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Genomic and Functional Approaches to Understanding Cancer Aneuploidy.
Taylor AM, Shih J, Ha G, Gao GF, Zhang X, Berger AC, Schumacher SE, Wang C, Hu H, Liu J, Lazar AJ, Cancer Genome Atlas Research Network, Cherniack AD, Beroukhim R, Meyerson M
(2018) Cancer Cell 33: 676-689.e3
MeSH Terms: Aneuploidy, Carcinoma, Squamous Cell, Cell Cycle, Cell Proliferation, Chromosome Aberrations, Chromosome Deletion, Chromosomes, Human, Pair 3, Databases, Genetic, Genomics, Humans, Mutation Rate, Tumor Suppressor Protein p53
Show Abstract · Added October 30, 2019
Aneuploidy, whole chromosome or chromosome arm imbalance, is a near-universal characteristic of human cancers. In 10,522 cancer genomes from The Cancer Genome Atlas, aneuploidy was correlated with TP53 mutation, somatic mutation rate, and expression of proliferation genes. Aneuploidy was anti-correlated with expression of immune signaling genes, due to decreased leukocyte infiltrates in high-aneuploidy samples. Chromosome arm-level alterations show cancer-specific patterns, including loss of chromosome arm 3p in squamous cancers. We applied genome engineering to delete 3p in lung cells, causing decreased proliferation rescued in part by chromosome 3 duplication. This study defines genomic and phenotypic correlates of cancer aneuploidy and provides an experimental approach to study chromosome arm aneuploidy.
Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.
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Loss of CENP-F results in distinct microtubule-related defects without chromosomal abnormalities.
Pfaltzgraff ER, Roth GM, Miller PM, Gintzig AG, Ohi R, Bader DM
(2016) Mol Biol Cell 27: 1990-9
MeSH Terms: Animals, Cell Cycle, Centromere, Chromosomal Proteins, Non-Histone, Chromosome Aberrations, Chromosome Segregation, Fibroblasts, Interphase, Kinetochores, Mice, Mice, Knockout, Microfilament Proteins, Microtubules, Mitosis, Protein Binding
Show Abstract · Added March 29, 2017
Microtubule (MT)-binding centromere protein F (CENP-F) was previously shown to play a role exclusively in chromosome segregation during cellular division. Many cell models of CENP-F depletion show a lag in the cell cycle and aneuploidy. Here, using our novel genetic deletion model, we show that CENP-F also regulates a broader range of cellular functions outside of cell division. We characterized CENP-F(+/+) and CENP-F(-/-) mouse embryonic fibroblasts (MEFs) and found drastic differences in multiple cellular functions during interphase, including cell migration, focal adhesion dynamics, and primary cilia formation. We discovered that CENP-F(-/-) MEFs have severely diminished MT dynamics, which underlies the phenotypes we describe. These data, combined with recent biochemical research demonstrating the strong binding of CENP-F to the MT network, support the conclusion that CENP-F is a powerful regulator of MT dynamics during interphase and affects heterogeneous cell functions.
© 2016 Pfaltzgraff et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).
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15 MeSH Terms
Community-Acquired Pneumonia Hospitalization among Children with Neurologic Disorders.
Millman AJ, Finelli L, Bramley AM, Peacock G, Williams DJ, Arnold SR, Grijalva CG, Anderson EJ, McCullers JA, Ampofo K, Pavia AT, Edwards KM, Jain S
(2016) J Pediatr 173: 188-195.e4
MeSH Terms: Adolescent, Case-Control Studies, Cerebral Palsy, Child, Child, Preschool, Chromosome Aberrations, Community-Acquired Infections, Developmental Disabilities, Down Syndrome, Epilepsy, Female, Hospitalization, Humans, Intensive Care Units, Length of Stay, Male, Patient Admission, Pneumonia, Spinal Cord, Tennessee, Utah
Show Abstract · Added July 27, 2018
OBJECTIVE - To describe and compare the clinical characteristics, outcomes, and etiology of pneumonia among children hospitalized with community-acquired pneumonia (CAP) with neurologic disorders, non-neurologic underlying conditions, and no underlying conditions.
