Efficient variant phasing utilizing a replication cycle reaction system.

Akihiko Mitsutake, Hiroyuki Ishiura, Takashi Matsukawa, Jun Mitsui, Shoji Tsuji, Tatsushi Toda

Abstract read

In one paragraph

Article in Genetics in medicine open, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it

0cells of the map it votes in

0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

6 authors.

Akihiko MitsutakeDepartment of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.

Hiroyuki IshiuraDepartment of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.

Takashi MatsukawaDepartment of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.

Jun MitsuiDepartment of Precision Medicine Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.

Shoji TsujiDepartment of Precision Medicine Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.

Tatsushi TodaDepartment of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Purpose: When 2 heterozygous variants are detected in autosomal recessive disease genes, determining whether they are in cis or in trans is essential. Subcloning polymerase chain reaction products or complementary DNA is limited by variant distance (up to 10 kb) and complementary DNA availability. Droplet digital polymerase chain reaction, effective up to 100 kb, faces probe design challenges. We used replication cycle reaction (RCR), which replicates large DNA fragments based on Methods: Circular DNA molecules were formed by ligating CRISPR/Cas9-cleaved genomic fragments with an Results: RCR amplified genomic regions up to 104 kb. Lower gDNA-to-cassette ratios favored monoallelic amplification, enabling straightforward phasing, whereas higher ratios yielded biallelic products requiring transformation-based allele separation. For variants 152 kb apart, an intervening single-nucleotide variant enabled phased reconstruction. Ultimately, RCR confirmed compound heterozygosity in all 7 patients. Conclusion: This method effectively phases multiple heterozygous variants across large genomic distances.

Indexed as

Autosomal recessive inheritanceCompound heterozygosityReplication cycle reactionVariant phasing

Identifiers

PMID41210371

DOI10.1016/j.gimo.2025.103457

PMCPMC12590433

What OpenQuestion holds

Textmetadata

LicenceCC BY

Read underepoch 390

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.