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  • 1
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    Rare, Protein-Altering Variants in AS3MT and Arsenic Metabolism Efficiency: A Multi-Population Association Study
    Environmental Health Perspectives ; 2021
    In:  Environmental Health Perspectives Vol. 129, No. 4 ( 2021-04)
    Details
    In: Environmental Health Perspectives, Environmental Health Perspectives, Vol. 129, No. 4 ( 2021-04)
    Type of Medium: Online Resource
    ISSN: 0091-6765 , 1552-9924
    URL: Article
    DOI: 10.1289/EHP8152
    Language: English
    Publisher: Environmental Health Perspectives
    Publication Date: 2021
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    Sequencing-based fine-mapping and in silico functional characterization of the 10q24.32 arsenic metabolism efficiency locus across multiple arsenic-exposed populations
    Public Library of Science (PLoS) ; 2023
    In:  PLOS Genetics Vol. 19, No. 1 ( 2023-1-20), p. e1010588-
    Details
    In: PLOS Genetics, Public Library of Science (PLoS), Vol. 19, No. 1 ( 2023-1-20), p. e1010588-
    Abstract: Inorganic arsenic is highly toxic and carcinogenic to humans. Exposed individuals vary in their ability to metabolize arsenic, and variability in arsenic metabolism efficiency (AME) is associated with risks of arsenic-related toxicities. Inherited genetic variation in the 10q24.32 region, near the arsenic methyltransferase ( AS3MT ) gene, is associated with urine-based measures of AME in multiple arsenic-exposed populations. To identify potential causal variants in this region, we applied fine mapping approaches to targeted sequencing data generated for exposed individuals from Bangladeshi, American Indian, and European American populations (n = 2,357, 557, and 648 respectively). We identified three independent association signals for Bangladeshis, two for American Indians, and one for European Americans. The size of the confidence sets for each signal varied from 4 to 85 variants. There was one signal shared across all three populations, represented by the same SNP in American Indians and European Americans (rs191177668) and in strong linkage disequilibrium (LD) with a lead SNP in Bangladesh (rs145537350). Beyond this shared signal, differences in LD patterns, minor allele frequency (MAF) (e.g., rs12573221 ~13% in Bangladesh ~0.2% among American Indians), and/or heterogeneity in effect sizes across populations likely contributed to the apparent population specificity of the additional identified signals. One of our potential causal variants influences AS3MT expression and nearby DNA methylation in numerous GTEx tissue types (with rs4919690 as a likely causal variant). Several SNPs in our confidence sets overlap transcription factor binding sites and cis-regulatory elements (from ENCODE). Taken together, our analyses reveal multiple potential causal variants in the 10q24.32 region influencing AME, including a variant shared across populations, and elucidate potential biological mechanisms underlying the impact of genetic variation on AME.
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    ISSN: 1553-7404
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    DOI: 10.1371/journal.pgen.1010588
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    Language: English
    Publisher: Public Library of Science (PLoS)
    Publication Date: 2023
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  • 3
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    Lower levels of human milk adiponectin predict offspring weight for age: a study in a lean population of F ilipinos
    Wiley ; 2016
    In:  Maternal & Child Nutrition Vol. 12, No. 4 ( 2016-10), p. 790-800
    Details
    In: Maternal & Child Nutrition, Wiley, Vol. 12, No. 4 ( 2016-10), p. 790-800
    Abstract: Prior studies have reported a significant, inverse association between adiponectin in human milk and offspring growth velocity. Less is known about this association in populations characterised by a loss of weight for age z ‐scores ( WAZs ) in early life. We investigated the association between maternal body composition and milk adiponectin in a sample of F ilipino mothers. We then tested for an association between milk adiponectin and size for age in their infants. A total of 117 F ilipino mothers nursing infants from 0 to 24 months were recruited from C ebu, P hilippines. Anthropometrics, interviews and milk samples were collected and analysed using standard protocols. Mean milk adiponectin in this sample was 7.47 ± 5.75 ng mL −1 . Mean infant WAZ and weight for length ( WLZ ) decreased with age. Maternal body composition was not associated with milk adiponectin content. Milk adiponectin had a significant, positive association with infant WAZ and WLZ . Prior reports have found an inverse association between milk adiponectin and infant WAZ . Here, we report that in lean populations with lower milk adiponectin, there is a positive association with infant WAZ , possibly reflecting pleiotropic biological functions of adiponectin for post‐natal growth. This study increases the understanding of normal biological variation in milk adiponectin and the consequences of low levels of milk adiponectin for offspring growth.
