Evidence map›Paper›PMID 27142425›Full record

ArticleBMC genomics2016

Selecting SNPs informative for African, American Indian and European Ancestry: application to the Family Investigation of Nephropathy and Diabetes (FIND).

Robert C Williams, Robert C Elston, Pankaj Kumar, William C Knowler, Hanna E Abboud, Sharon Adler, Donald W Bowden, Jasmin Divers, Barry I Freedman, Robert P Igo and 24 more

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

Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
0.3field-weighted citation impact, top 27% 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

2 citing papers in PubMed, 2 citations in OpenAlex.

  1. Article
  2. 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

34 authors at 18 institutions in 3 countries.

Robert C WilliamsPhoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ, 85014, USA. williamsr@mail.nih.gov.
Robert C ElstonGenetic Analysis and Data Coordinating Center, Case Western Reserve University, Cleveland, OH, 44104, USA.
Pankaj KumarPhoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ, 85014, USA.
William C KnowlerPhoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ, 85014, USA.
Hanna E AbboudDivision of Nephrology, The University of Texas Health Science Center, San Antonio, TX, 78229, USA.
Sharon AdlerDepartment of Nephrology, Harbor-UCLA Medical Center, Torrance, CA, 90502, USA.
Donald W BowdenWake Forest School of Medicine, Winston-Salem, NC, 27157, USA.
Jasmin DiversWake Forest School of Medicine, Winston-Salem, NC, 27157, USA.
Barry I FreedmanWake Forest School of Medicine, Winston-Salem, NC, 27157, USA.
Robert P IgoGenetic Analysis and Data Coordinating Center, Case Western Reserve University, Cleveland, OH, 44104, USA.
Eli IppDepartment of Nephrology, Harbor-UCLA Medical Center, Torrance, CA, 90502, USA.
Sudha K IyengarGenetic Analysis and Data Coordinating Center, Case Western Reserve University, Cleveland, OH, 44104, USA.
Paul L KimmelNational Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, 20892, USA.
Michael J KlagWelch Center for Prevention, Epidemiology, and Clinical Research, Baltimore, MD, 21205, USA.
Orly KohnThe University of Chicago Medical Center, Chicago, IL, 60637, USA.
Carl D LangefeldWake Forest School of Medicine, Winston-Salem, NC, 27157, USA.
David J LeeheyLoyola University Medical Center, Chicago, IL, 60153, USA.
Robert G NelsonPhoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ, 85014, USA.
Susanne B NicholasDivisions of Nephrology and Endocrinology, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA.
Madeleine V PahlDivision of Nephrology and Hypertension, Department of Medicine, UC Irvine School of Medicine, University of California, Orange, 92868, CA, USA.
Rulan S ParekhHospital for Sick Children, University Health Network and the University of Toronto, Ontario, M5G1X8, Canada.
Jerome I RotterInstitute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, 90502, USA.
Jeffrey R SchellingDepartments of Medicine and Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, 44104, USA.
John R SedorDepartments of Medicine and Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, 44104, USA.
Vallabh O ShahThe University of New Mexico, Albuquerque, NM, 87131, USA.
Michael W SmithNational Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA.
Kent D TaylorInstitute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, 90502, USA.
Farook ThameemDivision of Nephrology, The University of Texas Health Science Center, San Antonio, TX, 78229, USA.
Denyse Thornley-BrownThe University of Alabama at Birmingham, Birmingham, AL, 35233, USA.
Cheryl A WinklerCenter for Cancer Research, National Cancer Institute, NIH, Leidos Biomedical, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA.
Xiuqing GuoInstitute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, 90502, USA.
Phillip ZagerThe University of New Mexico, Albuquerque, NM, 87131, USA.
Robert L HansonPhoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ, 85014, USA.
FIND Research Group
Case Western Reserve University · USNational Institute of Diabetes and Digestive and Kidney Diseases · USWake Forest University · USHarbor–UCLA Medical Center · USNational Institutes of Health · USThe University of Texas Health Science Center at San Antonio · USUniversity of New Mexico · USLeidos (United States) · USLoyola University Medical Center · USNational Human Genome Research Institute · USThe Lundquist Institute · USUCLA Medical Center · USUniversity of Alabama at Birmingham · USUniversity of California, Irvine · USUniversity of California, Los Angeles · USUniversity of Chicago Medical Center · USUniversity of Toronto · CAWelch Foundation · US

