Evidence map›Paper›PMID 26098870›Full record

ArticleNature genetics2015

Structural forms of the human amylase locus and their relationships to SNPs, haplotypes and obesity.

Christina L Usher, Robert E Handsaker, Tõnu Esko, Marcus A Tuke, Michael N Weedon, Alex R Hastie, Han Cao, Jennifer E Moon, Seva Kashin, Christian Fuchsberger and 9 more

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

Article in Nature genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
82citing papers in PubMed, 1 pooled it
15.1field-weighted citation impact, top 1% 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

82 citing papers in PubMed, 1 synthesis or guideline pooled it, 150 citations in OpenAlex.

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22 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

19 authors at 9 institutions in 3 countries.

Christina L UsherDepartment of Genetics, Harvard Medical School, Boston, Massachusetts, USA.
Robert E Handsaker1] Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA. [2] Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [3] Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.ORCID 0000000231283547
Tõnu Esko1] Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA. [2] Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [3] Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, Massachusetts, USA. [4] Division of Endocrinology, Boston Children's Hospital, Boston, Massachusetts, USA. [5] Estonian Genome Center, University of Tartu, Tartu, Estonia.ORCID 0000000319826569
Marcus A TukeGenetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK.
Michael N WeedonGenetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK.
Alex R HastieBioNano Genomics, San Diego, California, USA.
Han CaoBioNano Genomics, San Diego, California, USA.
Jennifer E Moon1] Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA. [2] Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [3] Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, Massachusetts, USA. [4] Division of Endocrinology, Boston Children's Hospital, Boston, Massachusetts, USA.
Seva Kashin1] Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [2] Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Christian Fuchsberger1] Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA. [2] Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA.
Andres Metspalu1] Estonian Genome Center, University of Tartu, Tartu, Estonia. [2] Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
Carlos N PatoDepartment of Psychiatry and the Behavioral Sciences, University of Southern California, Los Angeles, California, USA.
Michele T PatoDepartment of Psychiatry and the Behavioral Sciences, University of Southern California, Los Angeles, California, USA.
Mark I McCarthy1] Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. [2] Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK. [3] Oxford National Institute for Health Research (NIHR) Biomedical Research Centre, Churchill Hospital, Headington, Oxford, UK.
Michael Boehnke1] Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA. [2] Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA.
David M Altshuler1] Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA. [2] Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [3] Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.ORCID 0000000272504107
Timothy M FraylingGenetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK.
Joel N Hirschhorn1] Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA. [2] Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [3] Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, Massachusetts, USA. [4] Division of Endocrinology, Boston Children's Hospital, Boston, Massachusetts, USA.
Steven A McCarroll1] Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA. [2] Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [3] Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Broad Institute · USBoston Children's Hospital · USUniversity of Exeter · GBBioNano Genomics (United States) · USUniversity of Michigan · USUniversity of Southern California · USCentre for Human Genetics · GBHarvard University · USUniversity of Tartu · EE

Funding

Regional Pilot And Feasibility Study Grants ProgramP30DK020572 · NIDDK · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI DAVID P OLSON · 2013 to 2026
$24.3M
Genomic Psychiatry CohortR01MH085548 · NIMH · UNIVERSITY OF SOUTHERN CALIFORNIA · PI PATO, CARLOS N, PATO, MICHELE T · 2008 to 2012
$16.3M
Cell Interactions in the Inflamed Intestinal MucosaR01DK075787 · NIDDK · BOSTON CHILDREN'S HOSPITAL · PI JOEL N HIRSCHHORN · 2007 to 2026
$13.1M
Identifying Genes for Type 2 Diabetes: FUSIONU01DK062370 · NIDDK · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI BOEHNKE, MICHAEL L, SCOTT, LAURA J. · 2009 to 2021
$11.6M
Structurally complex genome loci in human populations and human phenotypesR01HG006855 · NHGRI · HARVARD MEDICAL SCHOOL · PI Steven Andrew McCarroll · 2012 to 2026
$8.2M
Identifying Genes for Type 2 Diabetes:FUSIONR01DK062370 · NIDDK · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI BOEHNKE, MICHAEL L, SCOTT, LAURA J. · 2003 to 2025
$6.7M
Identifying Genes for Type 2 Diabetes: FUSIONR56DK062370 · NIDDK · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI BOEHNKE, MICHAEL L · 2008 to 2008
$500k
Medical Research Council G0500070Medical Research Council G0601261NHGRI NIH HHS R01 HG006855NIDDK NIH HHS DK062370NIDDK NIH HHS P30 DK020572NIDDK NIH HHS R01 DK062370NIDDK NIH HHS R01 DK075787NIDDK NIH HHS R56 DK062370NIDDK NIH HHS U01 DK062370NIMH NIH HHS R01 MH085548Wellcome TrustWellcome Trust WT097835MF
6 · The paper itself

Abstract

Hundreds of genes reside in structurally complex, poorly understood regions of the human genome. One such region contains the three amylase genes (AMY2B, AMY2A and AMY1) responsible for digesting starch into sugar. Copy number of AMY1 is reported to be the largest genomic influence on obesity, although genome-wide association studies for obesity have found this locus unremarkable. Using whole-genome sequence analysis, droplet digital PCR and genome mapping, we identified eight common structural haplotypes of the amylase locus that suggest its mutational history. We found that the AMY1 copy number in an individual's genome is generally even (rather than odd) and partially correlates with nearby SNPs, which do not associate with body mass index (BMI). We measured amylase gene copy number in 1,000 obese or lean Estonians and in 2 other cohorts totaling ∼3,500 individuals. We had 99% power to detect the lower bound of the reported effects on BMI, yet found no association.

Indexed as

HaplotypesPolymorphism, Single NucleotideAdolescentAdultAmylasesBody Mass IndexCohort StudiesFemaleGene DosageGene FrequencyGenetic Predisposition to DiseaseGenome-Wide Association StudyGenotypeHumansMaleMiddle AgedAmylases

Identifiers

PMID26098870
PMCPMC4712930
OpenAlexW2114610435

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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.