    Type of Medium: Online Resource
    ISSN: 1740-8695 , 1740-8709
    URL: Issue
    URL: Article
    DOI: 10.1111/mcn.2016.12.issue-4
    DOI: 10.1111/mcn.12216
    Language: English
    Publisher: Wiley
    Publication Date: 2016
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    Abstract 3632: Differential DNA methylation in the benign and cancerous prostate tissue of African American and European American men
    American Association for Cancer Research (AACR) ; 2022
    In:  Cancer Research Vol. 82, No. 12_Supplement ( 2022-06-15), p. 3632-3632
    Details
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 82, No. 12_Supplement ( 2022-06-15), p. 3632-3632
    Abstract: In this study, we compare patterns of differential DNA methylation (DNAm) distinguishing tumor and benign prostate tissue in European American (EA) and African American (AA) men to improve our understanding of biological mechanisms that may underlie prostate cancer (PCa) disparities. In the United States, AA men are more likely to be diagnosed with and to die of PCa compared with EA men. Changes in DNAm accompany tumor development and progression, and differences in DNAm across ancestry groups may be an important lens through which to study PCa disparities. We collected paired tumor and histologically benign formalin-fixed paraffin-embedded tissue blocks from 151 (76 AA, 75 EA) PCa patients undergoing prostatectomy at the University of Chicago. DNA was extracted and genome-wide DNAm was measured at ~850,000 CpG sites using the Illumina MethylationEpic Array. After quality control, 682,694 CpGs remained for analysis. We conducted differential methylation analyses, adjusting for batch, age, and individual and identified 29,236 and 38,035 tumor-associated CpGs in AA and EA respectively (p & lt;5x10-8 and Δβ & gt;0.3) with 25,263 CpGs common to both sets. There was a depletion of differentially methylated CpGs in CpG islands and promoters in both groups, but depletion was stronger in AA. Tumor-associated CpGs within islands and in promoters were more likely to be hypermethylated for both groups, though this was stronger in EA. We identified 2,392 genes with differentially methylated promoters common to both ancestry groups; 223 and 1,045 were unique to AA and EA respectively. Shared gene regions included GSTP1, APC, RARB, and GRASP, which have been previously reported. We assigned CpG sites to genes and used Gene Set Enrichment Analysis to identify differentially methylated pathways. The identified pathways include several previously associated with cancer development including the epithelial mesenchymal transition. We also identified ancestry-specific pathways including the early and late estrogen response pathways in AA. Examining the predictive ability of our differentially methylated CpGs, we found that relatively few CpGs (~10) were sufficient to distinguish tumor and benign tissue in AA and EA men (AUC & gt;0.9). Scores constructed from differentially methylated CpGs in EA were able to predict tumor vs benign in AA (and vice versa) with high accuracy. Finally, we examined the association between ancestry and DNAm in both tumor and benign tissue. Here, 89 and 423 ancestry-associated CpGs were identified in tumor and benign respectively. Overall, we find that differential methylation patterns distinguishing tumor and benign tissue are generally similar for EA and AA men. However, differenced in tumor-associated DNAm as well as the presence of ancestry-associated CpGs provide a rich area for future studies exploring the impact of these differences on cancer development in AA and EA men. Citation Format: Meytal B. Chernoff, Marc Gillard, Kathryn Demanelis, Dayana Delgado, Anthony Williams, Donald Vander Griend, Brandon L. Pierce. Differential DNA methylation in the benign and cancerous prostate tissue of African American and European American men [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3632.
