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Theories and Applications for Sequencing Randomly Selected Clones

Michael C. Wendl, Marco A. Marra, LaDeana W. Hillier, Asif T. Chinwalla, Richard K. Wilson, Robert H. Waterston
2001 Genome Research  
Theory is developed for the process of sequencing randomly selected large-insert clones. Genome size, library depth, clone size, and clone distribution are considered relevant properties and perfect overlap detection for contig assembly is assumed. Genome-specific and nonrandom effects are neglected. Order of magnitude analysis indicates library depth is of secondary importance compared to the other variables, especially as clone size diminishes. In such cases, the well-known Poisson coverage
more » ... w is a good approximation. Parameters derived from these models are used to examine performance for the specific case of sequencing random human BAC clones. We compare coverage and redundancy rates for libraries possessing uniform and nonuniform clone distributions. Results are measured against data from map-based human-chromosome-2 sequencing. We conclude that the map-based approach outperforms random clone sequencing, except early in a project. However, simultaneous use of both strategies can be beneficial if a performance-based estimate for halting random clone sequencing is made. Results further show that the random approach yields maximum effectiveness using nonbiased rather than biased libraries.
doi:10.1101/gr.133901 fatcat:l2lzoa2smfe4nb7stxvcxnfd2e

Histidine Protects Against Zinc and Nickel Toxicity in Caenorhabditis elegans

John T. Murphy, Janelle J. Bruinsma, Daniel L. Schneider, Sara Collier, James Guthrie, Asif Chinwalla, J. David Robertson, Elaine R. Mardis, Kerry Kornfeld, Kaveh Ashrafi
2011 PLoS Genetics  
Statistical analysis To compare two sets of values, we used the Student's T Test when the number of samples was greater than two and the Fisher's Exact T Test when there were two samples (Microsoft Excel  ...  The mutation is a C to T transition in the wobble position of codon 296 that changes a tryptophan to a stop codon ( Figure 3B ).  ... 
doi:10.1371/journal.pgen.1002013 pmid:21455490 pmcid:PMC3063764 fatcat:vrovhupt2ra27dydffp4hzdnam

Design and implementation of a generalized laboratory data model

Michael C Wendl, Scott Smith, Craig S Pohl, David J Dooling, Asif T Chinwalla, Kevin Crouse, Todd Hepler, Shin Leong, Lynn Carmichael, Mike Nhan, Benjamin J Oberkfell, Elaine R Mardis (+2 others)
2007 BMC Bioinformatics  
Investigators in the biological sciences continue to exploit laboratory automation methods and have dramatically increased the rates at which they can generate data. In many environments, the methods themselves also evolve in a rapid and fluid manner. These observations point to the importance of robust information management systems in the modern laboratory. Designing and implementing such systems is non-trivial and it appears that in many cases a database project ultimately proves
more » ... e. Results: We describe a general modeling framework for laboratory data and its implementation as an information management system. The model utilizes several abstraction techniques, focusing especially on the concepts of inheritance and meta-data. Traditional approaches commingle eventoriented data with regular entity data in ad hoc ways. Instead, we define distinct regular entity and event schemas, but fully integrate these via a standardized interface. The design allows straightforward definition of a "processing pipeline" as a sequence of events, obviating the need for separate workflow management systems. A layer above the event-oriented schema integrates events into a workflow by defining "processing directives", which act as automated project managers of items in the system. Directives can be added or modified in an almost trivial fashion, i.e., without the need for schema modification or re-certification of applications. Association between regular entities and events is managed via simple "many-to-many" relationships. We describe the programming interface, as well as techniques for handling input/output, process control, and state transitions. Conclusion: The implementation described here has served as the Washington University Genome Sequencing Center's primary information system for several years. It handles all transactions underlying a throughput rate of about 9 million sequencing reactions of various kinds per month and has handily weathered a number of major pipeline reconfigurations. The basic data model can be readily adapted to other high-volume processing environments.
doi:10.1186/1471-2105-8-362 pmid:17897463 pmcid:PMC2194795 fatcat:xthtg72eynb23i57n3yndsfasa

