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Method: Parallel analysis of replication timing, gene expression and copy number with PARTAGE
- Lakshana Sruthi Sadu Murari,
- Quinn Dickinson,
- Silvia Meyer-Nava,
- and Juan Carlos Rivera-Mulia
Genome Res. March 19, 2026 gr.281532.125; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
...recovered between 151 92% and 100% of the ENCODE CNV events (Figure 4B). The statistical significance of the overlap 152 between ENCODE and PARTAGE CNVs was assessed using ProOvErlap (Gualandi et al. 2025), 153 confirming that the concordance is substantially greater than expected by chance (Figure 4B). 154...
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Research: Copy number variation underlies complex phenotypes in domestic dog breeds and other canids
- Aitor Serres-Armero,
- Brian W. Davis,
- Inna S. Povolotskaya,
- Carlos Morcillo-Suarez,
- Jocelyn Plassais,
- David Juan,
- Elaine A. Ostrander,
- and Tomas Marques-Bonet
Genome Res. May 2021 31: 762-774; Published in Advance April 16, 2021, doi:10.1101/gr.266049.120
...study of structural variation as it relates to breed-specific phenotypes is lacking. We have generated whole CNV maps for more than 300 canids. Our data set extends the canine structural variation landscape to more than 100 dog breeds, including novel variants that cannot be assessed using microarray...
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Resource: Analysis of copy number variations among diverse cattle breeds
- George E. Liu,
- Yali Hou,
- Bin Zhu,
- Maria Francesca Cardone,
- Lu Jiang,
- Angelo Cellamare,
- Apratim Mitra,
- Leeson J. Alexander,
- Luiz L. Coutinho,
- Maria Elena Dell'Aquila,
- Lou C. Gasbarre,
- Gianni Lacalandra,
- Robert W. Li,
- Lakshmi K. Matukumalli,
- Dan Nonneman,
- Luciana C. de A. Regitano,
- Tim P.L. Smith,
- Jiuzhou Song,
- Tad S. Sonstegard,
- Curt P. Van Tassell,
- Mario Ventura,
- Evan E. Eichler,
- Tara G. McDaneld,
- and John W. Keele
Genome Res. May 2010 20: 693-703; Published in Advance March 8, 2010, doi:10.1101/gr.105403.110
...CNV regions identified in normal individuals. These data sets alone correspond to over 910Mb of structurally variant DNA. More than 9000 genes have beenmapped within or near regions of human structural variation. While SNPs aremore frequent,CNVs involvemore genomic sequences andhave potentially more...
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Resource: Detecting copy number variation with mated short reads
- Paul Medvedev,
- Marc Fiume,
- Misko Dzamba,
- Tim Smith,
- and Michael Brudno
Genome Res. November 2010 20: 1613-1622; Published in Advance August 30, 2010, doi:10.1101/gr.106344.110
...-variable regions. Such methods, however, are hindered by sequencing biases that lead certain regions of the genome to be over- or undersampled, lowering their resolution and ability to accurately identify the exact breakpoints of the variants. In this work, we develop a method for CNV detection that supplements...
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Research: Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize
- Baoxing Song,
- Edward S. Buckler,
- Hai Wang,
- Yaoyao Wu,
- Evan Rees,
- Elizabeth A. Kellogg,
- Daniel J. Gates,
- Merritt Khaipho-Burch,
- Peter J. Bradbury,
- Jeffrey Ross-Ibarra,
- Matthew B. Hufford,
- and M. Cinta Romay
Genome Res. July 2021 31: 1245-1257; Published in Advance May 27, 2021, doi:10.1101/gr.266528.120
...(Luu et al. 2017). The overlap between these regions and pan-And-CNS was substantially less than would be expected by chance, suggesting recent selection in maize has mainly favored variants that do not modify these constrained functional regions (Supplemental Fig. S21).CNS variation is associated...
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Perspective: Genetic architecture of quantitative traits in mice, flies, and humans
- Jonathan Flint and
- Trudy F.C. Mackay
Genome Res. May 2009 19: 723-733; doi:10.1101/gr.086660.108
...and ultimately the sequence variants has proved more difficult, so that our information on the molecular basis of quantitative variation remains limited. Nevertheless, available data indicate that many variants lie outside genes, presumably in regulatory regions of the genome, where they act by altering gene...
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Method: Estimation of alternative splicing variability in human populations
- Mar Gonzàlez-Porta,
- Miquel Calvo,
- Michael Sammeth,
- and Roderic Guigó
Genome Res. March 2012 22: 528-538; Published in Advance November 23, 2011, doi:10.1101/gr.121947.111
...used to perform transcriptome-wide analysis of gene expression, and many methods have been developed to measure gene expression variability and to compare gene expression between conditions. Because RNA-seq is also becoming increasingly popular for transcriptome characterization, the possibility exists...
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Research: The origin, evolution, and functional impact of short insertion–deletion variants identified in 179 human genomes
- Stephen B. Montgomery,
- David L. Goode,
- Erika Kvikstad,
- Cornelis A. Albers,
- Zhengdong D. Zhang,
- Xinmeng Jasmine Mu,
- Guruprasad Ananda,
- Bryan Howie,
- Konrad J. Karczewski,
- Kevin S. Smith,
- Vanessa Anaya,
- Rhea Richardson,
- Joe Davis,
- The 1000 Genomes Project Consortium,
- Daniel G. MacArthur,
- Arend Sidow,
- Laurent Duret,
- Mark Gerstein,
- Kateryna D. Makova,
- Jonathan Marchini,
- Gil McVean,
- and Gerton Lunter
Genome Res. May 2013 23: 749-761; Published in Advance March 11, 2013, doi:10.1101/gr.148718.112
...(particularly for indels in tandem repeats) as expected from the improved mapping and modified filtering stages. To assess our power to detect indels more formally, we used variants identified in high-quality fosmid data of a single individual of European ancestry (NA12878 from CEU) (Kidd et al. 2010). Although...
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Resource: Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing
- Thomas Zichner,
- David A. Garfield,
- Tobias Rausch,
- Adrian M. Stütz,
- Enrico Cannavó,
- Martina Braun,
- Eileen E.M. Furlong,
- and Jan O. Korbel
Genome Res. March 2013 23: 568-579; Published in Advance December 6, 2012, doi:10.1101/gr.142646.112
...the aforementioned PCR-based FDR estimates of 4%–6%). Zichner et al. 572 Genome Research www..org The impact of SVs on genomic annotation The high resolution of our SV map further enabled us to assess the functional impact of our SVs in detail. To this end, we initially investigated functional impact by relating our...
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Method: Calling amplified haplotypes in next generation tumor sequence data
- Ninad Dewal,
- Yang Hu,
- Matthew L. Freedman,
- Thomas LaFramboise,
- and Itsik Pe'er
Genome Res. February 2012 22: 362-374; Published in Advance November 16, 2011, doi:10.1101/gr.122564.111
...purposes, to infer amplified alleles and haplotypes in regions of copy number gain. Our method is designed to handle rare variants and biases in read data. We assess the performance of HATS using simulated amplified regions generated from varying copy number and coverage levels, followed by amplicons...

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