STUDY DESIGN - Children <18 years old hospitalized with clinical and radiographic CAP were enrolled at 3 US children's hospitals. Neurologic disorders included cerebral palsy, developmental delay, Down syndrome, epilepsy, non-Down syndrome chromosomal abnormalities, and spinal cord abnormalities. We compared the epidemiology, etiology, and clinical outcomes of CAP in children with neurologic disorders with those with non-neurologic underlying conditions, and those with no underlying conditions using bivariate, age-stratified, and multivariate logistic regression analyses.
RESULTS - From January 2010-June 2012, 2358 children with radiographically confirmed CAP were enrolled; 280 (11.9%) had a neurologic disorder (52.1% of these individuals also had non-neurologic underlying conditions), 934 (39.6%) had non-neurologic underlying conditions only, and 1144 (48.5%) had no underlying conditions. Children with neurologic disorders were older and more likely to require intensive care unit (ICU) admission than children with non-neurologic underlying conditions and children with no underlying conditions; similar proportions were mechanically ventilated. In age-stratified analysis, children with neurologic disorders were less likely to have a pathogen detected than children with non-neurologic underlying conditions. In multivariate analysis, having a neurologic disorder was associated with ICU admission for children ≥2 years of age.
CONCLUSIONS - Children with neurologic disorders hospitalized with CAP were less likely to have a pathogen detected and more likely to be admitted to the ICU than children without neurologic disorders.
Published by Elsevier Inc.
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Comparison of 60 and 80 mg/m of daunorubicin in induction therapy of acute myeloid leukaemia.
Vaezi M, Bahar B, Mousavi A, Yaghmai M, Kasaeian A, Souri M, Jahani M, Alimoghaddam K, Ghavamzadeh A
(2017) Hematol Oncol 35: 101-105
MeSH Terms: Adolescent, Adult, Antibiotics, Antineoplastic, Chromosome Aberrations, Cytarabine, Daunorubicin, Disease-Free Survival, Dose-Response Relationship, Drug, Drug Administration Schedule, Febrile Neutropenia, Female, Follow-Up Studies, Humans, Kaplan-Meier Estimate, Leukemia, Myeloid, Acute, Male, Middle Aged, Mycoses, Neutropenia, Prevalence, Prospective Studies, Remission Induction, Treatment Outcome, Young Adult
Show Abstract · Added September 28, 2015
For finding better method of acute myeloid leukaemia (AML) induction, we designed a prospective clinical trial to find a more effective regimen with least toxicity for induction therapy of AML. Hence, we examined different accepted doses of daunorubicin and their outcomes. Total of 114 patients were included in the study. Fifty-five patients received 60 mg/m of daunorubicin (arm 1) 1 h IV infusion for 3 days, and the remaining 59 received 80 mg/m (arm 2) 1 h IV infusion for 3 days. Continuous infusion of 100 mg/m /day of cytosine arabinozide IV for 24 h for 7 days was given in both groups. Complete remission rate was 77.78% in group 1 and 76.92% in group 2 (p = 0.92). One-year overall survival was 55.85% [standard error (SE) = 8.05%] in arm 1 and 57.94% (SE = 7.32%) in arm 2. Median follow-up time was 11.1 (SE = 1.43) and 10.28 (SE = 1.29) months, respectively. One-year disease-free survival was 64.41% (SE = 7.39%) in arm 1 and 54.86% (SE = 7.53%) in arm 2. Complete remission, overall survival and disease-free survival were statistically the same in both groups (p = 0.92, 0.697, 0.31). Toxicity and safety profile were similar in two groups but need to transfusion was higher in arm 2. Febrile neutropenia, days of antibiotics consumption and invasive fungal infection prevalence did not show any difference. Mean transfused packed cells and platelets rate were higher in the group that received higher dose of daunorubicin. Considering these results, we found that 60 mg/m of daunorubicin would be more rational and as effective with lower toxicity to 80 mg/m in induction therapy of AML patients at least as scheduled in our trial. Copyright © 2015 John Wiley & Sons, Ltd.
Copyright © 2015 John Wiley & Sons, Ltd.
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24 MeSH Terms
Genetic and chromosomal alterations in Kenyan Wilms Tumor.