Mapping copy number variation by population-scale genome sequencing

Ryan E. Mills, Klaudia Walter, Chip Stewart, Robert E. Handsaker, Ken Chen, Can Alkan, Alexej Abyzov, Seungtai Chris Yoon, Kai Ye, R. Keira Cheetham, Asif Chinwalla, Donald F. Conrad (+45 others)
2011 Nature  
All rights reserved ©2011 F E B R U A R Y 2 0 1 1 | V O L 4 7 0 | N A T U R E | 6 3Macmillan Publishers Limited. All rights reserved ©2011  ... 
doi:10.1038/nature09708 pmid:21293372 pmcid:PMC3077050 fatcat:zuhvie54ubfn5emfirigmni7be

The DNA sequence of human chromosome 7

LaDeana W. Hillier, Robert S. Fulton, Lucinda A. Fulton, Tina A. Graves, Kymberlie H. Pepin, Caryn Wagner-McPherson, Dan Layman, Jason Maas, Sara Jaeger, Rebecca Walker, Kristine Wylie, Mandeep Sekhon (+95 others)
2003 Nature  
200 kb and 38 megabases (Mb), respectively, with the latter residing on 7q and containing the cystic fibrosis gene, the ST7 tumour suppressor gene 10 , olfactory and taste receptors 11, 12 , and the T-cell  ... 
doi:10.1038/nature01782 pmid:12853948 fatcat:fv2z3hsqnndx5fwjf4e2um5ija

Genome analysis of the platypus reveals unique signatures of evolution

Wesley C. Warren, LaDeana W. Hillier, Jennifer A. Marshall Graves, Ewan Birney, Chris P. Ponting, Frank Grützner, Katherine Belov, Webb Miller, Laura Clarke, Asif T. Chinwalla, Shiaw-Pyng Yang, Andreas Heger (+90 others)
2008 Nature  
A list of authors and their affiliations appears at the end of the paper We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic
more » ... tions. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation.
doi:10.1038/nature06936 pmid:18464734 pmcid:PMC2803040 fatcat:alnex64ie5hnfbrm5ctzgs6vdu

Generation and annotation of the DNA sequences of human chromosomes 2 and 4

LaDeana W. Hillier, Tina A. Graves, Robert S. Fulton, Lucinda A. Fulton, Kymberlie H. Pepin, Patrick Minx, Caryn Wagner-McPherson, Dan Layman, Kristine Wylie, Mandeep Sekhon, Michael C. Becker, Ginger A. Fewell (+110 others)
2005 Nature  
We thank T. Hubbard, J. Ashurst, J. Gilbert and S. Keenan for Ensembl pipeline assistance.  ...  In contrast, the region upstream of ZFHX1B is enriched in conserved segments in T. rubripes as well as in dog and mouse.  ... 
doi:10.1038/nature03466 pmid:15815621 fatcat:bb3aowy35ngbziogaqliqsyqmm

Page 34 of None Vol. 37, Issue 2 [page]

1995 None  
We thank Chong Oon Park and Asif Chinwalla for excellent technical assistance. This work was supported by National Institute of Neurological Disorders and Stroke Grant NS-21045.  ...  J., T. S. Park, E. R. Gonzales, and J. M. Gidday. Adenosine and cerebrovascular hyperemia during insulin-induced  ... 

Comparative and demographic analysis of orang-utan genomes

Devin P. Locke, LaDeana W. Hillier, Wesley C. Warren, Kim C. Worley, Lynne V. Nazareth, Donna M. Muzny, Shiaw-Pyng Yang, Zhengyuan Wang, Asif T. Chinwalla, Pat Minx, Makedonka Mitreva, Lisa Cook (+89 others)
2011 Nature  
doi:10.1038/nature09687 pmid:21270892 pmcid:PMC3060778 fatcat:uochv4fxkba7dcgdlszsavjlim

RNA-Seq 2G: Online Analysis Of Differential Gene Expression With Comprehensive Options Of Statistical Methods [article]

Zhe Zhang, Yuanchao Zhang, Perry Evans, Asif Chinwalla, Deanne Taylor
2017 bioRxiv   pre-print
For example, while the ranges of p values differed by over 2 orders between Student's t test and SAM, their p value . CC-BY 4.0 International license peer-reviewed) is the author/funder.  ...  Speed Paired Logged Norm Distribution Test R Function StudentsT Fast Yes Yes No Normal Student's t test, equal variance TDist {stats} limma Fast Yes Yes No Normal Empirical Bayes  ... 
doi:10.1101/122747 fatcat:ymumrmnto5ew3bpgrksdws53pe

