Evidence map›Paper›PMID 38168337›Full record

ArticlebioRxiv : the preprint server for biology2023

The complete diploid reference genome of RPE-1 identifies human phased epigenetic landscapes.

Emilia Volpe, Luca Corda, Elena Di Tommaso, Franca Pelliccia, Riccardo Ottalevi, Danilo Licastro, Andrea Guarracino, Mattia Capulli, Giulio Formenti, Evelyne Tassone and 1 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. 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

5 · Who and what money

Authors and funding

11 authors.

Emilia VolpeGiunta Laboratory of Genome Evolution, Department of Biology and Biotechnologies Charles Darwin, University of Rome "Sapienza", Piazzale Aldo Moro 5, 00185 Rome, Italy.
Luca CordaGiunta Laboratory of Genome Evolution, Department of Biology and Biotechnologies Charles Darwin, University of Rome "Sapienza", Piazzale Aldo Moro 5, 00185 Rome, Italy.
Elena Di TommasoGiunta Laboratory of Genome Evolution, Department of Biology and Biotechnologies Charles Darwin, University of Rome "Sapienza", Piazzale Aldo Moro 5, 00185 Rome, Italy.
Franca PellicciaGiunta Laboratory of Genome Evolution, Department of Biology and Biotechnologies Charles Darwin, University of Rome "Sapienza", Piazzale Aldo Moro 5, 00185 Rome, Italy.
Riccardo OttaleviDepartment of Bioinformatic, Dante Genomics Corp Inc., 667 Madison Avenue, New York, NY 10065 USA and S.s.17, 67100, L'Aquila, Italy.
Danilo LicastroArea Science Park, Padriciano 99, 34149 Trieste, Italy.
Andrea GuarracinoDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA.ORCID 0000-0001-9744-131X
Mattia CapulliDepartment of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy.
Giulio FormentiThe Rockefeller University, 1230 York Avenue, 10065 New York, USA.ORCID 0000-0002-7554-5991
Evelyne TassoneGiunta Laboratory of Genome Evolution, Department of Biology and Biotechnologies Charles Darwin, University of Rome "Sapienza", Piazzale Aldo Moro 5, 00185 Rome, Italy.
Simona GiuntaGiunta Laboratory of Genome Evolution, Department of Biology and Biotechnologies Charles Darwin, University of Rome "Sapienza", Piazzale Aldo Moro 5, 00185 Rome, Italy.ORCID 0000-0002-6666-9271

Funding

ELSI Administrative Supplement - Center for Human Reference Genome DiversityU01HG010971 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI EICHLER, EVAN, JARVIS, ERICH D · 2019 to 2023
$18.4M
NHGRI NIH HHS U01 HG010971
6 · The paper itself

Abstract

Comparative analysis of recent human genome assemblies highlights profound sequence divergence that peaks within polymorphic loci such as centromeres. This raises the question about the adequacy of relying on human reference genomes to accurately analyze sequencing data derived from experimental cell lines. Here, we generated the complete diploid genome assembly for the human retinal epithelial cells (RPE-1), a widely used non-cancer laboratory cell line with a stable karyotype, to use as matched reference for multi-omics sequencing data analysis. Our RPE1v1.0 assembly presents completely phased haplotypes and chromosome-level scaffolds that span centromeres with ultra-high base accuracy (>QV60). We mapped the haplotype-specific genomic variation specific to this cell line including t(X

Indexed as

centromere assemblyde novo assemblydiploid genomeepigeneticsexperimental cell linehuman polymorphismHuman referenceisogenomic referencelaboratory cell linematched genome referencemulti-omics analysis

Identifiers

PMID38168337
PMCPMC10760208

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.