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Method: Pangenome-based genome inference using integer programming
- Ghanshyam Chandra,
- Md Helal Hossen,
- Stephan Scholz,
- Alexander T. Dilthey,
- Daniel Gibney,
- and Chirag Jain
Genome Res. December 2025 35: 2661-2670; Published in Advance August 21, 2025, doi:10.1101/gr.280567.125
...-023-06173-7 ↵Grytten I, Dagestad Rand K, Sandve GK. 2022. KAGE: fast alignment-free graph-based genotyping of SNPs and short indels. Genome Biol 23: 209. doi:10.1186/s13059-022-02771-2 ↵Harris L, McDonagh EM, Zhang X, Fawcett K, Foreman A, Daneck P, Sergouniotis PI, Parkinson H, Mazzarotto F, Inouye M, et al. 2024...
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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...nucleotide polymorphisms (SNPs).View larger version: In this window In a new window Figure 1. Methods to detect -wide 5mC. DNAm can be detected through enrichment, bisulfite conversion, enzymatic modification, or single-molecule approaches. (A) Enrichment methods use restriction enzymes...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...haplotypes were analyzed from the Zambian population.Figure 5A shows the Integrative Genomics Viewer (IGV) plots of two windows flanking the histone locus. We label the flanking SNPs in relation to the position of the histone cluster. Distal positions start with −1 and become more negative the more distal...
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Method: Full-resolution HLA and KIR gene annotations for human genome assemblies
- Ying Zhou,
- Li Song,
- and Heng Li
Genome Res. November 2024 34: 1931-1941; Published in Advance June 5, 2024, doi:10.1101/gr.278985.124
...the CDS of all C4 genes sequences in our data, C4A and C4B were clearly separated, but the long and short forms were mixed in both the C4A and C4B clades (Supplemental Fig. S8). In addition to the five SNPs in exon 26 that are often used to distinguish C4A and C4B, four SNPs in exon 28 can also separate...
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Method: Efficient and accurate KIR and HLA genotyping with massively parallel sequencing data
- Li Song,
- Gali Bai,
- X. Shirley Liu,
- Bo Li,
- and Heng Li
Genome Res. May 11, 2023 gr.277585.122; Published in Advance May 11, 2023, doi:10.1101/gr.277585.122
...the precision by 2.6% in this evaluation. The phased reference s also provide the ground truth of novel genomics variations. We evaluated the unambiguous SNPs in the correct alleles predicted by T1K and found that 95.0% of these SNPs inferred by T1K can be validated on the phased (Figure S3). T1K could...
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Method: Simultaneous assessment of human genome and methylome data in a single experiment using limited deamination of methylated cytosine
- Bo Yan,
- Duan Wang,
- and Laurence Ettwiller
Genome Res. June 2024 34: 904-913; Published in Advance June 10, 2024, doi:10.1101/gr.278294.123
.... The evaluation of EM-seq conversion efficiency (>99.7%) was performed by utilizing unmethylated lambda genomic DNA as a spike-in.Reference and other annotation filesWe used the GRCh38 human reference (hg38), UCSC human CGI annotation, and known human SNP files used for GATK base quality recalibration...
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Research: Ancestral aneuploidy and stable chromosomal duplication resulting in differential genome structure and gene expression control in trypanosomatid parasites
- João L. Reis-Cunha,
- Samuel A. Pimenta-Carvalho,
- Laila V. Almeida,
- Anderson Coqueiro-dos-Santos,
- Catarina A. Marques,
- Jennifer A. Black,
- Jeziel Damasceno,
- Richard McCulloch,
- Daniella C. Bartholomeu,
- and Daniel C. Jeffares
Genome Res. March 2024 34: 441-453; Published in Advance April 11, 2024, doi:10.1101/gr.278550.123
...the least deleterious mutations (impact 3) (Mann–Whitney U test P-value 0.0125) (Fig. 4F). Taken together, these data suggest that TASC may be purging highly deleterious SNPs from the population more efficiently while maintaining low-impactful SNPs in higher proportions than other chromosomes...
