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Research: Centromeric instability and chromoanasynthesis observed in nine supernumerary marker chromosomes resolved with long-read genome sequencing
- Kristine Bilgrav Saether,
- Angelo Salazar Mantero,
- Marlene Ek,
- Maria Pettersson,
- Elisabeth Syk Lundberg,
- Christopher M. Grochowski,
- Claudia M.B. Carvalho,
- Jesper Eisfeldt,
- and Anna Lindstrand
Genome Res. March 25, 2026 ; Published in Advance March 25, 2026, doi:10.1101/gr.281175.125
...of the Helsinki Declaration. Short-read sequencing srGS was performed using the HiSeq Xten platform. The samples were sequenced using 2×150 bp paired-end reads, on one flow cell for each sample, which resulted in 30× median coverage. The data were aligned to T2T-CHM13 (chm13v2.0) (Nurk et al. 2022) using BWA...
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Resource: Complete sequencing of a cynomolgus macaque major histocompatibility complex haplotype
- Julie A. Karl,
- Trent M. Prall,
- Hailey E. Bussan,
- Joshua M. Varghese,
- Aparna Pal,
- Roger W. Wiseman,
- and David H. O'Connor
Genome Res. March 2023 33: 448-462; Published in Advance February 28, 2023, doi:10.1101/gr.277429.122
...Fi coverage of an MHC-homozygous MCM, creating the most complete macaque MHC sequence to date. This full genomic MHC region assembly provides an important new comparator for understanding differences between macaque and human MHC and, in turn, cellular immunity. It establishes a new paradigm for sequencing...
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Method: Quantification of somatic mutation flow across individual cell division events by lineage sequencing
- Yehuda Brody,
- Robert J. Kimmerling,
- Yosef E. Maruvka,
- David Benjamin,
- Juniper J. Elacqua,
- Nicholas J. Haradhvala,
- Jaegil Kim,
- Kent W. Mouw,
- Kristjana Frangaj,
- Amnon Koren,
- Gad Getz,
- Scott R. Manalis,
- and Paul C. Blainey
Genome Res. December 2018 28: 1901-1918; Published in Advance November 20, 2018, doi:10.1101/gr.238543.118
..., and the acquisition of drug resistance. However, available -wide methods have a limited ability to resolve rare somatic variants and the relationships between these variants. Here, we present lineage sequencing, a new sequencing approach that enables somatic event reconstruction by providing quality somatic mutation...
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Method: Haplotype and population structure inference using neural networks in whole-genome sequencing data
- Jonas Meisner and
- Anders Albrechtsen
Genome Res. August 2022 32: 1542-1552; Published in Advance July 6, 2022, doi:10.1101/gr.276813.122
...Haplotype and population structure inference using neural networks in whole- sequencing data Jonas Meisner and Anders Albrechtsen Department of Biology, Bioinformatics Center, University of Copenhagen, DK-2200 Copenhagen, Denmark Corresponding author: jonas...
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Method: SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data
- Hamim Zafar,
- Nicholas Navin,
- Ken Chen,
- and Luay Nakhleh
Genome Res. November 2019 29: 1847-1859; Published in Advance October 18, 2019, doi:10.1101/gr.243121.118
...SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell sequencing data Hamim Zafar1,2, Nicholas Navin3, Ken Chen2 and Luay Nakhleh1 1Department of Computer Science, Rice University, Houston, Texas 77005, USA; 2Department of Bioinformatics...
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Method: High-throughput single-cell DNA sequencing of acute myeloid leukemia tumors with droplet microfluidics
- Maurizio Pellegrino,
- Adam Sciambi,
- Sebastian Treusch,
- Robert Durruthy-Durruthy,
- Kaustubh Gokhale,
- Jose Jacob,
- Tina X. Chen,
- Jennifer A. Geis,
- William Oldham,
- Jairo Matthews,
- Hagop Kantarjian,
- P. Andrew Futreal,
- Keyur Patel,
- Keith W. Jones,
- Koichi Takahashi,
- and Dennis J. Eastburn
Genome Res. September 2018 28: 1345-1352; Published in Advance August 7, 2018, doi:10.1101/gr.232272.117
...tumors that was not observable with bulk sequencing. We anticipate that this approach will make feasible the routine analysis of AML heterogeneity, leading to improved stratification and therapy selection for the disease.Current tumor sequencing paradigms are inadequate to fully characterize many...
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Resource: Long-read sequencing reveals intra-species tolerance of substantial structural variations and new subtelomere formation in C. elegans
- Chuna Kim,
- Jun Kim,
- Sunghyun Kim,
- Daniel E. Cook,
- Kathryn S. Evans,
- Erik C. Andersen,
- and Junho Lee
Genome Res. June 2019 29: 1023-1035; Published in Advance May 23, 2019, doi:10.1101/gr.246082.118
...These authors contributed equally to this work. Corresponding author: elegans@snu.ac.krAbstractLong-read sequencing technologies have contributed greatly to comparative genomics among species and can also be applied to study genomics within a species. In this study, to determine how substantial genomic changes...
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Research: Single-cell DNA sequencing reveals a late-dissemination model in metastatic colorectal cancer
- Marco L. Leung,
- Alexander Davis,
- Ruli Gao,
- Anna Casasent,
- Yong Wang,
- Emi Sei,
- Eduardo Vilar,
- Dipen Maru,
- Scott Kopetz,
- and Nicholas E. Navin
Genome Res. August 2017 27: 1287-1299; Published in Advance May 25, 2017, doi:10.1101/gr.209973.116
...a diploid (2N) and aneuploid (3.3N) distribution in the primary tumor and a diploid (2N) and aneuploid (3N) distribution in the liver metastasis (Fig. 1B). Millions of cells from the D and A peaks were gated and flow-sorted for exome and targeted cancer gene panel sequencing in CRC1 and CRC2. Single nuclei...
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Research: Genome-wide evidence for speciation with gene flow in Heliconius butterflies
- Simon H. Martin,
- Kanchon K. Dasmahapatra,
- Nicola J. Nadeau,
- Camilo Salazar,
- James R. Walters,
- Fraser Simpson,
- Mark Blaxter,
- Andrea Manica,
- James Mallet,
- and Chris D. Jiggins
Genome Res. November 2013 23: 1817-1828; Published in Advance September 17, 2013, doi:10.1101/gr.159426.113
...of the H. cydno/timareta clade (Fig. 1), and carry out amuchmore powerful -wide test for gene flow than was possible with the sequenced fragments hitherto studied. We analyzed 31 resequenced individuals (30 of which were newly sequenced in this study) from replicate sympatric species pairs of the two...
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Method: HySA: a Hybrid Structural variant Assembly approach using next-generation and single-molecule sequencing technologies
- Xian Fan,
- Mark Chaisson,
- Luay Nakhleh,
- and Ken Chen
Genome Res. May 2017 27: 793-800; Published in Advance January 19, 2017, doi:10.1101/gr.214767.116
...in human s and the limitations of existing sequencing technologies call for the development of novel assembly methods that can leverage the complementary strengths of multiple technologies. We propose a Hybrid Structural variant Assembly (HySA) approach that integrates sequencing reads from next...

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