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Review: Leveraging the power of long reads for targeted sequencing
- Shruti V. Iyer,
- Sara Goodwin,
- and William Richard McCombie
Genome Res. November 2024 34: 1701-1718; doi:10.1101/gr.279168.124
...reads long enough to span and resolve complex or repetitive regions of the . Several groups have shown the power of long reads in detecting thousands of genomic and epigenomic features that were previously missed by short-read sequencing approaches. While these studies demonstrate how long reads can...
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Research: The Chinese longsnout catfish genome provides novel insights into the feeding preference and corresponding metabolic strategy of carnivores
- Yulong Liu,
- Gang Zhai,
- Jingzhi Su,
- Yulong Gong,
- Bingyuan Yang,
- Qisheng Lu,
- Longwei Xi,
- Yutong Zheng,
- Jingyue Cao,
- Haokun Liu,
- Junyan Jin,
- Zhimin Zhang,
- Yunxia Yang,
- Xiaoming Zhu,
- Zhongwei Wang,
- Gaorui Gong,
- Jie Mei,
- Zhan Yin,
- Rodolphe E. Gozlan,
- Shouqi Xie,
- and Dong Han
Genome Res. July 2024 34: 981-996; Published in Advance August 9, 2024, doi:10.1101/gr.278476.123
...ratio of 99.40% and the coverage ratio of 98.95% suggest that our assembled exhibits satisfactory uniformity (Supplemental Table S7). The heterozygous single-nucleotide polymorphism (SNP) ratio and the homozygous SNP ratio were 0.138745% and 0.001405%, respectively, indicating that the assembly has...
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Research: Cancer-associated rs6983267 SNP and its accompanying long noncoding RNA CCAT2 induce myeloid malignancies via unique SNP-specific RNA mutations
- Maitri Y. Shah,
- Manuela Ferracin,
- Valentina Pileczki,
- Baoqing Chen,
- Roxana Redis,
- Linda Fabris,
- Xinna Zhang,
- Cristina Ivan,
- Masayoshi Shimizu,
- Cristian Rodriguez-Aguayo,
- Mihnea Dragomir,
- Katrien Van Roosbroeck,
- Maria Ines Almeida,
- Maria Ciccone,
- Daniela Nedelcu,
- Maria Angelica Cortez,
- Taghi Manshouri,
- Steliana Calin,
- Muharrem Muftuoglu,
- Pinaki P. Banerjee,
- Mustafa H. Badiwi,
- Jan Parker-Thornburg,
- Asha Multani,
- James William Welsh,
- Marcos Roberto Estecio,
- Hui Ling,
- Ciprian Tomuleasa,
- Delia Dima,
- Hui Yang,
- Hector Alvarez,
- M. James You,
- Milan Radovich,
- Elizabeth Shpall,
- Muller Fabbri,
- Katy Rezvani,
- Leonard Girnita,
- Ioana Berindan-Neagoe,
- Anirban Maitra,
- Srdan Verstovsek,
- Riccardo Fodde,
- Carlos Bueso-Ramos,
- Mihai Gagea,
- Guillermo Garcia Manero,
- and George A. Calin
Genome Res. April 2018 28: 432-447; Published in Advance March 22, 2018, doi:10.1101/gr.225128.117
...mice. The RNA transcribed from the SNP locus in malignant hematopoietic cells have different allelic composition from the corresponding genomic DNA, a phenomenon rarely observed in normal cells. Our findings provide fundamental insights into the functional role of rs6983267 SNP and CCAT2 in myeloid...
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Research: Low-pass sequencing increases the power of GWAS and decreases measurement error of polygenic risk scores compared to genotyping arrays
- Jeremiah H. Li,
- Chase A. Mazur,
- Tomaz Berisa,
- and Joseph K. Pickrell
Genome Res. April 2021 31: 529-537; Published in Advance February 3, 2021, doi:10.1101/gr.266486.120
...using haplotype tags: a class of tests and the determinants of statistical power. Hum Hered 56: 18–31. doi:10.1159/000073729 ↵Das S, Abecasis G, Fuchsberger C. 2015. Minimac4: a next generation imputation tool for mega reference panels (Abstract 1278W). Presented at the 65th Annual Meeting...
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Research: A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility
- Angelo A. Ruggieri,
- Luca Livraghi,
- James J. Lewis,
- Elizabeth Evans,
- Francesco Cicconardi,
- Laura Hebberecht,
- Yadira Ortiz-Ruiz,
- Stephen H. Montgomery,
- Alfredo Ghezzi,
- José Arcadio Rodriguez-Martinez,
- Chris D. Jiggins,
- W. Owen McMillan,
- Brian A. Counterman,
- Riccardo Papa,
- and Steven M. Van Belleghem
Genome Res. October 2022 32: 1862-1875; Published in Advance September 15, 2022, doi:10.1101/gr.276839.122
...for structural variation to serve as raw material for adaptive evolution.Structural variants (SVs) in s are a ubiquitous component of within and between species genomic variation (Mérot et al. 2020; Zhang et al. 2021). The larger size of SVs, when compared with single nucleotide polymorphisms (SNPs), may...
