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  • Cybergenetics :: A genome-wide search for alcoholism susceptibility genes
    Article Abstract Alcoholism is currently one of the most serious public health problems in the US Lifetime prevalence rates are relatively high with one in five men and one in 12 women meeting criteria for this condition Identification of genetic loci conferring an increased susceptibility to developing alcohol dependence could strengthen prevention efforts by informing individuals of their risk before abusive drinking ensues Families identified through a double proband methodology

    Original URL path: http://www.cybgen.com/information/publication/2004/AJMG/Hill-Allan-A-genome-wide-search-for-alcoholism-susceptibility-genes/page.shtml (2016-02-12)
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  • Cybergenetics :: Validation study of the TrueAllele® automated data review system
    L A and Duceman B W Validation study of the TrueAllele 174 automated data review system Journal of Forensic Sciences 49 4 1 8 2004 Downloads Full Article Abstract The New York State Convicted Offender DNA Databank is the first U S lab to complete an internal validation of the TrueAllele 174 expert data review system TrueAllele is designed to assess short tandem repeat STR DNA data based on several key features such as peak height shape area and position relative to a standard ladder and use this information to make accurate allele calls The software then prioritizes the allele calls based on several user defined rules As a result the user need only review low quality data The validation of this system consisted of an extensive optimization phase and a large concordance phase During optimization the rule settings were tailored to minimize the amount of high quality data viewed by the user In the concordance phase a large dataset was typed in parallel with the ABI software Gene Scan and Genotyper manual review and TrueAllele automated review for comparison of allele calls and sample state assignment Only one significant difference was discovered out of 2048 samples in the concordance

    Original URL path: http://www.cybgen.com/information/publication/2004/JFS/Kadash-Duceman-Validation-study-of-the-TrueAllele-automated-data-review-system/page.shtml (2016-02-12)
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  • Cybergenetics :: Determining sequence length or content in zero, one, and two dimensions
    in zero one and two dimensions Human Mutation 19 4 2002 Downloads Full Article Abstract High throughput assays are essential for the practical application of mutation detection in medicine and research Moreover such assays should produce informative data of high quality that have a low error rate and a low cost Unfortunately this is not currently the case Instead we typically witness legions of people reviewing imperfect data at astronomical expense yielding uncertain results To address this problem for the past decade we have been developing methods that exploit the inherent quantitative nature of DNA experiments By generating high quality data careful DNA signal quantification permits robust analysis for determining true alleles and certainty measures We will explore several assays and methods In a one dimensional readout short tandem repeat STR data display interesting artifacts Even with high quality data PCR artifacts such as stutter and relative amplification can confound correct or automated scoring However by appropriate mathematical analysis these artifacts can be essentially removed from the data The result is fully automated data scoring quality assessment and new types of DNA analysis These approaches enable the accurate analysis of pooled DNA samples for both genetic and forensic applications On

    Original URL path: http://www.cybgen.com/information/publication/2002/HM/Perlin-Szabady-Determining-sequence-length-or-content-in-zero-one-and-two-dimensions/page.shtml (2016-02-12)
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  • Cybergenetics :: Linear Mixture Analysis: a Mathematical Approach to Resolving Mixed DNA Samples
    Journal of Forensic Sciences 46 6 pp 1372 77 2001 Downloads Download Full Manuscript Full Article Abstract With the advent of PCR based STR typing systems mixed samples can be separated into their individual DNA profiles Quantitative peak information can help in this analysis However despite such advances forensic mixture analysis still remains a laborious art with the high cost and effort often precluding timely reporting We introduce here a