Funding

ZOVIRAX CREAM TO TREAT HERPES LABIALIS IN ADOLESCENTSM01RR000827 · NCRR · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI CHANG, R JEFFREY · 1985 to 2010
$74.3M
ZONA-FREE HAMSTER OVA ASSAY AS AN INDICATOR OF MALE FERTILITYM01RR000425 · NCRR · LUNDQUIST INSTITUTE FOR BIOMEDICAL INNOVATION AT HARBOR-UCLA MEDICAL CENTER · PI ANDERSON, GAIL V · 1985 to 2011
$74.2M
UCLA Clinical and Translational Science InstituteUL1TR000124 · NCATS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI DUBINETT, STEVEN M. · 2012 to 2015
$57.0M
Transgenic & Knock-out MouseP30DK063491 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI PETER J TONTONOZ · 2003 to 2026
$40.4M
WORKER PROTECTION AGAINST AIRBORNE INFLUENZA - A PILOT STUDYM01RR007122 · NCRR · WAKE FOREST UNIVERSITY HEALTH SCIENCES · PI HUNDLEY, WILLIAM GREGORY · 1992 to 2010
$35.2M
ZUNI KIDNEY PROJECT STUDY I--POPULATION BASED SURVEY OF RENAL DISEASEM01RR000997 · NCRR · UNIVERSITY OF NEW MEXICO · PI ROLDAN, CARLOS A · 1985 to 2010
$30.0M
ZOLEDRONATE VS AREDIA IN MULTIPLE MYELOMA/BREAST CANCER W /BONE DISORDERSM01RR001346 · NCRR · UNIVERSITY OF TEXAS HLTH SCIENCE CENTER · PI FERRER, ROBERT L · 1985 to 2008
$23.1M
Zosuquidar trihydrochloride for acute myeloid leukemia &refractory anemiaM01RR000080 · NCRR · UNIVERSITY HOSPITALS OF CLEVELAND · PI DAVIS, PAMELA B · 1985 to 2007
$22.2M
University of Alabama at Birmingham's Diabetes Research CenterP30DK079626 · NIDDK · UNIVERSITY OF ALABAMA AT BIRMINGHAM · PI Kirk Michael Habegger · 2013 to 2026
$19.5M
Institute for Integration of Medicine & Science: A Partnership to Improve HealthUL1TR001120 · NCATS · UNIVERSITY OF TEXAS HLTH SCIENCE CENTER · PI CLARK, ROBERT A, HARGREAVES, KENNETH M · 2013 to 2017
$16.5M
LINKAGE CONSORTIUM FOR END-STAGE RENAL DISEASEU01DK057292 · NIDDK · CASE WESTERN RESERVE UNIVERSITY · PI IYENGAR, SUDHA K · 1999 to 2009
$13.1M
Genetics of Renal Disease in African AmericansZIABC010022 · NCI · DIVISION OF BASIC SCIENCES - NCI · PI WINKLER, CHERYL · 2009 to 2022
$8.9M
AHRQ HHS R01 HS008365NCATS NIH HHS UL1 TR000124NCATS NIH HHS UL1 TR001120NCRR NIH HHS M01 RR000080NCRR NIH HHS M01 RR000425NCRR NIH HHS M01 RR000827NCRR NIH HHS M01 RR000997NCRR NIH HHS M01 RR001346NCRR NIH HHS M01 RR007122NHGRI NIH HHS N01 HG065403NHLBI NIH HHS R01 HL062985NIDDK NIH HHS F32 DK080617NIDDK NIH HHS P30 DK063491NIDDK NIH HHS P30 DK079626NIDDK NIH HHS R01 DK053591NIDDK NIH HHS R01 DK070941NIDDK NIH HHS R01 DK084149NIDDK NIH HHS U01 DK057249NIDDK NIH HHS U01 DK057292NIDDK NIH HHS U01 DK057295NIDDK NIH HHS U01 DK057298NIDDK NIH HHS U01 DK057300NIDDK NIH HHS U01 DK057303NIDDK NIH HHS U01 DK057304NIDDK NIH HHS U01 DK057329NIDDK NIH HHS U01 DK070657
6 · The paper itself

Abstract

backgroundThe presence of population structure in a sample may confound the search for important genetic loci associated with disease. Our four samples in the Family Investigation of Nephropathy and Diabetes (FIND), European Americans, Mexican Americans, African Americans, and American Indians are part of a genome- wide association study in which population structure might be particularly important. We therefore decided to study in detail one component of this, individual genetic ancestry (IGA). From SNPs present on the Affymetrix 6.0 Human SNP array, we identified 3 sets of ancestry informative markers (AIMs), each maximized for the information in one the three contrasts among ancestral populations: Europeans (HAPMAP, CEU), Africans (HAPMAP, YRI and LWK), and Native Americans (full heritage Pima Indians). We estimate IGA and present an algorithm for their standard errors, compare IGA to principal components, emphasize the importance of balancing information in the ancestry informative markers (AIMs), and test the association of IGA with diabetic nephropathy in the combined sample.

resultsA fixed parental allele maximum likelihood algorithm was applied to the FIND to estimate IGA in four samples: 869 American Indians; 1385 African Americans; 1451 Mexican Americans; and 826 European Americans. When the information in the AIMs is unbalanced, the estimates are incorrect with large error. Individual genetic admixture is highly correlated with principle components for capturing population structure. It takes ~700 SNPs to reduce the average standard error of individual admixture below 0.01. When the samples are combined, the resulting population structure creates associations between IGA and diabetic nephropathy.

conclusionsThe identified set of AIMs, which include American Indian parental allele frequencies, may be particularly useful for estimating genetic admixture in populations from the Americas. Failure to balance information in maximum likelihood, poly-ancestry models creates biased estimates of individual admixture with large error. This also occurs when estimating IGA using the Bayesian clustering method as implemented in the program STRUCTURE. Odds ratios for the associations of IGA with disease are consistent with what is known about the incidence and prevalence of diabetic nephropathy in these populations.

Indexed as

Polymorphism, Single NucleotideAlgorithmsBlack or African AmericanChromosome MappingDiabetic NephropathiesGenetic MarkersGenetic Predisposition to DiseaseGenome-Wide Association StudyHumansIndians, North AmericanLikelihood FunctionsMexican AmericansModels, GeneticOligonucleotide Array Sequence AnalysisPrincipal Component AnalysisUnited StatesGenetic MarkersDiabetic nephropathyIndividual genetic ancestryPopulation structureSNP

Identifiers

PMID27142425
PMCPMC4855449
OpenAlexW2346312249

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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.