M3: an improved SNP calling algorithm for Illumina BeadArray data

Li, Gengxin; Kranzler, Henry R.; Zhao, Hongyu

doi:10.1093/bioinformatics/btr673

Cited by 29 publications

(34 citation statements)

References 18 publications

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“…The four extraction methods were then evaluated further based on the genotyping quality at each SNP locus assessed by the corresponding call rate. Call rate is defined as the proportion of genotype calls for a SNP assigned a genotype other than unknown [ 37 ]. Values range from 0 to 100% and higher values are desirable.…”

Section: Methodsmentioning

confidence: 99%

Comparison of Eleven Methods for Genomic DNA Extraction Suitable for Large-Scale Whole-Genome Genotyping and Long-Term DNA Banking Using Blood Samples

et al. 2015

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Over the recent years, next generation sequencing and microarray technologies have revolutionized scientific research with their applications to high-throughput analysis of biological systems. Isolation of high quantities of pure, intact, double stranded, highly concentrated, not contaminated genomic DNA is prerequisite for successful and reliable large scale genotyping analysis. High quantities of pure DNA are also required for the creation of DNA-banks. In the present study, eleven different DNA extraction procedures, including phenol-chloroform, silica and magnetic beads based extractions, were examined to ascertain their relative effectiveness for extracting DNA from ovine blood samples. The quality and quantity of the differentially extracted DNA was subsequently assessed by spectrophotometric measurements, Qubit measurements, real-time PCR amplifications and gel electrophoresis. Processing time, intensity of labor and cost for each method were also evaluated. Results revealed significant differences among the eleven procedures and only four of the methods yielded satisfactory outputs. These four methods, comprising three modified silica based commercial kits (Modified Blood, Modified Tissue, Modified Dx kits) and an in-house developed magnetic beads based protocol, were most appropriate for extracting high quality and quantity DNA suitable for large-scale microarray genotyping and also for long-term DNA storage as demonstrated by their successful application to 600 individuals.

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Section: Methodsmentioning

confidence: 99%

Comparison of Eleven Methods for Genomic DNA Extraction Suitable for Large-Scale Whole-Genome Genotyping and Long-Term DNA Banking Using Blood Samples

et al. 2015

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“…Single nucleotide polymorphisms were called using bcftools-1.3.1 call (-v -c). A PCA plot was created from the resulting variant call format file (vcf; Li et al, 2012) using the R package SNPRelate-1.6.4 (Zheng et al, 2012). From the PCA plot it was clear that the four trees were clonal replicates (Supplemental Figure 6).…”

Section: Rna-seq Preprocessingmentioning

confidence: 99%

AspWood: High-Spatial-Resolution Transcriptome Profiles Reveal Uncharacterized Modularity of Wood Formation in Populus tremula

et al. 2017

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Trees represent the largest terrestrial carbon sink and a renewable source of ligno-cellulose. There is significant scope for yield and quality improvement in these largely undomesticated species, and efforts to engineer elite varieties will benefit from improved understanding of the transcriptional network underlying cambial growth and wood formation. We generated highspatial-resolution RNA sequencing data spanning the secondary phloem, vascular cambium, and wood-forming tissues of Populus tremula. The transcriptome comprised 28,294 expressed, annotated genes, 78 novel protein-coding genes, and 567 putative long intergenic noncoding RNAs. Most paralogs originating from the Salicaceae whole-genome duplication had diverged expression, with the exception of those highly expressed during secondary cell wall deposition. Coexpression network analyses revealed that regulation of the transcriptome underlying cambial growth and wood formation comprises numerous modules forming a continuum of active processes across the tissues. A comparative analysis revealed that a majority of these modules are conserved in Picea abies. The high spatial resolution of our data enabled identification of novel roles for characterized genes involved in xylan and cellulose biosynthesis, regulators of xylem vessel and fiber differentiation and lignification. An associated web resource (AspWood, http://aspwood.popgenie.org) provides interactive tools for exploring the expression profiles and coexpression network.

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“…SNPs were called using bcftools-1.3.1 call (-v -c). A PCA plot was created from the resulting variant call format file (vcf; Li et al (2012)) using the R package SNPRelate-1.6.4 (Zheng et al, 2012). From the PCA plot it was clear that the four trees were clonal replicates ( Figure S6).…”

Section: Rna-seq Preprocessingmentioning

confidence: 99%

AspWood: High-spatial-resolution transcriptome profiles reveal uncharacterized modularity of wood formation inPopulus tremula

Sundell

Street

Kumar

et al. 2016

Preprint

116

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Trees represent the largest terrestrial carbon sink and a renewable source of ligno-cellulose. There is significant scope for yield and quality improvement in these largely undomesticated species, however, efforts to engineer new, elite varieties are constrained by the lack of a comprehensive understanding of the transcriptional network underlying cambial growth and wood formation. We generated RNA Sequencing transcriptome data for four mature, wild-growing aspens (Populus tremula) from high-spatial-resolution tangential cryosection series spanning the secondary phloem, vascular cambium, expanding and secondary cell wall forming xylem cells, cell death zone and the previous year's annual ring. The transcriptome comprised 28,294 expressed, previously annotated protein-coding genes, 78 novel protein-coding genes and 567 long intergenic non-coding RNAs. Most paralogs originating from the Salicaceae whole genome duplication had diverged expression, with the notable exception of those with high expression during secondary cell wall deposition. We performed coexpression network analysis to identify central transcriptional modules and associated several of these with known biological processes. This revealed previously uncharacterized complexity underlying the regulation of cambial growth and wood formation, with modules forming a continuum of activated processes across the tissues. The high spatial resolution suggested novel roles for known genes involved in xylan and cellulose biosynthesis, regulators of xylem vessel and fiber differentiation and components of lignification. The associated web resource (AspWood, http://aspwood.popgenie.org) integrates the data within a set of interactive tools for exploring the co-expression network of cambial growth and wood formation.

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M3: an improved SNP calling algorithm for Illumina BeadArray data

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 29 publications

References 18 publications

Comparison of Eleven Methods for Genomic DNA Extraction Suitable for Large-Scale Whole-Genome Genotyping and Long-Term DNA Banking Using Blood Samples

Comparison of Eleven Methods for Genomic DNA Extraction Suitable for Large-Scale Whole-Genome Genotyping and Long-Term DNA Banking Using Blood Samples

AspWood: High-Spatial-Resolution Transcriptome Profiles Reveal Uncharacterized Modularity of Wood Formation in Populus tremula

AspWood: High-spatial-resolution transcriptome profiles reveal uncharacterized modularity of wood formation inPopulus tremula

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