Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Paper: "Rapid whole-genome mutational profiling using next-gen technolgies"

    Interesting paper out in Genome Research comparing resequencing performance using the three leading platforms.

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

    Douglas R. Smith1,7,9, Aaron R. Quinlan2,7, Heather E. Peckham3,7, Kathryn Makowsky1, Wei Tao1, Betty Woolf1, Lei Shen1, William F. Donahue1, Nadeem Tusneem1, Michael P. Stromberg2, Donald A. Stewart2, Lu Zhang2, Swati S. Ranade3, Jason B. Warner3, Clarence C. Lee3, Brittney E. Coleman3, Zheng Zhang3,4, Stephen F. McLaughlin3, Joel A. Malek3, Jon M. Sorenson3,4, Alan P. Blanchard3, Jarrod Chapman5, David Hillman5, Feng Chen5, Daniel S. Rokhsar5, Kevin J. McKernan3, Thomas W. Jeffries6, Gabor T. Marth2,9, and Paul M. Richardson5,8,9

    1 Agencourt Bioscience Corporation, Beverly, Massachusetts 01915, USA; 2 Boston College Biology Department, Higgins Hall, Chestnut Hill, Massachusetts 02467, USA; 3 Applied Biosystems, Beverly, Massachusetts 01915, USA; 4 Appplied Biosystems, Foster City, California 94404, USA; 5 US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA; 6 Institute for Microbial and Biochemical Technology, US Forest Products Laboratory, Madison, Wisconsin 53726, USA

    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.

  • #2
    in fact i first saw this presented at a meeting by Gabor about 1 year ago - which implies the data are very old. Gabor is a bit more circumspect about the meaning of the results in his associated genomeweb interview. Its not the only paper to come out comparing the state of platfoms over a year earlier. I just dont think the analsys->submission-<review and publication cycle is fast enough to keep pace with the rate of development of the technologies.

    Comment


    • #3
      Originally posted by clivey View Post
      I just dont think the analsys->submission-<review and publication cycle is fast enough to keep pace with the rate of development of the technologies.
      Good job we have SEQanswers!


      Thus, this approach could help accelerate the
      development of novel organisms for bioenergy and biotechnol-
      ogy applications as well as facilitate traditional forward and re-
      verse genetic screens.
      Last edited by dan; 09-24-2008, 05:53 AM. Reason: Added a nice quote from the paper
      Homepage: Dan Bolser
      MetaBase the database of biological databases.

      Comment


      • #4
        SNP discovery

        Thanks for an encouraging paper. I have been setting up SNP discovery with 454 sequencing and I get a lot of false-positives: the validated approach used will help me identify sensitive steps for accuracy improvement. Is anyone else working in this area?

        Comment


        • #5
          Originally posted by Pathfinder View Post
          Thanks for an encouraging paper. I have been setting up SNP discovery with 454 sequencing and I get a lot of false-positives: the validated approach used will help me identify sensitive steps for accuracy improvement. Is anyone else working in this area?
          Not with 454, but rather the Illumina GA. In our first trial project we encountered many FPs as well.

          Comment


          • #6
            We are now setting up a small trial run with higher coverage and known samples to improve detection. Will this work?

            Comment


            • #7
              Originally posted by acnoll View Post
              Not with 454, but rather the Illumina GA. In our first trial project we encountered many FPs as well.
              recalibrate the base scores. use a snp-caller that understands them.

              Comment


              • #8
                I think you´re right. We already have the results and are reprocessing the base calling with PyroBayes. Do you know of other efficient basecalling softwares?

                Comment

                Latest Articles

                Collapse

                • seqadmin
                  Best Practices for Single-Cell Sequencing Analysis
                  by seqadmin



                  While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
                  06-06-2024, 07:15 AM
                • seqadmin
                  Latest Developments in Precision Medicine
                  by seqadmin



                  Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

                  Somatic Genomics
                  “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
                  05-24-2024, 01:16 PM

                ad_right_rmr

                Collapse

                News

                Collapse

                Topics Statistics Last Post
                Started by seqadmin, 06-21-2024, 07:49 AM
                0 responses
                14 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 06-20-2024, 07:23 AM
                0 responses
                14 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 06-17-2024, 06:54 AM
                0 responses
                16 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 06-14-2024, 07:24 AM
                0 responses
                25 views
                0 likes
                Last Post seqadmin  
                Working...
                X