Searching journal content for articles similar to Li et al. 19 (6): 1124.

Displaying results 1-10 of 28

For checked items

view abstracts
download to citation manager

Select this article
Method: Detection of long repeat expansions from PCR-free whole-genome sequence data
- Egor Dolzhenko,
- Joke J.F.A. van Vugt,
- Richard J. Shaw,
- Mitchell A. Bekritsky,
- Marka van Blitterswijk,
- Giuseppe Narzisi,
- Subramanian S. Ajay,
- Vani Rajan,
- Bryan R. Lajoie,
- Nathan H. Johnson,
- Zoya Kingsbury,
- Sean J. Humphray,
- Raymond D. Schellevis,
- William J. Brands,
- Matt Baker,
- Rosa Rademakers,
- Maarten Kooyman,
- Gijs H.P. Tazelaar,
- Michael A. van Es,
- Russell McLaughlin,
- William Sproviero,
- Aleksey Shatunov,
- Ashley Jones,
- Ahmad Al Khleifat,
- Alan Pittman,
- Sarah Morgan,
- Orla Hardiman,
- Ammar Al-Chalabi,
- Chris Shaw,
- Bradley Smith,
- Edmund J. Neo,
- Karen Morrison,
- Pamela J. Shaw,
- Catherine Reeves,
- Lara Winterkorn,
- Nancy S. Wexler,
- The US–Venezuela Collaborative Research Group,
- David E. Housman,
- Christopher W. Ng,
- Alina L. Li,
- Ryan J. Taft,
- Leonard H. van den Berg,
- David R. Bentley,
- Jan H. Veldink,
- and Michael A. Eberle
Genome Res. November 2017 27: 1895-1903; Published in Advance September 8, 2017, doi:10.1101/gr.225672.117
...to generation, pathogenic repeats may show little or no linkage disequilibrium with the surrounding variants. Thus, association studies based solely on SNPs may be blind to these highly polymorphic risk alleles. An important result highlighted in Figures 3 and 4 is that ExpansionHunter is able to size both...
OPEN ACCESS ARTICLE
Select this article
Method: Detection and phasing of single base de novo mutations in biopsies from human in vitro fertilized embryos by advanced whole-genome sequencing
- Brock A. Peters,
- Bahram G. Kermani,
- Oleg Alferov,
- Misha R. Agarwal,
- Mark A. McElwain,
- Natali Gulbahce,
- Daniel M. Hayden,
- Y. Tom Tang,
- Rebecca Yu Zhang,
- Rick Tearle,
- Birgit Crain,
- Renata Prates,
- Alan Berkeley,
- Santiago Munné,
- and Radoje Drmanac
Genome Res. March 2015 25: 426-434; Published in Advance February 11, 2015, doi:10.1101/gr.181255.114
...pools of DNA are unlikely to repeatedly occur exclusively on one parental chromosome. By linking these SNVs to the surrounding heterozygous SNPs, one can assess whether the variant is in phase with one or both haplotypes. Those SNVs that are found to be in phase with both haplotypes, an impossibility...
OPEN ACCESS ARTICLE
Select this article
Resource: Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads
- Rei Kajitani,
- Kouta Toshimoto,
- Hideki Noguchi,
- Atsushi Toyoda,
- Yoshitoshi Ogura,
- Miki Okuno,
- Mitsuru Yabana,
- Masayuki Harada,
- Eiji Nagayasu,
- Haruhiko Maruyama,
- Yuji Kohara,
- Asao Fujiyama,
- Tetsuya Hayashi,
- and Takehiko Itoh
Genome Res. August 2014 24: 1384-1395; Published in Advance April 22, 2014, doi:10.1101/gr.170720.113
...of the scaffolds according to the numbers of mismatches (SNPs) and indels (<5 bp) reported in the GAGE evaluations of the C. elegans data in the absence of simulated heterozygosity (Table 2). The raw heterozygosity of the C. elegans was estimated to be 1.85 3 103%, and the expected number of variants...
OPEN ACCESS ARTICLE
Select this article
Resource: Whole-genome resequencing allows detection of many rare LINE-1 insertion alleles in humans
- Adam D. Ewing and
- Haig H. Kazazian, Jr.
Genome Res. June 2011 21: 985-990; Published in Advance October 27, 2010, doi:10.1101/gr.114777.110
...variants on a large scale using array-based technologies in order to identify genotype-phenotype associations, especially in complex human genetic diseases. We believe that RIPs should be considered alongside SNPs and CNVs in studies of human genomic variation. Methods Data sources Sequence data for 307...
Select this article
Research: Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolution
- Hoon Kim,
- Siyuan Zheng,
- Seyed S. Amini,
- Selene M. Virk,
- Tom Mikkelsen,
- Daniel J. Brat,
- Jonna Grimsby,
- Carrie Sougnez,
- Florian Muller,
- Jian Hu,
- Andrew E. Sloan,
- Mark L. Cohen,
- Erwin G. Van Meir,
- Lisa Scarpace,
- Peter W. Laird,
- John N. Weinstein,
