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HUMAN MUTATION 0,1^8,2007 METHODS Multiplex PCR-Based Real-Time Invader Assay (mPCR-RETINA): A Novel SNP-Based Method for Detecting Allelic Asymmetries Within Copy Number Variation Regions

by Yozo Ohnishi, Yusuke Nakamura
"... We report the development of a real-time Invader assay combined with multiplex PCR (mPCR-RETINA), an SNP-based approach that can measure the allelic ratio in copy number variation (CNV) regions of a genome. RETINA monitors the real-time fluorescence intensity of each allele during the Invader assay ..."
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We report the development of a real-time Invader assay combined with multiplex PCR (mPCR-RETINA), an SNP-based approach that can measure the allelic ratio in copy number variation (CNV) regions of a genome. RETINA monitors the real-time fluorescence intensity of each allele during the Invader assay

Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees.

by Koichiro Tamura , Masatoshi Nei - Mol Biol Evol , 1993
"... Examining the pattern of nucleotide substitution for the control region of mitochondrial DNA ( mtDNA ) in humans and chimpanzees, we developed a new mathematical method for estimating the number of transitional and transversional substitutions per site, as well as the total number of nucleotide sub ..."
Abstract - Cited by 925 (4 self) - Add to MetaCart
Examining the pattern of nucleotide substitution for the control region of mitochondrial DNA ( mtDNA ) in humans and chimpanzees, we developed a new mathematical method for estimating the number of transitional and transversional substitutions per site, as well as the total number of nucleotide

Analysis of relative gene expression data using real-time quantitative

by Kenneth J. Livak, Thomas D. Schmittgen - PCR and 2 ���CT method. Methods 25 , 2001
"... of the target gene relative to some reference group The two most commonly used methods to analyze data from real-time, quantitative PCR experiments are absolute quantifica-such as an untreated control or a sample at time zero tion and relative quantification. Absolute quantification deter- in a time ..."
Abstract - Cited by 2666 (6 self) - Add to MetaCart
variations of the 2 ���CT method that may be script copy number and reporting the relative change useful in the analysis of real-time, quantitative PCR data. � 2001 in gene expression will suffice. For example, stating

The Cache Performance and Optimizations of Blocked Algorithms

by Monica S. Lam, Edward E. Rothberg, Michael E. Wolf - In Proceedings of the Fourth International Conference on Architectural Support for Programming Languages and Operating Systems , 1991
"... Blocking is a well-known optimization technique for improving the effectiveness of memory hierarchies. Instead of operating on entire rows or columns of an array, blocked algorithms operate on submatrices or blocks, so that data loaded into the faster levels of the memory hierarchy are reused. This ..."
Abstract - Cited by 574 (5 self) - Add to MetaCart
is highly sensitive to the stride of data accesses and the size of the blocks, and can cause wide variations in machine performance for different matrix sizes. The conventional wisdom of trying to use the entire cache, or even a fixed fraction of the cache, is incorrect. If a fixed block size is used for a

The diploid genome sequence of an individual human

by Samuel Levy, Granger Sutton, Pauline C. Ng, Lars Feuk, Aaron L. Halpern, Brian P. Walenz, Nelson Axelrod, Jiaqi Huang, Ewen F. Kirkness, Gennady Denisov, Yuan Lin, Jeffrey R. Macdonald, Andy Wing, Chun Pang, Mary Shago, Timothy B. Stockwell, Alexia Tsiamouri, Vineet Bafna, Vikas Bansal, Saul A. Kravitz, Dana A. Busam, Karen Y. Beeson, Tina C. Mcintosh, Karin A. Remington, Josep F. Abril, John Gill, Jon Borman, Yu-hui Rogers, Marvin E. Frazier, Stephen W. Scherer, Robert L. Strausberg, J. Craig Venter - PLoS Biol
"... Presented here is a genome sequence of an individual human. It was produced from;32 million random DNA fragments, sequenced by Sanger dideoxy technology and assembled into 4,528 scaffolds, comprising 2,810 million bases (Mb) of contiguous sequence with approximately 7.5-fold coverage for any given r ..."
Abstract - Cited by 293 (6 self) - Add to MetaCart
inversions, as well as numerous segmental duplications and copy number variation regions. Non-SNP DNA variation accounts for 22 % of all events identified in the donor, however they involve 74 % of all variant bases. This suggests an important role for non-SNP genetic alterations in defining the diploid

