Evidence map›Paper›PMID 41172993›Full record

ArticleAmerican journal of human genetics2025

Using the ancestral recombination graph to study the history of rare variants in founder populations.

Alejandro Mejia-Garcia, Alex Diaz-Papkovich, Guillaume Sillon, Daniela D'Agostino, Anne-Laure Chong, George Chong, Ken Sin Lo, Laurence Baret, Nancy Hamel, Vincent Chapdelaine and 5 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in American journal of human genetics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing 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

5 citing papers in PubMed.

  1. Article
  2. Article
  3. A Pandemic-Scale Ancestral Recombination Graph for SARS-CoV-2.bioRxiv : the preprint server for biology · 2025
    Article
  4. Article
  5. 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

15 authors.

Alejandro Mejia-GarciaDepartment of Human Genetics, McGill University, Montreal, QC, Canada.
Alex Diaz-PapkovichDepartment of Human Genetics, McGill University, Montreal, QC, Canada.
Guillaume SillonDivision of Medical Genetics, Departments of Medicine and Human Genetics, McGill University Health Center, Montreal, QC, Canada.
Daniela D'AgostinoDivision of Medical Genetics, Departments of Medicine and Human Genetics, McGill University Health Center, Montreal, QC, Canada.
Anne-Laure ChongCancer Axis, Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada.
George ChongMolecular Pathology Centre, Jewish General Hospital, Montreal, QC, Canada.
Ken Sin LoCARTaGENE, CHU Sainte-Justine, Montreal, QC, Canada.
Laurence BaretDivision of Medical Genetics, Departments of Medicine and Human Genetics, McGill University Health Center, Montreal, QC, Canada.
Nancy HamelCancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada.
Vincent ChapdelaineCanada Excellence Research Chair in Genomic Medicine, McGill University, Montréal, QC, Canada.
William D FoulkesDepartment of Human Genetics, McGill University, Montreal, QC, Canada; Cancer Axis, Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada; Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada.
Daniel TaliunDepartment of Human Genetics, McGill University, Montreal, QC, Canada; Canada Excellence Research Chair in Genomic Medicine, McGill University, Montréal, QC, Canada.
Adam J ShapiroDepartment of Pediatrics, Research Institute of the McGill University Health Centre, Montréal, QC, Canada.
Guillaume LettreCARTaGENE, CHU Sainte-Justine, Montreal, QC, Canada.
Simon GravelDepartment of Human Genetics, McGill University, Montreal, QC, Canada. Electronic address: simon.gravel@mcgill.ca.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Gene genealogies represent the shared ancestry of a sample and are often encoded as ancestral recombination graphs (ARGs). It has recently become possible to infer these gene genealogies from sequencing or genotyping data and use them for many evolutionary and statistical genetics applications. Here, we use the ARG inference software ARG-needle and the pedigree imputation software ISGen to impute and trace the transmission of disease variants in founder populations where long shared haplotypes allow for accurate timing of relatedness. We applied these methods to the population of Quebec, where multiple founder events led to an uneven distribution of pathogenic variants across regions and where extensive population pedigrees are available via the BALSAC project. We validated this approach with nine founder mutations for the Saguenay-Lac-Saint-Jean region, demonstrating high accuracy for mutation age, imputation, and regional frequency estimation. We used imputed carrier status in a longitudinal cohort to highlight heterozygote effects for known recessive alleles. These heterozygote effects, together with regional frequency estimates, can inform the design of screening programs.

Indexed as

Founder EffectGenetics, PopulationGenetic VariationRecombination, GeneticGene FrequencyHaplotypesHeterozygoteHumansModels, GeneticMutationPedigreeQuebecSoftwareancestral recombination graphFrench CanadiangenealogyimputationpedigreeQuebecrare variantscreening

Identifiers

PMID41172993
PMCPMC12808987

What OpenQuestion holds

Textmetadata
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.