A map of human genome variation from population-scale sequencing

Richard M. Durbin, David L. Altshuler, Richard M. Durbin, Gonçalo R. Abecasis, David R. Bentley, Aravinda Chakravarti, Andrew G. Clark, Francis S. Collins, Francisco M. De La Vega, Peter Donnelly, Michael Egholm, Paul Flicek (+540 others)
2010 Nature  
Birney (European Bioinformatics Institute); T Hunkapiller and Q. Doan (Life Technologies) for their advice and coordination; N. Kälin (German Aerospace Center [DLR]); F.  ... 
doi:10.1038/nature09534 pmid:20981092 pmcid:PMC3042601 fatcat:52pv24sjnna5jmy4qvvgwwdo2u

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

Roger McLendon, Allan Friedman, Darrell Bigner, Erwin G. Van Meir, Daniel J. Brat, Gena M. Mastrogianakis, Jeffrey J. Olson, Tom Mikkelsen, Norman Lehman, Ken Aldape, W. K. Alfred Yung, Oliver Bogler (+219 others)
2008 Nature  
Human cancer cells typically harbour multiple chromosomal aberrations, nucleotide substitutions and epigenetic modifications that drive malignant transformation. The Cancer Genome Atlas (TCGA) pilot project aims to assess the value of large-scale multi-dimensional analysis of these molecular characteristics in human cancer and to provide the data rapidly to the research community. Here we report the interim integrative analysis of DNA copy number, gene expression and DNA methylation aberrations
more » ... in 206 glioblastomas-the most common type of primary adult brain cancer-and nucleotide sequence aberrations in 91 of the 206 glioblastomas. This analysis provides new insights into the roles of ERBB2, NF1 and TP53, uncovers frequent mutations of the phosphatidylinositol-3-OH kinase regulatory subunit gene PIK3R1, and provides a network view of the pathways altered in the development of glioblastoma. Furthermore, integration of mutation, DNA methylation and clinical treatment data reveals a link between MGMT promoter methylation and a hypermutator phenotype consequent to mismatch repair deficiency in treated glioblastomas, an observation with potential clinical implications. Together, these findings establish the feasibility and power of TCGA, demonstrating that it can rapidly expand knowledge of the molecular basis of cancer.
doi:10.1038/nature07385 pmid:18772890 pmcid:PMC2671642 fatcat:kqk3jmxow5bt5kp6pviaa7miui

A physical map of the chicken genome

John W. Wallis, Jan Aerts, Martien A. M. Groenen, Richard P. M. A. Crooijmans, Dan Layman, Tina A. Graves, Debra E. Scheer, Colin Kremitzki, Mary J. Fedele, Nancy K. Mudd, Marco Cardenas, Jamey Higginbotham (+26 others)
2004 Nature  
Hemmatian, J. van der Poel, T. Veenendaal and R. Dijkhof for their help fingerprinting the WAG BAC library and, along with J. Price and C.  ... 
doi:10.1038/nature03030 pmid:15592415 fatcat:mhpmmdobqvb7jopflr7sl3nzju

Lane tracking software for four-color fluorescence-based electrophoretic gel images

M L Cooper, D R Maffitt, J D Parsons, L Hillier, D J States
1996 Genome Research  
The authors would also like to acknowledge the review of the code by Darren Platt and Asif Chinwalla, the readings of this manuscript by Elaine Mardis, and the direction of Richard Wilson and Robert Waterston  ...  Lane Behavior Models I I...oad Filter Images T (Tr~k I.  ...  Image i i (Identify Gel Charaderistics ) I Lorm Vertically Integrated Ga~ file Over C~rent Windowfl I Locate Lanes (Maxima) And Edi~ Locations With Previous Lane / Locations ~ fl i T  ... 
doi:10.1101/gr.6.11.1110 pmid:8938435 fatcat:wutshwyxfzdyxbg7xsm5c23cuu

Roughness penalties on finite domains

J.A. O'Sullivan
1995 IEEE Transactions on Image Processing  
ACKNOWLEDGMENT Some simulations were run by Asif Chinwalla, a graduate student. The data for the radar images were obtained from McDonnell Douglas.  ...  Assume that x(t) is nonnegative and integrable.  ...  Let x(t) E L1(R) be a probability density function to be es?imated.  ... 
doi:10.1109/83.413170 pmid:18292022 fatcat:fk5u5hmh7bfmpe7smjoryobt74
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