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Research: Genome-wide strand asymmetry in massively parallel reporter activity favors genic strands
- Brian S. Roberts,
- E. Christopher Partridge,
- Bryan A. Moyers,
- Vikram Agarwal,
- Kimberly M. Newberry,
- Beth K. Martin,
- Jay Shendure,
- Richard M. Myers,
- and Gregory M. Cooper
Genome Res. May 2021 31: 866-876; Published in Advance April 20, 2021, doi:10.1101/gr.270751.120
...Institute for Precision Medicine, University of Washington, Seattle, Washington 98195, USA Corresponding authors: rmyers@hudsonalpha.org, gcooper@hudsonalpha.orgAbstractMassively parallel reporter assays (MPRAs) are useful tools to characterize regulatory elements in human s. An aspect of MPRAs...
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Perspective: Challenges and considerations for reproducibility of STARR-seq assays
- Maitreya Das,
- Ayaan Hossain,
- Deepro Banerjee,
- Craig Alan Praul,
- and Santhosh Girirajan
Genome Res. April 2023 33: 479-495; Published in Advance May 2, 2023, doi:10.1101/gr.277204.122
...-seq), like other episomal massively parallel reporter assays (MPRAs) (Melnikov et al. 2012; Patwardhan et al. 2012), directly quantifies enhancer activity by relying on transcription factors within a host cell system, thereby removing any chromatin-associated biases (Arnold et al. 2013). STARR-seq takes...
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Method: Integration of hyperspectral imaging and transcriptomics from individual cells with SpectralSeq
- Yike Xie,
- Abbas Habibalahi,
- Ayad G. Anwer,
- Kanu Wahi,
- Jacqueline Bailey,
- Francis Lin,
- Catherine Gatt,
- Emma M.V. Johansson,
- Tatyana Chtanova,
- Jeff Holst,
- Ewa Goldys,
- and Fabio Zanini
Genome Res. August 2025 35: 1809-1820; Published in Advance July 8, 2025, doi:10.1101/gr.280014.124
....goldys@unsw.edu.auAbstractMicroscopy and omics are complementary approaches to probe cellular molecular states in health and disease, combining granularity with scalability. However, integrating both imaging- and sequencing-based assays on the same cell has proven challenging. This study demonstrates a new approach called Spectral...
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Research: Sequence determinants of polyadenylation-mediated regulation
- Ilya Vainberg Slutskin,
- Adina Weinberger,
- and Eran Segal
Genome Res. October 2019 29: 1635-1647; Published in Advance September 17, 2019, doi:10.1101/gr.247312.118
...for accurate cleavage site prediction is yet to be established.Recent progress in large-scale DNA synthesis promoted the establishment of massively parallel reporter assays (MPRAs) (Sharon et al. 2012; Goodman et al. 2013; Kheradpour et al. 2013; Mogno et al. 2013; Smith et al. 2013; Noderer et al. 2014...
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Method: Detection and phasing of single base de novo mutations in biopsies from human in vitro fertilized embryos by advanced whole-genome sequencing
- Brock A. Peters,
- Bahram G. Kermani,
- Oleg Alferov,
- Misha R. Agarwal,
- Mark A. McElwain,
- Natali Gulbahce,
- Daniel M. Hayden,
- Y. Tom Tang,
- Rebecca Yu Zhang,
- Rick Tearle,
- Birgit Crain,
- Renata Prates,
- Alan Berkeley,
- Santiago Munné,
- and Radoje Drmanac
Genome Res. March 2015 25: 426-434; Published in Advance February 11, 2015, doi:10.1101/gr.181255.114
...with thousands of distinct barcodes, and the error reduction process as described in this study provide a fundamental solution for accurate and phased WGS from IVF biopsies (and other scarce samples), applicable for both current massively parallel short-read technologies and future longer read, single...
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Method: Sequencing Illumina libraries at high accuracy on the ONT MinION using R2C2
- Alexander Zee,
- Dori Z.Q. Deng,
- Matthew Adams,
- Kayla D. Schimke,
- Russell Corbett-Detig,
- Shelbi L. Russell,
- Xuan Zhang,
- Robert J. Schmitz,
- and Christopher Vollmers
Genome Res. November/December 2022 32: 2092-2106; Published in Advance November 9, 2022, doi:10.1101/gr.277031.122
...MinION flowcell to be flushed, stored, and ultimately reused.DiscussionThe capabilities of the dominant Illumina sequencing technology—producing massive numbers of short reads—have shaped the development of sequencing-based assays more than any other single factor.Although long-read sequencers...
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Method: Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation
- Joseph B. Hiatt,
- Colin C. Pritchard,
- Stephen J. Salipante,
- Brian J. O'Roak,
- and Jay Shendure
Genome Res. May 2013 23: 843-854; Published in Advance February 4, 2013, doi:10.1101/gr.147686.112
...microbial evolution to human cancer genetics. However, despite the cost and throughput advances associated with massively parallel sequencing, it remains challenging to reliably detect mutations that are present at a low relative abundance in a given DNA sample. Here we describe smMIP, an assay...
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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
...genotyping arrays; for example, (1) there is a lack of ascertainment bias with regard to which variants/sites on the are assayed, (2) sequence data can be used to discover novel variation both at the sample or population level (such as in Tran et al. 2020; Liu et al. 2018), (3) massively parallel low...
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Perspective: Genomic approaches for understanding the genetics of complex disease
- William L. Lowe, Jr. and
- Timothy E. Reddy
Genome Res. October 2015 25: 1432-1441; doi:10.1101/gr.190603.115
..., and we will focus on two widely used approaches, chromatin accessibility mapping and ChIP-seq. The accessibility of chromatin to various enzymes such as DNase I is a well-established indicator of genomic regulatory activity. High-throughput sequencing-based assays such as DNase-seq and ATAC-seq exploit...
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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
...of samples, as these approaches are not easily scalable. Alfano et al. (2022) evaluated a multiplex Cas9 enrichment approach using nCATS with ONT native barcoding (EXP-NBD104 kit) and reported >10-fold lower enrichment compared to a singleplex run, with 70% unclassified reads. These results were consistent...
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