolchik D, Bruen TC, Bevan R, Cutler DJ, Schwartz S, Elnitski L, Idol JR, Prasad AB, Lee-Lin SQ, Maduro VVB, Summers TJ, Portnoy ME, Dietrich NL, Akhter N, Ayele K, Benjamin B, Cariaga K, Brinkley CP, Brooks SY, Granite S, Guan X, Gupta J, Haghighi P, Ho SL, Huang MC, Karlins E, Laric PL, Legaspi R, Lim MJ, Maduro QL, Masiello CA, Mastrian SD, McCloskey JC, Pearson R, Stantripop S, Tiongson EE, Tran JT, Tsurgeon C, Vogt JL, Walker MA, Wetherby KD, Wiggins LS, Young AC, Zhang LH, Osoegawa K, Zhu B, Zhao B, Shu CL, De Jong PJ, Lawrence CE, Smit AF, Chakravarti A, Haussler D, Green P, Miller W, Green ED. Comparative analyses of multi-species sequences from targeted genomic regions. Nature 2003; 424:788-93. [PMID: 12917688 DOI: 10.1038/nature01858] [Citation(s) in RCA: 421] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2003] [Accepted: 06/16/2003] [Indexed: 11/08/2022]
Abstract
The systematic comparison of genomic sequences from different organisms represents a central focus of contemporary genome analysis. Comparative analyses of vertebrate sequences can identify coding and conserved non-coding regions, including regulatory elements, and provide insight into the forces that have rendered modern-day genomes. As a complement to whole-genome sequencing efforts, we are sequencing and comparing targeted genomic regions in multiple, evolutionarily diverse vertebrates. Here we report the generation and analysis of over 12 megabases (Mb) of sequence from 12 species, all derived from the genomic region orthologous to a segment of about 1.8 Mb on human chromosome 7 containing ten genes, including the gene mutated in cystic fibrosis. These sequences show conservation reflecting both functional constraints and the neutral mutational events that shaped this genomic region. In particular, we identify substantial numbers of conserved non-coding segments beyond those previously identified experimentally, most of which are not detectable by pair-wise sequence comparisons alone. Analysis of transposable element insertions highlights the variation in genome dynamics among these species and confirms the placement of rodents as a sister group to the primates.
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170
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Chakravarti A, Chaklader A, Latham D, Delaney M, Loeffler J. Survivin increases resistance to radiation-induced cell death and is upregulated by AKT signaling in primary human glioblastoma cell lines. Int J Radiat Oncol Biol Phys 2002. [DOI: 10.1016/s0360-3016(02)03359-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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171
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Puri A, Gupta VK, Chakravarti A, Mehra M. Measles vaccine efficacy evaluated by case reference technique. Indian Pediatr 2002; 39:556-60. [PMID: 12084949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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172
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Zwick ME, Cutler DJ, Chakravarti A. Patterns of genetic variation in Mendelian and complex traits. Annu Rev Genomics Hum Genet 2002; 1:387-407. [PMID: 11701635 DOI: 10.1146/annurev.genom.1.1.387] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This review discusses the prospects for understanding the genetic basis of complex traits in humans. We take the view that work done on Drosophila melanogaster can serve as a model for understanding complex traits in humans, and the literature on this model system, as well as on humans, is reviewed. The prospects for success in understanding the genetic basis of complex traits depend, in part, on the nature of the forces acting on genetic variation. We suggest that different experimental approaches should be undertaken for traits caused by common genetic variants versus those arising from rare genetic variants.
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173
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Okunieff P, Hammond E, Grignon D, Langer C, Pajak TF, Ang K, Bruner DW, Travis E, Greven K, Guha A, Moulder J, Pollack A, Scarantino C, Sneige N, Watson J, Amin M, Bondy M, Chakravarti A, Chapman JD, Dicker A, Harris J, Koch W, Komaki R, Lange C, McBride W, Mitchell J, Milas L, Movsas B, Pandya K, Pienta K, Regine W, Ritter M, Rubin P, Safran H, Sauter E, Schell M, Stevens C, Trotti A, Vikram B. Radiation Therapy Oncology Group. Research Plan 2002-2006. Translational Research Program. Int J Radiat Oncol Biol Phys 2002; 51:75-87. [PMID: 11641020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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174
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Rawat D, Chakravarti A, Yadav S. Study of measles antibody in children. Indian Pediatr 2001; 38:1286-9. [PMID: 11721070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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175
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Abstract
We present two interesting cases of a 24-year-old man and a 14-year-old boy, uncle and nephew, with lower urinary tract symptoms, café au lait patches and subcutaneous nodules. Ultrasonography and computed tomography scans showed a large, irregular lobulated soft tissue mass between the bladder and sacrum. Cystoscopy, laparotomy and biopsies revealed neurofibromatosis involving the urinary bladder. No enlargement of the tumor or upper urinary tract obstruction has occurred during the long-term follow up. We recommend meticulous follow up of patients with giant intrapelvic neurofibromatosis.
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