    Type of Medium: Online Resource
    ISSN: 1538-7445
    URL: Article
    DOI: 10.1158/1538-7445.AM2022-3632
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2022
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    Abstract 160: Identifying differential methylation patterns of benign and tumor prostate tissue in African American and European American prostate cancer patients
    American Association for Cancer Research (AACR) ; 2020
    In:  Cancer Research Vol. 80, No. 16_Supplement ( 2020-08-15), p. 160-160
    Details
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 80, No. 16_Supplement ( 2020-08-15), p. 160-160
    Abstract: This study aims to identify biological features and processes underlying disparities in prostate cancer (PCa) between African American (AA) and European American (EA) men using DNA methylation (DNAm). Changes in genome-wide DNAm accompany tumor development and progression. Differences in genome-wide DNAm across ancestry groups may be an important mechanism to understand the higher incidence and poorer prognosis among AA men. We collected paired tumor and histologically benign tissue from formalin fixed and paraffin embedded (FFPE) blocks from 150 prostate cancer patients (75 AA, 75 EA) at the University of Chicago. DNA was extracted and genome-wide DNAm was measured at ~850,000 CpG sites in benign and tumor tissue using the Illumina Infinium MethylationEpic BeadChip. After CpG and sample-level QC and normalization, we conducted differential methylation analyses, comparing tumor and benign tissue within each ancestry group, adjusting for batch, age, and tissue pair. We then used Gene Set Enrichment Analysis (GSEA) to examine enrichment of GO and Hallmark terms. 682,694 CpGs passed QC filtering. For AA and EA, CpGs hyper-methylated in cancer tissue were enriched in CpG islands while hypo-methylated CpGs were enriched in open seas. We identified 39,768 and 25,405 tumor-associated CpGs in AA and EA respectively (p & lt;5 × 10-8 and absolute change in methylation 0.25). Of these, 23,068 CpGs were common to both sets. In AA, a higher proportion of tumor-associated CpGs were hypo-methylated compared to EA (40.5% vs 18.6%, p & lt;2 × 10-16). A larger proportion tumor-associated CpGs annotated to non-CpG islands in AA compared to EA (67.7% vs 62%) (p=2 × 10-16). We also observed an increased proportion of differentially methylated CpGs in promoter regions in EA compared with AA. Consistent with prior studies, among the common, tumor-associated CpGs, we observed differential methylation of GSTP1 and APC, both involved in PCa development. We observed enrichment in 6 genesets in both AA and EA, including the epithelial mesenchymal transition and estrogen response. In AA we observed additional enrichment in 2 genesets including hedgehog signaling (FDR & lt;0.05). Comparing the ancestry groups, adjusting for age and batch, we found 219 differentially methylated CpGs between AA and EA in tumor and 151 in benign tissue. Overall, we identified higher frequencies of differential methylation and more differentially methylated genes in AA compared with EA; despite slightly more favorable clinical features in the AA in our sample. We also found differential methylation by ancestry within each tissue type. These results suggest the existence of epigenetic alterations unique to AA and EA that may contribute to the biological basis of PCa disparities. Moving forward we will refine our analyses, adjusting for cell type proportion and further examining the differentially methylated pathways. Citation Format: Meytal B. Chernoff, Kathryn Demanelis, Marc Gillard, Dayana Delgado, Donald J. Vander Griend, Brandon L. Pierce. Identifying differential methylation patterns of benign and tumor prostate tissue in African American and European American prostate cancer patients [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 160.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    URL: Article
    DOI: 10.1158/1538-7445.AM2020-160
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2020
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    Abstract 4233: Racial differences in patterns of cytogenetic abnormalities in multiple myeloma
    American Association for Cancer Research (AACR) ; 2018
    In:  Cancer Research Vol. 78, No. 13_Supplement ( 2018-07-01), p. 4233-4233
    Details
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 78, No. 13_Supplement ( 2018-07-01), p. 4233-4233
    Abstract: Introduction: African American (AA) patients with Multiple Myeloma (MM) are diagnosed at younger ages and show an age-adjusted incidence twice as high as that seen in European Americans (EA); however, a study by Waxman et al found higher disease specific survival in AA. A recent study showed differences in chromosomal aberrations between AA and EA, but further work is needed to understand racial differences in cytogenetics through Fluorescent In Situ Hybridization (FISH) using an extensive array of probes. Methods: We identified 470 consecutive patients with MM from the University of Chicago Cancer Cytogenetics Laboratory from October 2003-January 2017. Of those, 127 (22%) patients had abnormal karyotypes and 343 were evaluated by FISH using a panel of 18 probes. Twenty-two patients who self-identified as Hispanic, Multiracial, Asian, or Indian were dropped from the analysis due to low numbers. For the remaining 311 patients, we obtained data on IGH translocations (partner genes