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Method: Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus
- Mari B. Gornitzka,
- Egil Røsjø,
- Uddalok Jana,
- Easton E. Ford,
- Alan Tourancheau,
- William D. Lees,
- Zachary Vanwinkle,
- Melissa L. Smith,
- Corey T. Watson,
- and Andreas Lossius
Genome Res. October 2025 35: 2240-2251; Published in Advance August 21, 2025, doi:10.1101/gr.280400.125
...and adaptive sampling with a bioinformatic pipeline to produce haplotype-resolved, annotated IGH assemblies. Notably, our strategy overcomes prior limitations in phasing resolution, enabling single-contig haplotype assemblies that span the entire IGH locus. We apply this method to four individuals and validate...
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Perspective: Challenges in identifying mRNA transcript starts and ends from long-read sequencing data
- Ezequiel Calvo-Roitberg,
- Rachel F. Daniels,
- and Athma A. Pai
Genome Res. November 2024 34: 1719-1734; doi:10.1101/gr.279559.124
...DNA molecules. The largest shift in length, however, is likely introduced by polymerase chain reaction (PCR) steps at the end of library preparation, which favors the amplification of shorter fragments (Fig. 2A; Shagin et al. 1999; Parekh et al. 2016). This bias should again equally affect misrepresentation...
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Research: Locus-resolution analysis of L1 regulation and retrotransposition potential in mouse embryonic development
- Patricia Gerdes,
- Dorothy Chan,
- Mischa Lundberg,
- Francisco J. Sanchez-Luque,
- Gabriela O. Bodea,
- Adam D. Ewing,
- Geoffrey J. Faulkner,
- and Sandra R. Richardson
Genome Res. September 2023 33: 1465-1481; Published in Advance October 5, 2023, doi:10.1101/gr.278003.123
...′ monomeric region of each L1 was PCR amplified. Amplicons were pooled and sequenced as 2 × 300-mer Illumina reads. Circles represent methylated (black circles) and unmethylated (white circles) CpG dinucleotides in L1 5′ UTR. (C) Methylation of a de novo L1 promoter sequence (Insertion 2) shown...
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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
...-edge approaches, some regions, especially chromosome ends, lacked support or were poorly resolved. Subsequent whole- sequencing data remain unassembled or in a large number of contigs.In 2015, the CpIRef was reannotated using new RNA-seq evidence, and a new C. hominis sequence from a recent human isolate (UdeA01...
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Research: A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice
- Mikhail O. Maksimov,
- Cynthia Wu,
- David G. Ashbrook,
- Flavia Villani,
- Vincenza Colonna,
- Nima Mousavi,
- Nichole Ma,
- Lu Lu,
- Jonathan K. Pritchard,
- Alon Goren,
- Robert W. Williams,
- Abraham A. Palmer,
- and Melissa Gymrek
Genome Res. May 2023 33: 689-702; Published in Advance May 1, 2023, doi:10.1101/gr.277576.122
..., as well as a current drug target against Huntington's disease. The D haplotype at this locus harbors a cluster of variants near the 5′ end of Msh3, including multiple missense variants near the DNA mismatch recognition domain. In contrast, the B haplotype contains a unique retrotransposon insertion...
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Method: NanoPARE: parallel analysis of RNA 5′ ends from low-input RNA
- Michael A. Schon,
- Max J. Kellner,
- Alexandra Plotnikova,
- Falko Hofmann,
- and Michael D. Nodine
Genome Res. December 2018 28: 1931-1942; Published in Advance October 24, 2018, doi:10.1101/gr.239202.118
...to TSOs and inserted transposase adapter sequences. The resulting amplicons were then used for final PCR amplification with indexed Illumina-adapter primers for next-generation sequencing. Additionally, tagmented products corresponding to nonterminal, or body, regions of transcripts were amplified...