Bioprospector: Discovering Conserved Dna Motifs In Upstream Regulatory Regions Of Co-Expressed Genes

by X. Liu, D. L. Brutlag, J. S. Liu - Pac. Symp. Biocomput , 2001
"... ms. For a copy of the program and documentation for UNIX systems, please contact xliu@smi.stanford.edu. 1 Introduction Over the last ten years, genomic sequencing has started in over 600 organisms, and over 50 complete genomes are sequenced. The DNA microarray technology permits the measurement o ..."
Abstract - Cited by 354 (23 self) - Add to MetaCart
ms. For a copy of the program and documentation for UNIX systems, please contact xliu@smi.stanford.edu. 1 Introduction Over the last ten years, genomic sequencing has started in over 600 organisms, and over 50 complete genomes are sequenced. The DNA microarray technology permits the measurement

Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers.

by T D Kocher , W K Thomas , A Meyer , S V Edwards , S Paabo , F X Villablancatt , A C Wilson - Proc. Natl. Acad. Sci. USA , 1989
"... ABSTRACT With a standard set of primers directed toward conserved regions, we have used the polymerase chain reaction to amplify homologous segments of mtDNA from more than 100 animal species, including mammals, birds, amphibians, fishes, and some invertebrates. Amplification and direct sequencing ..."
Abstract - Cited by 310 (3 self) - Add to MetaCart
ABSTRACT With a standard set of primers directed toward conserved regions, we have used the polymerase chain reaction to amplify homologous segments of mtDNA from more than 100 animal species, including mammals, birds, amphibians, fishes, and some invertebrates. Amplification and direct sequencing

New Copy Number Variations in Schizophrenia

by Chiara Magri, Emilio Sacchetti, Michele Traversa, Paolo Valsecchi, Rita Gardella, Ra Minelli, Massimo Gennarelli, Sergio Barlati , 2010
"... Genome-wide screenings for copy number variations (CNVs) in patients with schizophrenia have demonstrated the presence of several CNVs that increase the risk of developing the disease and a growing number of large rare CNVs; the contribution of these rare CNVs to schizophrenia remains unknown. Using ..."
Abstract - Cited by 9 (0 self) - Add to MetaCart
Genome-wide screenings for copy number variations (CNVs) in patients with schizophrenia have demonstrated the presence of several CNVs that increase the risk of developing the disease and a growing number of large rare CNVs; the contribution of these rare CNVs to schizophrenia remains unknown

A Hidden Markov Model approach to variation among sites in rate of evolution.

by Joseph Felsenstein , Gary A Churchill , Joe Felsenstein - Mol Biol Evol , 1996
"... Abstract The method of hidden Markov models is used to allow for unequal and unknown evolutionary rates at different sites in molecular sequences. Rates of evolution at different sites are assumed to be drawn from a set of possible rates, with a finite number of possibilities. The overall likelihoo ..."
Abstract - Cited by 244 (1 self) - Add to MetaCart
Abstract The method of hidden Markov models is used to allow for unequal and unknown evolutionary rates at different sites in molecular sequences. Rates of evolution at different sites are assumed to be drawn from a set of possible rates, with a finite number of possibilities. The overall

HW: Whole Genome Distribution and Ethnic Differentiation of Copy Number Variation in Caucasian and Asian Populations. PLoS One 2009

by Jian Li, Tielin Yang, Liang Wang, Han Yan, Yinping Zhang, Yan Guo, Feng Pan, Yumei Peng, Qi Zhou, Lina He, Xuezhen Zhu, Hongyi Deng, Shawn Levy, Christopher J, Betty M. Drees, James J. Hamilton, Robert R. Recker, Jing Cheng, Hong-wen Deng - He L, Zhu X, Deng H, Levy S, Papasian CJ, Drees BM, Hamilton JJ, Recker RR, Cheng J, Deng
"... Although copy number variation (CNV) has recently received much attention as a form of structure variation within the human genome, knowledge is still inadequate on fundamental CNV characteristics such as occurrence rate, genomic distribution and ethnic differentiation. In the present study, we used ..."
Abstract - Cited by 6 (1 self) - Add to MetaCart
individuals were identified, with a mean length of 296 kb. Among these CNVs, 190 had frequencies greater than 1 % in at least one ethnic group, and 109 showed significant ethnic differences in frequencies (p,0.01). After merging overlapping CNVs, 1135 copy number variation regions (CNVRs), covering
Results 1 - 10 of 6,026