Successful use of whole genome amplified DNA from multiple source types for high-density Illumina SNP microarrays
Abstract Background The recommended genomic DNA input requirements for whole genome single nucleotide polymorphism microarrays can limit the scope of molecular epidemiological studies. We performed a large-scale evaluation of whole genome amplified DNA as input into high-density, whole-genome Illumi...
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| Format: | Article |
| Language: | English |
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BMC
2018-03-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-018-4572-6 |
| _version_ | 1818016057579798528 |
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| author | Casey L. Dagnall Lindsay M. Morton Belynda D. Hicks Shengchao Li Weiyin Zhou Eric Karlins Kedest Teshome Salma Chowdhury Kerrie S. Lashley Joshua N. Sampson Leslie L. Robison Gregory T. Armstrong Smita Bhatia Gretchen A. Radloff Stella M. Davies Margaret A. Tucker Meredith Yeager Stephen J. Chanock |
| author_facet | Casey L. Dagnall Lindsay M. Morton Belynda D. Hicks Shengchao Li Weiyin Zhou Eric Karlins Kedest Teshome Salma Chowdhury Kerrie S. Lashley Joshua N. Sampson Leslie L. Robison Gregory T. Armstrong Smita Bhatia Gretchen A. Radloff Stella M. Davies Margaret A. Tucker Meredith Yeager Stephen J. Chanock |
| author_sort | Casey L. Dagnall |
| collection | DOAJ |
| description | Abstract Background The recommended genomic DNA input requirements for whole genome single nucleotide polymorphism microarrays can limit the scope of molecular epidemiological studies. We performed a large-scale evaluation of whole genome amplified DNA as input into high-density, whole-genome Illumina® Infinium® SNP microarray. Results Overall, 6622 DNA samples from 5970 individuals were obtained from three distinct biospecimen sources and genotyped using gDNA and/or wgaDNA inputs. When genotypes from the same individual were compared with standard, native gDNA input amount, we observed 99.94% mean concordance with wgaDNA input. Conclusions Our results demonstrate that carefully conducted studies with wgaDNA inputs can yield high-quality genotyping results. These findings should enable investigators to consider expansion of ongoing studies using high-density SNP microarrays, currently challenged by small amounts of available DNA. |
| first_indexed | 2024-04-14T07:06:52Z |
| format | Article |
| id | doaj.art-371d8d142e9f4e97baedf052bf07d0ac |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-14T07:06:52Z |
| publishDate | 2018-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-371d8d142e9f4e97baedf052bf07d0ac2022-12-22T02:06:33ZengBMCBMC Genomics1471-21642018-03-0119111010.1186/s12864-018-4572-6Successful use of whole genome amplified DNA from multiple source types for high-density Illumina SNP microarraysCasey L. Dagnall0Lindsay M. Morton1Belynda D. Hicks2Shengchao Li3Weiyin Zhou4Eric Karlins5Kedest Teshome6Salma Chowdhury7Kerrie S. Lashley8Joshua N. Sampson9Leslie L. Robison10Gregory T. Armstrong11Smita Bhatia12Gretchen A. Radloff13Stella M. Davies14Margaret A. Tucker15Meredith Yeager16Stephen J. Chanock17Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH)Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH)Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH)Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH)Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH)Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH)Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH)Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH)Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH)Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH)Department of Epidemiology and Cancer Control, St. Jude Children’s Research HospitalDepartment of Epidemiology and Cancer Control, St. Jude Children’s Research HospitalDepartment of Population Sciences, City of HopeDepartment of Pediatrics, Cincinnati Children’s Hospital Medical CenterDepartment of Pediatrics, Cincinnati Children’s Hospital Medical CenterDivision of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH)Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH)Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH)Abstract Background The recommended genomic DNA input requirements for whole genome single nucleotide polymorphism microarrays can limit the scope of molecular epidemiological studies. We performed a large-scale evaluation of whole genome amplified DNA as input into high-density, whole-genome Illumina® Infinium® SNP microarray. Results Overall, 6622 DNA samples from 5970 individuals were obtained from three distinct biospecimen sources and genotyped using gDNA and/or wgaDNA inputs. When genotypes from the same individual were compared with standard, native gDNA input amount, we observed 99.94% mean concordance with wgaDNA input. Conclusions Our results demonstrate that carefully conducted studies with wgaDNA inputs can yield high-quality genotyping results. These findings should enable investigators to consider expansion of ongoing studies using high-density SNP microarrays, currently challenged by small amounts of available DNA.http://link.springer.com/article/10.1186/s12864-018-4572-6Whole genome amplificationGenome-wide association studyHigh-density microarrayCCSS clinical trial |
| spellingShingle | Casey L. Dagnall Lindsay M. Morton Belynda D. Hicks Shengchao Li Weiyin Zhou Eric Karlins Kedest Teshome Salma Chowdhury Kerrie S. Lashley Joshua N. Sampson Leslie L. Robison Gregory T. Armstrong Smita Bhatia Gretchen A. Radloff Stella M. Davies Margaret A. Tucker Meredith Yeager Stephen J. Chanock Successful use of whole genome amplified DNA from multiple source types for high-density Illumina SNP microarrays BMC Genomics Whole genome amplification Genome-wide association study High-density microarray CCSS clinical trial |
| title | Successful use of whole genome amplified DNA from multiple source types for high-density Illumina SNP microarrays |
| title_full | Successful use of whole genome amplified DNA from multiple source types for high-density Illumina SNP microarrays |
| title_fullStr | Successful use of whole genome amplified DNA from multiple source types for high-density Illumina SNP microarrays |
| title_full_unstemmed | Successful use of whole genome amplified DNA from multiple source types for high-density Illumina SNP microarrays |
| title_short | Successful use of whole genome amplified DNA from multiple source types for high-density Illumina SNP microarrays |
| title_sort | successful use of whole genome amplified dna from multiple source types for high density illumina snp microarrays |
| topic | Whole genome amplification Genome-wide association study High-density microarray CCSS clinical trial |
| url | http://link.springer.com/article/10.1186/s12864-018-4572-6 |
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