High Quality Genome-Wide Genotyping from Archived Dried Blood Spots without DNA Amplification
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{"title"=>"High Quality Genome-Wide Genotyping from Archived Dried Blood Spots without DNA Amplification", "type"=>"journal", "authors"=>[{"first_name"=>"Krystal R.", "last_name"=>"St. Julien", "scopus_author_id"=>"55989488500"}, {"first_name"=>"Laura L.", "last_name"=>"Jelliffe-Pawlowski", "scopus_author_id"=>"8569120300"}, {"first_name"=>"Gary M.", "last_name"=>"Shaw", "scopus_author_id"=>"7401773618"}, {"first_name"=>"David K.", "last_name"=>"Stevenson", "scopus_author_id"=>"7402384031"}, {"first_name"=>"Hugh M.", "last_name"=>"O'Brodovich", "scopus_author_id"=>"7006287464"}, {"first_name"=>"Mark A.", "last_name"=>"Krasnow", "scopus_author_id"=>"7004230522"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"369039398", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "sgr"=>"84878495450", "issn"=>"19326203", "pmid"=>"23737996", "scopus"=>"2-s2.0-84878495450", "doi"=>"10.1371/journal.pone.0064710"}, "id"=>"79bb0189-5854-3b27-8553-4f417ce26e6c", "abstract"=>"Spots of blood are routinely collected from newborn babies onto filter paper called Guthrie cards and used to screen for metabolic and genetic disorders. The archived dried blood spots are an important and precious resource for genomic research. Whole genome amplification of dried blood spot DNA has been used to provide DNA for genome-wide SNP genotyping. Here we describe a 96 well format procedure to extract DNA from a portion of a dried blood spot that provides sufficient unamplified genomic DNA for genome-wide single nucleotide polymorphism (SNP) genotyping. We show that SNP genotyping of the unamplified DNA is more robust than genotyping amplified dried blood spot DNA, is comparable in cost, and can be done with thousands of samples. This procedure can be used for genome-wide association studies and other large-scale genomic analyses that require robust, high-accuracy genotyping of dried blood spot DNA.", "link"=>"http://www.mendeley.com/research/high-quality-genomewide-genotyping-archived-dried-blood-spots-without-dna-amplification", "reader_count"=>36, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>3, "Researcher"=>7, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>8, "Student > Postgraduate"=>3, "Student > Master"=>3, "Other"=>2, "Student > Bachelor"=>4, "Lecturer"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>3, "Researcher"=>7, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>8, "Student > Postgraduate"=>3, "Student > Master"=>3, "Other"=>2, "Student > Bachelor"=>4, "Lecturer"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Nursing and Health Professions"=>1, "Biochemistry, Genetics and Molecular Biology"=>5, "Materials Science"=>1, "Medicine and Dentistry"=>9, "Agricultural and Biological Sciences"=>15, "Psychology"=>2}, "reader_count_by_subdiscipline"=>{"Materials Science"=>{"Materials Science"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>9}, "Psychology"=>{"Psychology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>15}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Unspecified"=>{"Unspecified"=>3}}, "reader_count_by_country"=>{"United States"=>1, "Brazil"=>1, "United Kingdom"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1070955"], "description"=>"<p>Genomic DNA (gDNA) extracted from two 2 mm punches obtained from archived dried blood spots (DBS) from nine individuals (1–9) was genotyped on an Illumina Infinium 300,000 SNP test chip (set “a”, 1a–9a). For six of the DBS (1,3,4,5,7,8), a set (set “b”) of extraction duplicates (duplicate extractions from the same DBS) was prepared and genotyped in the same way. A 1 µl aliquot of each of these 15 samples of gDNA was whole genome amplified (wgaDNA) and then genotyped in the same way as sets “a” and “b”: set “c” wgaDNA samples (1c–9c) were amplified from set “a” gDNA samples, and set “d” wgaDNA samples (1d, 3d, 4d, 5d, 7d, 8d) were amplified from set “b” gDNA samples. (A) Performance quality of the gDNA and wgaDNA samples on genome-wide SNP genotyping. Successful, Marginal, and Failed sample performance parameters are given in Results. (B) SNP genotyping replication error. The number of SNP discrepancies for each sample was determined using gDNA set “a” as the reference. Replication error (the number of discrepancies among SNPs called in both the sample and reference divided by the total number of SNPs called in both) was 1.6×10<sup>−5</sup> for set “b”, 1.5×10<sup>−4</sup> for set “c”, and 1.2×10<sup>−4</sup> for set “d”. These replication error values are provisional because we do not know the true genotype of the discrepant loci and there may be gDNA-specific and/or wgaDNA-specific artifacts.