Evidence map›Paper›PMID 24412158›Full record

ArticleGenomics2014

One in four individuals of African-American ancestry harbors a 5.5kb deletion at chromosome 11q13.1.

Kayvan Zainabadi, Anuja V Jain, Frank X Donovan, David Elashoff, Nagesh P Rao, Vundavalli V Murty, Settara C Chandrasekharappa, Eri S Srivatsan

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Article
  2. Article
  3. Review
  4. 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

8 authors.

Kayvan ZainabadiDivision of General Surgery, Department of Surgery, VAGLAHS West Los Angeles, David Geffen School of Medicine at UCLA, Los Angeles, CA 90073, USA.
Anuja V JainDivision of General Surgery, Department of Surgery, VAGLAHS West Los Angeles, David Geffen School of Medicine at UCLA, Los Angeles, CA 90073, USA.
Frank X DonovanGenome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
David ElashoffDepartment of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90025, USA.
Nagesh P RaoDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90025, USA.
Vundavalli V MurtyDepartment of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA.
Settara C ChandrasekharappaGenome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Eri S SrivatsanDivision of General Surgery, Department of Surgery, VAGLAHS West Los Angeles, David Geffen School of Medicine at UCLA, Los Angeles, CA 90073, USA. Electronic address: esrivats@ucla.edu.

Funding

UCLA Clinical and Translational Science InstituteUL1TR000124 · NCATS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI DUBINETT, STEVEN M. · 2012 to 2015
$57.0M
NHGRI/DIR Genomics CoreZICHG200346 · NHGRI · NATIONAL HUMAN GENOME RESEARCH INSTITUTE · PI CHANDRASEKHARAPPA, SETTARA · 2010 to 2025
$14.5M
POSITIONAL CLONING OF THE MEN1 GENEZIAHG000029 · NHGRI · NATIONAL HUMAN GENOME RESEARCH INSTITUTE · PI CHANDRASEKHARAPPA, SETTARA · 2009 to 2025
$13.3M
Howard Hughes Medical InstituteIntramural NIH HHS ZIC HG200346NCATS NIH HHS UL1 TR000124
6 · The paper itself

Abstract

Cloning and sequencing of 5.5 kb deletion at chromosome 11q13.1 from the HeLa cells, tumorigenic hybrids and two fibroblast cell lines have revealed homologous recombination between AluSx and AluY resulting in the deletion of intervening sequences. Long-range PCR of the 5.5 kb sequence in 494 normal lymphocyte samples showed heterozygous deletion in 28.3% of African-American ancestry samples but only in 4.8% of Caucasian samples (p<0.0001). This observation is strengthened by the copy number variation (CNV) data of the HapMap samples which showed that this deletion occurs in 27% of YRI (Yoruba--West African) population but none in non-African populations. The HapMap analysis further identified strong linkage disequilibrium between 5 single nucleotide polymorphisms and the 5.5 kb deletion in people of African ancestry. Computational analysis of 175 kb sequence surrounding the deletion site revealed enhanced flexibility, low thermodynamic stability, high repetitiveness, and stable stem-loop/hairpin secondary structures that are hallmarks of common fragile sites.

Indexed as

Chromosome DeletionChromosomes, Human, Pair 11Polymorphism, Single NucleotideBase SequenceBlack or African AmericanChromosome Fragile SitesDNA Copy Number VariationsFemaleFounder EffectHapMap ProjectHeLa CellsHeterozygoteHumansLinkage DisequilibriumMaleMolecular Sequence Data5.5kb deletionAfrican American ancestryCervical cancerChromosome 11q13.1Common fragile siteLinkage disequilibriumSingle nucleotide polymorphisms

Identifiers

PMID24412158
PMCPMC4162346

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Registered trials

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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.