Lovvorn HN, Pierce J, Libes J, Li B, Wei Q, Correa H, Gouffon J, Clark PE, Axt JR, Hansen E, Newton M, O'Neill JA, Kenyan Wilms Tumor Consortium
(2015) Genes Chromosomes Cancer 54: 702-15
MeSH Terms: Child, Preschool, Chromosome Aberrations, Cohort Studies, Female, Gene Dosage, Genes, Wilms Tumor, High-Throughput Nucleotide Sequencing, Humans, Kenya, Kidney Neoplasms, Male, Mutation, Proto-Oncogene Proteins p21(ras), Wilms Tumor
Show Abstract · Added October 1, 2015
Wilms tumor (WT) is the most common childhood kidney cancer worldwide and poses a cancer health disparity to black children of sub-Saharan African ancestry. Although overall survival from WT at 5 years exceeds 90% in developed countries, this pediatric cancer is alarmingly lethal in sub-Saharan Africa and specifically in Kenya (36% survival at 2 years). Although multiple barriers to adequate WT therapy contribute to this dismal outcome, we hypothesized that a uniquely aggressive and treatment-resistant biology compromises survival further. To explore the biologic composition of Kenyan WT (KWT), we completed a next generation sequencing analysis targeting 10 WT-associated genes and evaluated whole-genome copy number variation. The study cohort was comprised of 44 KWT patients and their specimens. Fourteen children are confirmed dead at 2 years and 11 remain lost to follow-up despite multiple tracing attempts. TP53 was mutated most commonly in 11 KWT specimens (25%), CTNNB1 in 10 (23%), MYCN in 8 (18%), AMER1 in 5 (11%), WT1 and TOP2A in 4 (9%), and IGF2 in 3 (7%). Loss of heterozygosity (LOH) at 17p, which covers TP53, was detected in 18% of specimens examined. Copy number gain at 1q, a poor prognostic indicator of WT biology in developed countries, was detected in 32% of KWT analyzed, and 89% of these children are deceased. Similarly, LOH at 11q was detected in 32% of KWT, and 80% of these patients are deceased. From this genomic analysis, KWT biology appears uniquely aggressive and treatment-resistant.
© 2015 The Authors. Genes, Chromosomes & Cancer Published by Wiley Periodicals, Inc.
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14 MeSH Terms
Global and local ancestry in African-Americans: Implications for Alzheimer's disease risk.
Hohman TJ, Cooke-Bailey JN, Reitz C, Jun G, Naj A, Beecham GW, Liu Z, Carney RM, Vance JM, Cuccaro ML, Rajbhandary R, Vardarajan BN, Wang LS, Valladares O, Lin CF, Larson EB, Graff-Radford NR, Evans D, De Jager PL, Crane PK, Buxbaum JD, Murrell JR, Raj T, Ertekin-Taner N, Logue MW, Baldwin CT, Green RC, Barnes LL, Cantwell LB, Fallin MD, Go RC, Griffith P, Obisesan TO, Manly JJ, Lunetta KL, Kamboh MI, Lopez OL, Bennett DA, Hardy J, Hendrie HC, Hall KS, Goate AM, Lang R, Byrd GS, Kukull WA, Foroud TM, Farrer LA, Martin ER, Pericak-Vance MA, Schellenberg GD, Mayeux R, Haines JL, Thornton-Wells TA, Alzheimer Disease Genetics Consortium
(2016) Alzheimers Dement 12: 233-43
MeSH Terms: ATP-Binding Cassette Transporters, African Americans, Aged, Aged, 80 and over, Alzheimer Disease, Apolipoproteins E, Chi-Square Distribution, Chromosome Aberrations, Cohort Studies, Female, Genetic Association Studies, Genetic Predisposition to Disease, Genotype, Humans, Male, Polymorphism, Single Nucleotide, Sialic Acid Binding Ig-like Lectin 3
Show Abstract · Added April 10, 2018
INTRODUCTION - African-American (AA) individuals have a higher risk for late-onset Alzheimer's disease (LOAD) than Americans of primarily European ancestry (EA). Recently, the largest genome-wide association study in AAs to date confirmed that six of the Alzheimer's disease (AD)-related genetic variants originally discovered in EA cohorts are also risk variants in AA; however, the risk attributable to many of the loci (e.g., APOE, ABCA7) differed substantially from previous studies in EA. There likely are risk variants of higher frequency in AAs that have not been discovered.
