Evidence map›Paper›PMID 36995666›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2023

ASIS-Seq: Transgene Insertion Site Mapping by Nanopore Adaptive Sampling.

Charles Yu, Roger Caothien, Anna Pham, Lucinda Tam, Tuija Alcantar, Natasha Bacarro, Juan Reyes, Marques Jackson, Brian Nakao, Merone Roose-Girma

Abstract read
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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Charles YuGenentech, Inc., Department of Molecular Biology, South San Francisco, CA, USA.
Roger CaothienGenentech, Inc., Department of Molecular Biology, South San Francisco, CA, USA.
Anna PhamGenentech, Inc., Department of Molecular Biology, South San Francisco, CA, USA.
Lucinda TamGenentech, Inc., Department of Molecular Biology, South San Francisco, CA, USA.
Tuija AlcantarGenentech, Inc., Department of Molecular Biology, South San Francisco, CA, USA.
Natasha BacarroGenentech, Inc., Department of Molecular Biology, South San Francisco, CA, USA.
Juan ReyesGenentech, Inc., Department of Molecular Biology, South San Francisco, CA, USA.
Marques JacksonGenentech, Inc., Department of Molecular Biology, South San Francisco, CA, USA.
Brian NakaoGenentech, Inc., Department of Molecular Biology, South San Francisco, CA, USA.
Merone Roose-GirmaGenentech, Inc., Department of Molecular Biology, South San Francisco, CA, USA. girma.meron@gene.com.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Generation of transgenic mice by direct microinjection of foreign DNA into fertilized ova has become a routine technique in biomedical research. It remains an essential tool for studying gene expression, developmental biology, genetic disease models, and their therapies. However, the random integration of foreign DNA into the host genome that is inherent to this technology can lead to confounding effects associated with insertional mutagenesis and transgene silencing. Locations of most transgenic lines remain unknown because the methods are often burdensome (Nicholls et al., G3: Genes Genomes Genetics 9:1481-1486, 2019) or have limitations (Goodwin et al., Genome Research 29:494-505, 2019). Here, we present a method that we call Adaptive Sampling Insertion Site Sequencing (ASIS-Seq) to locate transgene integration sites using targeted sequencing on Oxford Nanopore Technologies' (ONT) sequencers. ASIS-Seq requires only about 3 ug of genomic DNA, 3 hours of hands-on sample preparation time, and 3 days of sequencing time to locate transgenes in a host genome.

Indexed as

NanoporesAnimalsBase SequenceGenomeHigh-Throughput Nucleotide SequencingMiceMice, TransgenicSequence Analysis, DNATransgenesAdaptive samplingGridIONMinIONNanopore sequencingNext-generation sequencing (NGS)Oxford Nanopore Technologies (ONT)Transgene insertion site mappingTransgenic mice

Identifiers

PMID36995666

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.