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome analysis tools", "Genome-wide association studies", "Genome sequencing", "population genetics", "Genetic polymorphism", "Evolutionary biology", "genetics", "Human genetics", "Population biology", "Public health", "Health screening", "genotyping", "genomic", "amplified", "dna"], "article_id"=>709203, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Krystal R. St. Julien", "Laura L. Jelliffe-Pawlowski", "Gary M. Shaw", "David K. Stevenson", "Hugh M. O’Brodovich", "Mark A. Krasnow"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0064710.g001", "stats"=>{"downloads"=>1, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Success_and_accuracy_of_genotyping_with_genomic_or_amplified_DNA_from_dried_blood_spots_/709203", "title"=>"Success and accuracy of genotyping with genomic or amplified DNA from dried blood spots.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-05-30 02:33:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/1070956"], "description"=>"<p>The genotyping performance of the gDNA samples (A) and wgaDNA samples (B) described in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0064710#pone-0064710-g001\" target=\"_blank\">Figure 1</a> is plotted against the DNA concentration of the sample as determined by Qubit for gDNA and Picogreen for wgaDNA (bottom axis) and total amount of DNA used (4 µl) during each genotyping run (top axis). Picogreen was used for wgaDNA because Qubit does not discern concentrations above 100 ng/µl. Note that all gDNA samples with DNA concentrations above 5 ng/µl (∼20 ng DNA) were genotyped successfully (A). No similar threshold was observed for wgaDNA samples (B).</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome analysis tools", "Genome-wide association studies", "Genome sequencing", "population genetics", "Genetic polymorphism", "Evolutionary biology", "genetics", "Human genetics", "Population biology", "Public health", "Health screening", "gdna"], "article_id"=>709204, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Krystal R. St. Julien", "Laura L. Jelliffe-Pawlowski", "Gary M. Shaw", "David K. Stevenson", "Hugh M. O’Brodovich", "Mark A. Krasnow"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0064710.g002", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genotyping_performance_as_a_function_of_gDNA_concentration_/709204", "title"=>"Genotyping performance as a function of gDNA concentration.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-05-30 02:33:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/1070957"], "description"=>"<p>gDNA was extracted from two 2 mm punches of seven different archived DBS (1–7), and the process was repeated with fresh punches from the same DBS on a separate day. DNA was quantitated by Qubit. Different DBS showed ∼5-fold difference in DNA yield, whereas extraction duplicates of the same DBS gave almost identical DNA yield (103% ±15%, mean ± S.D.).</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome analysis tools", "Genome-wide association studies", "Genome sequencing", "population genetics", "Genetic polymorphism", "Evolutionary biology", "genetics", "Human genetics", "Population biology", "Public health", "Health screening", "gdna", "yields"], "article_id"=>709205, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Krystal R. St. Julien", "Laura L. Jelliffe-Pawlowski", "Gary M. Shaw", "David K. Stevenson", "Hugh M. O’Brodovich", "Mark A. Krasnow"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0064710.g003", "stats"=>{"downloads"=>0, "page_views"=>32, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Reproducibility_of_gDNA_yields_from_the_same_dried_blood_spot_/709205", "title"=>"Reproducibility of gDNA yields from the same dried blood spot.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-05-30 02:33:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/1070958"], "description"=>"<p>The indicated number of punches was obtained from 19 archived DBS for gDNA extraction. DNA yield was determined by Qubit (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0064710#pone.0064710.s002\" target=\"_blank\">Table S1</a>) and the values (mean ± S.D.) were normalized to the yield for a single punch. p<0.0001, one-way ANOVA.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome analysis tools", "Genome-wide association studies", "Genome sequencing", "population genetics", "Genetic polymorphism", "Evolutionary biology", "genetics", "Human genetics", "Population biology", "Public health", "Health screening"], "article_id"=>709206, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Krystal R. St. Julien", "Laura L. Jelliffe-Pawlowski", "Gary M. Shaw", "David K. Stevenson", "Hugh M. O’Brodovich", "Mark A. Krasnow"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0064710.g004", "stats"=>{"downloads"=>2, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_gDNA_yield_increases_with_increasing_number_of_dried_blood_spot_punches_/709206", "title"=>"gDNA yield increases with increasing number of dried blood spot punches.