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Resource: Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions
- Rodrigo P. Baptista,
- Yiran Li,
- Adam Sateriale,
- Mandy J. Sanders,
- Karen L. Brooks,
- Alan Tracey,
- Brendan R.E. Ansell,
- Aaron R. Jex,
- Garrett W. Cooper,
- Ethan D. Smith,
- Rui Xiao,
- Jennifer E. Dumaine,
- Peter Georgeson,
- Bernard J. Pope,
- Matthew Berriman,
- Boris Striepen,
- James A. Cotton,
- and Jessica C. Kissinger
Genome Res. January 2022 32: 203-213; Published in Advance November 11, 2021, doi:10.1101/gr.275325.121
.... Only 136 isolates from a small geographic region have been sampled here. Newer techniques such as hybrid capture bait set techniques (Mamanova et al. 2010) are a powerful future alternative to characterize and select Cryptosporidium population variants and better characterize genetic diversity.The new...
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Resource: Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci
- Jonathan M. Mudge,
- Irwin Jungreis,
- Toby Hunt,
- Jose Manuel Gonzalez,
- James C. Wright,
- Mike Kay,
- Claire Davidson,
- Stephen Fitzgerald,
- Ruth Seal,
- Susan Tweedie,
- Liang He,
- Robert M. Waterhouse,
- Yue Li,
- Elspeth Bruford,
- Jyoti S. Choudhary,
- Adam Frankish,
- and Manolis Kellis
Genome Res. December 2019 29: 2073-2087; Published in Advance September 19, 2019, doi:10.1101/gr.246462.118
...PCCRs. (C) PhyloCSF tracks in UCSC Genome Browser showing the “−” strand of C. elegans Chromosome X. Upper six green and red “PhyloCSFraw” tracks show the raw PhyloCSF score for each codon in each of six reading frames. The black “PhyloCSF power” track indicates the relative branch length of the local...
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Research: The population genomics of rhesus macaques (Macaca mulatta) based on whole-genome sequences
- Cheng Xue,
- Muthuswamy Raveendran,
- R. Alan Harris,
- Gloria L. Fawcett,
- Xiaoming Liu,
- Simon White,
- Mahmoud Dahdouli,
- David Rio Deiros,
- Jennifer E. Below,
- William Salerno,
- Laura Cox,
- Guoping Fan,
- Betsy Ferguson,
- Julie Horvath,
- Zach Johnson,
- Sree Kanthaswamy,
- H. Michael Kubisch,
- Dahai Liu,
- Michael Platt,
- David G. Smith,
- Binghua Sun,
- Eric J. Vallender,
- Feng Wang,
- Roger W. Wiseman,
- Rui Chen,
- Donna M. Muzny,
- Richard A. Gibbs,
- Fuli Yu,
- and Jeffrey Rogers
Genome Res. December 2016 26: 1651-1662; Published in Advance October 17, 2016, doi:10.1101/gr.204255.116
....68 49.22 49.90 71.21 Number of nonsense (×103) 1.47 1.22 0.67 0.69 0.88 Average number of SNVs per sample (×106) 9.14 11.25 3.44 3.43 4.21 Average number heterozygous SNVs per sample (×106) 6.10 6.94 2.09 1.96 2.79 Human data from The 1000 Genomes Project Consortium (2012) and annotations from dbSNP138...
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Method: Gene discovery by chemical mutagenesis and whole-genome sequencing in Dictyostelium
- Cheng-Lin Frank Li,
- Balaji Santhanam,
- Amanda Nicole Webb,
- Blaž Zupan,
- and Gad Shaulsky
Genome Res. September 2016 26: 1268-1276; Published in Advance June 15, 2016, doi:10.1101/gr.205682.116
...% of the entire and ∼10% of the coding exons did not pass the read depth filter and were therefore excluded from SNP calling (Supplemental Fig. S1B), we probably underestimated the number of NTG-induced mutations per . Nevertheless, this relatively small number of mutations per suggested that it would be possible...
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RESOURCE: An Efficient SNP System for Mouse Genome Scanning and Elucidating Strain Relationships
- Petko M. Petkov,
- Yueming Ding,
- Megan A. Cassell,
- Weidong Zhang,
- Gunjan Wagner,
- Evelyn E. Sargent,
- Steven Asquith,
- Victor Crew,
- Kevin A. Johnson,
- Phil Robinson,
- Valerie E. Scott,
- and Michael V. Wiles
Genome Res. September 2004 14: 1806-1811; doi:10.1101/gr.2825804
...(Supplemental Table 1). All assays were identified by their physical position in the mouse and by their refSNP ID in the dbSNP ( http://www.ncbi.nlm.nih.gov/SNP ). The average distance between them was 1.56 Mb, or about 0.8 cM ( Table 1 ), with a minimum resolution power of 5 Mb for most chromosomal regions...

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