Evidence map›Paper›PMID 26072482›Full record

ArticleBioinformatics (Oxford, England)2015

Inferring parental genomic ancestries using pooled semi-Markov processes.

James Y Zou, Eran Halperin, Esteban Burchard, Sriram Sankararaman

Open access · hybridAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.

0numbers the graph read from it
0cells of the map it votes in
10citing papers in PubMed
1.0field-weighted citation impact, top 19% of its field
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

10 citing papers in PubMed, 20 citations in OpenAlex.

  1. Article
  2. Article
  3. A general approach for inferring the ancestry of recent ancestors of an admixed individual.Proceedings of the National Academy of Sciences of the United States of America · 2024
    Article
  4. Article
  5. Article
  6. Human genetic admixture through the lens of population genomics.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022
    Review
  7. Article
  8. Article
  9. Article
  10. Genetic and socioeconomic study of mate choice in Latinos reveals novel assortment patterns.Proceedings of the National Academy of Sciences of the United States of America · 2015
    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

4 authors at 3 institutions in 2 countries.

James Y ZouMicrosoft Research, One Memorial Drive, Cambridge, MA 02142, USA, Blavatnik School of Computer Science, Tel Aviv University, Tel-Aviv 69978, Israel, Department of Bioengineering and Therapeutic Sciences and Department of Medicine, University of California, San Francisco, CA 94158 and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
Eran HalperinMicrosoft Research, One Memorial Drive, Cambridge, MA 02142, USA, Blavatnik School of Computer Science, Tel Aviv University, Tel-Aviv 69978, Israel, Department of Bioengineering and Therapeutic Sciences and Department of Medicine, University of California, San Francisco, CA 94158 and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
Esteban BurchardMicrosoft Research, One Memorial Drive, Cambridge, MA 02142, USA, Blavatnik School of Computer Science, Tel Aviv University, Tel-Aviv 69978, Israel, Department of Bioengineering and Therapeutic Sciences and Department of Medicine, University of California, San Francisco, CA 94158 and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA Microsoft Research, One Memorial Drive, Cambridge, MA 02142, USA, Blavatnik School of Computer Science, Tel Aviv University, Tel-Aviv 69978, Israel, Department of Bioengineering and Therapeutic Sciences and Department of Medicine, University of California, San Francisco, CA 94158 and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
Sriram SankararamanMicrosoft Research, One Memorial Drive, Cambridge, MA 02142, USA, Blavatnik School of Computer Science, Tel Aviv University, Tel-Aviv 69978, Israel, Department of Bioengineering and Therapeutic Sciences and Department of Medicine, University of California, San Francisco, CA 94158 and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
Microsoft (United States) · USHarvard University · USUniversity of California, San Francisco · US

Funding

Statistical methods to infer structure and impact of ancient admixtureK99GM111744 · NIGMS · HARVARD MEDICAL SCHOOL · PI SANKARARAMAN, SRIRAM · 2014 to 2015
$128k
NIGMS NIH HHS K99 GM111744
6 · The paper itself

Abstract

motivationA basic problem of broad public and scientific interest is to use the DNA of an individual to infer the genomic ancestries of the parents. In particular, we are often interested in the fraction of each parent's genome that comes from specific ancestries (e.g. European, African, Native American, etc). This has many applications ranging from understanding the inheritance of ancestry-related risks and traits to quantifying human assortative mating patterns.

resultsWe model the problem of parental genomic ancestry inference as a pooled semi-Markov process. We develop a general mathematical framework for pooled semi-Markov processes and construct efficient inference algorithms for these models. Applying our inference algorithm to genotype data from 231 Mexican trios and 258 Puerto Rican trios where we have the true genomic ancestry of each parent, we demonstrate that our method accurately infers parameters of the semi-Markov processes and parents' genomic ancestries. We additionally validated the method on simulations. Our model of pooled semi-Markov process and inference algorithms may be of independent interest in other settings in genomics and machine learning.

Indexed as

AlgorithmsChildFemaleGenetics, PopulationGenomicsGenotyping TechniquesHumansMaleMarkov ChainsMexicoParentsPuerto RicoRacial Groups

Identifiers

PMID26072482
PMCPMC4765873
OpenAlexW2295940159

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
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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.