METHODS - We performed a comprehensive analysis of genetically determined local and global ancestry in AAs with regard to LOAD status.
RESULTS - Compared to controls, LOAD cases showed higher levels of African ancestry, both globally and at several LOAD relevant loci, which explained risk for AD beyond global differences.
DISCUSSION - Exploratory post hoc analyses highlight regions with greatest differences in ancestry as potential candidate regions for future genetic analyses.
Copyright © 2016 The Alzheimer's Association. All rights reserved.
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Detectable clonal mosaicism and its relationship to aging and cancer.
Jacobs KB, Yeager M, Zhou W, Wacholder S, Wang Z, Rodriguez-Santiago B, Hutchinson A, Deng X, Liu C, Horner MJ, Cullen M, Epstein CG, Burdett L, Dean MC, Chatterjee N, Sampson J, Chung CC, Kovaks J, Gapstur SM, Stevens VL, Teras LT, Gaudet MM, Albanes D, Weinstein SJ, Virtamo J, Taylor PR, Freedman ND, Abnet CC, Goldstein AM, Hu N, Yu K, Yuan JM, Liao L, Ding T, Qiao YL, Gao YT, Koh WP, Xiang YB, Tang ZZ, Fan JH, Aldrich MC, Amos C, Blot WJ, Bock CH, Gillanders EM, Harris CC, Haiman CA, Henderson BE, Kolonel LN, Le Marchand L, McNeill LH, Rybicki BA, Schwartz AG, Signorello LB, Spitz MR, Wiencke JK, Wrensch M, Wu X, Zanetti KA, Ziegler RG, Figueroa JD, Garcia-Closas M, Malats N, Marenne G, Prokunina-Olsson L, Baris D, Schwenn M, Johnson A, Landi MT, Goldin L, Consonni D, Bertazzi PA, Rotunno M, Rajaraman P, Andersson U, Beane Freeman LE, Berg CD, Buring JE, Butler MA, Carreon T, Feychting M, Ahlbom A, Gaziano JM, Giles GG, Hallmans G, Hankinson SE, Hartge P, Henriksson R, Inskip PD, Johansen C, Landgren A, McKean-Cowdin R, Michaud DS, Melin BS, Peters U, Ruder AM, Sesso HD, Severi G, Shu XO, Visvanathan K, White E, Wolk A, Zeleniuch-Jacquotte A, Zheng W, Silverman DT, Kogevinas M, Gonzalez JR, Villa O, Li D, Duell EJ, Risch HA, Olson SH, Kooperberg C, Wolpin BM, Jiao L, Hassan M, Wheeler W, Arslan AA, Bueno-de-Mesquita HB, Fuchs CS, Gallinger S, Gross MD, Holly EA, Klein AP, LaCroix A, Mandelson MT, Petersen G, Boutron-Ruault MC, Bracci PM, Canzian F, Chang K, Cotterchio M, Giovannucci EL, Goggins M, Hoffman Bolton JA, Jenab M, Khaw KT, Krogh V, Kurtz RC, McWilliams RR, Mendelsohn JB, Rabe KG, Riboli E, Tjønneland A, Tobias GS, Trichopoulos D, Elena JW, Yu H, Amundadottir L, Stolzenberg-Solomon RZ, Kraft P, Schumacher F, Stram D, Savage SA, Mirabello L, Andrulis IL, Wunder JS, Patiño García A, Sierrasesúmaga L, Barkauskas DA, Gorlick RG, Purdue M, Chow WH, Moore LE, Schwartz KL, Davis FG, Hsing AW, Berndt SI, Black A, Wentzensen N, Brinton LA, Lissowska J, Peplonska B, McGlynn KA, Cook MB, Graubard BI, Kratz CP, Greene MH, Erickson RL, Hunter DJ, Thomas G, Hoover RN, Real FX, Fraumeni JF, Caporaso NE, Tucker M, Rothman N, Pérez-Jurado LA, Chanock SJ
(2012) Nat Genet 44: 651-8
MeSH Terms: Aged, Aging, Chromosome Aberrations, Female, Humans, Male, Middle Aged, Mosaicism, Neoplasms, Risk
Show Abstract · Added February 26, 2014
