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Method: Quantification of somatic mutation flow across individual cell division events by lineage sequencing
- Yehuda Brody,
- Robert J. Kimmerling,
- Yosef E. Maruvka,
- David Benjamin,
- Juniper J. Elacqua,
- Nicholas J. Haradhvala,
- Jaegil Kim,
- Kent W. Mouw,
- Kristjana Frangaj,
- Amnon Koren,
- Gad Getz,
- Scott R. Manalis,
- and Paul C. Blainey
Genome Res. December 2018 28: 1901-1918; Published in Advance November 20, 2018, doi:10.1101/gr.238543.118
...calling across multiple data setsIn order to produce a list of provisional SNVs for each lineage experiment, sequence data from all pairs of subclones were analyzed with MuTect1 (Cibulskis et al. 2013) using the hg19 reference (Genome Reference Consortium GRCh37). SNVs that arose de novo during...
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Resource: Genome-wide discovery of human splicing branchpoints
- Tim R. Mercer,
- Michael B. Clark,
- Stacey B. Andersen,
- Marion E. Brunck,
- Wilfried Haerty,
- Joanna Crawford,
- Ryan J. Taft,
- Lars K. Nielsen,
- Marcel E. Dinger,
- and John S. Mattick
Genome Res. February 2015 25: 290-303; Published in Advance January 5, 2015, doi:10.1101/gr.182899.114
..., corresponding to ;10.6-fold more reads (;133million reads) that align to introns relative to matched RNAseq controls (Supplemental Fig. 1C,D). Figure 1. Identification of splicing branchpoints. Splicing joins the 59 splice site to the branchpoint (BP) nucleotide near the 39 end of the intron to form a lariat...
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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
...that have modest effects on disease ( Wang et al. 2005 ). In contrast, -wide association studies offer a promising approach for mapping associated loci. The completion of the human sequence ( Lander et al. 2001 ; Venter et al. 2001 ) enabled the identification of millions of single nucleotide polymorphisms...
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Research: A matter of life or death: How microsatellites emerge in and vanish from the human genome
- Yogeshwar D. Kelkar,
- Kristin A. Eckert,
- Francesca Chiaromonte,
- and Kateryna D. Makova
Genome Res. December 2011 21: 2038-2048; Published in Advance October 12, 2011, doi:10.1101/gr.122937.111
...-values provided in Supplemental Fig. S10). Microsatellite l ife cycle in primates Genome Research 2041 www..org To investigate births/deaths across L1PA elements of different ages, we created three groups with integration times similar to those ofAlu subfamilies: (a) L1PA3–L1PA6 (13–26MY); (b) L1PA7–L1PA10 (31...
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Chicken Special/Letters: Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes
- Erik Axelsson,
- Matthew T. Webster,
- Nick G.C. Smith,
- David W. Burt,
- and Hans Ellegren
Genome Res. January 2005 15: 120-125; Published in Advance December 8, 2004, doi:10.1101/gr.3021305
...: 555 -556. ↵ Zhao, Z. and Boerwinkle, E. 2002 . Neighboring-nucleotide effects on single nucleotide polymorphisms: A study of 2.6 million polymorphisms across the human . Genome Res. 12 : 1679 -1686. Comparison of the chicken and turkey s reveals a higher rate of nucleotide divergence...
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Research: A-to-I RNA editing contributes to the persistence of predicted damaging mutations in populations
- Te-Lun Mai and
- Trees-Juen Chuang
Genome Res. November 2019 29: 1766-1776; Published in Advance September 12, 2019, doi:10.1101/gr.246033.118
...1000 Genomes Project Consortium 2015]) and the RNA-seq data of the corresponding LCL samples from the Geuvadis project (Lappalainen et al. 2013). For each A/G SNP site, there are three possible genotypes across the LCL population: AA, AG, and GG. We selected individuals with the homozygous genotype AA...
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Resource: PRISM offers a comprehensive genomic approach to transcription factor function prediction
- Aaron M. Wenger,
- Shoa L. Clarke,
- Harendra Guturu,
- Jenny Chen,
- Bruce T. Schaar,
- Cory Y. McLean,
- and Gill Bejerano
Genome Res. May 2013 23: 889-904; Published in Advance February 4, 2013, doi:10.1101/gr.139071.112
..., high-quality library from more than 800 public transcription factor motifs, covering all major DNA binding domains, and predict 3.3 million binding sites for all factors across the human and mouse s. We then place GREAT (McLean et al. 2010), a tool for functional analysis of a set of cis...
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Resource: Low-coverage sequencing: Implications for design of complex trait association studies
- Yun Li,
- Carlo Sidore,
- Hyun Min Kang,
- Michael Boehnke,
- and Gonçalo R. Abecasis
Genome Res. June 2011 21: 940-951; Published in Advance April 1, 2011, doi:10.1101/gr.117259.110
...allow genomic variation to be surveyed in much greater detail than previously possible. While detailed analysis of a single individual typically requires deep sequencing, when many individuals are sequenced it is possible to combine shallow sequence data across individuals to generate accurate calls...
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Research: Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes
- Chun-Long Chen,
- Aurélien Rappailles,
- Lauranne Duquenne,
- Maxime Huvet,
- Guillaume Guilbaud,
- Laurent Farinelli,
- Benjamin Audit,
- Yves d'Aubenton-Carafa,
- Alain Arneodo,
- Olivier Hyrien,
- and Claude Thermes
Genome Res. April 2010 20: 447-457; Published in Advance January 26, 2010, doi:10.1101/gr.098947.109
...in Methods (DNA Methylation section). Mutation rates and replication timing in mammals Genome Research 453 www..org Two replicate experiments (Experiments 1 and 2) were performed that produced seven to 15 million sequence reads for each fraction of the S phase (Supplemental Table S6). The sequence reads were...
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Letter: HapMap methylation-associated SNPs, markers of germline DNA methylation, positively correlate with regional levels of human meiotic recombination
- Martin I. Sigurdsson,
- Albert V. Smith,
- Hans T. Bjornsson,
- and Jon J. Jonsson
Genome Res. April 2009 19: 581-589; Published in Advance January 21, 2009, doi:10.1101/gr.086181.108
...( Bjornsson et al. 2006 ). Using the recently released HapMap data set of 3.1 million SNPs, we created a model of human germline methylation. We then used this model to test if DNA methylation of the human germline was directly and independently correlated with meiotic recombination. The results suggest...

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