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Method: Sequences of 95 human MHC haplotypes reveal extreme coding variation in genes other than highly polymorphic HLA class I and II
- Paul J. Norman,
- Steven J. Norberg,
- Lisbeth A. Guethlein,
- Neda Nemat-Gorgani,
- Thomas Royce,
- Emily E. Wroblewski,
- Tamsen Dunn,
- Tobias Mann,
- Claudia Alicata,
- Jill A. Hollenbach,
- Weihua Chang,
- Melissa Shults Won,
- Kevin L. Gunderson,
- Laurent Abi-Rached,
- Mostafa Ronaghi,
- and Peter Parham
Genome Res. May 2017 27: 813-823; Published in Advance March 30, 2017, doi:10.1101/gr.213538.116
...diamonds: Genes that are involved in immunity. Black diamonds: Other genes. Red text: Classical HLA class I and II genes. Areas of significant structural diversity are indicated with green brackets; these are HLA-DR and C4A/C4B. Build 142 of dbSNP was used, which has 225,302 SNP sites mapped to the target...
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Research: Thousands of human mutation clusters are explained by short-range template switching
- Ari Löytynoja
Genome Res. August 2022 32: 1437-1447; Published in Advance June 27, 2022, doi:10.1101/gr.276478.121
...(Supplemental Data S1)—but none of the manually confirmed cases supported by both short-read data sets was completely absent from the dbSNP database (Sherry et al. 2001). Although dbSNP correctly lists many studied loci as multinucleotide variants (MNVs), all loci were also present as multiple SNVs and indels...
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Resource: SNP detection for massively parallel whole-genome resequencing
- Ruiqiang Li,
- Yingrui Li,
- Xiaodong Fang,
- Huanming Yang,
- Jian Wang,
- Karsten Kristiansen,
- and Jun Wang
Genome Res. June 2009 19: 1124-1132; Published in Advance May 6, 2009, doi:10.1101/gr.088013.108
..., for multi-individual data sets, the likelihood information of each individual can be integrated and used to build a statistic frame to infer the genotype for each allele. We also showed that using dbSNP genotypes for prior probability calculation substantially helps in distinguishing real heterozygotes from...
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LETTER: Single Nucleotide Variation Analysis in 65 Candidate Genes for CNS Disorders in a Representative Sample of the European Population
- Yun Freudenberg-Hua,
- Jan Freudenberg,
- Nadine Kluck,
- Sven Cichon,
- Peter Propping,
- and Markus M. Nöthen
Genome Res. October 2003 13: 2271-2276; doi:10.1101/gr.1299703
...selection and thus could play a role in the etiology of genetically complex diseases. Footnotes [Supplemental material is available online at www.genome.org. The sequence data from this study have been submitted to dbSNP under accession nos. ss12586678-ss12587076.] Article...
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Method: A comprehensively molecular haplotype-resolved genome of a European individual
- Eun-Kyung Suk,
- Gayle K. McEwen,
- Jorge Duitama,
- Katja Nowick,
- Sabrina Schulz,
- Stefanie Palczewski,
- Stefan Schreiber,
- Dustin T. Holloway,
- Stephen McLaughlin,
- Heather Peckham,
- Clarence Lee,
- Thomas Huebsch,
- and Margret R. Hoehe
Genome Res. October 2011 21: 1672-1685; Published in Advance August 3, 2011, doi:10.1101/gr.125047.111
...://www.molgen.mpg.de/;geneticvariation/MaxPlanckOneUCSC) and Ensembl Genome Browsers (http://www.ebi.ac.uk/das-srv/easydas/MP1/das/sources). The phased variants have been annotated for their status of novelty (against dbSNP129) and potential for being damaging (Adzhubei et al. 2010), and can be examined for each of the two haplotypes separately. In addition...
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Resource: Genome-based analysis of the nonhuman primate Macaca fascicularis as a model for drug safety assessment
- Martin Ebeling,
- Erich Küng,
- Angela See,
- Clemens Broger,
- Guido Steiner,
- Marco Berrera,
- Tobias Heckel,
- Leonardo Iniguez,
- Thomas Albert,
- Roland Schmucki,
- Hermann Biller,
- Thomas Singer,
- and Ulrich Certa
Genome Res. October 2011 21: 1746-1756; Published in Advance August 23, 2011, doi:10.1101/gr.123117.111
...high-resolution genotyping and microarray-based gene-expression profiling for animal stratification, thereby allowing the use of well-characterized animals for safety testing. Finally, the genome sequence presented here is a significant contribution to the global “3R” animal welfare initiative, which...