In an analysis of 31,717 cancer cases and 26,136 cancer-free controls from 13 genome-wide association studies, we observed large chromosomal abnormalities in a subset of clones in DNA obtained from blood or buccal samples. We observed mosaic abnormalities, either aneuploidy or copy-neutral loss of heterozygosity, of >2 Mb in size in autosomes of 517 individuals (0.89%), with abnormal cell proportions of between 7% and 95%. In cancer-free individuals, frequency increased with age, from 0.23% under 50 years to 1.91% between 75 and 79 years (P = 4.8 × 10(-8)). Mosaic abnormalities were more frequent in individuals with solid tumors (0.97% versus 0.74% in cancer-free individuals; odds ratio (OR) = 1.25; P = 0.016), with stronger association with cases who had DNA collected before diagnosis or treatment (OR = 1.45; P = 0.0005). Detectable mosaicism was also more common in individuals for whom DNA was collected at least 1 year before diagnosis with leukemia compared to cancer-free individuals (OR = 35.4; P = 3.8 × 10(-11)). These findings underscore the time-dependent nature of somatic events in the etiology of cancer and potentially other late-onset diseases.
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10 MeSH Terms
Detectable clonal mosaicism from birth to old age and its relationship to cancer.
Laurie CC, Laurie CA, Rice K, Doheny KF, Zelnick LR, McHugh CP, Ling H, Hetrick KN, Pugh EW, Amos C, Wei Q, Wang LE, Lee JE, Barnes KC, Hansel NN, Mathias R, Daley D, Beaty TH, Scott AF, Ruczinski I, Scharpf RB, Bierut LJ, Hartz SM, Landi MT, Freedman ND, Goldin LR, Ginsburg D, Li J, Desch KC, Strom SS, Blot WJ, Signorello LB, Ingles SA, Chanock SJ, Berndt SI, Le Marchand L, Henderson BE, Monroe KR, Heit JA, de Andrade M, Armasu SM, Regnier C, Lowe WL, Hayes MG, Marazita ML, Feingold E, Murray JC, Melbye M, Feenstra B, Kang JH, Wiggs JL, Jarvik GP, McDavid AN, Seshan VE, Mirel DB, Crenshaw A, Sharopova N, Wise A, Shen J, Crosslin DR, Levine DM, Zheng X, Udren JI, Bennett S, Nelson SC, Gogarten SM, Conomos MP, Heagerty P, Manolio T, Pasquale LR, Haiman CA, Caporaso N, Weir BS
(2012) Nat Genet 44: 642-50
MeSH Terms: Adolescent, Adult, Aged, Aged, 80 and over, Aging, Child, Child, Preschool, Chromosome Aberrations, Chromosome Mapping, DNA Copy Number Variations, Female, Genome-Wide Association Study, Humans, Infant, Infant, Newborn, Male, Middle Aged, Mosaicism, Neoplasms
Show Abstract · Added March 20, 2014
We detected clonal mosaicism for large chromosomal anomalies (duplications, deletions and uniparental disomy) using SNP microarray data from over 50,000 subjects recruited for genome-wide association studies. This detection method requires a relatively high frequency of cells with the same abnormal karyotype (>5-10%; presumably of clonal origin) in the presence of normal cells. The frequency of detectable clonal mosaicism in peripheral blood is low (<0.5%) from birth until 50 years of age, after which it rapidly rises to 2-3% in the elderly. Many of the mosaic anomalies are characteristic of those found in hematological cancers and identify common deleted regions with genes previously associated with these cancers. Although only 3% of subjects with detectable clonal mosaicism had any record of hematological cancer before DNA sampling, those without a previous diagnosis have an estimated tenfold higher risk of a subsequent hematological cancer (95% confidence interval = 6-18).
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19 MeSH Terms
Return of individual research results from genome-wide association studies: experience of the Electronic Medical Records and Genomics (eMERGE) Network.
