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Research: T2T-CHM13 improves read mapping and detection of clinically relevant genetic variation in the Swedish population
- Daniel Schmitz,
- Adam Ameur,
- and Åsa Johansson
Genome Res. November 2025 35: 2377-2388; Published in Advance September 16, 2025, doi:10.1101/gr.279320.124
...but are functionally relevant, such as centromeres, promises to close the gap in quantifying the missing heritability.The resources provided by the T2T Consortium, such as lifted-over versions of dbSNP, allow for the adoption of existing workflows to the new reference as well as alignments and variant calls generated...
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Research: Discovery and genotyping of structural variation from long-read haploid genome sequence data
- John Huddleston,
- Mark J.P. Chaisson,
- Karyn Meltz Steinberg,
- Wes Warren,
- Kendra Hoekzema,
- David Gordon,
- Tina A. Graves-Lindsay,
- Katherine M. Munson,
- Zev N. Kronenberg,
- Laura Vives,
- Paul Peluso,
- Matthew Boitano,
- Chen-Shin Chin,
- Jonas Korlach,
- Richard K. Wilson,
- and Evan E. Eichler
Genome Res. May 2017 27: 677-685; Published in Advance November 28, 2016, doi:10.1101/gr.214007.116
...-deletion variants identified in 179 human s. Genome Res 23: 749–761. ↵Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. 2001. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 29: 308–311. ↵Shi L, Guo Y, Dong C, Huddleston J, Yang H, Han X, Fu A, Li Q, Li N, Gong S, et al...
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Resource: The landscape of human STR variation
- Thomas Willems,
- Melissa Gymrek,
- Gareth Highnam,
- The 1000 Genomes Project Consortium,
- David Mittelman,
- and Yaniv Erlich
Genome Res. November 2014 24: 1894-1904; Published in Advance August 18, 2014, doi:10.1101/gr.177774.114
...augments the level of knowledge of STR variation. Currently, dbSNP reports data for only 5500 STR loci. Our catalog provides data on close to 700,000 STR loci, which encompasses 97%of the STRswithmotifs of 2–6 bp in the , and contains more than 300,000 STR loci with a MAF of >1%. One caveat of our catalog...
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RESOURCE: Large-Scale Validation of Single Nucleotide Polymorphisms in Gene Regions
- Matthew R. Nelson,
- George Marnellos,
- Stefan Kammerer,
- Carolyn R. Hoyal,
- Michael M. Shi,
- Charles R. Cantor,
- and Andreas Braun
Genome Res. August 2004 14: 1664-1668; doi:10.1101/gr.2421604
...: 541 –550. ↵ Sherry, S.T., Ward, M.H., Kholodov, M., Baker, J., Phan, L., Smigielski, E.M., and Sirotkin, K. 2001 . dbSNP: The NCBI database of genetic variation. Nucleic Acids Res. 29 : 308 –311. ↵ Shifman, S., Pisante-Shalom, A., Yakir, B., and Darvasi, A. 2002 . Quantitative technologies for allele...
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RESOURCE: Single Nucleotide Polymorphisms Associated With Rat Expressed Sequences
- Victor Guryev,
- Eugene Berezikov,
- Rainer Malik,
- Ronald H.A. Plasterk,
- and Edwin Cuppen
Genome Res. July 2004 14: 1438-1443; doi:10.1101/gr.2154304
...and haplotypes obtained in this study were submitted to dbSNP (accession numbers: ss12535137–ss12568440, ss12588074–ss12588105). The database is publicly available at http://cascad.niob.knaw.nl ; all scripts are freely available upon request from the authors. Prediction of Effect of Nonsynonymous Candidate SNPs...
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Research: Novel determinants of mammalian primary microRNA processing revealed by systematic evaluation of hairpin-containing transcripts and human genetic variation
- Christine Roden,
- Jonathan Gaillard,
- Shaveta Kanoria,
- William Rennie,
- Syndi Barish,
- Jijun Cheng,
- Wen Pan,
- Jun Liu,
- Chris Cotsapas,
- Ye Ding,
- and Jun Lu
Genome Res. March 2017 27: 374-384; Published in Advance January 13, 2017, doi:10.1101/gr.208900.116
...minor alleles (Supplemental Fig. S6A,B).View larger version: In this window In a new window Figure 5. The effects of human SNPs on pri-miRNA processing. (A) Human SNPs in dbSNP human Build 142 that are located close to human pri-miRNAs were evaluated for their impact on hairpin structure and sequence...
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LETTER: A Population Threshold for Functional Polymorphisms
- Gane Ka-Shu Wong,
- Zhiyong Yang,
- Douglas A. Passey,
- Miho Kibukawa,
- Marcia Paddock,
- Chun-Rong Liu,
- Lars Bolund,
- and Jun Yu
Genome Res. August 2003 13: 1873-1879; doi:10.1101/gr.1324303
..., insertion-deletion polymorphisms identified in a special class of minimal introns appeared to be functional only for minor allele frequencies of below 6% ( Yu et al. 2002 ). Aside from being a potentially important clue to understanding the basis of human genetic variation, the threshold has a practical...
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RESOURCE: Expression-based Genetic/Physical Maps of Single-Nucleotide Polymorphisms Identified by the Cancer Genome Anatomy Project
- Robert Clifford,
- Michael Edmonson,
- Ying Hu,
- Cu Nguyen,
- Titia Scherpbier,
- and Kenneth H. Buetow
Genome Res. August 1, 2000 10: 1259-1265; doi:10.1101/gr.10.8.1259
....A. , Stein L.D. , Gyapay G. , Rice K. , White R.E. , Rodriguez-Tomé P. , Aggarwal A. , Bajorek E. , et al. ( 1996 ) A gene map of the human . Science 274 : 540 – 546 . ↵ Sherry S.T. , Ward M. , Sirotkin K. ( 1999 ) dbSNP—Database for single nucleotide polymorphisms and other classes of minor genetic...
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LETTER: Accounting for Human Polymorphisms Predicted to Affect Protein Function
- Pauline C. Ng and
- Steven Henikoff
Genome Res. March 1, 2002 12: 436-446; doi:10.1101/gr.212802
....-H. , Kholodov M. , Baker J. , Phan L. , Smigielski E.M. , Sirotkin K. ( 2001 ) dbSNP: The NCBI database of genetic variation. Nucleic Acids Res. 29 : 308 – 311 . ↵ Skibola C.F. , Smith M.T. , Kane E. , Roman E. , Rollinson S. , Cartwright R.A. , Morgan G. ( 1999 ) Polymorphisms in the methylenetetrahydrofolate...
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Research: Natural genetic variation caused by small insertions and deletions in the human genome
- Ryan E. Mills,
- W. Stephen Pittard,
- Julienne M. Mullaney,
- Umar Farooq,
- Todd H. Creasy,
- Anup A. Mahurkar,
- David M. Kemeza,
- Daniel S. Strassler,
- Chris P. Ponting,
- Caleb Webber,
- and Scott E. Devine
Genome Res. June 2011 21: 830-839; Published in Advance April 1, 2011, doi:10.1101/gr.115907.110
...://www.ncbi.nlm.nih.gov/geo ) under accession no. GSE27889. The INDEL variants reported in this study have been deposited in the NCBI dbSNP database ( http://www.ncbi.nlm.nih.gov/projects/SNP/ ) (a complete listing of the accession numbers can be found in Supplemental Table 17).] Article published online before print...

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