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Rapid whole-genome mutational profiling using next-generation sequencing technologies.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Smith, Douglas R. Quinlan, Aaron R. Peckham, Heather E. Makowsky, Kathryn Tao, Wei Woolf, Betty Shen, Lei Donahue, William F. Tusneem, Nadeem Stromberg, Michael P. Stewart, Donald A. Zhang, Lu Ranade, Swati S. Warner, Jason B. Lee, Clarence C. Coleman, Brittney E. Zhang, Zheng McLaughlin, Stephen F. Malek, Joel A. Sorenson, Jon M. Blanchard, Alan P. Chapman, Jarrod Hillman, David Chen, Feng Rokhsar, Daniel S. McKernan, Kevin J. Jeffries, Thomas W. Marth, Gabor T. Richardson, Paul M.
Description	Country affiliation: United States Author Affiliation: Smith DR ( Agencourt Bioscience Corporation, Beverly, Massachusetts 01915, USA. douglas.smith@agencourt.com)
Abstract	Forward genetic mutational studies, adaptive evolution, and phenotypic screening are powerful tools for creating new variant organisms with desirable traits. However, mutations generated in the process cannot be easily identified with traditional genetic tools. We show that new high-throughput, massively parallel sequencing technologies can completely and accurately characterize a mutant genome relative to a previously sequenced parental (reference) strain. We studied a mutant strain of Pichia stipitis, a yeast capable of converting xylose to ethanol. This unusually efficient mutant strain was developed through repeated rounds of chemical mutagenesis, strain selection, transformation, and genetic manipulation over a period of seven years. We resequenced this strain on three different sequencing platforms. Surprisingly, we found fewer than a dozen mutations in open reading frames. All three sequencing technologies were able to identify each single nucleotide mutation given at least 10-15-fold nominal sequence coverage. Our results show that detecting mutations in evolved and engineered organisms is rapid and cost-effective at the whole-genome level using new sequencing technologies. Identification of specific mutations in strains with altered phenotypes will add insight into specific gene functions and guide further metabolic engineering efforts.
File Format	HTM / HTML
ISSN	10889051
e-ISSN	15495469
DOI	10.1101/gr.077776.108
Journal	Genome Research
Issue Number	10
Volume Number	18
Language	English
Publisher	Cold Spring Harbor Laboratory Press
Publisher Date	2008-10-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Discipline Genetics Discipline Genomics Dna Mutational Analysis Genome, Fungal Mutation Pichia Genetics Sequence Alignment Sequence Analysis, Dna
Content Type	Text
Resource Type	Article
Subject	Genetics Genetics (clinical)

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
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9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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