Evidence map›Paper›PMID 26421280›Full record

ArticleBioMed research international2015

Constructing a Genome-Wide LD Map of Wild A. gambiae Using Next-Generation Sequencing.

Xiaohong Wang, Yaw A Afrane, Guiyun Yan, Jun Li

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BioMed research international, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

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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

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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

3 citing papers in PubMed.

  1. Review
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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.

Xiaohong WangDepartment of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA.
Yaw A AfraneCentre for Global Health Research, Kenya Medical Research Institute, Kisumu 40100, Kenya.
Guiyun YanProgram in Public Health, University of California, Irvine, CA 92697, USA.
Jun LiDepartment of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA.

Funding

University of California Health Participation in the National COVID Cohort Collaborative (N3C)UL1TR001414 · NCATS · UNIVERSITY OF CALIFORNIA-IRVINE · PI COOPER, DAN M, VILAIN, ERIC J. · 2015 to 2023
$35.1M
Ecology of African Highland MalariaR01AI050243 · NIAID · UNIVERSITY OF CALIFORNIA-IRVINE · PI YAN, GUIYUN · 2001 to 2018
$8.8M
Gene Structure Variations and Malaria Resistance in Anopheles gambiaeR56AI081829 · NIAID · UNIVERSITY OF MINNESOTA · PI FALLON, ANN M · 2009 to 2009
$365k
NCATS NIH HHS UL1 TR001414NIAID NIH HHS 1R56AI081829NIAID NIH HHS R01 AI050243NIAID NIH HHS R56 AI081829
6 · The paper itself

Abstract

Anopheles gambiae is the major malaria vector in Africa. Examining the molecular basis of A. gambiae traits requires knowledge of both genetic variation and genome-wide linkage disequilibrium (LD) map of wild A. gambiae populations from malaria-endemic areas. We sequenced the genomes of nine wild A. gambiae mosquitoes individually using next-generation sequencing technologies and detected 2,219,815 common single nucleotide polymorphisms (SNPs), 88% of which are novel. SNPs are not evenly distributed across A. gambiae chromosomes. The low SNP-frequency regions overlay heterochromatin and chromosome inversion domains, consistent with the lower recombinant rates at these regions. Nearly one million SNPs that were genotyped correctly in all individual mosquitoes with 99.6% confidence were extracted from these high-throughput sequencing data. Based on these SNP genotypes, we constructed a genome-wide LD map for wild A. gambiae from malaria-endemic areas in Kenya and made it available through a public Website. The average size of LD blocks is less than 40 bp, and several large LD blocks were also discovered clustered around the para gene, which is consistent with the effect of insecticide selective sweeps. The SNPs and the LD map will be valuable resources for scientific communities to dissect the A. gambiae genome.

Indexed as

Genome, InsectAnimalsAnophelesGenes, InsectHigh-Throughput Nucleotide SequencingInternetKenyaLinkage DisequilibriumMolecular Sequence AnnotationPolymorphism, Single Nucleotide

Identifiers

PMID26421280
PMCPMC4573223

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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.