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Method: High-fidelity, large-scale targeted profiling of microsatellites
- Caitlin A. Loh,
- Danielle A. Shields,
- Adam Schwing,
- and Gilad D. Evrony
Genome Res. July 2024 34: 1008-1026; Published in Advance July 16, 2024, doi:10.1101/gr.278785.123
...-cell DNA sequencing and forensics, the amount of DNA available is low and requires amplification (Butler 2006; Evrony et al. 2015). Although high-depth whole- sequencing (WGS) of PCR-amplified libraries could achieve large-scale, high-fidelity profiling of microsatellites, this is not feasible to scale...
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Method: Secure discovery of genetic relatives across large-scale and distributed genomic data sets
- Matthew M. Hong,
- David Froelicher,
- Ricky Magner,
- Victoria Popic,
- Bonnie Berger,
- and Hyunghoon Cho
Genome Res. September 2024 34: 1312-1323; Published in Advance August 7, 2024, doi:10.1101/gr.279057.124
...-Relate on the UK Biobank and All of Us data sets. On a data set of 200,000 individuals split between two parties, SF-Relate detects 97% of third-degree or closer relatives within 15 h of runtime. Our work enables secure identification of relatives across large-scale genomic data sets.Collaborative studies that aim...
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Method: Automated interpretable artificial intelligence genomic prediction with AIGP
- Lei Wei,
- Ziqin Jiang,
- Baoliang Fan,
- Yidan Yan,
- Zhenqiang Xu,
- Xiaoxiang Hu,
- and Yuzhe Wang
Genome Res. March 5, 2026 gr.281006.125; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
...–455. 570 Benegas G, Albors C, Aw AJ, Ye C, Song YS. 2025. A DNA language model based on 571 multispecies alignment predicts the effects of -wide variants. Nat Biotechnol 43: 572 1960–1965. 573 Chen KM, Wong AK, Troyanskaya OG, Zhou J. 2022. A sequence-based global map of regulatory 574 activity...
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Method: Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations
- Yuwei Cao,
- Lauren Patel,
- Lauren Alcoser,
- Eric Mendenhall,
- Christopher Benner,
- Sven Heinz,
- and Alon Goren
Genome Res. January 2026 36: 129-141; Published in Advance December 12, 2025, doi:10.1101/gr.281320.125
..._PCR_Enrichment_Cleanup was run to clean up the input samples. At the end of the protocols, the ChIP library plate should contain ChIP library samples eluted in TT buffer.DNA quantification and sequencingThe size of the DNA libraries was estimated by running on a 2% agarose gel prestained with GelGreen. DNA libraries should have...
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Research: Assessing DNA methylation detection for primary human tissue using Nanopore sequencing
- Rylee Genner,
- Stuart Akeson,
- Melissa Meredith,
- Pilar Alvarez Jerez,
- Laksh Malik,
- Breeana Baker,
- Abigail Miano-Burkhardt,
- CARD-long-read Team,
- Benedict Paten,
- Kimberley J. Billingsley,
- Cornelis Blauwendraat,
- and Miten Jain
Genome Res. April 2025 35: 632-643; Published in Advance March 7, 2025, doi:10.1101/gr.279159.124
...different Nanopore chemistries using guided hypotheses. This work will facilitate comparison among Nanopore data cohorts derived using different chemistries from large-scale sequencing efforts, such as the NIH CARD Long Read Initiative.DNA methylation is an epigenetic mechanism that most commonly involves...
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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
...: In this window In a new window Figure 1. Overview of the experimental setup and bioinformatic pipeline. (A) Schematics of DNA sample preparation and sequencing. High-molecular-weight gDNA was extracted from peripheral blood mononuclear cells (PBMCs), isolated monocytes, or the HG002 Epstein–Barr virus...
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Method: Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR
- Artem Mikelov,
- George Nefediev,
- Alexander Tashkeev,
- Oscar L. Rodriguez,
- Diego Aguilar Ortmans,
- Valeriia Skatova,
- Mark Izraelson,
- Alexey N. Davydov,
- Stanislav Poslavsky,
- Souad Rahmouni,
- Corey T. Watson,
- Dmitriy Chudakov,
- Scott D. Boyd,
- and Dmitry Bolotin
Genome Res. December 2024 34: 2293-2303; Published in Advance October 21, 2024, doi:10.1101/gr.278775.123
...a/b Profiling Kit v2 (Takara Bio). Briefly, a rapid amplification of cDNA ends (RACE) approach with a template-switch effect was used to introduce 5′ adaptors during cDNA synthesis. cDNA corresponding to TRA and TRB transcripts was further amplified and prepared for sequencing, which was performed...
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Research: Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains
- Stephen J. Salipante,
- David J. Roach,
- Jacob O. Kitzman,
- Matthew W. Snyder,
- Bethany Stackhouse,
- Susan M. Butler-Wu,
- Choli Lee,
- Brad T. Cookson,
- and Jay Shendure
Genome Res. January 2015 25: 119-128; Published in Advance November 4, 2014, doi:10.1101/gr.180190.114
...system, TREK Diagnostic Systems). Use of specimens was approved by the University of Washington Human Subjects Review Committee. Library preparation and sequencing DNAwas extracted using the Wizard Genomic DNA Purification kit (Promega). Shotgun sequencing libraries were prepared using the Nextera system...
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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
...for which sequencing all the nucleic acids present in a sample is unnecessary and consumes resources. Targeted sequencing employs strategies that increase the proportion of specific DNA/RNA fragments in a sample, thus increasing the overall coverage of these regions of interest (ROIs). These approaches...
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Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
- Carolina Monzó,
- Adam Frankish,
- and Ana Conesa
Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
...Bio Kinnex or ONT cDNA/directRNA sequencing experiment. The depth of data now available challenges both our technical ability to identify and describe every transcript and our philosophical approach to producing reference annotation. Put simply, sampling depth will increase and many novel transcripts...
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