sequencing platforms complete genomics, (cgi)  (Complete Genomics Inc)

Journal: Nucleic Acids Research

Article Title: Ultra-fast local-haplotype variant calling using paired-end DNA-sequencing data reveals somatic mosaicism in tumor and normal blood samples

doi: 10.1093/nar/gkv953

Figure Lengend Snippet: LHV calling for a head and neck cancer (HNC) WES dataset with 30 pairs of matched tumor and normal samples. ( A ) A circos plot of prevalence of LHVs for five arbitrarily selected sample pairs. Each red dot indicates the existence of at least one LHV in the corresponding exonic region of 1M bps. The height of a red dot indicates the number of LHVs present in the segment of 1M bps long. A pair of matched tumor and normal samples are arranged as adjacent circles with grey and blue color, respectively. ( B ) Comparison of read depth for genome regions with and without LHVs. No apparent difference is observed. ( C ) Histogram showing the frequencies of DNA segments (vertical axis) with different numbers of haplotype calls (horizontal axis). Most regions have up to two haplotypes, i.e., no variants. Regions with greater than two haplotypes are variants implying genome mosaicism. ( D ) A total of 30 line plots, one for each pair of matched tumor (red) and normal (blue) samples from an individual patient. The number of LHVs is shown for each chromosome for each patient. In general, tumors exhibit more LHVs implying more mosaicism. ( E ) Summary of ( D ). For each chromosome, a blue dot is the median of the difference in the number of LHVs between tumor and its matched normal sample across 30 patients; point-wise confidence intervals are shown as purple bands. Tumors show much higher frequencies of LHVs on chromosomes 9, 14 and 17, indicating potential disease-related variations on these regions. ( F ) Summary of sequence mutations for the SNVs within called LHVs. Transitions are much more prevalent than transversions.

Article Snippet: In order to validate our results, we sequenced whole blood DNA from three members of a parent–child trio using two different sequencing platforms, Complete Genomics, Inc. (CGI) ( http://www.completegenomics.com/documents/DataFileFormats_Standard_Pipeline_2.5.pdf , http://cgatools.sourceforge.net/docs/1.8.0/cgatools-user-guide.pdf ) and Illumina whole genome sequencing (ILMN) ( http://www.illumina.com/applications/sequencing.html ).

Techniques: Comparison, Sequencing

Journal: Nucleic Acids Research

Article Title: Ultra-fast local-haplotype variant calling using paired-end DNA-sequencing data reveals somatic mosaicism in tumor and normal blood samples

doi: 10.1093/nar/gkv953

Figure Lengend Snippet: LHV calls for normal samples from a CEU trio of father, mother and daughter in the 1000 genome project based on WGS data. ( A ) A circos plot of prevalence of LHVs. Outer three arcs and inner three arcs represent results of TRIO samples filtered by type III filter and type I filter, respectively. See ‘Materials and Methods’ section for details of the filters. Each red dot indicates the existence of at least one LHV in the corresponding genomic region of 1M bp. The height of a red dot indicates the number of LHVs present in the region. ( B ) Comparison of the three family members in the number of LHVs per chromosome. The daughter has the smallest and the father has the largest number of LHVs in all chromosomes (autosome). ( C ) Histogram showing the frequencies of DNA segments (vertical axis) with different numbers of haplotype calls (horizontal axis). Most segments have up to two haplotypes indicating no variant. Segments with greater than two haplotypes are variants implying genome mosaicism. ( D ) Functional annotations of the genome regions where LHVs are found. Most are intergenic and intronic, with <1% LHVs in exons. ( E ) Summary of sequence mutations for the SNVs within called LHVs. Transitions are much more prevalent than transversions. ( F ) Copy number calls based on CNVnator are directly compared with LHVs for all three family members. In most cases, there are no copy number variations on genome regions where LHVs are found. Copy numbers are represented in the outer arc and LHVs are shown in the adjacent inner arc in the same color for each sample.

Article Snippet: In order to validate our results, we sequenced whole blood DNA from three members of a parent–child trio using two different sequencing platforms, Complete Genomics, Inc. (CGI) ( http://www.completegenomics.com/documents/DataFileFormats_Standard_Pipeline_2.5.pdf , http://cgatools.sourceforge.net/docs/1.8.0/cgatools-user-guide.pdf ) and Illumina whole genome sequencing (ILMN) ( http://www.illumina.com/applications/sequencing.html ).

Techniques: Comparison, Variant Assay, Functional Assay, Sequencing