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Resource: Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans
- Kohei Hamanaka,
- Daisuke Yamauchi,
- Eriko Koshimizu,
- Kei Watase,
- Kaoru Mogushi,
- Kinya Ishikawa,
- Hidehiro Mizusawa,
- Naomi Tsuchida,
- Yuri Uchiyama,
- Atsushi Fujita,
- Kazuharu Misawa,
- Takeshi Mizuguchi,
- Satoko Miyatake,
- and Naomichi Matsumoto
Genome Res. March 2023 33: 435-447; Published in Advance March 27, 2023, doi:10.1101/gr.277335.122
...-nucleotide polymorphisms (SNPs), small indels, and structural variations. Two linear regression models explaining the variation of each splicing event were compared using analysis of variance (ANOVA): one including nearby variants and the other additionally including a TR between the 10-kb upstream position from the donor...
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Resource: The western redcedar genome reveals low genetic diversity in a self-compatible conifer
- Tal J. Shalev,
- Omnia Gamal El-Dien,
- Macaire M.S. Yuen,
- Shu Shengqiang,
- Shaun D. Jackman,
- René L. Warren,
- Lauren Coombe,
- Lise van der Merwe,
- Ada Stewart,
- Lori B. Boston,
- Christopher Plott,
- Jerry Jenkins,
- Guifen He,
- Juying Yan,
- Mi Yan,
- Jie Guo,
- Jesse W. Breinholt,
- Leandro G. Neves,
- Jane Grimwood,
- Loren H. Rieseberg,
- Jeremy Schmutz,
- Inanc Birol,
- Matias Kirst,
- Alvin D. Yanchuk,
- Carol Ritland,
- John H. Russell,
- and Joerg Bohlmann
Genome Res. October 2022 32: 1952-1964; Published in Advance September 15, 2022, doi:10.1101/gr.276358.121
...-Interior (n = 9) (Fig. 1A). Using a panel of single-nucleotide polymorphisms (SNPs) that were genotyped via targeted sequence capture approach, we identified 2,454,925 variant and invariant sites, which were filtered separately and resulted in sets of 18,371 SNPs (Supplemental Data Set S5) and 2...
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Resource: Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines
- Wen Huang,
- Andreas Massouras,
- Yutaka Inoue,
- Jason Peiffer,
- Miquel Ràmia,
- Aaron M. Tarone,
- Lavanya Turlapati,
- Thomas Zichner,
- Dianhui Zhu,
- Richard F. Lyman,
- Michael M. Magwire,
- Kerstin Blankenburg,
- Mary Anna Carbone,
- Kyle Chang,
- Lisa L. Ellis,
- Sonia Fernandez,
- Yi Han,
- Gareth Highnam,
- Carl E. Hjelmen,
- John R. Jack,
- Mehwish Javaid,
- Joy Jayaseelan,
- Divya Kalra,
- Sandy Lee,
- Lora Lewis,
- Mala Munidasa,
- Fiona Ongeri,
- Shohba Patel,
- Lora Perales,
- Agapito Perez,
- LingLing Pu,
- Stephanie M. Rollmann,
- Robert Ruth,
- Nehad Saada,
- Crystal Warner,
- Aneisa Williams,
- Yuan-Qing Wu,
- Akihiko Yamamoto,
- Yiqing Zhang,
- Yiming Zhu,
- Robert R.H. Anholt,
- Jan O. Korbel,
- David Mittelman,
- Donna M. Muzny,
- Richard A. Gibbs,
- Antonio Barbadilla,
- J. Spencer Johnston,
- Eric A. Stone,
- Stephen Richards,
- Bart Deplancke,
- and Trudy F.C. Mackay
Genome Res. July 2014 24: 1193-1208; Published in Advance April 8, 2014, doi:10.1101/gr.171546.113
...to improve our understanding of the effects of naturally occurring genetic variation on molecular and organismal phenotypes. We used an integrated genotyping strategy to identify 4,853,802 single nucleotide polymorphisms (SNPs) and 1,296,080 non-SNP variants. Our molecular population genomic analyses show...
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