Targeted DNA Resequencing

Targeted DNA resequencing is a high resolution method of focused DNA sequencing. It can focus on as few as 10 to 50 genes to achieve high resolution detection of rare variants across a panel of patient samples. Because targeted resequencing methods specifically focus the sequencing reads on a small panel of genes, a modestly sized sequencing experiment can achieve high sequencing coverage across many samples.  Our in house Fluidigim Access Array provides a MIP based method for low cost targeted resequencing while hybrid capture methods, such as the Agilent SureSelect XT2 technology, are commonly used as well.

Sequencing Results

  • Raw Data:  Demultiplexed raw reads in compressed fastq format
  • Quality Control Report: Sequence data quality assessment based on FastQC package, including per-base read quality, over-represented sequences, and over-represented k-mers.
  • Alignment File: Sequenced reads are aligned to a reference genome to produce an aligned BAM file.  The BAM file may be subsequently filtered for duplicate reads (e.g. from PCR artifacts) and for unambiguously mapped, primary alignments.  Appropriate sorting and formatting may be added for integration with supplemental downstream analysis.

Standard Bioinformatics

  • Variant Calling: Variant calling is accomplished with either VarScan or the Genome Analysis Toolkit (GATK) HaplotypeCaller, which improves putative calls of small variants (SNPs, INDELS) via local de novo assembly.  Other  tools such as samtools (http://samtools.sourceforge.net) or the GATK UnifiedGenotyper are possible.  Filtering of common variants can be performed with supplemental information provided by public databases (e.g. dbSNP).  Standard VCF (Variant Call Format) files are provided as output.
  • Variant Annotation: The SnpEff tool may be used to provide additional annotation and functional prediction of the variants to guide downstream inspection and analysis.  SnpEff is designed to work seamlessly with other bioinformatics packages such as the GATK.   

Customized Bioinformatics

We can also perform customized analysis to meet specific needs of your projects.

Required Sample Inputs

  • Fluidigm Access Array: 50ng DNA
  • Agilent Custom Capture: 100ng DNA