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-05-30 02:33:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/1070959"], "description"=>"1<p>Time for two 96 well extraction plates, not including time to catalog samples; All iterations of samples from the original two 96 well plates typically fill two new 96 well plates (22 hours includes all iterations).</p>2<p>Mean SNP genotyping replication error rate from <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0064710#pone-0064710-g001\" target=\"_blank\">Figure 1B</a>.</p>3<p>Mean SNP genotyping failure rate (protocol development sample set); gDNA and wgaDNA failure rates are significantly different (p = 2.6×10<sup>−7</sup>, Student’s t-test).</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome analysis tools", "Genome-wide association studies", "Genome sequencing", "population genetics", "Genetic polymorphism", "Evolutionary biology", "genetics", "Human genetics", "Population biology", "Public health", "Health screening", "genomic", "dna", "genome", "amplified"], "article_id"=>709207, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Krystal R. St. Julien", "Laura L. Jelliffe-Pawlowski", "Gary M. Shaw", "David K. Stevenson", "Hugh M. O’Brodovich", "Mark A. Krasnow"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0064710.t001", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_genomic_DNA_and_whole_genome_amplified_DNA_from_DBS_/709207", "title"=>"Comparison of genomic DNA and whole genome amplified DNA from DBS.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-05-30 02:33:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/1070961", "https://ndownloader.figshare.com/files/1070962", "https://ndownloader.figshare.com/files/1070963", "https://ndownloader.figshare.com/files/1070964", "https://ndownloader.figshare.com/files/1070965", "https://ndownloader.figshare.com/files/1070966", "https://ndownloader.figshare.com/files/1070967"], "description"=>"<div><p>Spots of blood are routinely collected from newborn babies onto filter paper called Guthrie cards and used to screen for metabolic and genetic disorders. The archived dried blood spots are an important and precious resource for genomic research. Whole genome amplification of dried blood spot DNA has been used to provide DNA for genome-wide SNP genotyping. Here we describe a 96 well format procedure to extract DNA from a portion of a dried blood spot that provides sufficient unamplified genomic DNA for genome-wide single nucleotide polymorphism (SNP) genotyping. We show that SNP genotyping of the unamplified DNA is more robust than genotyping amplified dried blood spot DNA, is comparable in cost, and can be done with thousands of samples. This procedure can be used for genome-wide association studies and other large-scale genomic analyses that require robust, high-accuracy genotyping of dried blood spot DNA.</p></div>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome analysis tools", "Genome-wide association studies", "Genome sequencing", "population genetics", "Genetic polymorphism", "Evolutionary biology", "genetics", "Human genetics", "Population biology", "Public health", "Health screening", "genome-wide", "genotyping", "archived", "spots", "dna"], "article_id"=>709208, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Krystal R. St. Julien", "Laura L. Jelliffe-Pawlowski", "Gary M. Shaw", "David K. Stevenson", "Hugh M. O’Brodovich", "Mark A. Krasnow"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0064710.s001", "https://dx.doi.org/10.1371/journal.pone.0064710.s002", "https://dx.doi.org/10.1371/journal.pone.0064710.s003", "https://dx.doi.org/10.1371/journal.pone.0064710.s004", "https://dx.doi.org/10.1371/journal.pone.0064710.s005", "https://dx.doi.org/10.1371/journal.pone.0064710.s006", "https://dx.doi.org/10.1371/journal.pone.0064710.s007"], "stats"=>{"downloads"=>47, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_High_Quality_Genome_Wide_Genotyping_from_Archived_Dried_Blood_Spots_without_DNA_Amplification_/709208", "title"=>"High Quality Genome-Wide Genotyping from Archived Dried Blood Spots without DNA Amplification", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-05-30 02:33:28"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"13", "full-text"=>"14", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"4", "cited-by"=>"0", "year"=>"2018", "month"=>"9"}
  • {"unique-ip"=>"16", "full-text"=>"17", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"11", "cited-by"=>"0", "year"=>"2018", "month"=>"11"}
  • {"unique-ip"=>"11", "full-text"=>"16", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"10", "full-text"=>"9", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"3", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"10", "full-text"=>"11", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"6", "supp-data"=>"9", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"8", "full-text"=>"10", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"3", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
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Relative Metric

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