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ARTICLE: Pattern of Sequence Variation Across 213 Environmental Response Genes
- Robert J. Livingston,
- Andrew von Niederhausern,
- Anil G. Jegga,
- Dana C. Crawford,
- Christopher S. Carlson,
- Mark J. Rieder,
- Sivakumar Gowrisankar,
- Bruce J. Aronow,
- Robert B. Weiss,
- and Deborah A. Nickerson
Genome Res. October 2004 14: 1821-1831; Published in Advance September 13, 2004, doi:10.1101/gr.2730004
...and generated 2.1 million genotypes, which are cataloged at the GeneSNPs ( http://.utah.edu/genesnps ) and dbSNPs databases. Of the 23,443 SNPs, 17,538 (75%) were unique reports. Of the 17,538 new dbSNP submissions, 2928 (17%) were common, with a MAF &gt;5%, and 14,610 (83%) had a MAF ≤5%. Of the 25% of our...
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Method: Allele-specific RNA N⁶-methyladenosine modifications reveal functional genetic variants in human tissues
- Shuo Cao,
- Haoran Zhu,
- Jinru Cui,
- Sun Liu,
- Yuhe Li,
- Junfang Shi,
- Junyuan Mo,
- Zihan Wang,
- Hailan Wang,
- Jiaxin Hu,
- Lizhi Chen,
- Yuan Li,
- Laixin Xia,
- and Shan Xiao
Genome Res. August 2023 33: 1369-1380; Published in Advance September 15, 2023, doi:10.1101/gr.277704.123
...for downstream analysis. The variants were retained if they matched the criteria “neither found in UCSC RepeatMasker microsatellites (Tarailo-Graovac and Chen 2009) nor in RNA editing sites (RADAR database)” but were contained in the dbSNP database.Mapping bias correction using STAR-WASP pipelineSNVs were called...
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Research: Comparison against 186 canid whole-genome sequences reveals survival strategies of an ancient clonally transmissible canine tumor
- Brennan Decker,
- Brian W. Davis,
- Maud Rimbault,
- Adrienne H. Long,
- Eric Karlins,
- Vidhya Jagannathan,
- Rebecca Reiman,
- Heidi G. Parker,
- Cord Drögemüller,
- Jason J. Corneveaux,
- Erica S. Chapman,
- Jeffery M. Trent,
- Tosso Leeb,
- Matthew J. Huentelman,
- Robert K. Wayne,
- Danielle M. Karyadi,
- and Elaine A. Ostrander
Genome Res. November 2015 25: 1646-1655; Published in Advance July 31, 2015, doi:10.1101/gr.190314.115
...identified by GATK HaplotypeCaller, but did not pass variant quality score recalibration, were retained for use as a systematic error filter. Together with canine dbSNP (Sherry 2001) and a recently published variation survey (Axelsson et al. 2013), our canine Variation and Systematic Error Catalog (VSEC...
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Resource: Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly
- Valerie A. Schneider,
- Tina Graves-Lindsay,
- Kerstin Howe,
- Nathan Bouk,
- Hsiu-Chuan Chen,
- Paul A. Kitts,
- Terence D. Murphy,
- Kim D. Pruitt,
- Françoise Thibaud-Nissen,
- Derek Albracht,
- Robert S. Fulton,
- Milinn Kremitzki,
- Vincent Magrini,
- Chris Markovic,
- Sean McGrath,
- Karyn Meltz Steinberg,
- Kate Auger,
- William Chow,
- Joanna Collins,
- Glenn Harden,
- Timothy Hubbard,
- Sarah Pelan,
- Jared T. Simpson,
- Glen Threadgold,
- James Torrance,
- Jonathan M. Wood,
- Laura Clarke,
- Sergey Koren,
- Matthew Boitano,
- Paul Peluso,
- Heng Li,
- Chen-Shan Chin,
- Adam M. Phillippy,
- Richard Durbin,
- Richard K. Wilson,
- Paul Flicek,
- Evan E. Eichler,
- and Deanna M. Church
Genome Res. May 2017 27: 849-864; Published in Advance April 10, 2017, doi:10.1101/gr.213611.116
...sequences, we examined their effect at GRCh37 and GRCh38 genomic sites annotated with the subset of dbSNP Build 147 variations described in ClinVar (Landrum et al. 2014). In one analysis, we aligned reads from the Ashkenazi female sample NA24143 (Zook et al. 2016) with BWA-MEM (Li 2013) and evaluated Clin...
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