Evidence map›Paper›PMID 38168361›Full record

ArticlebioRxiv : the preprint server for biology2023

Personalized Pangenome References.

Jouni Sirén, Parsa Eskandar, Matteo Tommaso Ungaro, Glenn Hickey, Jordan M Eizenga, Adam M Novak, Xian Chang, Pi-Chuan Chang, Mikhail Kolmogorov, Andrew Carroll and 2 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

12 authors.

Jouni SirénUC Santa Cruz Genomics Institute, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.ORCID 0000-0001-5828-4139
Parsa EskandarUC Santa Cruz Genomics Institute, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.ORCID 0000-0001-7682-3140
Matteo Tommaso UngaroUC Santa Cruz Genomics Institute, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.ORCID 0000-0002-1107-3307
Glenn HickeyUC Santa Cruz Genomics Institute, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.ORCID 0000-0002-2280-9404
Jordan M EizengaUC Santa Cruz Genomics Institute, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.ORCID 0000-0001-8345-8356
Adam M NovakUC Santa Cruz Genomics Institute, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.ORCID 0000-0001-5828-047X
Xian ChangUC Santa Cruz Genomics Institute, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.ORCID 0000-0002-3801-4542
Pi-Chuan ChangGoogle LLC, 1600 Amphitheater Pkwy, Mountain View, CA 94043, USA.ORCID 0000-0003-3021-6446
Mikhail KolmogorovCenter for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.ORCID 0000-0002-5489-9045
Andrew CarrollGoogle LLC, 1600 Amphitheater Pkwy, Mountain View, CA 94043, USA.ORCID 0000-0002-4824-6689
Jean MonlongUC Santa Cruz Genomics Institute, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.ORCID 0000-0002-9737-5516
Benedict PatenUC Santa Cruz Genomics Institute, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.ORCID 0000-0001-8863-3539

Funding

The AnVIL Data Ecosystem DACReS SupplementU24HG010262 · NHGRI · BROAD INSTITUTE, INC. · PI Robert J Carroll, Jonathan Lawson · 2018 to 2026
$40.5M
The Integration of Trans-omics for Precision Medicine (TOPMED) and Other Heart, Lung, Blood and Sleep (HLBS) Data Sets with the Data CommonsOT3HL142481 · NHLBI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI GROSSMAN, ROBERT L., PATEN, BENEDICT · 2017 to 2020
$24.9M
Dockstore: The Community Platform for Reproducible Biomedical Workflows and ApplicationsU24HG011853 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI Jonathan Lawson, Benedict Paten · 2021 to 2026
$5.7M
Computational tools for uniform processing and integration of human reference atlas data [2 of 5]OT2OD033761 · OD · CARNEGIE-MELLON UNIVERSITY · PI PATEN, BENEDICT, RUFFALO, MATTHEW · 2022 to 2025
$4.2M
The construction and utility of reference pan-genome graphsU01HG010961 · NHGRI · DANA-FARBER CANCER INST · PI LI, HENG, PATEN, BENEDICT · 2020 to 2023
$3.2M
Enabling Comparative PangenomicsR01HG010485 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI HAUSSLER, DAVID H, MARTIN, FERGAL JAMES · 2020 to 2023
$2.6M
NHGRI NIH HHS R01 HG010485NHGRI NIH HHS U01 HG010961NHGRI NIH HHS U24 HG010262NHGRI NIH HHS U24 HG011853NHLBI NIH HHS OT3 HL142481NIH HHS OT2 OD033761
6 · The paper itself

Abstract

Pangenomes, by including genetic diversity, should reduce reference bias by better representing new samples compared to them. Yet when comparing a new sample to a pangenome, variants in the pangenome that are not part of the sample can be misleading, for example, causing false read mappings. These irrelevant variants are generally rarer in terms of allele frequency, and have previously been dealt with using allele frequency filters. However, this is a blunt heuristic that both fails to remove some irrelevant variants and removes many relevant variants. We propose a new approach, inspired by local ancestry inference methods, that imputes a personalized pangenome subgraph based on sampling local haplotypes according to

Identifiers

PMID38168361
PMCPMC10760139

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.