included IGH/FGFR3 fusion [t(4;14)(p16.3;q32)]; IGH/CCND1 fusion [t(11;14)(q13;q32)] ; IGH/MAF fusion [t(14;16)(q32;q23)]); TP53 loss [17p13.1] ; CDKN2C loss [1p32.3]; CKS1B gain [1q21] ; ATM losss [(11)(q22.3)11(q22.3)]; trisomy of chromosomes 3, 7, 9, 12, and 15; and chromosome 13 loss or interstitial deletion of 13q. We grouped the FISH results as high (loss of TP53, loss of CDKN2C; CKS1B gain, IGH/MAF fusion), intermediate (IGH/FGFR3 fusion), or standard (Trisomies 3, 7, 9, 15; Gain of TP53, Gain of ATM, chromosome 13 loss) prognostic risk markers. Results: Of 311 patients, 172 (55.3%) are self-reported EA, 130 (41.8%) are AA. Compared with EA, AA patients were more likely to be females (44.8% vs. 59.2%, respectively) and older than 65 years at diagnosis (47.7% vs. 56.2% respectively). Overall, 6.3% of patients were younger than 45 years at diagnosis, but there was no racial difference in the proportion of young patients. Compared with EA, AA patients assessed with standard risk probes were less likely to have standard risk cytogenetic features (48% vs. 66%; p-value=0.02). AA patients showed a lower percentage of hyperdiploidy, 36.5% of AA patients assessed were positive for hyperdiploidy compared with 57.1% of assessed EA (p=0.02). Despite the lower proportion of AA with cytogenetic markers associated with favorable prognosis, there was no significant difference between EA and AA patients in the prevalence of adverse prognostic markers, such as TP53 deletion, IGH/MAF fusions, or CKS1B gain. However, we did observe that AA patients were more likely to have loss of CDKN2C (16.7% vs 3.6%, p=0.02). Conclusions: We found that compared with EA, AA patients are less likely to have cytogenetic features associated with favorable prognosis (i.e. hyperdiploidy), yet AA do not have a higher prevalence of high risk cytogenetics. These findings suggest that cytogenetics alone may not fully explain racial/ethnic differences in MM mortality. [Meytal Chernoff and Madina Sukhanova are co-first authors of this abstract.] Citation Format: Meytal B. Chernoff, Madina Sukhanova, Liz Stepniak, Wei Zhang, Brian C. Chiu. Racial differences in patterns of cytogenetic abnormalities in multiple myeloma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4233.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    URL: Article
    DOI: 10.1158/1538-7445.AM2018-4233
    RVK:
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2018
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  • 7
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    Erratum: “Rare, protein-altering variants in AS3MT and arsenic metabolism efficiency: a multi-population association study”
    Environmental Health Perspectives ; 2021
    In:  Environmental Health Perspectives Vol. 129, No. 5 ( 2021-05)
    Details
    In: Environmental Health Perspectives, Environmental Health Perspectives, Vol. 129, No. 5 ( 2021-05)
    Type of Medium: Online Resource
    ISSN: 0091-6765 , 1552-9924
    URL: Article
    DOI: 10.1289/EHP9488
    Language: English
    Publisher: Environmental Health Perspectives
    Publication Date: 2021
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  • 8
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    Racial Differences in High-Risk Cytogenetic Mutations and Outcomes in Multiple Myeloma
    American Society of Hematology ; 2019
    In:  Blood Vol. 134, No. Supplement_1 ( 2019-11-13), p. 5494-5494
    Details
    In: Blood, American Society of Hematology, Vol. 134, No. Supplement_1 ( 2019-11-13), p. 5494-5494
    Abstract: Introduction: Multiple myeloma (MM) is more common in blacks compared to whites. Prior studies have shown that when blacks have equal access to anti-myeloma therapies as whites, they have similar or even superior relative survival. However, most of these studies included eras when proteasome inhibitors (PI) and immunomodulatory agents (IMiD) were not routinely used. In addition, it is unclear how pre-treatment high risk cytogenetic mutations (HRCM) affect response to therapy among races. We sought to assess differences in the frequencies and outcomes between blacks and whites stratified by cytogenetic risk in two cohorts of MM patients receiving modern treatment approaches. Methods: A retrospective chart review was conducted using the Multiple Myeloma Research Foundation (MMRF) CoMMpass registry (version IA13) and the University of Chicago cytogenetic database and medical records (UChicago). High risk cytogenetic mutations were defined as: deletion 17p/TP53, 1q gain, t(4;14), t(14;16), and t(14;20). The CoMMPass registry inferred cytogenetic changes from next-generation sequencing data; a deletion required that 21% of cells have at least a 1 copy deletion, a gain required that 23% of the cells have a 1 copy gain, and translocations required at least 30% of cells having the event. UChicago cytogenetics data were limited to analyses using fluorescent in situ hybridization on CD138+ selected bone marrow aspirate samples. Abstracted data included pre-treatment demographics, International Staging System (ISS), cytogenetics, induction regimen, autologous stem cell transplant (ASCT) and maintenance therapy use, and overall survival (OS). Comparisons were made using Chi-square or Fisher's exact test for categorical variables and Mann-Whitney U-test for continuous variables. Kaplan-Meier curves were used to display survival curves and Cox models were used to assess the association between cytogenetic