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Method: Detection and characterization of jagged ends of double-stranded DNA in plasma
- Peiyong Jiang,
- Tingting Xie,
- Spencer C. Ding,
- Ze Zhou,
- Suk Hang Cheng,
- Rebecca W.Y. Chan,
- Wing-Shan Lee,
- Wenlei Peng,
- John Wong,
- Vincent W.S. Wong,
- Henry L.Y. Chan,
- Stephen L. Chan,
- Liona C.Y. Poon,
- Tak Y. Leung,
- K.C. Allen Chan,
- Rossa W.K. Chiu,
- and Y.M. Dennis Lo
Genome Res. August 2020 30: 1144-1153; Published in Advance August 14, 2020, doi:10.1101/gr.261396.120
...to bisulfite treatment and PCR amplification. If a molecule contained jagged ends with a 5′ protruding single strand, the methylation levels at CG sites proximal to the 3′ end (e.g., read2) would be lower than that close to the 5′ end (e.g., read1). Filled lollipops represent methylated Cs, and unfilled...
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Research: SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission
- Nicolae Sapoval,
- Medhat Mahmoud,
- Michael D. Jochum,
- Yunxi Liu,
- R.A. Leo Elworth,
- Qi Wang,
- Dreycey Albin,
- Huw A. Ogilvie,
- Michael D. Lee,
- Sonia Villapol,
- Kyle M. Hernandez,
- Irina Maljkovic Berry,
- Jonathan Foox,
- Afshin Beheshti,
- Krista Ternus,
- Kjersti M. Aagaard,
- David Posada,
- Christopher E. Mason,
- Fritz J. Sedlazeck,
- and Todd J. Treangen
Genome Res. April 2021 31: 635-644; Published in Advance February 18, 2021, doi:10.1101/gr.268961.120
...variant (iSNV) and SNP similarity, albeit with differences in C > U changes. Second, iSNV and SNP patterns in SARS-CoV-2 are more similar to MERS-CoV than SARS-CoV-1. Third, a significant fraction of insertions and deletions contribute to the genetic diversity of SARS-CoV-2. Altogether, our findings...
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Method: Detection of long repeat expansions from PCR-free whole-genome sequence data
- Egor Dolzhenko,
- Joke J.F.A. van Vugt,
- Richard J. Shaw,
- Mitchell A. Bekritsky,
- Marka van Blitterswijk,
- Giuseppe Narzisi,
- Subramanian S. Ajay,
- Vani Rajan,
- Bryan R. Lajoie,
- Nathan H. Johnson,
- Zoya Kingsbury,
- Sean J. Humphray,
- Raymond D. Schellevis,
- William J. Brands,
- Matt Baker,
- Rosa Rademakers,
- Maarten Kooyman,
- Gijs H.P. Tazelaar,
- Michael A. van Es,
- Russell McLaughlin,
- William Sproviero,
- Aleksey Shatunov,
- Ashley Jones,
- Ahmad Al Khleifat,
- Alan Pittman,
- Sarah Morgan,
- Orla Hardiman,
- Ammar Al-Chalabi,
- Chris Shaw,
- Bradley Smith,
- Edmund J. Neo,
- Karen Morrison,
- Pamela J. Shaw,
- Catherine Reeves,
- Lara Winterkorn,
- Nancy S. Wexler,
- The US–Venezuela Collaborative Research Group,
- David E. Housman,
- Christopher W. Ng,
- Alina L. Li,
- Ryan J. Taft,
- Leonard H. van den Berg,
- David R. Bentley,
- Jan H. Veldink,
- and Michael A. Eberle
Genome Res. November 2017 27: 1895-1903; Published in Advance September 8, 2017, doi:10.1101/gr.225672.117
...WGS into precisionmedicine.We developed a software tool called ExpansionHunter that, using PCR-freeWGS short-read data, can genotype repeats at the locus of interest, even if the expanded repeat is larger than the read length. We applied our algorithm to WGS data from 3001 ALS patients who have been tested for the presence...
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ARTICLE: Generation of a high-resolution genetic map and a YAC contig of the Lurcher locus on mouse chromosome 6.
- J Zuo,
- P L De Jager,
- D J Norman,
- and N Heintz
Genome Res. November 1995 5: 381-392; doi:10.1101/gr.5.4.381
...) at the D6Rkf39 locus. We further charac- terized these 10 YACs by rescuing their end sequences, determining their insert sizes and analyzing their content of markers (Table 1). A total of 15 YAC ends were iso- lated by a combination of the in- verse PCR and homologous recom- bination methods (Hermanson et...

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