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Grant Details

Grant Number: 5R03CA173806-02 Interpret this number
Primary Investigator: Orlow, Irene
Organization: Sloan-Kettering Inst Can Research
Project Title: Validation of the Use of Whole-Genome Amplified DNA in a Population-Based Study
Fiscal Year: 2014


Abstract

DESCRIPTION (provided by applicant): Abstract Whole-genome amplification (WGA) technologies offer the opportunity to expand DNA from otherwise depleted native DNAs. This technique has the potential to facilitate the continued productivity of molecular epidemiological studies that have limited remaining DNA. Although allele amplification errors can occur, the performance of WGA in SNP genotyping has generally reported very good concordance and reproducibility. However the quality of WGA DNA obtained from buccal brushes has not been thoroughly evaluated for screening of mutations or sequencing, and published reports have mostly involved limited sets of DNA samples extracted from other sources and tested for the fidelity of non- PCR based WGA methods. The objective of this validation study is to determine the sensitivity and specificity of detecting germline mutations and polymorphisms in a large set of WGA DNA samples from a population-based study by direct sequencing. We plan to sequence the CDKN2A/p16 gene in 3580 DNA samples from buccal brushes that has been whole-genome amplified with the GenomePlex(R) kit, and then compare the sequencing data with those results already obtained in the original or native DNAs. We endeavor to demonstrate that we can use the WGA random fragmentation- PCR method to allow nearly unlimited future studies of germline DNA using this resource to investigate hypotheses in relation to melanoma risk and/or progression. The study also has a broader scientific relevance in that it will provide generalizable knowledge about the utility of buccal samples for future epidemiological investigations.



Publications

Disease-Associated Risk Variants in ANRIL Are Associated with Tumor-Infiltrating Lymphocyte Presence in Primary Melanomas in the Population-Based GEM Study.
Authors: Davari D.R. , Orlow I. , Kanetsky P.A. , Luo L. , Edmiston S.N. , Conway K. , Parrish E.A. , Hao H. , Busam K.J. , Sharma A. , et al. .
Source: Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology, 2021-10-04; , .
EPub date: 2021-10-04.
PMID: 34607836
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Association of Known Melanoma Risk Factors with Primary Melanoma of the Scalp and Neck.
Authors: Wood R.P. , Heyworth J.S. , McCarthy N.S. , Mauguen A. , Berwick M. , Thomas N.E. , Millward M.J. , Anton-Culver H. , Cust A.E. , Dwyer T. , et al. .
Source: Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology, 2020 11; 29(11), p. 2203-2210.
EPub date: 2020-08-20.
PMID: 32856602
Related Citations

Association of IRF4 single-nucleotide polymorphism rs12203592 with melanoma-specific survival.
Authors: Ward S.V. , Gibbs D.C. , Orlow I. , Thomas N.E. , Kanetsky P.A. , Luo L. , Cust A.E. , Anton-Culver H. , Gruber S.B. , Gallagher R.P. , et al. .
Source: The British journal of dermatology, 2020 07; 183(1), p. 163-165.
EPub date: 2020-02-19.
PMID: 31958143
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A risk prediction model for the development of subsequent primary melanoma in a population-based cohort.
Authors: Cust A.E. , Badcock C. , Smith J. , Thomas N.E. , Haydu L.E. , Armstrong B.K. , Law M.H. , Thompson J.F. , Kanetsky P.A. , Begg C.B. , et al. .
Source: The British journal of dermatology, 2020 05; 182(5), p. 1148-1157.
EPub date: 2019-11-27.
PMID: 31520533
Related Citations

Inherited Melanoma Risk Variants Associated with Histopathologically Amelanotic Melanoma.
Authors: Gibbs D.C. , Orlow I. , Vernali S. , Powell H.B. , Kanetsky P.A. , Luo L. , Busam K.J. , Sharma A. , Kricker A. , Armstrong B.K. , et al. .
Source: The Journal of investigative dermatology, 2020 04; 140(4), p. 918-922.e7.
EPub date: 2019-09-27.
PMID: 31568773
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Relationship of Chromosome Arm 10q Variants to Occurrence of Multiple Primary Melanoma in the Population-Based Genes, Environment, and Melanoma (GEM) Study.
Authors: Miles J.A. , Orlow I. , Kanetsky P.A. , Luo L. , Cust A.E. , Armstrong B.K. , Kricker A. , Anton-Culver H. , Gruber S.B. , Gallagher R.P. , et al. .
Source: The Journal of investigative dermatology, 2019 06; 139(6), p. 1410-1412.
EPub date: 2018-12-17.
PMID: 30571972
Related Citations

Inherited Genetic Variants Associated with Melanoma BRAF/NRAS Subtypes.
Authors: Thomas N.E. , Edmiston S.N. , Orlow I. , Kanetsky P.A. , Luo L. , Gibbs D.C. , Parrish E.A. , Hao H. , Busam K.J. , Armstrong B.K. , et al. .
Source: The Journal of investigative dermatology, 2018 11; 138(11), p. 2398-2404.
EPub date: 2018-05-09.
PMID: 29753029
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The interaction between vitamin D receptor polymorphisms and sun exposure around time of diagnosis influences melanoma survival.
Authors: Orlow I. , Shi Y. , Kanetsky P.A. , Thomas N.E. , Luo L. , Corrales-Guerrero S. , Cust A.E. , Sacchetto L. , Zanetti R. , Rosso S. , et al. .
Source: Pigment cell & melanoma research, 2018 03; 31(2), p. 287-296.
EPub date: 2017-11-05.
PMID: 28990310
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