- Eric S. Lander,
- Stacey Gabriel,
- Gad Getz,
- Matthew Meyerson,
- Lynda Chin,
- Jill S. Barnholtz-Sloan,
- and Roel G.W. Verhaak
Genome Res. March 2015 25: 316-327; Published in Advance February 3, 2015, doi:10.1101/gr.180612.114
...to that base, of exome and validation sequencingwere highly correlated (Pearson correlation = 0.93) (Supplemental Fig. 4). Copy number and LOH analysis For cohort II, Affymetrix SNP 6.0 arrays were preprocessed by either aroma.affymetrix (Bengtsson et al. 2009) or CopyNumberInferencePipeline in Gene...
Select this article
Methods: Rapid whole-genome mutational profiling using next-generation sequencing technologies
- Douglas R. Smith,
- Aaron R. Quinlan,
- Heather E. Peckham,
- Kathryn Makowsky,
- Wei Tao,
- Betty Woolf,
- Lei Shen,
- William F. Donahue,
- Nadeem Tusneem,
- Michael P. Stromberg,
- Donald A. Stewart,
- Lu Zhang,
- Swati S. Ranade,
- Jason B. Warner,
- Clarence C. Lee,
- Brittney E. Coleman,
- Zheng Zhang,
- Stephen F. McLaughlin,
- Joel A. Malek,
- Jon M. Sorenson,
- Alan P. Blanchard,
- Jarrod Chapman,
- David Hillman,
- Feng Chen,
- Daniel S. Rokhsar,
- Kevin J. McKernan,
- Thomas W. Jeffries,
- Gabor T. Marth,
- and Paul M. Richardson
Genome Res. October 2008 18: 1638-1642; Published in Advance September 4, 2008, doi:10.1101/gr.077776.108
...GIGABAYES, a new version of the POLYBAYES ( Marth et al. 1999 ) SNP discovery program (Methods). Color-space alignments of the SOLiD data were similarly screened using software supplied by Applied Biosystems. The 17 candidate mutations discovered among the three sequencing technologies were resequenced...
OPEN ACCESS ARTICLE
Select this article
Method: Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing
- Jamie K. Teer,
- Lori L. Bonnycastle,
- Peter S. Chines,
- Nancy F. Hansen,
- Natsuyo Aoyama,
- Amy J. Swift,
- Hatice Ozel Abaan,
- Thomas J. Albert,
- NISC Comparative Sequencing Program,
- Elliott H. Margulies,
- Eric D. Green,
- Francis S. Collins,
- James C. Mullikin,
- and Leslie G. Biesecker
Genome Res. October 2010 20: 1420-1431; Published in Advance September 1, 2010, doi:10.1101/gr.106716.110
...), and 91% (MGS) for 400 Mb. In contrast, all methods yielded similar accuracies of &gt;99.84% when compared to Infinium 1M SNP BeadChip-derived genotypes and &gt;99.998% when compared to 30-fold coverage whole-genome shotgun sequencing data. We also observed a low false-positive rate with all three methods...
Select this article
Resource: SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples
- Si Quang Le and
- Richard Durbin
Genome Res. June 2011 21: 952-960; Published in Advance October 27, 2010, doi:10.1101/gr.113084.110
...–1858. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078–2079. Li R, Li Y, Fang X, Yang H, Wang J, Kristiansen K, Wang J. 2009. SNP detection for massively parallel whole- resequencing...
OPEN ACCESS ARTICLE
Select this article
Methods: An MCMC algorithm for haplotype assembly from whole-genome sequence data
- Vikas Bansal,
- Aaron L. Halpern,
- Nelson Axelrod,
- and Vineet Bafna
Genome Res. August 2008 18: 1336-1346; doi:10.1101/gr.077065.108
...are useful for evaluating the power of these subsets to detect association at the untyped SNPs in human populations. Further, the haplotype data have also been used for fine-scale mapping of variants identified in association studies ( Gudmundsson et al. 2007 ) and for improving the power of whole...
Select this article
Method: Genome-wide detection of chromosomal rearrangements, indels, and mutations in circular chromosomes by short read sequencing
- Ole Skovgaard,
- Mads Bak,
- Anders Løbner-Olesen,
- and Niels Tommerup
Genome Res. August 2011 21: 1388-1393; Published in Advance May 9, 2011, doi:10.1101/gr.117416.110
...with the Comparative Genome Sequencing (CGS) service provided by Nimblegen Systems Inc. They reported that CGSwas efficient in detection of SNPs (single-nucleotide polymorphisms), small indels, IS element insertions, and deletions compared to a reference sequence, but they failed to detect the known rrn...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Li et al. 19 (6): 1124.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: