研究目的
Investigating the genetic basis of non-syndromic canine retinal degeneration in Miniature Schnauzers, specifically identifying and characterizing the PPT1dci variant associated with progressive retinal atrophy.
研究成果
The study identifies a complex structural variant in the PPT1 gene (PPT1dci) as causative for a non-syndromic form of progressive retinal atrophy in Miniature Schnauzers, showing incomplete penetrance. This variant involves duplication, deletion, and insertion events, leading to aberrant transcripts. The findings provide insights into retinal degeneration mechanisms and highlight the role of PPT1 beyond syndromic diseases, with implications for genetic testing and understanding variable expressivity in inherited disorders.
研究不足
The study has limitations including incomplete DNA for genotyping in some cases, reliance on blood instead of retinal tissue for transcript analysis, potential population stratification, and the inability to specify exact age of disease onset due to varied sample sources. Additionally, the incomplete penetrance of the PPT1dci variant suggests other genetic or environmental factors may influence disease expression.
1:Experimental Design and Method Selection:
The study employed genome-wide association study (GWAS), homozygosity mapping, targeted sequencing, whole genome sequencing (WGS), PCR, Sanger sequencing, and transcript characterization to identify and validate genetic variants. Theoretical models included Mendelian inheritance assumptions and bioinformatics tools for variant analysis.
2:Sample Selection and Data Sources:
DNA samples from 51 Miniature Schnauzers affected by PRA and 56 controls were collected. Additional data from the Dog Biomedical Variant Database Consortium (DBVDC) and European Nucleotide Archive were used for filtering.
3:List of Experimental Equipment and Materials:
Equipment included SNP genotyping arrays (Affymetrix canine SNP array, Illumina CanineHD Beadchip), sequencing platforms (Illumina HiSeq2000, HiSeq2500), PCR machines, capillary sequencers (ABI 3730), and various kits for DNA/RNA extraction and library preparation. Materials included primers, enzymes, and reagents.
4:Experimental Procedures and Operational Workflow:
Steps involved DNA extraction, SNP genotyping, GWAS analysis, homozygosity mapping, targeted sequencing of candidate regions, WGS of selected samples, variant calling and filtering, PCR validation, Sanger sequencing, RNA extraction from blood, cDNA synthesis, and transcript analysis.
5:Data Analysis Methods:
Data were analyzed using PLINK, BEAGLE, GenABEL, GATK, SnpEff, Delly2, FastQC, Kallisto, and other bioinformatics tools for statistical analysis, variant prediction, and expression quantification.
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Illustra DNA extraction kit
BACC2
GE Healthcare
DNA extraction from blood samples
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Affymetrix canine SNP array
Affymetrix
SNP genotyping
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Illumina CanineHD Beadchip
Illumina
SNP genotyping
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Agilent SureSelectXT2 Target Enrichment System
Agilent
Targeted sequencing library preparation
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Illumina HiSeq2000
Illumina
Sequencing
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Illumina HiSeq2500
Illumina
Sequencing
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AmpliTaqGold360Mastermix
Life Technologies
PCR amplification
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ABI 3730 capillary sequencer
Life Technologies
Sanger sequencing
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GeneJET RNA Purification Kit
Thermo Fisher
RNA extraction from blood
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Superscript III
Thermo Fisher
Reverse transcription
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TOPO-TA cloning plasmids pCRII
Thermo Fisher
Cloning of PCR products
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