Whole Genome Sequence Analysis

DNA genotyping technologies specifically target common known SNPs, not rare unknown variants. The only way to identify and evaluate these rare or unidentified variants is through whole-genome sequencing analysis. Whole-genome sequencing provides us with information on DNA variations such as single nucleotide variations (SNVs), copy number variations (CNVs), insertions and deletions (indels), inversions and translocations, substitutions.

Services Offered

A dedicated team of Jaivik data researchers harness both bioinformatics and computational approaches to analyze whole-genome sequencing data to identify, interpret and prioritize biologically relevant genetic variations. We use sophisticated computational methods and tools to perform mapping, data alignment and assembly and variant analysis of data generated by whole-genome sequencing to help answer a vast array of important biological questions.

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Exome Sequence Analysis

Exome sequencing is an efficient strategy to selectively sequence the coding regions of the genome as a cheaper alternative to whole genome sequencing. It is a powerful and cost-effective tool for dissecting the genetic basis of diseases and traits that have proved to be difficult for gene-discovery strategies. Exome sequencing has been widely applied in the identification of germline mutations underlying Mendelian disorders, somatic mutations in various cancers and de novo mutations in neurodevelopmental disorders.

Services Offered

Jaivik’s robust data analysis pipeline enables you to rapidly identify meaningful results. We offer multi-sample (case/control) comparison, analysis of family-based data, identification of somatic mutations, copy number variation (CNV) analysis and loss of heterozygosity (LOH) analysis.

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Transcriptome Analysis (RNA-Seq)

Transcriptome analysis is performed most commonly using next generation sequencing application called RNA-seq, in which RNA pool (total RNA, messenger RNA or noncoding RNA) is reverse-transcribed into cDNA, converted into a sequencing library, sequenced and analyzed. RNA-Seq analysis offers several advantages over DNA microarrays. The biggest advantage is that RNA-Seq works even for species for which no reference genome or DNA microarray exists. Complete sequencing of transcriptomes has become an important tool in the analysis of gene expression, alternative splice sites, allele specific expression and the discovery and analysis of rare or novel transcripts.

Services Offered

Jaivik Data offers wide variety of RNA-seq analyses, including short-read mapping, data alignment and assembly using different software, identification of splice junctions, transcript and isoform detection, quantitation, differential expression and functional analysis. Jaivik Data employs its in-house pipelines for performing a number of multi-step RNA-seq analyses automatically.

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Methylome Analysis (MethylC-Seq)

Methylome-seq is a comprehensive technique for understanding differential gene expression and regulation in development and disease studies at genomic level. Methylome data is primarily obtained from bisulfite sequencing (Bisulfite-seq) or methylated DNA immunoprecipitation sequencing (MeDIP-seq). Genome-wide DNA methylation patterns are analyzed by immunoprecipitation of methylated cytosines in MeDIP-seq or based on bisulfite conversion of methylated cytosines to uracil in Bisulfite-seq. These methods target vast majority of the methylome and are able to detect mC and mCG contexts.

Services Offered

Jaivik Data offers alignment of reads to the reference genome, mapping of methyl cyosine positions, identification of differentially methylated positions, gene-set enrichment and pathway analysis of differentially methylated genes, and biological interpretation and graphical visualization of the resulting data.

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