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Research: Evidence for selfing in a vertebrate from whole-genome sequencing
- Astrid Böhne,
- Zeynep Oğuzhan,
- Ioannis Chrysostomakis,
- Simon Vitt,
- Denis Meuthen,
- Sebastian Martin,
- Sandra Kukowka,
- and Timo Thünken
Genome Res. December 2023 33: 2133-2142; Published in Advance December 7, 2023, doi:10.1101/gr.277368.122
...of a heterozygosity reduction of 50% by selfing. Heterozygosity patterns along individual chromosomes do not point to alternative parthenogenetic reproductive mechanisms like automixis by terminal or central fusion. Facultative selfing may represent an adaptive strategy ensuring reproduction when mating partners...
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Method: Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples
- Shuangxi Ji,
- Tong Zhu,
- Ankit Sethia,
- and Wenyi Wang
Genome Res. April 2024 34: 633-641; Published in Advance April 8, 2024, doi:10.1101/gr.278456.123
...as a major contributing caller to reach final consensus calls by The Cancer Genome Atlas (TCGA) PanCanAtlas project (Ellrott et al. 2018), across approximately 13,000 tumor samples, and the International Cancer Genome Consortium Pan-Cancer Analysis of Whole Genomes (ICGC-PCAWG) initiative (The ICGC/TCGA Pan...
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Research: Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall
- William T. Harvey,
- Peter Ebert,
- Jana Ebler,
- Peter A. Audano,
- Katherine M. Munson,
- Kendra Hoekzema,
- David Porubsky,
- Christine R. Beck,
- Tobias Marschall,
- Kiran Garimella,
- and Evan E. Eichler
Genome Res. December 2023 33: 2029-2040; Published in Advance December 7, 2023, doi:10.1101/gr.278070.123
..., first generate ab initio a whole- assembly from LRS reads without guidance from a particular reference , and then proceed analogously by aligning this assembly to a reference to call variants using assembly-based calling algorithms. Many different tools implement variant-calling algorithms...
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Research: Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population
- Agnese Viluma,
- Øystein Flagstad,
- Mikael Åkesson,
- Camilla Wikenros,
- Håkan Sand,
- Petter Wabakken,
- and Hans Ellegren
Genome Res. March 2022 32: 449-458; Published in Advance February 8, 2022, doi:10.1101/gr.276070.121
...but appearing in a later was low. In the case of the second male, on the other hand, 32.5% of his inferred haplotypes not detected in 1994–2005 were seen in the 2006–2014 sample. This can probably be explained by the sampling strategy when choosing individuals for sequencing. Most of the “reappearing...
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Method: Whole-genome bisulfite sequencing with improved accuracy and cost
- Masako Suzuki,
- Will Liao,
- Frank Wos,
- Andrew D. Johnston,
- Justin DeGrazia,
- Jennifer Ishii,
- Toby Bloom,
- Michael C. Zody,
- Soren Germer,
- and John M. Greally
Genome Res. September 2018 28: 1364-1371; Published in Advance August 9, 2018, doi:10.1101/gr.232587.117
...to the Homo sapiens (hg19) reference using the Burrows-Wheeler Aligner version 0.7.13 (bwa mem –M –t <N> hg19.idxbase <R2 FASTQ> <R1 FASTQ>) (Li and Durbin 2009). Uniquely mapped reads were retained using SAMtools v0.1.19, followed by removal of mitochondrial reads by picard-tools v1.92 (Li et al. 2009...
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Method: TraDIS-Xpress: a high-resolution whole-genome assay identifies novel mechanisms of triclosan action and resistance
- Muhammad Yasir,
- A. Keith Turner,
- Sarah Bastkowski,
- David Baker,
- Andrew J. Page,
- Andrea Telatin,
- Minh-Duy Phan,
- Leigh Monahan,
- George M. Savva,
- Aaron Darling,
- Mark A. Webber,
- and Ian G. Charles
Genome Res. February 2020 30: 239-249; Published in Advance February 12, 2020, doi:10.1101/gr.254391.119
...organism in one massively parallel experiment in a controlled manner promises to be a hugely powerful strategy that has the potential to uncover new genotype–phenotype relationships.ResultsCreation of a high-density transposon insert library in E. coli strain BW25113E. coli BW25113 was transformed...
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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
...to this work. Corresponding author: manoli@mit.eduAbstractThe most widely appreciated role of DNA is to encode protein, yet the exact portion of the human that is translated remains to be ascertained. We previously developed PhyloCSF, a widely used tool to identify evolutionary signatures of protein...
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Method: INTEGRATE: gene fusion discovery using whole genome and transcriptome data
- Jin Zhang,
- Nicole M. White,
- Heather K. Schmidt,
- Robert S. Fulton,
- Chad Tomlinson,
- Wesley C. Warren,
- Richard K. Wilson,
- and Christopher A. Maher
Genome Res. January 2016 26: 108-118; Published in Advance November 10, 2015, doi:10.1101/gr.186114.114
...that causative mutations are not missed while minimizing false positives. Currently, there are many computational tools that predict structural variations (SV) and gene fusions using whole genome (WGS) and transcriptome sequencing (RNA-seq) data separately. However, as both WGS and RNA-seq have their limitations...
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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
...Comparison against 186 canid whole- sequences reveals survival strategies of an ancient clonally transmissible canine tumor Brennan Decker,1,2,7 Brian W. Davis,1,7 Maud Rimbault,1 Adrienne H. Long,3 Eric Karlins,1 Vidhya Jagannathan,4 Rebecca Reiman,5 Heidi G. Parker,1 Cord Drögemüller,4 Jason J...
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Resource: Whole-genome analysis of the methylome and hydroxymethylome in normal and malignant lung and liver
- Xin Li,
- Yun Liu,
- Tal Salz,
- Kasper D. Hansen,
- and Andrew Feinberg
Genome Res. December 2016 26: 1730-1741; Published in Advance October 13, 2016, doi:10.1101/gr.211854.116
...Whole-genome analysis of the methylome and hydroxymethylome in normal and malignant lung and liver Xin Li 1 , Yun Liu 1 , 2 , 3 , Tal Salz 1 , Kasper D. Hansen 1 , 4 , 5 and Andrew Feinberg 1 , 6 , 7 , 8 1Center...

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