Fullerton SM, Wolf WA, Brothers KB, Clayton EW, Crawford DC, Denny JC, Greenland P, Koenig BA, Leppig KA, Lindor NM, McCarty CA, McGuire AL, McPeek Hinz ER, Mirel DB, Ramos EM, Ritchie MD, Smith ME, Waudby CJ, Burke W, Jarvik GP
(2012) Genet Med 14: 424-31
MeSH Terms: Biomedical Research, Factor V, Genetics, Medical, Genome-Wide Association Study, Homozygote, Humans, Incidental Findings, Klinefelter Syndrome, Medical Informatics, Research Subjects, Sex Chromosome Aberrations, Truth Disclosure, Turner Syndrome
Show Abstract · Added December 10, 2013
PURPOSE - Return of individual genetic results to research participants, including participants in archives and biorepositories, is receiving increased attention. However, few groups have deliberated on specific results or weighed deliberations against relevant local contextual factors.
METHODS - The Electronic Medical Records and Genomics (eMERGE) Network, which includes five biorepositories conducting genome-wide association studies, convened a return of results oversight committee to identify potentially returnable results. Network-wide deliberations were then brought to local constituencies for final decision making.
RESULTS - Defining results that should be considered for return required input from clinicians with relevant expertise and much deliberation. The return of results oversight committee identified two sex chromosomal anomalies, Klinefelter syndrome and Turner syndrome, as well as homozygosity for factor V Leiden, as findings that could warrant reporting. Views about returning findings of HFE gene mutations associated with hemochromatosis were mixed due to low penetrance. Review of electronic medical records suggested that most participants with detected abnormalities were unaware of these findings. Local considerations relevant to return varied and, to date, four sites have elected not to return findings (return was not possible at one site).
CONCLUSION - The eMERGE experience reveals the complexity of return of results decision making and provides a potential deliberative model for adoption in other collaborative contexts.
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13 MeSH Terms
Genetic disease in the children of Danish survivors of childhood and adolescent cancer.
Winther JF, Olsen JH, Wu H, Shyr Y, Mulvihill JJ, Stovall M, Nielsen A, Schmiegelow M, Boice JD
(2012) J Clin Oncol 30: 27-33
MeSH Terms: Adolescent, Antineoplastic Agents, Child, Chromosome Aberrations, Cohort Studies, Congenital Abnormalities, Denmark, Female, Genetic Diseases, Inborn, Germ-Line Mutation, Gonads, Humans, Infant Mortality, Infant, Newborn, Male, Neoplasms, Pregnancy, Pregnancy Outcome, Radiotherapy, Radiotherapy Dosage, Registries, Risk Assessment, Risk Factors, Stillbirth, Survivors
Show Abstract · Added March 10, 2014
PURPOSE - Preconception radiation and chemotherapy have the potential to produce germ cell mutations leading to genetic disease in the next generation. Dose-response relationships were evaluated between cancer treatments and untoward pregnancy outcomes.
PATIENTS AND METHODS - A case-cohort study was conducted involving 472 Danish survivors of childhood and adolescent cancer and their 1,037 pregnancies. Adverse outcomes included 159 congenital malformations, six chromosomal abnormalities, seven stillbirths, and nine neonatal deaths. Preconception radiation doses to the gonads, uterus, and pituitary gland and administered chemotherapy were quantified based on medical records and related to adverse outcomes using a generalized estimating equation model.
RESULTS - No statistically significant associations were found between genetic disease in children and parental treatment with alkylating drugs or preconception radiation doses to the testes in male and ovaries in female cancer survivors. Specifically, the risk of genetic disease was similar among the children of irradiated survivors when compared with nonirradiated survivors (relative risk [RR], 1.02; 95% CI, 0.59 to 1.44; P = .94). A statistically significant association between abdomino-pelvic irradiation and malformations, stillbirths, and neonatal deaths was not seen in the children of female survivors overall (P = .07) or in the children of mothers receiving high uterine doses (mean, 13.5 Gy; max, 100 Gy; RR, 2.3; 95% CI, 0.95 to 5.56).
CONCLUSION - Mutagenic chemotherapy and radiotherapy doses to the gonads were not associated with genetic defects in children of cancer survivors. However, larger studies need to be conducted to further explore potential associations between high-dose pelvic irradiation and specific adverse pregnancy outcomes.
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25 MeSH Terms