    Original URL path: http://www.cybgen.com/information/publication/2001/JFS/Perlin-Szabady-Linear-mixture-analysis-a-mathematical-approach-to-resolving-mixed-DNA-samples/page.shtml (2016-02-12)
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  • Cybergenetics :: Using quality measures to facilitate allele calling in high-throughput genotyping
    Stefánsson K and Gulcher J Using quality measures to facilitate allele calling in high throughput genotyping Genome Research 9 10 1002 1012 1999 Downloads Full Article Abstract Currently the main limitation in high throughput microsatellite genotyping is the required manual editing of allele calls Even though programs for automated allele calling have been available for several years they have limited capability because accurate data could only be assured by manual inspection of the electropherograms for confirmation Here we describe the development of a parametric approach to allele call quality control that eliminates much of the time required for manual editing of the data This approach was implemented in an editing tool Decode GT that works downstream of the allele calling program TrueAllele TA Decode GT reads the output data from TA displays the underlying electropherograms for the genotypes and sorts the allele calls into three categories good bad and ambiguous It discards the bad calls accepts the good calls and suggests that the user inspect the ambiguous calls thereby reducing dependence on manual editing For the categorization we use the following parameters 1 the quality value for each allele call from TrueAllele 2 the peak height of the alleles and

    Original URL path: http://www.cybgen.com/information/publication/1999/GR/Palsson-Gulcher-Using-quality-measures-to-facilitate-allele-calling-in-high-throughput-genotyping/page.shtml (2016-02-12)
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  • Cybergenetics :: Genotyping of pooled microsatellite markers by combinatorial optimization techniques
    optimization techniques Discrete Applied Math 88 1 3 291 314 1998 Downloads Full Article Abstract An important everyday task for geneticists and molecular biologists is that of isolating and analyzing some particular DNA regions markers each drawn from a limited and known set of possible values alleles This procedure is called genotyping and is based on DNA amplification and size separation In order to increase the throughput of genotyping recently

    Original URL path: http://www.cybgen.com/information/publication/1998/DAM/Lancia-Perlin-Genotyping-of-pooled-microsatellite-markers-by-combinatorial-optimization-techniques/page.shtml (2016-02-12)
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  • Cybergenetics :: Toward fully automated genotyping: genotyping microsatellite markers by deconvolution
    with average densities of 2 9 cM and 0 35 cM respectively These genetic maps are crucial for mapping both Mendelian and complex traits and are useful in clinical genetic diagnosis Current maps are largely comprised of abundant easily assayed and highly polymorphic PCR based microsatellite markers primarily dinucleotide CA n repeats One key limitation of these length polymorphisms is the PCR stutter or slippage artifact that introduces additional stutter

    Original URL path: http://www.cybgen.com/information/publication/1995/AJHG/Perlin-Lancia-Ng-Toward-fully-automated-genotyping-genotyping-microsatellite-markers-by-deconvolution/page.shtml (2016-02-12)
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  • Cybergenetics :: Toward fully automated genotyping: allele assignment, pedigree construction, phase determination, and recombination detection in Duchenne muscular dystrophy
    phase determination and recombination detection in Duchenne muscular dystrophy American Journal of Human Genetics 55 4 777 787 1994 Downloads Full Article Abstract Human genetic maps have made quantum leaps in the past few years because of the characterization of 2 000 CA dinucleotide repeat loci these PCR based markers offer extraordinarily high PIC and within the next year their density is expected to reach intervals of a few centimorgans per marker These new genetic maps open new avenues for disease gene research including large scale genotyping for both simple and complex disease loci However the allele patterns of many dinucleotide repeat loci can be complex and difficult to interpret with genotyping errors a recognized problem Furthermore the possibility of genotyping individuals at hundreds or thousands of polymorphic loci requires improvements in data handling and analysis The automation of genotyping and analysis of computer derived haplotypes would remove many of the barriers preventing optimal use of dense and informative dinucleotide genetic maps Toward this end we have automated the allele identification genotyping phase determinations and inheritance consistency checks generated by four CA repeats within the 2 5 Mbp 10 cM X linked dystrophin gene using fluorescein labeled multiplexed PCR products

    Original URL path: http://www.cybgen.com/information/publication/1994/AJHG/Perlin-Hoffman-Toward-fully-automated-genotyping-allele-assignment-pedigree-construction-phase-determination-and-recombination-detection-in-Duchenne-muscular-dystrophy/page.shtml (2016-02-12)
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