mutations and outcomes. Baseline HRCM frequencies from the MMRF and UChicago were pooled; outcomes from the MMRF registry are provided here, and combined survival analysis with UChicago data will be presented. Results: We identified 639 MM patients (113 black and 526 white) in the MMRF CoMMpass registry and 110 (47 black and 63 white) in the UChicago database with complete baseline cytogenetic data available. Median age was 64.5 yrs for whites vs 63 yrs for blacks (p=0.2); 349/589 (59%) whites and 93/160 (58%) blacks were male (p=0.9). There was a similar distribution in the number of HRCMs between the two groups (p=0.7), and no statistical differences in individual HRCMs. In analyzing outcomes in the MMRF cohort, blacks and whites had similar pre-treatment ISS stage and bone marrow plasmacytosis. Blacks were less likely to receive triplet therapies, including combined PI/IMiD-based or alkylator-based triplet therapy (55% vs 73%, p 〈 0.001). First line ASCT was performed in 260/526 (49%) whites compared to 44/113 (39%) blacks (p=0.05). A triplet induction combined with first line ASCT was performed in 231/526 (44%) whites and 37/113 (33%) blacks (p=0.04). Of those who received ASCT, equal numbers received post-ASCT maintenance therapy (60% vs 59%, p=0.9). For the entire MMRF cohort, OS was shorter for blacks compared to whites (Hazard Ratio (HR) 1.59, 95% confidence interval (CI) 1.13-2.27, p=0.01) (Fig. 1A). Estimated 3-yr OS was 67% for blacks vs 76% for whites (p=0.05). In patients who specifically received a triplet regimen followed by ASCT (Fig. 1B), there was no difference in OS between races (HR 1.86, 95% CI 0.75-4.63, p=0.2). Among patients with no HRCM present at diagnosis, there was also no difference between races (p=0.6) (Fig. 2A). There was a trend toward inferior OS in blacks vs whites with one or more HRCMs, which did not reach significance (p=0.13) (Fig. 2B). Results from pooled analyses with the UChicago cohort will be presented at the ASH meeting. Conclusions: There was a similar distribution of HRCMs between blacks and whites. Utilization rates of both triplets and ASCT were higher for both races than previously reported; however, there was a higher use of triplet regimens and ASCT in whites vs blacks. Access to a combination of frontline triplet regimens and ASCT appears to mitigate disparities in outcomes for patients with standard risk cytogenetics, but it is unclear if this is true for those with HRCMs. This requires further investigation of the biological differences in MM among races. Disclosures Jakubowiak: Adaptive Biotechnologies: Consultancy, Honoraria; Takeda: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; GSK: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; Celgene: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; KaryoPharm Therapeutics: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; Millennium: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; Sanofi: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; SkyLineDx: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; Juno: Consultancy, Honoraria; AbbVie: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; Janssen: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; BMS: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; Amgen: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
    URL: Article
    DOI: 10.1182/blood-2019-126304
    RVK:
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2019
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    Determinants of telomere length across human tissues
    American Association for the Advancement of Science (AAAS) ; 2020
    In:  Science Vol. 369, No. 6509 ( 2020-09-11)
    Details
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 369, No. 6509 ( 2020-09-11)
    Abstract: Telomere shortening is a hallmark of aging. Telomere length (TL) in blood cells has been studied extensively as a biomarker of human aging and disease; however, little is known regarding variability in TL in nonblood, disease-relevant tissue types. Here, we characterize variability in TLs from 6391 tissue samples, representing 〉 20 tissue types and 952 individuals from the Genotype-Tissue Expression (GTEx) project. We describe differences across tissue types, positive correlation among tissue types, and associations with age and ancestry. We show that genetic variation affects TL in multiple tissue types and that TL may mediate the effect of age on gene expression. Our results provide the foundational knowledge regarding TL in healthy tissues that is needed to interpret epidemiological studies of TL and human health.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    URL: Article
    DOI: 10.1126/science.aaz6876
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2020
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    DNA methylation QTL mapping across diverse human tissues provides molecular links between genetic variation and complex traits
    Springer Science and Business Media LLC ; 2023
    In:  Nature Genetics Vol. 55, No. 1 ( 2023-01), p. 112-122
    Details
    In: Nature Genetics, Springer Science and Business Media LLC, Vol. 55, No. 1 ( 2023-01), p. 112-122
    Type of Medium: Online Resource
    ISSN: 1061-4036 , 1546-1718
    URL: Article
    DOI: 10.1038/s41588-022-01248-z
    RVK:
    XA 10000
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 1494946-5
    SSG: 12
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