Evidence map›Paper›PMID 26925373›Full record

ArticleMeta gene2015

Exploring genetic polymorphism in innate immune genes in Indian cattle (Bos indicus) and buffalo (Bubalus bubalis) using next generation sequencing technology.

Shreya M Patel, Prakash G Koringa, Neelam M Nathani, Namrata V Patel, Tejash M Shah, Chaitanya G Joshi

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

Article in Meta gene, 2015. 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
0.7field-weighted citation impact, top 30% 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

4 citing papers in PubMed, 13 citations in OpenAlex.

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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

6 authors at 1 institution in 1 country.

Shreya M PatelDepartment of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388001, Gujarat, India.
Prakash G KoringaDepartment of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388001, Gujarat, India.
Neelam M NathaniDepartment of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388001, Gujarat, India.
Namrata V PatelDepartment of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388001, Gujarat, India.
Tejash M ShahDepartment of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388001, Gujarat, India.
Chaitanya G JoshiDepartment of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388001, Gujarat, India.
Anand Agricultural University · IN

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Activation of innate immunity initiates various cascades of reactions that largely contribute to defense against physical, microbial or chemical damage, prompt for damage repair and removal of causative organisms as well as restoration of tissue homeostasis. Genetic polymorphism in innate immune genes plays prominent role in disease resistance capabilities in various breeds of cattle and buffalo. Here we studied single nucleotide variations (SNP/SNV) and haplotype structure in innate immune genes viz CHGA, CHGB, CHGC, NRAMP1, NRAMP2, DEFB1, BNBD4, BNBD5, TAP and LAP in Gir cattle and Murrah buffalo. Targeted sequencing of exonic regions of these genes was performed by Ion Torrent PGM sequencing platform. The sequence reads obtained corresponding to coding regions of these genes were mapped to reference genome of cattle BosTau7 by BWA program using genome analysis tool kit (GATK). Further variant analysis by Unified Genotyper revealed 54 and 224 SNPs in Gir and Murrah respectively and also 32 SNVs was identified. Among these SNPs 43, 36, 11,32,81,21 and 22 variations were in CHGA, CHGB, CHGC, NRAMP1, NRAMP2, DEFB1 and TAP genes respectively. Among these identified 278 SNPs, 24 were found to be reported in the dbSNP database. Variant analysis was followed by structure formation of haplotypes based on multiple SNPs using SAS software revealed a large number of haplotypes. The SNP discovery in innate immune genes in cattle and buffalo breeds of India would advance our understanding of role of these genes in determining the disease resistance/susceptibility in Indian breeds. The identified SNPs and haplotype data would also provide a wealth of sequence information for conservation studies, selective breeding and designing future strategies for identifying disease associations involving samples from distinct populations.

Indexed as

BAM, Binary Alignment MapBNBD4, Neutrophil beta-defensin 4BNBD5, Neutrophil beta-defensin 5BWA, Burrows–Wheeler AlignerCHGA, Chromagranin ACHGB, Chromagranin BCHGC, Chromagranin CDEFB1, Beta defensin 1EM, Expectation MaximizationGATK, Genome Analysis Tool KitHaplotypeIndian cattle and buffaloInnate immune genesLAP, Lingual Antimicrobial PeptideLD, Linkage DisequilibriumNCBI, National Center for Biotechnology InformationNext generation sequencingNRAMP1, Natural Resistance associated macrophage protein 1NRAMP2, Natural Resistance associated macrophage protein 2PCR, Polymerase Chain ReactionPGM, Personal Genome MachineRFLP, Restriction Fragment Length PolymorphismSAM, Sequence Alignment MapSAS, Statistical Analysis SystemSingle nucleotide polymorphismSLC11, Solute Carrier Family 11SNP, Single Nucleotide PolymorphismSNV, Single Nucleotide VariantTAP, Tracheal Antimicrobial PeptideTLR, Toll Like ReceptorUTR, Untranslated Region

Identifiers

PMID26925373
PMCPMC4722485
OpenAlexW2033902841

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

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.